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ZANCO JOURNAL OF PURE AND APPLIED SCIENCES The official scientific journal of Salahaddin University-Erbil

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ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 1-17 http://dx.doi.org/10.21271/ZJPAS.29.2.1

Cytogenetic and molecular genetic studies of number of chronic mylogenous leukemia in Erbil province

Mustafa S. Al-Attar and Govand M. Qader University of Salahaddin -Erbil, College of science, Biology Department

A R T I C L E I N F O A B S T R A C T

Article History: Chronic myeloid leukemia (CML) is amyeloprolirative disorder

Received: 04/05/2016 characterized by the Philadelphia chromosome originates from the Accepted: 25/08/2016 translocation of chromosome 9 and 22 t (9;22) (q34;q11), creating a Published:07 /06 /2017 Keywords: BCR-ABL fusion gene which results in the constitutive activation Philadelphia Chronic BCR-ABL tyrosine kinase. Patients of BCR-ABL fusion gene myelogenous leukemia, positive in (CML) are treated by an effective therapy called Imatinib chromosome, cytogenetics mutation, ABL gene (Gleevec). Point mutations alter the conformation of the ATP binding ASO-PCR. site that disturbs the binding of therapy to its target which leading to *Corresponding Author: imatinib resistance. Fifty CML patients were collected from Nanakali Mustafa S. Al-Attar Hospital in Erbil city which were diagnosed by physicians. The age Email: [email protected] of the patients from 9 to 80 years, 62% were male and 39% were female, median age of the patients were 38 years. The present study deals with two different aspects; conventional cytogenetic (G- banding) analysis to diagnose the Philadelphia chromosome as a (CML) marker and using Allele Specific Oligonucleotide Polymerase Chain Reaction (ASO-PCR) assay for screening the mutant allele at the three codons 351, 311 and 315 of the BCR-ABL ATP binding domain in Imatinib resistant CML patients. The phenotype of fifteen CML patients were successfully analyzed, thirteen patients were in complete cytogenetic response state (Philadelphia 0%) only two of those patients showed the Philadelphia chromosome. Three point mutations T1052C, T932C and C944T were identified by allele specific oligonucleotide polymerase chain reaction (ASO-PCR). One patient showed T1052C mutation, T932C was detected in three patients and two patients showed the C944T ATP binding domain mutation. In conclusion, conventional cytogenetic and molecular genetic tests are complementary techniques to show the exact types of abnormalities, which allow better evaluation of the genomic aberration involved in CML patients, specifically for kinase domain mutation that plays an important role in different diagnosis, prognosis, therapy treatment and drug resistant management of chronic myeloid leukemia.

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Hydroxyurea is an inhibitor of the INTRODUCTION ribonucleotide reductase as well as decrease the Chronic myeloid leukemia (CML) is a tumor mass, however hydroxyurea prolonged clonal disorder of myeloid stem cells (Witte, the duration of chronic phase as compared with 2001; Mark et al., 2006), accounting 15% of busulfan while busulfan is an alkalating agent adult leukemias (Kaur et al., 2012). It was first that used as a second line treatment after recognized in 1845 (Rachel & Mary, 2007; hydroxyurea resistant or intolerance that act as McCann, 2012). The median age of CML anti-tumor activity at stem cell level ( patients is 45 to 55 years (Faderl et al., 1999). Hehlmann et al., 1993; Paci, 2013). In contrast, It is the first malignant disorder which is found interferon alpha used in response to antigenic to be associated with a chromosome aberration stimuli such as those that occur with viral called Philadelphia (Ph) chromosome (Chin et infection and malignant disease as well as it al., 1996 ;Hamad et al., 2013). has pleiotropic effect involving antiviral, The high exposure to ionizing radiation, antiproliferative and antiangiogenic activities pesticide, and herbicide are factors that lead to (Faderl et al., 1999), however interferon alpha CML (Moloney, 1987; Kaur et al., 2012). The prolonged survival as compared to typical symptoms of CML are leukocytosis, hydroxyurea with low risk due to expose of fatigue, splenomegaly, thrombocytosis and significant toxicity (Eiring et al., 2011). anemia (Faderl et al., 1999; Nestal et al., When a fragment of ABL gene is fused with 2012). BCR gene thus the activation loop in BCR-ABL The induction of the genomic aberration fusion gene would be in the open conformation which lead to the formation of BCR-ABL fusion and phosphorylation, in contrast when Imatinib genes are due to environmental factors, life binds with an active site of the tyrosine kinase style, natural individual genotype difference, at ATP binding site, Imatinib mesylate exposure to radioactivity and carcinogen switches off downstream signaling, cells stop substances play an important role (Iqbal, 2011; proliferating and apoptosis by preventing Bhat et al., 2012). Cytogenetic analysis is the tyrosine autophosphorylation (Guido, 2003; standard tool for initial evaluation, diagnosis, Al-achkar et al., 2009; Dhara et al., 2010). management of hematological malignancy of a Despite response to Imatinib in the majority patient that suspected to cancer (Goh et al., of patients with chronic myeloid leukemia, 2006) and used as a prognostic indicator for CML patients show primary or acquire monitoring therapy (Parikh and Tefferi, 2012). resistance (Parker et al., 2011). Generally there Also it provides evidence of the progression of are two kinds of BCR-ABL mechanism disease at an earlier phase than hematological resistant, first BCR-ABL independent marker (Alachkar et al., 2013) by detecting mechanism of resistance belong to decreasing various chromosomal aberrations and has a in the intracellular level of Imatinib due to significant role at the time of CML diagnosis complication with drug efflus, drug influx or (Razelle et al., 1990; Boronova & Sotak, drug concentration which lead to signal 2007). activation of Ras/MEK and STAT (Hamad et The first an older therapy for CML is al., 2013). Arsenic trioxide that has apro-apoptic effect While the BCR-ABL dependent which increase apoptosis and a significant mechanism of resistance involves duplication decline BCR-ABL protein level (Cheryl, 2012; or over amplification of BCR-ABL oncogene Rachel & Mary, 2007; Melda & Guray, 2013). that leads to elevated ABL kinase, among them the most frequent dependent mechanism is Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17 mutation in the ABL kinase domain. Mutation Sample Collection can affect directly the proper binding of A total of three to five ml venous blood Imatinib to the target molecule as well as samples of fifty CML patients were collected binding of ATP (Alimena, 2009; Hamad et al., from Nanakali Hospital in Erbil city which 2013). were diagnosed by physicians, fifteen of the The BCR-ABL domain mutation include samples were subjected to the cytogenetic of four major regions P-loop ATP-binding site, technique. Sample collection and transport was catalytic domain and activation loop, the two completed at the same day on ice. The age of major categories of mutation have been defined the patients from 9 to 80 years, 62% were male as those at positions where direct contact with and 39% were female, median age of the imatinib occurs and those that affect the patients were 38 years. conformation of BCR-ABL thus preventing imatinib binding. The first category mutation A-Cytogenetic method: namely T315I located in the ATP-binding site Cytogenetic analysis: that prevents the formation of hydrogen bonds Peripheral blood samples were collected in with imatinib and F359V mutation located in lethium heparin tubes (Gersen & Keagle, the catalytic domain. The second category 2005). It was performed on (24-48) hours on comprises mutations in the P-loop (Y253H and peripheral blood cell culture (Joaquín et al., E255K) and H396R/P mutation in A-loop (Tali 2000; Farkhondeh et al., 2001) using standard & Ninette, 2012; Menon, 2013). protocol for preparation of GTG-banding The most frequent mutations are namely metaphase (Talwar, 2003; Boronova & Sotak, C944T (cytosine to thymine substitution at 2007) and chromosome karyotype was ABL gene in position 944 I exon3) which lead described according to International System to amino acid change of threonine to isoleusine Cytogenetic Nomenclature (ISCN) guidelines at position 315(Thr315Ile). T932C (thymine to for human Cytogenetic Nomenclature, using cytosine substitution at ABL gene position 932) cytovision system for image analysis (Qureshi, causing change the amino acid of 2008). The number of metaphase were phenylalanine to leucine at position analyzed on each sample were at least 20 311(Phe311Leu) and T1052C (thymine to metaphases (Al-achkar et al., 2007). The cytosine substitution at ABL gene position prepared metaphase slides (metaphase 1052) which converts the amino acid analyzing) had been read in laboratory of methionine to threonine at position medical genetics in Iran/Tehran. 351(Met351Thr) that forms apart of BCR-ABL The absence of any Ph+ metaphase cells is fusion gene and hence BCR-ABL onco-protein indicating a complete cytogenetic response (Catherine et al., 2002; Mahon, 2006). (CyR) (Alice et al., 2007). The aims of the current study were diagnose the Philadelphia chromosome by Preparation of Metaphase Banding Human cytogenetic analysis and then confirmation of Chromosome: it’s by screening various mutations (T1052C, The protocol used according to (Moorhead T932C and C944T) in the BCR-ABL ATP et al., 1960; Fan, 2003; Gersen & eagle, 2005). binding domain by allele specific oligonucleotide polymerase chain reaction (ASO-PCR) assay. Specimens Collection and Handling: MATERIALS AND METHODS Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Three ml of venous blood was drew by a Allele specific oligonucleotide polymerase sterile syringe and collected in a vacuum tubes chain reaction technique uses three primers, containing anticoagulant lithium heparin. first primer wild type allele specific second Specimens were transported on ice box and primer mutant allele specific and third common were kept in refrigerator at 4°C till culturing. primer. The primer wild type and mutant allele The specimens were cultured within 24 hours specific usually differ by only one nucleotide of collection for best result. that gives them a high specifity to the corresponding wild type or mutant allele, the Karyotype Procedure (Culture of two allele specific primer are combined with leukocytes): the common primer in separate reaction tubes 0.5ml of heparinized whole blood was (Delia et al., 2008), the primers are listed in mixed with 4.5ml of PAA culture medium that (Table 1). The tubes were placed in the PCR contain all requirements like (RPMI machine for amplification depending on the 1640,Phytohaemagglutinin, Fetal bovine PCR program file in (Table 2 and 3). Then the serum, L-glutamine and antibiotics) for cell PCR product was run on agarose gel proliferation. The cultured cells were incubated electrophoresis (2%). at 37°C for (65-70) h. PCR Mix preparation: A 20 µl PCR reaction was performed B- Molecular method: containing 2µl of DNA, 2X lyophilized DNA Extraction: Accupower master mix (Bioneer, Korea) and Genomic DNA was extracted from whole 1.5µl was added for each of the forward and blood by using Genomic DNA kit (Genaid, reverse primers then the mixture was UK), depending on manufacturer’s completed by adding 15 µl of nuclease free instructions. The qualification and water. quantitification of extracted DNA were done by gel electrophoresis and Nano-Drop respectively.

Allele specific Oligonucleotide Polymerase Chain reaction (ASO-PCR) To determine the most useful protocol in clinical practice (Catherine et al., 2002 ) was developed ASO-PCR assay using primer sets detecting the three common point mutations in BCR-ABL fusion gene ATP binding domain known as T1052C (Met351Thr), T932C (Phe311Leu) and C944T (Thr315Ile). ASO- PCR assay can amplified the mutated or wild type sequences in CML patients specifically in the PCR reaction (Zafar, 2004; Kim, 2006; Aamir et al., 2011).

Table 1: Identities and sequences of primers used in ASO-PCR assay for mutant allele detection in CML Gleevec resistant patients (Catherine et al., 2002). Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Mutation Primer Polarity Recognition sequence (5’—3’) Amplicon Type length (bp)

NP Forward CCA CTC AGA TCT CGT CAG T1052C CCAT* ASO Forward CCA CTC AGA TCT CGT CAG CCA 112 (bp) C* Common Reverse GCC CTG AGA CCT CCT AGG CT

NP Forward CAC CCG GGA GCC CCC GT* T932C ASO Forward CAC CCG GGA GCC CCC GC* 172 (bp)

Common Reverse CCC CTA CCT GTG GAT GAA GT

NP Forward GCC CCC GTTCTA TAT CATCAC*

C944T ASO Forward GCC CCC GTTCTA TAT CATCAT* 158 (bp)

Common Reverse GGA TGA AGT TTT TCT TCT CCA

Table (2): Thermal cycling conditions of ASO-PCR technique for mutation C944T and T932C (Catherine et al., 2002).

Steps Tempreture (ºC) Time Number of cycles

Initial denaturation 94 12 minutes 1

Denaturation 95 1 minute Annealing 64 1 minute 35 Extension 72 1 minute

Final extension 72 5 minutes 1

Table (3): Reaction cycling program of ASO-PCR technique for mutation T1052C (Catherine et al., 2002).

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17 Steps Tempreture (ºC) Time Number of cycles

Initial denaturation 94 12 minutes 1

Denaturation 95 1 minute Annealing 68 1 minute 35 Extension 72 1 minute

Final extension 72 5 minutes 1

Results and Discussion: be exists at the time of CML diagnosis patients Cytogenetic studies: but this disorder are not clinically Out of the fifteen diagnosed CML patients, distinguishable from those with philadelphia two CML patients showed philadelphia positive. positive Figure (2) while thirteen patients’ On other hand Current results were specimen have a normal karyotype that is supported by the previous finding such as Goh philadelphia negative Figure (1). In the current et al., (2006) illustrated that the analyzed study the number of philadelphia positive was metaphase were philadelphia negative this is lower than that reported by Al -Attar, (2004), due to complete cytogenetic response or who found fourteen positive cases among masked philadelphia chromosome (Hochhaus, twenty six patient samples. Philadelphia 2006; Boronova & Sotak, 2007) Table (4) negative belong to many reasons one of them shows the cytogenetic analysis of CML patient. reported by Razelle etal., (1990) that ph- can

Figure (1): GTG-banding of human chromosome. 46,XY Normal male karyotype (negative Philadelphia chromosome) in CML patient (1000X).

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Figure (2): GTG-banding of human chromosome. Female 46,XX,t(9;22) that revealed Philadelphia chromosome in CML patient (1000X).

Table (4): Patient’s characteristics and results of cytogenetic analysis.

Sample Age Sex Therapy Karyotype

Case 1 70 M Nilotinib Ph-

Case 2 59 F Gleevec Ph-

Case 3 40 M Nilotinib Ph-

Case 4 58 M Nilotinib Ph-

Case 5 38 M Gleevec Ph-

Case 6 49 M Nilotinib Ph-

Case 7 13 F Gleevec Ph+

Case 8 52 M Gleevec Ph-

Case 9 40 F Gleevec Ph-

Case 10 45 M Gleevec Ph-

Case 11 55 F Gleevec Ph-

Case 12 30 M Nilotinib Ph-

Case 13 39 F Gleevec Ph-

Case 14 55 F Gleevec Ph+

Case 15 51 M Gleevec Ph-

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Molecular studies: mutated type allele of 351.This mutation can be Molecular detection of BCR-ABL kinase partially impairs the binding of the Imatinib to domain mutation that associated with its target and thus lead to partial drug resistance Imatinib resistance: that overcome actively by administering full Mutation analysis was performed by using therapeutic dose escalation of Imatinib as a a sensitive technique ASO-PCR for CML first line therapy from 600mg/day to cases. Out of the 50 chronic phase (CP) CML 1600mg/day (Zafar, 2004; Hochhaus, 2006). patients examined according to the presence of The incidence of T1052C (1 of 50 patients, the BCR-ABL tyrosine kinase mutation, six 2%) was lower than that reported by (Catherine patients (12%) were found to harbor the mutant et al., 2002), (1 of 24, 4.1%) and (Zafar, 2004), allele at the three codon 351, 311 and 315 of (6 of 68, 4.4%). the BCR-ABL fusion gene Table (5). Thirty four patients (68%) had the wild type allele of Table (5): Patient’s characteristics and positive 351, 311 and 315, the remaining patients were results of different types of ATP Binding Domain 10 (20%) that there were no any indicator Mutation by ASO-PCR. (normal band) on the gel electrophoresis to have wild type of the 311 and 315 alleles. ID Sample Age Sex Mutation type Delia et al., (2008) which supports that the Case 2 59 F T1052C mutant specific primer was designed for high specifity, it binds when the exact Case 5 38 M T932C complementary sequence for it must be present Case 6 41 M T932C in DNA of the CML patients otherwise amplification is not occurred, then we Case 7 40 F T932C confirmed our results on the same patients by using normal primer and also there was no any Case 29 35 F C944T normal bands after running PCR products on Case 39 40 M C944T the gel electrophoresis, in this case we were interpreted that these CML patients (20%) have another mutation. Each of these mutations were detected alone which are in concordance with results of

(Catherine et al., 2002; Aamir et al., 2011) and there was no any double mutation in a single patient which is disconcordance with the results that reported by (Zafar, 2004).

Our data showed that the BCR-ABL

Met351Thr (T1052C) already described gene mutation in one of the fifty CML cases with using ASO-PCR technique that supported by the previous study such as (Catherine et al.,

2002; Zafar, 2004), Figure (3) shows specific band (112bp) after amplification the target sequence of CML patient with normal primer and one of them not amplified with normal primer. Figures (4) show wild (normal) and

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Figure 3: Analysis of T1052C mutation by ASO-PCR. Lane 1 and 20: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (Control DNA amplified with normal primer), Lane 4: Control DNA not amplified with mutant specific primer, Lane 11: Patient sample not amplified with normal primer and the rest are Patient samples amplified with normal primer.

Figure 4: Analysis of T1052C mutation by ASO-PCR. Lane 1 and 15: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (Control DNA amplified with normal primer), Lane 4: Control DNA not amplified with mutant specific primer, Lane 5: Patient sample amplified with mutated specific primer T1052C and Lane 6-14: Patient samples amplified with normal primer.

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

BCR-ABL ATP binding mutation (T932C) of (158bp) of mutated ABL gene Thr315Ile the ABL gene was checked by ASO-PCR (T315I) on the gel electrophoresis by (Zafar, 2004). Figure (5) shows specific band amplification of DNA patient with mutant (172bp) of CML patients with normal primer specific primer (ASO-Primer). This mutation and three mutations Phe311Leu (T932C) out of was formed by a single amino acid substitution the fifty CML patients after using ASO-Primer at location 315 (Gorre et al., 2001), normally for their amplifications. Figure (6) shows three site chain of threonine 315 provide oxygen CML patients were not amplified with normal atom that form a crucial hydrogen bond with primer while the same patients were positive Imatinib (Gorre et al., 2001) but in the absence for mutated primer like in previous figure and of an oxygen atom in the substitution the rest are patient samples amplified with isoleucine prevents bond formation that lead to normal primer. The incidence of T932C inhibit binding (Massimo & Giuliana, 2009). mutation (3 of 50 CML patients, 6%) was C944T mutation completely impaired the higher than that reported by (Catherine et al., therapy binding leading to complete drug 2002) (1 of 24 CML patients, 4.1%) but lower resistance. Complete Imatinib resistance can be than that found by (Aamir et al., 2011) (7 of 40 controlled by combination of therapies (Zafar, CML patients, 17.75%). 2004). Imatinib plus arsenic (Hamad et al., 2013), Imatinib plus Cytarabine (Kantarjian et The first identified mutation in CML al., 2003), interferon alpha plus Cytarabine patients was the C944T (T315I) in a male 53 (Vigil et al., 2011) And Imatinib plus years old that described by Gorre et al in 2001 pegylated interferon alpha are used for those (Francis et al., 2007; Massimo & Giuliana, CML patients whom show complete resistance 2009). Cytosine to Thymine mutation at to Imatinib (Zafar, 2004; Jayakar, 2012; position 944 of ABL gene (Al-achkar et al., Radich, 2012). Figure (8) shows those patients 2013) was detected by ASO-PCR assay were amplified with normal primer. The (Waggas & Abdel-Muhsin, 2011; Maysaa, incidence of C944T was lower than that 2013). Figure (7) shows three CML patients showed in the previous study by (Gorre et al., that not amplified with normal primer then we 2001) (6 of 9, 66.6%), (Catherine et al., 2002) used ASO-Primer for the same samples, we (3 of 24, 12.5%), (Zafar, 2004) (6 of 68, 8.8%) observed the band of specific PCR product and (Aamir et al., 2011) (3 of 40, 7.5%).

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Figure 5: Agarose gel Electrophoresis showing 172bp ASO-PCR fragments corresponding to BCR-ABL Gene ATP binding domain T932C mutation. Lane 1 and 15: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (non CML DNA amplified with normal primer), Lane 4: non CML not amplified with mutant specific primer, Lane 5,6 and 7: Patient sample amplified with mutated specific primer T932C and Lane 8-15: Patient samples amplified with normal primer.

Figure 6: Agarose gel Electrophoresis showing 172bp ASO-PCR fragments corresponding to BCR-ABL Gene ATP binding domain T932C mutation. Lane 1 and 19: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (non CML DNA amplified with normal primer), Lane 4: non CML DNA not amplified with mutant specific primer, Lane 11,12 and 13: Patient samples not amplified with normal primer and the rest are Patient samples amplified with normal primer.

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Figure 7: Detection of mutation C944T by ASO-PCR. Lane 1 and 15: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (Normal DNA amplified with normal primer), Lane 4: Normal DNA not amplified with mutant specific primer, Lane 5, 6 and 10: Patient samples amplified with ASO- Primer,Lane 7-9: CML patient samples not amplified with normal primer and the rest Patient samples amplified with normal primer.

Figure 8: Detection of mutation C944T by ASO-PCR. Lane 1 and 15: DNA ladder of 1kb and 50bp respectively, Lane 2: Negative control, Lane 3: Positive control (Normal DNA amplified with normal primer), Lane 4: Normal DNA not amplified with mutant specific primer and Lane 5-15: Patient samples amplified with normal Primer.

Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

Imatinib has fascinated the physicians, and sensitive technique for detection of known clinicians, patients and researchers by its high mutations (Catherine et al., 2002), short effectiveness against BCR-ABL positive CML turnaround time of analysis, lower cost and patients (Zafar, 2004), that stops the oncogenic simple procedure (Kim, 2006). Direct activity of BCR-ABL onco-protien by binding sequencing of the ABL kinase domain is the to its ATP binding site on the ABL kinase most common mutation analysis technique but leading to inhibition of substrate has a limited sensitivity for detection (Waggas phosphorylation of protein BCR-ABL and & Abdel-Muhsin, 2011; Parker et al., 2011) so preventing the activation of downstream ASO-PCR method is more sensitive than signaling pathways (Hofmann et al., 2003; mutation detection by sequencing of ABL ATP Mathisen et al., 2011). binding domain because DNA sequencing is Imatinib interacts with kinase through useful to detect point mutation when proportion hydrogen bond; any mutation affecting amino of mutated cells is more than 30% (Catherine et acid residues in the active site of ABL could al., 2002; Zafar, 2004). Also sequence analysis induce a structural change effect, making the for mutation detection is quite costly, time drug unable to inhibit ABL kinase activity consuming and laborious (Zafar, 2004; (Catherine et al., 2002). Massimo & Giuliana, 2009). The molecular genetic changes (DNA On the other hand ASO-PCR is suitable for damage) in CML patients affect the action of rapid and routine screening of mutations and targeted therapy causing drug resistance like with a satisfying cost effectiveness value (Delia Imatinib, specifically that forms abnormal et al., 2008). The ASO-PCR was founded that BCR-ABL fusion gene that lead to genomic able to detect one mutated cell Imatinib instability of leukemic clone (Cortes, 2009 ) resistant cell out of 10,000 normal cells (Zafar, which induce point mutation in BCR-ABL 2004). Strong specifity of the method was kinase domain leading to shortened survival of demonstrated by the constant lack of CML patients due to failure to response to amplification of mutant allele specific fragment Imatinib. On other hand exposure to Imatinib in healthy individuals who served as a control may induce the genetic instability eventually for the study (Catherine etal., 2002 ; Delia et cause the high frequency of mutation in wild al., 2008). BCR-ABL fusion gene ATP binding type ABL kinase domain (Neil et al., 2002). domain mutation have been founded in another The most frequent mechanism that change tyrosine kinase inhibitor like Nilotinib and Imatinib sensitivity in BCR-ABL transformed Dasatinib which cause resistance formation in cells (Massimo & Giuliana, 2009; Mathisen et Nilotinib and Dasatinib (Simona et al., 2007; al., 2011) and finally cause Imatinib resistant is Michele et al., 2013). The mutation number mutation in the BCR-ABL kinase domain that that formed by Nilotinib treatment is lower impair Imatinib binding either by direct affect than that formed by Gleevec treatment the proper binding of Imatinib to the target (Massimo & Giuliana, 2009) and the molecule binding of ATP or lead to mechanism of Nilotinib resistance belong to conformation changes of the protein which over expression of BCR-ABL fusion gene reduce the affinity to Imatinib (Hochhaus, (Nestal et al., 2012). 2006; Massimo & Giuliana, 2009) The The best way to avoid Imatinib resistance occurrence of the mutations in patients whom in CML can be achieved by dose escalation. develop Imatinib resistant is from 30% to 90% Administering full therapeutic doses as early as (Delia et al., 2008). Allele specific possible such as 800mg/day as a first line oligonucleotide ASO-PCR is a very specific therapy in newly diagnosed chronic phase Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

CML patients causes the maximal depletion of Al-Attar, M.S. (2004). Evaluation of pesticides toxicity leukemic cells (Jeffrey & Helen, 2003; on laboratory mice and human chromosomes in Iraq-Kurdistan, Ph.D. Thesis,University of Hochhaus, 2006). Also higher doses (standard Salahaddin/Erbil-Iraq. dose, 800mg/day) of Imatinib reinduce hematologic response or impair cytogenetic Alice, F., Martin, C., Philipp, E., Tanja, L., Michelle, G., Oliver, F., Wolfgang, S., Rüdiger, H. & Andreas, response (Kantarjian et al., 2003). H. (2007). Dynamics of cytogenetic aberrations in BCR-ABL positive CML patients require Philadelphia chromosome positive and negative immediate attention not only by local hematopoiesis during dasatinib therapy of chronic physicians and oncologists but international myeloid leukemia patients after imatinib failure. community should also go many stages to work haematologica/the hematology journal, 92(06), 834-837. in collaboration with local personnel for this issue, to find out the reasons, molecular maker Alimena, M. (2009). Resistance to Imatinib in Chronic Myeloid Leukemia and Therapeutic Approaches to of the disease and drug targets. Circumvent the Problem. Cardiovascular and Haematological Disorders-Drug Targets,9(1), 21- Conclusion 28. Conventional cytogenetic and molecular Bhat, G., Bhat, A., Wani, A., Sadiq, N., Jeelani, S., Kaur, genetic tests are complementary techniques to R. & Ganai, B.(2012). Polymorphic Variation in show the exact types of abnormalities, that Glutathione-S-transferase Genes and Risk of allow better evaluation of the genomic Chronic Myeloid Leukaemia in the Kashmiri aberration involved in CML patients, Population. Asian Pacific Journal of Cancer specifically for kinase domain mutation that Prevention, 13(1), 69-73. plays an important role in different diagnosis, Boronova, I. & Sotak, M. (2007). Detection of prognosis, therapy treatment and drug resistant Philadelphia in patients with Chronic meyeloid management of CML patients like selection the leukemia from the presov region in Slovakia. Bratisl Lek listy Journal 108, 433-436. specific tyrosine kinase inhibitor when Imatinib mesylate treatment has been failed. Catherine, R., Nathalie, G., Jean, L., Nathalie, P., Thierry, F., Pierre, F. & Claude, P. (2002 ). Several types of mutations of the Abl gene can be found in chronic myeloid leukemia patients resistant to REFERENCES STI571, and they can pre-exist to the onset of treatment. The American Society of Hematology, Aamir, R., Sabir, H., Nazia, R., Shaukat, A., Ghulam, 100, 3, 1014-1018. M., Shahzad, B. & Ammad, A. (2011). Chronic myeloid leukemia: Attributes of break point cluster Cheryl, A. (2012). Treating Chronic Myeloid Leukemia region-abelson (BCR-ABL). Journal of Cancer Improving Management Through Understanding of Research and Experimental Oncology 3(6), 62-66. the Patient Experience. Clinical Journal of Oncology Nursing, 17(1), 13-20. Al-achkar, W.,Wafa, A. & Nwedar, M. (2007). A complex translocation t(5;9;22) in philadelphia Chin, Y., Wang, L. & Zubaidah, Z. (1996). Chromosome cells involving the short arm of chromosome 5 in Aberration in philadelphia chromosome positive case of chronic Myelogenous Leukemia. Journal Chronic Myeloid Leukemia. Genetics Society of experimental Clinical Cancer Research 26(3), 411- Malaysia Journal, 2, 258-261. 415. Cortes, A. (2009). Molecular biology of bcr-abl-positive Al-achkar, W., Wafa, A., Moassass, F., Klein, E. & chronic myeloid leukemia. The American Society of Liehr, T. (2013). Multiple copies of BCR-ABL Hematology, 113, 1619-1630. fusion gene on two isodicentric Philadelphia Delia, D., Andrei, C., Radu, P., Mariana, P. & Ljubomir, chromosomes in an imatinib mesylate-resistant P. (2008). Monitoring T315I mutation in chronic chronic myeloid leukemia patient. Oncology myeloid leukemia by amplification refractory Letters, 5, 1579-1582. mutation system PCR. Revista Română de Medicină de Laborator, 13, 17-20. Mustafa S. and Qader /ZJPAS: 2017, 29(2): 1-17

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ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2016), 29 (2); 18-23 http://dx.doi.org/10.21271/ZJPAS.29.2.2

Measurement of white blood cells count, immunoglobulins and complement proteins in patients with scabies in Erbil- Iraq

1 2 3 Alaa Abdulrahman Sulaiman , Samir Jawdat Bilal , Sarhang Hasan Aziz

1-College of Medicine, Hawler Medical Univ. 2- Dept. Fish Res. Aquatic Anim., Coll. Agriculture, Salahaddin Univ. 3- Dept. Biology, Coll. Education, Salahaddin Univ.

A R T I C L E I N F O A B S T R A C T

Article History: The present study was conducted from November 2014 to March Received: 03/05/2016 2015. Seventy four patients aged from six to forty five years old were Accepted: 20/10/2016 examined. The present study aims to determine white blood cell Published: 07/06/2017 counts, antibody response and some complement components levels Keywords: Scabies WBC changes in the serum of patients with scabies. Immunological Immunoglobulins reaction to scabies evaluated were including leucocyte count, which Complements. was significantly increased, and Immunologic reactions mediated by immunoglobulins including IgG, IgM, IgA and IgE. All of them were *Corresponding Author: significantly increased except IgA. Concerning complement protein Samir J. Bilal levels (C3 and C4) non-significant changes were seen in their levels. [email protected] None of these reactions have been shown to eliminate all mites from the skin surface in patients who followed by the clinic reports, but

locally these reactions may prevent the epidemic multiplication of scabies' organisms on the skin surface.

1. INTRODUCTION wrists, axillae, areolae, umbilicus, lower Scabies is parasitic infection caused by a abdomen, genitals and buttocks (James et al.; mite, called Sarcoptes scabiei var. hominis, 2011). (the itch mite), it is an oval, ventrally flattened The immune system of human interacts with environmental, metabolic and endocrine factors mite with dorsal spines. The fertilized female burrows into the stratum corneum and deposits as well as with infectious agents’ bidirectional her eggs. Scabies is characterized by pruritic and is arranged genetically. Scabies is one of papular lesions, excoriations, and burrows. the most important parasitic skin diseases with Sites of predilection include the finger webs, global distribution and continues to persist all over the world at all-time despite the 19 availability and using of many acaricides and determine the immunological responses in therapeutic tools. Although the infestation is scabies infestation. not life-threatening, it is a nuisance disease that The study aimed to clear the immune system is commonly found in health care facilities and response against the skin parasitic infestation can result in crisis, fear and panic. Scabies with Sarcoptes scabiei and the effects of this outbreaks can be difficult to control and may parasite on total and differential leukocytes easily reoccur if not properly contained and count, also, the role of complement proteins treated (Beggs et al., 2005). Patients with (C3 and C4) in controlling of the infestation scabies react to the infestation mainly by were studied. generating cell-mediated immune response and humoral immunity (Şenol et al., 1997). 2. MATERIALS AND METHODS More than 300 million cases of scabies were reported worldwide every year. Anybody 2.1. Patients and Control might be in contact with the mite being able to catch scabies. This parasite can affect people The study involved 74 patients attended a from all socioeconomic levels, also age, sex, private clinic in Erbil from November 2014 to race or standards of personal hygiene not March 2015. Their ages ranged from 6- 45 related to the infestation (Gurevitch, 1985). years with a mean of 25.54±2.37 years. Scabies The female mite digs bore small tunnels in was suspected if a patient has a suspicious skin epidermis for lying the eggs and elicits a very lesion accompanied by itching for at least one itchy papule that is often excoriated. In some week. Information was collected from each cases ulcerated papules, nodules and vasculitis case through direct interview and a develop as a result of other immunologic questionnaire form and the age was detected. reactions in skin. An intact immunity entails all Concerning controls, 30 healthy persons were the forces and systems involved in recognition, selected with matched age group with the specific response and removal of foreign patients. objects after they again enter into the body of the host. The cell-mediated immune reaction in 2.2. Lab diagnosis the skin and the circulating antibodies act in a Confirmation of the diagnosis was done by parallel manner in clearing of the mites, eggs skin scraping which was performed by placing and debris. Studies related to humoral immune a drop of microscope immersion oil over the response to scabies are limited whereas T-cell lesion and scraping off the epidermis over the mediated immune response to scabies is well suspected site of scabies infestation. The documented (Cabrera et al., 1993; Morsy et al., specimen was then placed on a microscope 1993; Arlian et al., 1994; Arlian et al., 2007). slide and examined by light microscopy for the In the present study total white blood cell demonstration of mites or eggs (Gurevitch, count, differential counts (lymphocytes, 1985). Thirty healthy individuals were selected monocytes, neutrophils, eosinophils, as control group; they were matched with basophils), the serum levels of IgG, IgM, IgA, patients by age group. IgE, C3 and C4 were evaluated in seventy four patients with scabies with no secondary 2.3. Blood sample collection infection or other parasitic infestations and compared with thirty non-infested healthy Venous blood samples (7 ml) were collected individuals as control group aimed to from patients and control group using sterile disposable syringes. Blood samples were 20 divided into two parts, 2 ml were collected into sample T- test. P-value < 0.05 was considered ethylene diamine tetra acetic acid (EDTA) statistically significant. containing tubes for estimation of total white blood cell count (WBC) and differential leukocyte count. The other part (5 ml) were collected into plain universal tubes and allowed to clot, then centrifuged at 3000 rpm for 15 3. RESULTS minutes to separate the serum which dispensed into sterile Eppendorf tubes and stored at -20 The mean of the total white blood cell count for patient group in the present study was °C to be used for immunological investigations 3 (Mancini et al., 1965; Nutman, 2007). 9.1±3.71 X 10 , there was a significant increase of total WBC and differential counts in patients 2.4. Methods when compared with that of controls 7.1±2.13 X 103 (P< 0.05). 2.4.1 Determination of total and differential leukocyte count The absolute leukocytes counts for patient groups were recorded: Lymphocytes White blood cell and differential counts 1.34±0.95, monocytes 0.71±0.4, neutrophils including absolute lymphocytes, monocytes, 5.12±2.17, eosinophils 0.41±0.21 and basophils and granulocytes counts were measured by 0.096±0.03), while for control group: coulter counter (ACT, 5 diff, USA, 2007) for Lymphocytes 1.23±0.7, monocytes 0.63±0.23, patients and control group. neutrophils 4.85±1.1, eosinophils 0.28±0.1 and basophils 0.088±0.024) and the differences 2.4.2 Determination of serum were significant (P< 0.05) except that for immunoglobulins (IgG, IgA, IgE and IgM) and certain complement components (C3 neutrophils which was non-significant (Table and C4) 1).

Five µl of serum were added to wells in It was observed that the mean serum IgG an agarose gel using radial immunodiffusion levels for the patient group were: plate containing monospecific antisera for IgG, 1356.54±654.12 mg/dl, IgM levels were IgA, IgM, C3 and C4, the sample diffused 211.67±98.43 mg/dl, IgA levels were radially through the gel and the substance being assayed forms a precipitation ring with 213.21±76.21 mg/ dl, IgE levels were the specific antisera after 72 hours of 321.54±101.37 IU/ ml, C3 values were incubation except for IgM which was 97.4±19.56 mg/dl and C4 levels were determined after 96 hours. Ring diameter was 29.87±9.43 mg/dl, on another hand for control measured and reference values were correlated group they were found to be 1145.65±556.9 to reach actual concentration. IgE was mg/dl for IgG, 119.21±48.97 mg/dl for IgM, evaluated by ELISA kit (Mancini et al., 1965; 221.19±98.45 mg/dl for IgA, 321.54±101.37 Walton et al., 2010). mg/ dl for IgE, 86.5±28.59 IU/ml for C3 and 2.5 Statistical analysis 31.38±6.43 mg/dl for C4, significant differences were noticed for IgG, IgM and IgE Data were analyzed by SPSS (statistical levels (P< 0.05), while non-significant package for social science) version 19. Results differences for IgA, C3 and C4 were seen were expressed as (Mean± S.E.). Statistical (p>0.05) (Table 2). differences were determined by independent

Table 1 Mean ± S.E of total and absolute leukocytes counts for patients and controls.

Parameters Patients Control P value

3 WBC (10 /ml) 9.1±3.71 7.1±2.13 0.034

Lymphocytes 1.34±0.95 1.23±0.7 0.046 (cell/mm3)

Monocytes (cell/mm3) 0.71±0.4 0.63±0.23 0.041

Neutrophils (cell/mm3) 5.12±2.17 4.85±1.1 0.053

Eosinophils (cell/mm3) 0.41±0.21 0.28±0.1 0.029

3 Basophils (cell/mm ) 0.096±0.03 0.088±0.024 0.045

Table 2: Mean ± S.E of the humoral immunologic parameters for patients and controls.

Parameters Patients Control P value IgE (IU/ ml) 321.54±101.37 115.34±26.96 0.01

IgG (mg/ dl) 1356.54±654.12 1145.65±55.69 0.02

IgM (mg/ dl) 211.67±98.43 119.21±18.97 0.03

IgA (mg/ dl) 213.21±76.21 221.19±28.45 0.07

C3 (mg/ dl) 97.4±19.56 86.5±8.59 0.054

C4 (mg/ dl) 29.87±9.43 31.38±6.43 0.059

4- DISCUSSION observed by (Cabrera et al., 1993; Morsy et al., S. scabiei lives only in the avascular part of 1993; Morsy et al., 1994; Arlian et al., 1994, the skin, both humoral and cellular immune Arlian et al., 1996; Nutman, 2007). On the responses against the mite antigens are other hand, Morsy et al. (1995) and Walton developed, because of this, the mite antigens (2010) observed non-significant increase in must be diffused through the epidermis and IgM levels of patients. Non-significant stimulate the antigen presenting cells (APCs) difference was observed in IgA values among or the langerhans cells in the dermis. The patients compared to controls. Similar results ‘diffusible’ antigens are likely to be soluble in were found by other investigators, (Arlian et nature and secreted or excreted by the mite, not al., 1994; Morsy et al., 1994). On the other the structural components of the mites (Arlian hand, other studies, showed decreased levels of et al., 1994; Arlian et al., 1996; Walton et al., IgA in patients compared to controls (Morsy et 2010). al., 1993; Hill et al., 1995; Arlian et al., 1995). The normal level (or decreased sub-normal) in Cell-mediated immune responses of host have the IgA may be due to the mite or its products been identified primarily by histopathological which interfere with its synthesis (Şenol et al., examination of skin biopsy specimens from 1997). scabietic lesions. Mite burrows are surrounded by inflammatory cell infiltrates comprising IgE levels were significantly higher in the lymphocytes, monocytes, eosinophils and present study among patient groups compared to the control group. These results were in basophils. In most cases, the histological appearance is that of nonspecific, delayed agreement with observations reported by hypersensitivity with superficial and deep different researchers (Cabrera et al., 1993; perivascular inflammatory mononuclear cell Morsy et al., 1993; Morsy et al., 1994; Arlian infiltrates with numerous eosinophils, papillary et al., 1994; Morsy et al., 1995; Arlian et al., edema, and epidermal spongiosis (Falk and 1996; Nutman, 2007; Adedayo et al., 2009). Eide, 1981; Shelley and Bart, 2007), previous The same contradiction as in IgA is present notices agreed with the results of the present also here, some studies have indicated that study when increasing in lymphocytic cells measurement of total serum IgE would be of no reported. benefit in the preliminary clinical investigation of a suspected host as there is no significant In the literature, there are controversial increasing in its level (Walton et al., 2010), this results on this issue. Morsy et al. (1993) could be due to secondary bacterial infections reported that IgG levels were significantly of the patients since they have elevated levels higher among patients with scabies than among of IgG. The changes in the IgG, IgM, and in controls treatment of the disease. Similar particularly IgE may be a specific response to results were reported by (Hill et al., 1995; the parasite or a nonspecific reaction to the Adedayo et al., 2009), they noticed high levels dead parasite or its feces and debris. (Şenol et of IgG in patients with scabies. While another al., 1997; Nutman, 2007; Adedayo et al., study showed a non-significant increase in IgG 2009). in scabietic patients (Morsy et al., 1995; Walton et al., 2010). No significant differences in complement proteins levels were found between patients The current study showed significant and controls which were in agreement with increase in the IgM levels in patients than in conclusions obtained in other studies (Cabrera controls, these results were agreed with that et al., 1993; Morsy et al., 1993; Şenol et al., 22

1997; Mika et al., 2011) studies have indicated similar results, whereas in other studies, 5- CONCLUSION elevated levels of complement C3 were The present study showed that the observed (Arlin et al., 1994; Christian, 2015). immunological reactions involved in scabies High numbers of lymphocytes, monocytes, infestation includes both cellular and humoral eosinophils and basophils in patients with immune response, the most elevated leukocyte scabies were noticed by Pardo and Kerdel level is eosinophils, concerning humoral (1994). Cadman and Lawrence (2010) stated response IgE showed most elevated levels that granulocytes are innate effector cells in the among patients compared to controls. host immune defense against many However, these results are not absolute since multicellular parasites. Data’s now highlights there are papers from literatures showed similar granulocytes with immunomodulatory roles as results to the present study, while others well, able to produce cytokines and reported different ones concerning both cellular chemokines that can bias the immune response and humoral immune responses, for this itis in a particular direction. Eosinophils, mast cells recommend that studies on larger population and basophils are reported as responsible for groups perform in future works. the initiation and ongoing regulation of Th2 responses. They can be rapidly recruited to sites of infection and draining lymph nodes Ethical consideration where they produce IL-4 and ⁄ or IL-13 An explanation of the objectives of the (Cadman and Lawrence, 2010). Walton et al. study was done and an informed verbal consent (2008) reported blood eosinophilia and was obtained from all patients. In the case of enhanced production of IgE, these results are in minors, parents or guardians were asked for the agreements with that of the present study consent. The study was approved by the where significant changes in numbers of Research Ethics Committee of the College of lymphocytes, monocytes, eosinophils and Medicine, Hawler Medical University, Erbil – basophils were noticed (P< 0.05). Iraq

REFERENCES development of protective immunity in canine scabies. Vet. Parasitol., 62: 133-142. ADEDAYO, O.; GRELL, G. AND BELLOT, P. (2009). Mites and HTLV-1 at the Crux of a 10-year Itch ARLIAN, L. G.; MORGAN, M. S.; VYSZENSKI- and Plaque-Like Lesions (Human T-cell MOHER, D. L. AND STEMMER, B. L. (1994). Lymphotropic Virus 1). Infections in Medicine, Sarcoptes scabiei: the circulating antibody 26(4): 126-130. response and induced immunity to scabies. Exp. Parasitol., 78: 37-50. ARLIAN, L.G.; FALL, N. AND MORGAN, M.S. (2007). In vivo evidence that Sarcoptes scabiei ARLIAN, L. G.; RAPP, C. M. AND MORGAN, M. S. (Acari: Sarcoptidae) is the source of molecules (1995). Resistance and immune response in that modulate splenic gene expression. Journal of scabies-infested hosts immunized with Medical Entomology, 4(6): 1054–1063. Dermatophagoides mites. Am. J. Trop. Med. Hyg., 52: 539-545. ARLIAN, L. G.; MORGAN, M. S.; RAPP, C. M. AND VYSZENSKI-MOHER, D. L. (1996). The 23

CABRERA, R.; AGAR, A. AND DAHL, M. V. (1993). MORSY, T. A.; EL ALFY, M. S.; ARAFA, M. A. S.; The immunology of scabies. Seminaris in SALAMA, M. M. AND HABIB, K. S. (1995). Dermatology, 12(1): 15-21. Serum levels of tumour necrosis factor alpha (TNF-alpha) versus immunoglobulins (IgG, IgM, CADMAN, E. T. AND LAWRENCE, R. A. (2010). and IgE) in Egyptian scabietic children. J. Egypt Granulocytes: effector cells or Soc. Parasitol., 25 (3): 773-786. immunomodulators in the immune response to helminth infection? Parasite Immunol., 32: 1–19. MORSY, T. A.; ZOHDI, H. W.; ABDALLA, K. F.; NASR, M. E.; IBRAHIM, A. A.; EL SAID, A. CHRISTIAN, L. D. (2015).The role of endogenous M. AND KHALIL, H. T. (1994). scabies mite complement inhibitors in the Immunoglobulins in patients with atopic development of Streptococcus pyogenes skin dermatitis due to mites infestation in Qualyobia infections. M.Sc. Thesis, School of Biomedical Governorate, Egypt. J. Egypt Soc. Parasitol., 24 Sciences/ Institute of Health and Biomedical (3): 495-504. Innovation/ Faculty of Health Queensland University of Technology & QIMR Berghofer ŞENOL, M.; ӦZERAL, H. I.; ӦZERAL, E.; ŞAŞMAZ, Medical Research Institute, 89 pp. S.; TURAN, F. AND SOYTÜRK, D. (1997). Serum Immunoglobulin and Complement Levels FALK, E. S. AND EIDE, T. J. (1981). Histologic and in Scabies. J. Turgut Özal Med. Cen.; 4(1): 37- clinical findings in human scabies. Int. J. 39. Dermatol., 20 (9):600–605. NUTMAN, T. B. (2007). Evaluation and differential GUREVITCH, A. W. (1985). Symposium on parasitic diagnosis of marked, persistent eosinophilia. infections. Scabies and Lice. Ped Clin of North Immunol Allergy Clin North Am., 27(3): 529– America, 32(4):987-1018. 549. HILL, P. B.; MORIELLO, K. A. AND DE BOER, D. J. PARDO, J. R. AND KERDEL, F. A. (1994). Parasites, (1995). Concentrations of total serum IgE, IgA, arthropods, hazardous animals and tropical and IgG in atopic and parasitized dogs. Vet dermatology. In: Moschella SL, Hurley HJ, eds. Immunol. Immunopathol., 44: 105-113. Dermatol. 3rd edn. Philadelphia: WB JAMES, W. D.; BERGER, T. G. AND ELSTON, D. M. Saunders:1923–2004. (2011). Parasitic Infestations, Stings, and Bites. PODDAT, A. AND NASIRIAN, H. (2007). Prevalence In: Andrews Disease of the Skin: Clinical of Pediculosis and scabies in the prisoners of Dermatology, 11th edn. Philadelphia: WB Bander Abbas, Hormozgan province, Iran. Saunders Compan; 20: 442. Pakistan J. Biol. Sci., 10: 3967-3969. BEGGS, J. C.; BEZZANT, J.; COLE, D. C.; DYKE, J.; SHELLEY, F. W. AND BART, J. C. (2007). Problems EHNIS, W.; ENNESS, S.; FOSTER, E.; in diagnosing scabies, a global disease in human HOEGEMEYER, P.; JEMISON, C.; and animal populations. Clinic. Microbiol. Revi., KAUFMAN, M.; KENYON, J.; LAWHORNE, 20 (2): 268–279. L.; LEBBON, R.; MASTON, B.; RYE, R. A.; SCOTT, L.; SOMSEL, P.; SPIELDENNER, S.; WALTON, S. F.; BEROUKAS, D.; ROBERTS- STOBIERSKI, M. G.; SUNSTRUM, J.; THOMSON, P. AND CURRIE, B. J. (2008). SZLACSKY, M.; VANVLIET, P. AND New insights into disease pathogenesis in crusted WALKER, E. D. (2005). Scabies prevention and (Norwegian) scabies: the skin immune response control manual. Wer. 1, Michigan Department of in crusted scabies. Br. J. Dermatol., 158: 1247– Community Health, 57 pp. 1255. MANCINI, G.; CARBONARA, A. O. AND WALTON, S. F.; PIZZUTTO, S.; SLENDER, A.; HEREMANS, J. F. (1965). Immunochemical VIBERG, L.; HOLT, D.; HALES, B. J.; KEMP, quantitation of antigens by single radial D. J.; CURRIE, B. J.; ROLLAND, J. M. AND Immunodiffusion. Immunochem., 2: 235- 254. HEHIR, R. O. (2010). Increased allergic immune MIKA, A.; GOH, P.; HOLT, D. C.; KEMP, D. J. AND response to Sarcoptes scabiei antigens in crusted FISCHER, K. (2011). Scabies Mite Peritrophins versus ordinary Scabies. Clinical and Vaccine are potential targets of human host innate Immunology, 17(9): 1428–1438. immunity. PLOS Neglected Tropical Diseases, 5(9): 1-14. MORSY, T. A.; KENAWI, M. Z.; ZOHDY, H. A.; ABDALLA, K. F. AND EL FAKAHANY, A. F. (1993). Serum immunoglobulin and complement values in scabietic patients. J Egypt Soc Parasitol, 23: 221-229.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 24-31 http://dx.doi.org/10.21271/ZJPAS.29.2.3

The Economy Feasibility of Implementation WDS Project in Mala Omer Catchment Area

1 2 Dana Mawlood and Awaz Jalal Hussein 1- Civil Engineering Department, college of Engineering, University of Salahaddin

2- Construction Engineering and Management, KRG Ministry of Municipalities and Tourism, Head of Zakho Municipalities

A R T I C L E I N F O A B S T R A C T

Article History: The aim of the present study was to evaluate the Water Distribution System Received: 07/05/2016 (WDS) and water distribution economy feasibility in light of Mala Omer research Accepted: 15/11/2016 area that belongs to KR-I. Data have been collected regarded Mala Omer through Published: 07/06/2017 site visits and interviews with stakeholders and it was then analyzed for Keywords: information abstraction to assess the water distribution feasibility. Operation Mala Omer expenditures (OPEX) were estimated to 39% of the total revenue. The WDS WDS Assessment network was not sufficient and new water paradigm was proposed working by gravity. The costs and revenue have been analyzed, the capital cost will require Water price about five years. While the Internal Rate of Return (IRR) was 33.4%. The results Economy Feasibility of the study showed insufficient WDS with significance of the economy feasibility of the project. Family size should have significance consideration in water *Corresponding Author: consumption and price rates. Dana Mawlood [email protected]

1. INTRODUCTION restricts the usage by others, and therefore, Human kind cannot survive more than few there is a cost involved in the action (Mays, days without water. No developments and 2009). The use of water charges to generate human achievements would have been resources for maintenance and to reduce achieved without water (Brooks et al., 2009). demand is widely advocated (Perry, 2001). A Poor water management mostly hurts poor key component of pricing and institutional people (Mays, 2009). The target on equitable, reform is to establish water prices that reflect participatory and accountable water the full cost of water consumption and provide governance will require strong political incentives for efficient water-use decisions, commitment, appropriate policy and legal including those relating to investment in new frameworks, effective institutional structures, potable supplies, alternative sources and water efficient administrative systems and capable savings. The purpose of consumption-based human resources aligned with required pricing is to encourage more efficient water use investments (Biswas et al., 2008).Thus, it by aligning water bills and water consumption needs to be recognized that using water (National Water Commission, 2011). 25 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

The current study is conducted in drinking water (Roy et al., 2010); no study has Kurdistan Region of Iraq government, which been undertaken in Kurdistan Region of Iraq represents the primary investor in water government for determining economic infrastructure of the research area Mala Omer. feasibility of water thus far. The research area is a small community belongs to Erbil province. Therefore, this study is conducted to study the feasibility of the water economy within the The main concerns of the community are research area. The approach is interested in improper water distribution system and assessing the project’s ability to generate the continue deficit in amounts supplied. This is revenue streams so as to cover financial costs mainly because of irrational exploitation of the over time. “Water has an economic value in all aquifer and lack of capacity in water sector. its competing uses and should be recognized as The pricing reform aims to make the economic an economic good, for example, having efficiency of water use and the industry as a ensured basic human needs, allocating water to whole getting better. Efficient water pricing its highest value, and moving towards full cost helps ensure that water-related production and pricing, rational use and cost recovery” [Mays, consumption decisions across all sectors should 2009; Rahaman, 2009]. be reflective of the costs they require, that way driving national economic productivity and societal welfare gains (National Water 2. METHODOLOGY Commission, 2011) . However, the effect of pricing on water conservation and elsewhere 2.1. Location of Research Area has been effectively demonstrated like in The selected case study is the water Tucson (Beecher et al., 1994) and for distribution network in Mala Omer. It is a agricultural water in Morocco (Lionboui et al., small community of KRI, belongs to Erbil 2014). There should be an assessment to province and it is located in coordinates evaluate the cost and benefits of water supply. 36°18�0ʺ N and 44°8�3ʺ E. The topography People pay water fees in most Kurdistan of the research area face a huge difference in Region Government places; however, in Mala elevation changes since the lowest and highest Omer, yet, the government provides water free points range are between (548 and 901 m) of charge for people living there. The provided above S.L. water is not enough and does not fill the people needs as there is yet a shortage in water supplying similarly as in some cities in India, 2.2. Data Collection and Analysis for instance, Kolkata (Roy et al., 2010). It was There is no unique method of collecting shown previously that Water Resources and data which is perfect in all terms, besides there Economics is addressing the economic and being no reliable database system within financial dimensions that affect the use of Kurdistan Region Government (KRG). In the water resources, across different economic present study, questionnaires and personal sectors, including rural and urban water supply interviews were used for data collection. The (Roy et al., 2010; Barde and Lehmann, 2014). amount of the consumed water in the research The study in Kolkata used the artificial neural area was difficult to be accurately estimated. network technique for estimating cost of water. The sources of water were determined by People were willing to pay for supply of personal interviews with Mala Omer water 26 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

wells operators and private owner wells. for population growth rate forecast. Internal Global Positioning System (GPS) was used to Rate of Return (IRR) and capital recovery determine wells location, and then, payback period methods were used for Geographical Information System (GIS) was economic feasibility. Microsoft Excel was used used to determine the location, topography, for financial calculations and sensitivity graph distance measurement between wells, and land and analysis. use map, Fig. 1. Exponential equation was used

Figure 1: Wells Location Map of the Research Area and Land Use.

3. RESULTS AND DISCUSSION 3.1. Water Distribution System (WDS) The water distribution systems used within the research area are mainly through direct Eighty-five wells were observed to pumping and also pumping from storage water abstract water from the groundwater within the tanks. There are about 5,000 meters of old research area, but ten wells were dried and water distribution pipes within the research were not suitable for abstracting water. Twenty area. The system misses manholes in general, eight wells of them are used for domestic water especially, in case of old water distribution supply within the research area and eighteen of pipes that cause delay in identifying the them are operated by government and the other leakage, and broken pipes that lay under houses are personnel by public people, some of them and causes mixing of wastewater with drinking are shared for domestic and agricultural (KRG- water beside the improper design and pipe MM). 27 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

erection methods that result in traffic disruption 3.2 Evaluation of the Water Supply Network (KRG-MM). The supplied water has been decreased due In fact, water is distributed from many to the groundwater continuous depletion wells in different places. In addition, the (Iglesias et al., 2009) as a result of lack topography of Mala Omer faces huge integrated water planning. Therefore, it is difference in elevation. There is no equity in recommended that the unifying WDS and water distribution among served number of supplying water to be reliable. This is because families provided with water, and about 1% of the old existed pipes are not reliable and they the served population has no water connection faced unplanned growth in land use changes to their houses. Other houses are provided with and constructions have buried some pipes. at least one connection; whereas, there are Besides, it cannot provide the required families does not having enough water, pressure, aligned with higher costs of pumping because of insufficient pressure in water that from different areas duplicate costs aligned make it difficult to reach them. In addition, with more drawdown. operation and maintenance costs for water As mentioned earlier, the reliability of the network maintenance are also insufficient and existing aging systems is continually not provided on time to cover the required decreasing (Mays, 1999). In addition, the maintenance. existed WDS network does not provide the Every year, the required amount of water is desired pressures. It was concluded that, it is increasing, but wells’ yield is decreasing more effective for consistent and effective (KRG-MM). Therefore, wells have become WDS to design a new one, which will be based unable to provide the required water; thus, new on the design criteria for allowable pressures water pipe was driven from Pirmam city to the and velocities. In addition, it is more research area passing through the main old economical and easier for operation because it road of research area (KRG-MM). This does not need pumps. includes an 8 inches ductile pipe and connected The population of Mala Omer was 3000 to the existed main pipes that are four inches in persons by 1997 (Sharif, 1998) and reached diameter. Thus, consequently, that pipe to be 11655 persons by 2013 (KRG-MM), research connected to the existed wells and storage area is facing a big increment in population, tanks within the research area that have a total which is estimated to be 7.98% using capacity of 220 m3. Implementing with existing exponential equation (Rubin and Davidson, topography conditions and tank positions at 2001). It is extreme when compared to Erbil first place, the project includes providing more population incremental rate, depending on manholes to the area (KRG-MM). Erbil population data (KRG-MP, 2014) using The amount of the consumed water in the the same exponential equation estimated to research area is frequently difficult to be equals 2.32%. This difference in the population accurately estimated. This is due to the absence increase is due to the location of the research of any measuring meters, storage tanks with area, which is close to Erbil city that made specified times and also missing records of people settle to the research area. daily amount abstracted from wells; because Therefore, the government should take the main source of water is ground-water wells serious actions to balance the development in for supplying water for domestic purposes, urbanization. As well as controlling the agricultural and commercial purposes (Roy et population growth by considering that all parts al., 2010). of the KRG area require to be planned on basis 28 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

of providing the same welfare and flows in each node, velocity in each pipe. The entertainment. Hence, people can obtain their WDS network was redesigned with correct life requirements equally. According to this diameter. Valve positions were identified, and basis, the design rate of increment for the pressure ranges between 15m and 61m. future should be the same of Erbil city. Velocity ranges between 0.3 and 1.8m/sec A new WDS network paradigm was (KRG-MMT) it is also allowable to pass that proposed for the community of the research ranges to 2.5 m/s in some cases (Mays, 1999) area. The population estimation was 11,655 and fire hydrants were also identified. The persons per 1,500 homes by the end of 2013. In gravity distribution was used for the design average, ~8 people per home (KRG-MM). because the storage tank could be placed in After population estimation, based on the area above the community level (Stul and Mc questionnaire conducted within the Mala Omer Ghee, 1982). Gravity flow water distribution community, the daily water required per capita systems are reliable and cost effective over was estimated, that equal 125 LPCD for pumping systems as no external power is domestic purposes. Fifty liters were added for required to maintain the flow (Swamee and public use (Stul and Mc Ghee, 1982) and 20% Sharma, 2000). Pipes of ductile type have been was calculated for the losses and illegal taps used in all sizes. The lengths and diameters are (Arnalich, 2011). The total required water shown in Fig.2. The storage tank capacity was equals to [(125+50)*1.2], which equals to 210 estimated to (20.74*9.76*4.88) m length, width LPCD. The proposed network design should and height, respectively. Seven Air Relief serve a specified period of time extends to Valves was required. In addition seven future that has been designed for 2030. In pressures sustain valves and three pressures addition, the projected population has been reduce valves are required. Worth to mention estimated for future demands. ductile pipes can undertake pressure until 70m Then, Nodes that have been determined and (Chin, 2015). Also Twenty-six Gate valves are the demands in each node have been calculated required. A check valve was required and Six as well as the diameters for pipes have been Fire Hydrants were added. assumed. The water for fire demands are added to the storage tank and are calculated as follows: Fire demand = 1000 gal/min (Mays, 1999) = 1000 * 3.78= 3780 liter/minute for two hours fire duration Maximum number of fires happening in the research area is one per any time (KRG-MM)

Data have been projected to EPANET Figure 2: Pipes diameter and lengths of the proposed program for WDS network analysis, it is free water distribution network paradigm. download program developed by EPA for The layout of WDS networks perform water network analysis (Rossman, 2000) which better when designed on regular areas. is selected for analysis, furthermore there are Irregular areas increase cost of pipes because other commercial programs that could be used relatively more lengths of pipes are required. for same purposes like WaterCAD and KYpipe More number of valves is required. In addition net. The program analysis the pressure and 29 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

the calculation of pipe sizes are more complicated. Furthermore, for more reliable water distribution system and effective water resources management, other water consumption sectors, such as industrial and agricultural sectors, should be included in WDS. The best indicator of how the total water is distributed to the community is land use (Mays, 1999). Water distribution system Figure 3: estimated revenue of water use costs by the should be designed at first stages after land use community households and public service buildings. planning of an area. In addition, avoid many While operation expenditures (OPEX) was differences in paths and provide as much as estimated to 14,000,000 IQD/month. Thus possible equal water distribution system lines OPEX was estimated to be equal to 39% of and more fluent paths for design, revenue as shown in Fig.4. implementation and maintenance.

3.3. Financial Analysis The water distribution tariffs recently started to be required by consumers. Until the end of 2014, there were no water costs payments by consumers, and for consumers, there were no water metering and unitization.

Water is not for free and there are prices for Figure 4: Capital cost, annual revenue, and water. Based on the proposed KRG policy of expenditures. pricing water, the estimated annual revenue Attention should be paid to cost recovery from water is shown in Fig. 3, which is equal to for the project Payback period that starts after 300 Iraqi Dinar (IQD)/m3 for the first 15 m3 per project completion by one month and whole month, it becomes 500 IQD/m3 for 16 – 30m3 capital recovery need 4 years and 11 months. per month, it becomes 1000 ID for 31-60 m3 Therefore in November 2018 whole capital will per month (KRG-MMT). For public and be recovered as shown in Fig. 5. governmental building, the price is 1000 IQD/m3. The consumption has been estimated to 1m3/day/household. In addition, the estimated Capital Expenditures (CAPEX) was 1344810000 IQD. The revenue estimated for 2014 to be 428,703,750 IQD and increases as water population increases to reach 636,195,629IQD.

Figure 5: Capital cost recovery payback period. 30 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

In order to estimate the profits of the and not economic. In addition the existed WDS project income, we found IRR, which is equal doesn’t provide the required pressure and to 33.4%, as follows: velocity. Aligned with high population growth that was estimated to 7.98% and this fact had Find Present Worth of the future revenue and putted more pressure on water system. adventures Therefore it is essential to restrict the Given F (P /F,i,n) P = F(1+ i)-n (Newnan, 1991) population growth in balance with Erbil city At i% PWV is equal to = - CAPEX + Total that estimated to 2.32%. Based on KRG water estimated PWC (REVENUE-OPEX) authorities proposed water prices the financial IRR = 33.4%. The economy feasibility of the analysis of revenue showed the positive project was positive and it is feasible economy feasibility of the project. However, economically. While the price policy was for more researches are required to price water domestic purposes and no prices were assigned based on family size and also for agricultural for agricultural, also the family size has no sector to conserve water in mentioned sector. consideration in pricing policy. However, Also, it is of great significance to consider Fig.6, illustrates the differentiation between water pattern consumption change to be input parameters and output results of the considered if the changes will effect on the financial analysis, and the most affecting revenue and economy balance condition. factors are quantity and price of cubic meter of water, however the water consumption Acknowledgements increases the cost to consumer increase. Thanks to Kurdistan Regional Government. Special thanks to Salahadin University, College of Engineering. Many thanks to the research area, Mala Omer, authorities and people.

REFERENCES Arnalich, S., 2011. Epanet and Development. How to Calculate Water Networks by Computer. Arnalich. Barde, J.A. and Lehmann, P., 2014. Distributional effects of water tariff reforms–an empirical study for Lima, Peru. Water Resources and Economics, 6, pp.30-57. Figure 6: Sensitivity graph for financial Beecher, J.A., Mann, P.C., Hegazy, Y. and Stanford, analysis J.D., 1994. Revenue Effects of Water Conservation and Conservation Pricing: Issues and Practices. From figure 6, it is shown that the main Columbus, OH: National Regulatory Research affecting factors on revenue are the price and Institute. Biswas, A.K., Rached, E. and Tortajada, C., 2008. Water the quantity and whenever the quantity of as a human right for the Middle East and North consumed water decreases the revenue Africa. Idrc. decreases and this affect the economy balance Brooks, D.B., Brandes, O.M. and Gurman, S., 2009. Making the most of the water we have: The soft path of the project. approach to water management. Earthscan. Chin, D. A. (2015) Water Resources Engineering (3rd edn.). Pearson. 4. CONCLUSIONS Newnan, D.G., 1991. Engineering economic analysis It was concluded from the present study (Vol. 1). Engineering Press. Iglesias, A., Garrote, L., Cancelliere, A., Cubillo, F. and that the existed WDS network was unreliable Wilhite, D.A. eds., 2009. Coping with drought risk in 31 Mawlood and Hussein /ZJPAS: 2017, 29(2): 24-31

agriculture and water supply systems: Drought Perry, C.J., 2001. Charging for irrigation water: The management and policy development in the issues and options, with a case study from Iran (Vol. Mediterranean (Vol. 26). Springer Science & 52). IWMI. Business Media. Rahaman, M.M., 2009. INTEGRATED WATER Kurdistan Region Government, Ministry of Municipality RESOURCES MANAGEMENT: Constraints and and Tourism (KRG-MMT), General Directorate of opportunities with a focus on the Ganges and the Water and Sewerage, Design Department. Brahmaputra River Basins. Teknillinen korkeakoulu. Kurdistan Region Government, Ministry of Rossman, L.A., 2000. EPANET 2: user’s manual. Municipalities (KRG-MM), General Directorate of Roy, K.D., Thakur, B., Konar, T.S. and Chakrabarty, Erbil Municipalities, Mala Omer Municipality S.N., 2010. Rapid evaluation of water supply project Kurdistan Region Government, Ministry of Planning feasibility in Kolkata, India. Drink. Water Eng. Sci, (KRG-MP), Kurdistan Region Statistics Office, 3(1), pp.29-42. Population Projection Report for KRI for period Rubin, E.S. and Davidson, C.I., 2001. Introduction to (2009-2020), 2014 Engineering and the Environment. New York: Lionboui, H., Fadlaoui, A., Elame, F. and McGraw-Hill. Benabdelouahab, T., 2014. Water pricing impact on Sharif, A. J. (1998) Study of Local Climate Comparison, the economic valuation of water resources. Erbil Area Climate (Doctoral Thesis in Philosophy of International Journal of Education and Research, Geography, College of Art, Sallahadin University- 2(6), pp.147-166. Hawler). Mays, L. ed., 2009. Integrated Urban Water Stul, E.W. and Mc Ghee, T.J., 1982. Water supply and Management: Arid and Semi-Arid Regions: sewerage. McGraw-Hill International Book UNESCO-IHP (Vol. 3). CRC Press. Company. Mays, L.W., 1999. Water distribution system handbook. Swamee, P.K. and Sharma, A.K., 2000. Gravity flow New York, NY, USA: McGraw-Hill Professional water distribution system design. Journal of Water Publishing. Supply: Research and Technology-Aqua, 49(4), National Water Commission, 2011. Review of pricing pp.169-179. reform in the Australian water sector.

ZANKO Mawlud Journal S. et ofal./ PureZJPAS: and 2017 Applied, 29(2): 32- 42Science

The official scientific journal of Salahaddin University-Erbil

ZJPAS (2017), 29 (2); 32-42 http://dx.doi.org/10.21271/ZJPAS.29.2.4

Structural characterization and Thermal Behavior of Sm3+ Ions Doped Sodium Tellurite Glasses

1,2Saman Q. Mawlud, 1Mudhafar M. Ameen, 2Md. Rahim Sahar, 1,2Kasim F. Ahmed

1Department of Physics, College of Education, University of Salahaddin, Erbil, Kurdistan Region, Iraq. 2Advanced Optical Material Research Group, Department of Physics, Faculty of Science, University of Technology Malaysia, Skudai, Johor, Malaysia.

A RT I C L E I N FO A B ST R AC T

ArticleHistory: +3 The influence of Sm ions concentration doped sodium Received:27/08/2016 tellurite glasses on structural characterizationand thermal Accepted:20/11/2016 parameters have been investigated. Glass samples with molar Published:07/06/2017 composition (80-x) TeO2-20Na2O-xSm2O3 glasses (x=0, 0.3, 0.6, Keywords: 1, 1.2, 1.5) are prepared by conventionalmelt quenching Tellurite glass, technique.Crystallization temperature (Tc), melting temperature Rare Earth, (Tm) and glass transition temperature (Tg) are measured by using Glass transition, FTIR, Raman spectra differential thermal analysis (DTA),it is found that the stability factor (ΔT) of the glassincreases from (58.5to97.8) ºC with the

increasingSm O . The amorphous phase nature of the glass *CorrespondingAuthor: 2 3 samplesare observed by using X-ray diffraction (XRD), scanning Saman Q. Mawlud electron microscopy (SEM) and energy dispersive x-ray (EDX) Email: [email protected] analysisspectrometer are applied to study the structural properties of the glass samples. Values of Thedensity (ρ), molar volume (VM), and ionic packing density (Vt) were calculated for each of the glass compositions.The effect of the Sm2O3 on the glass structure has been investigated by using Fourier transform infrared (FTIR)and Raman spectroscopies, the FTIR spectra are -1 characterized by a band of 637 cm for the telluride glass, high -1 frequency peak at 668 cm presented by Raman spectra which indicates that these glasses network arebasically consists of TeO4 and TeO3/TeO3+1structural units. The Raman spectra of shows the presence of Sm-O bond, Na-O bond, Te-O-Te bridging configurations, vibrations of Te-O-Te bonds and stretching modes of non-bonding oxygen found on the TeO3/TeO3+1 structural unit.

1. INTRODUCTION theaidof the secondary material component Under normal quenching conditions which is called a network modifier.This tellurium dioxide (TeO2) does not possess the specific feature makes TeO2a conditional ability of forming a glassy network without glass former (El-Mallawany, 2011; Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42

Çelikbileket al., 2011).Manystudies indicate of the Sm2O3 doped glasses has been studied that heavy metal oxide (HMO) glasses have through Raman and FTIR Spectra. been found to be more promising convenient glassy materials especially for photonic 2. MATERIALS AND METHODS applications with acceptable low phonon TeO2-Na2O-Sm2O3glass samples energies (Sun et. al., 2006;Pan et. al., possessing compositions(80-x) TeO2- 1996),their wide advantages of tellurite 20Na2O-xSm2O3 with glasses makes them to be represented as a (x=0,0.3,0.6,1,1.2,1.5)are prepared using melt more attractive structure among the HMO quenching techniquewhich is essentially the glasses such as low temperature of melting, amorphous solid can be formed by the good corrosion resistance, excellent chemical continuous hardening (namely increase in durability, low glass transition temperature viscosity) of the melt,, glasses code of the

Tg, better thermal stability, high thermal samples and their molar ratio of the expansion coefficient, low phonon energy, compositions are listed in Table 1.High purity wide optical transmission region (especially 99.9% of raw materials from Sigma in the infrared region) (0.36μm–6.3μm), high Aldrichwith an appropriate amounts of refractive index and required rare earth chemicals for 15gm batch were weighed by concentration in the matrices (Xuet al., using electronic balance Precisa 205A SCS

2005).Basically, the structure of TeO2 glasses model with accuracy ±0.001gm,the chemical contains of three dimensional network of compositions were mixed well by using a

TeO4 trigonal bipiramids (tpb) units having milling machine. Platinum crucible of about two each of oxygen at two equatorial and 30ml capacity containing the batch was used axial sites with one other equatorial site being and preheated at 250ºC for about minutes for occupied by a lone pair of electrons, once the reducing the batch blanket coverage on the modifier is introduced to the structure, the top of the glass and enlarges the free non three dimensional network will break down coverage glass melt surface(Saharat al., with the conversion of TeO4 units into 2007).Then the batch is melted at 900 ºC for TeO3+1 and TeO3 units (Kiefferet al., 2006; 40 min by a controlled electric furnace. The Radaet al. 2011). melts are poured on to a stainless steel mold In addition to the glass former and annealed at 250 ºC for 3hours, then the conditionality and fast quenching sample cooled down tothe room temperature, requirements properties of tellurite glasses, sample powder of the glass prepared and used they are also counted as a good host for the for characterizing each of Tg, Tc and Tmby formation of rare earth doped glasses.The Te– Pyris Dymond TG/DTA technique at a O bonds are weak and canbe broken easilyby heating rate 50°C-1000°C at 10°C/min.To addingheavy metal and the rare earth atoms analysis the amorphous state of the samples (Muraliet al., 2005). In the literature there are an advanced powder XRD Bruker D8 were relatively few reports on structural of glasses used, the CuKα radiation specification was doped with Sm3O ions (Bolundutet al., (1.54A°) at 40 kV, 100mA and scanning 2015;Yusoffet al. 2015). Accordingly the angel 2θ ranges between 10°-80°. A Perkin– present work aims to investigate the influence Elmer FTIR double beam spectrometer over of Sm3+ ion on the structural and thermal the range 400-4000 cm-1 are used for studying properties of TeO2-Na2O glasses. The the transmission measurements, the spectra thermal modification of the glass system were resolution of 4 cm-1at room temperature made analyzed by DTA technique and the structure by using KBr pelletswere investigated.Raman analysisis performed using a confocal Horbia Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 Jobin Yvon (Model HR800 UV) with Argon glass samplesis shown in Figure 1, it can be ion laser (excitation wavelength 514.55 nm) seen thatthe density of TNS glass system operates at 20 mW in the range of 100-900 increasesfrom 4.903 gcm-3 for x=0 mol% to cm-1. Relatively fine glass powders are used 5.019g cm-3 forx=1.2 mol% of Sm3+ion. for Raman and FTIR measurements. Higher molecular mass of Sm3O2(348.74 g -1 - Traditional Archimedes method is mol ) andthose for TeO2(159.60 g mol used for determining the density of the glass 1)might be responsible for increase its density sample after measuring the weight of the [15]. The decrease in density at x=1.5mol% sample by using a sensitive analytical balance might be caused by Sm3+ ions which PrecisaXT220A, toluene ( =0.8669 gcm-3)is participatein the structure of glass and make used as an immersed liquid.Thedensity the density decreased(Yusoff and Sahar, iscalculatedusingtheexpression (Azmiet al., 2016).A molar volume of the TNS 2015): glassagainst Sm2O3 % is plotted in the Figure1, it reveals that the molar volumeof glass increased from TNS1 to TNS3 as the

Sm3+content increased from 0 mol% to 0.6 WhereWaand Wt are weightoftheglasssampleinairand in toluene mol%, while the molar volume of glass TNS4 3+ respectively, is the density of air and is and TNS5 decreased with increasing of Sm the density of the toluene. The molar volume content,this behaviorcan be explained as the Sm3+mole friction content increased the (VM) of the glasses was calculated from density values according to (Yusoff and structure of glasses willget more compact due Sahar, 2015): to increase in packing density of oxygen (Yusoff and Sahar, 2016), thisis indicate that the structureof TNS glasses changed, this

manners of molar volume is in consistent with where M is the molar weight and ρ is the increasing behavior of rigidity and the density of the glass. The ionic packing compactness of glass samples(Hajeret al., density (Vt) is calculated using Makishima 2014). and Mackenzie approach (Yusoff and Sahar, 2015; kareemet al., 2011), 29.0 5.02 Molar Volume (cm ρ 28.9

) 5.00 VM -3 28.8 where xi is the mole fraction (mol%) 4.98 3 28.7 and Vi is packing density parameter (m /mol). 4.96 28.6 For an oxide glass of the form MxOY, the 4.94 3

28.5 mol value of Viyields (Yusoff and Sahar, 2015): 4.92 Density (gm cm Density (gm

28.4 -1

4.90 ) 28.3 - 0.0 0.3 0.6 0.9 1.2 1.5 whereNA is Avogadro’s number (mol Sm O (mol%) 1 2 3 ), rM and roare the Shannon’s ionic radius of metal and oxygen, respectively. Table Figure 1: Density and molar volume of the

1represents the glass sample code and their glasses (80-x) TeO2-20Na2O-xSm2O3 as a molar ratio effect on each of the density, function of Sm2O3 mol%. molar volume and ionic packing density.The effect of Sm2O3%on both of the density and molar volume for each composition of the Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42

Table 1: Glasses sample code and calculated density, molar volume and ionic packing density. Sample TeO Na O Sm O M V ρ 2 2 2 3 V M Code % % % g mol-1 t cm3 mol-1 g cm-3 TNS1 80 20 0 140.07 0.4012 28.571 4.903 TNS2 79.7 20 0.3 140.64 0.4017 28.623 4.914 TNS3 79.4 20 0.6 141.21 0.4019 28.700 4.920 TNS4 79 20 1 141.97 0.4051 28.593 4.965 TNS5 78.8 20 1.2 142.34 0.4092 28.359 5.019 TNS6 78.5 20 1.5 142.91 0.4025 28.919 4.942

3. RESULTS AND DISCUSSION The EDX spectra evaluate the amount of eachelement present in the glasses.It is 3.1 XRD Analyses important to mark that EDX measured In order to check the non-crystalline elements by calculating the area under the nature of the glass samples, the XRD peak of each identified element(Noran, measurement is performed for all samples and 1999).SEM-EDX investigations were the result can be seen in Figure 2. The performed on the (80-x) TeO2-20Na2O- presence of a broad hump between 25 − 35° xSm2O3 with (x=1)% molefraction glasses in without any sharp crystallization peaks order to confirms the amorphous nature of the identifychangesinmorphologyandchemicalco prepared glass samples. It can be seen thatthe mposition.The typical EDX spectrum of results did not reveal any kinds of sharp TNS4 glass sample from selected area as peaks, therefore,proving the amorphous shown in Figure 3 exhibits Te, O, Na, Na and nature structure of the present glass.In this the weak Sm peak which is attributed to the study, no sharp characteristic peak of Sm is elemental traces in the glass matrix evidenced due to its small concentration in the surrounding.The presence of detected samples. elements confirms the successfulpreparation of the desired glass samples. A quantitative analysis of the EDX spectra are listed in Table 2. It shows theelements with their respective weight% and atomic%. K, L and M represent the innershell electrons. The intense peak located at 0.5 keV isconnected with the domination of oxygen (O) in the sample. However, there is a discrepencies between the experimental and calculatedpercentages (weight% and atomic%) of elements. This discrepencies is due to EDXanalyses which Figure 2: Typical XRD pattern of (80-x) quantify elements by calculating the area TeO2-20Na2O-xSm2O3 glasses (x=0, 0.3, under the peak of eachidentified 0.6, 1, 1.2, 1.5)glasses. element(Fultz and Howe, 2013) SimilarresultswereobtainedforallinvestigatedT 3.2 SEM-EDX Spectra eO2-Na2O-Sm2O3glass samples. Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 SEM micrograph in Figure 3 for the glass and this structure can be observed for other containing 1% mole of Sm2O3has glass samples. This confirmed homogeneous shownhomogeneous glassy phase. Both and amorphous nature of the prepared glasses dimensions show irregular shape of grains (Pal et al., 2011) .

Table 2: Calculated and EDX-measured weight of elements for sample containing 1 mol % Sm2O3 (TNS4 glass). Experimental Calculated Element Line Weight% Atomic% Weight% Atomic% O K 30.28 71.35 31.17 72.56 Na K 6.01 9.86 6.81 10.26 Te L 62.79 18.55 65.79 19.88 Sm L 0.92 0.23 0.98 0.28

Figure 3: EDX spectra and SEM micrograph of TNS4 sample.

3.3 DTA Spectral Analysis mol% Sm2O3 into the composition,the Tg The DTA thermogram for (80-x) value wasincreased to 267.6 °C. Obtained

TeO2-20Na2O-xSm2O3 glasses sample are results indicate that by increasing the amount shown in Figure4. The endothermic peaks due of mol% Sm2O3, the Tgof the samples also to the glass transition and melting point increases, the small increase of Tg in these andthe exothermic peak due to the glasses shows that the structure is strongly crystallization are clearly observed.The Tg and progressively modified(Pereira et al., value of 80TeO2-20Na2O have been 2016). The thermal stabilities ΔT of the TNS determined to be 265.8°C and by adding 0.3 reference glass and Sm+3: TNS glass have Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 been evaluated from their Tg, Tc and Tm (Saddeeket al., 2008). A large ΔT indicates values, the results are listed in the table 2. ΔT strong inhibition of nucleation and is generally used as a rough measure of glass crystallization (Özen et al., 2001). thermal stability and it is desirable for a glass host to have ΔT as large as possible

Table 3: Thermal parameters of (80-x) TeO2-20Na2O-xSm2O3 derived from the DTA profiles. Sample Name

TNS1 0 265.8 323.6 489.5 57.8 0.349 TNS2 0.3 267.6 334.1 490.2 66.5 0.426 TNS3 0.6 269.1 343.5 486.9 74.3 0.518 TNS4 1 273.8 350.4 486.4 76.6 0.563 TNS5 1.2 281.7 362.2 478.6 80.6 0.692 TNS6 1.5 273.1 370.6 483.0 97.5 0.868 Figure5 shows the effect of increasing %

Sm2O3 onΔT,Tc, Tg, Tm and Hruby’s parameter (H) (Kavaklıoğlu et al., 2015).

Figure 4: DTA traces of the (80-x) TeO2- 20Na2O-xSm2O3 glasses at a heating rate is 10°C/min.

The ΔT of present glasses are calculated to be in the range of (58.5-97.8) ºC, it is noted that the ΔT increases with Figure 5: Effect of Sm2O3% on each of the increasing % Sm2O3 to the composition, this on ΔT, T , T , T and Hruby’s parameter. results indicate that the present glass c g m possesses good thermal stability and anti- 3.4 FTIR Spectral Study crystallization ability.

Another factor to determine the In order to understand the structural tendency of the system to become a glass units of glasses, FTIR transmission spectra of rather than a crystal is Hruby’s parameter TNS glasses and pure KBr have been which can be defined by (Sidek et al., 2006). recorded in the range of 400-4000 cm–1 as Hruby’s parameter also calculated by using shown in Figure6. This range was used in eq. (5), the greater values of the Hruby’s order to study the fundamental vibrations and parameter indicate thehigher glass forming associated rotational-vibrational structure. tendency, andthe values of H in our glasses From Figure 6 it can be seen there are seven increased with the addition of the Sm2O3. Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 important absorption peaks appear in the FTIR spectra is divided into three regions: FTIR transmission spectra. The identical 400-900 cm-1, 1000-2500 cm-1 and 2500- peaks assignments are listed in Table 3. For 4000cm-1as shown in Figure7,Figure 8 and better clarity about the FTIR spectra, the Figure 9respectively.

-1 Table 4: Peaks position (in cm ) in the FTIR spectra of (80-x) TeO2-20Na2O- xSm2O3 glass.

Sample Sm2O3 Na-O TeO4 TeO3 M-OH Hydrogen Hydrogen OH- Code (mol%) Bonding Bonding Group Pure KBr - - - - 1637.53 2855.22 2933.75 3447.77 TNS1 0 471.80 637.51 759.61 1633.99 2851.32 2923.83 3443.73 TNS2 0.3 472.19 637.21 760.20 1627.15 2853.64 2923.07 3389.21 TNS3 0.6 473.30 635.9 765.61 1629.76 2855.22 2922.24 3395.65 TNS4 1 478.36 637.31 759.35 1630.26 2768.96 2927.44 3400.04 TNS5 1.2 475.12 619.19 759.95 1623.00 2848.98 2915.79 3382.01 TNS6 1.5 476.65 636.42 759.63 1632.26 2848.92 2921.24 3370.68 759.6/637.5cm-1represents the relative

concentrations of the TeO3 and TeO4structural units, which is absolutely dependent on the glass composition. According to the electronegativity theory, which is a measure of the tendency of an atom to attract a bonding pair of electrons, the covalency of the bond will become stronger with decreasing of the difference of electronegativity between cation and anion Figure 6: FTIR spectra of (80-x) TeO - 2 ions. From the periodic Table (Emsley, 1989) 20Na O-xSm O glass in the range of 400- 2 2 3 since the values of electronegativity for Te, 4000cm-1. Na, Sm and O elements are 2.1, 0.9, 1.17 and Figure7representthree bands at optical 3.5, respectively, the covalency of Te-O are visible range759.6, 637.5 and 471.8 cm–1and stronger than Na-O and Sm-O, respectively are assigned to stretching vibrations of TeO3 (Radaet al., 2011). As a result, the higher or TeO3+1, TeO4structural units and bending affinity of the tellurium ions to attract oxygen vibrations of Te-O-Te or O-Te-O linkages atoms yields the apparition of TeO4 structural with Na-O respectively.The change in sodium units (Hager and El-Mallawany, 2010). These tellurite structure can be predicted as the shift three bands are not exist in the pure KBr in the position is attributed to the change in spectra. the bonding length predicting (Sarithaet al., 2008; Saharet al., 1997).The shifts in the stretching vibration of TeO4 and TeO3 towards 637.5 and 759.6 cm-1are observed by increasingthe Sm3+ion concentration up to 1 mol %.This shift in the transmission bands is attributed to the deformation of TeO4 group into TeO3 throughTeO3+1 intermediate coordinate formation (Radaet al., 2011; Upenderet al., 2009).The ratio of Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42

Figure 7: FTIR spectra of (80-x) TeO2- 20Na2O-xSm2O3glass in the range of 400- Figure 9:FTIR spectra of (80-x)TeO2- -1 1000cm . 20Na2O-xSm2O3glass in the range of 2500- 4000cm-1. Figure8 shows the hydroxyl-metal (M- OH) stretching vibrations bond which is -1 observed at 1637.53 cm . This band is shifted to 1632.26 cm-1 with increasing amount of 3+ Sm concentration. This shift might be due to 3.5 Raman Spectra the addition of rare earth in the host matrix of One of the most well-known types of glasses that slightly increase the IR vibrational spectroscopy is an energy transmission and shift it to longer wavelength sensitive method Raman spectroscopy. It is (Nazabalet al., 2003). M-OH stretching considered as a finger print about structural vibration peaks also appeared for pure KBr information of the glass. The Raman spectra sample spectra. of TNS glass series in the frequency range of 100-900 cm-1is shown in Figure10, and the de-convoluted of the Raman spectra for sample TNS2 is presented in Figure11.The observed spectrum is then fitted to Gaussian peaks andto get four distinct solid line peaks named by (A, B, C and D).The sum of these picks are represented by a dotted line which is well coincide with the obtained solid line from the Raman spectra.These peaksare centered at 294.43 (A), 471.09 (B), 668.33 -1 Figure 8:FTIR spectra of (80-x)TeO2- (C) and 760.52 (D) cm .The corresponding 20Na2O-xSm2O3glass in the range of 1000- absorption peak shifts are listed in Table(4).It 2500cm-1. can be observed that the shift is dominant by -1 The IR transmission bands occur all band regions around 279.4-306.63 cm , -1 -1 around 2900 and 3400 cm-1 belong to 465.11-473.45 cm , 668.33-684.12 cm and -1 stretching vibration of the hydroxyl group and 759.06-773.3 cm . The hydrogen bond (Kumaret al., 2010). This is Raman band in the region around -1 observed clearly in Figure 9, the band ranges 279.4-306.63 cm can be assigned to both 2768.96-2927.44 cm-1 and 3400.04-3447.77 Sm3+-O and TeO3 tp which indicate thatthe cm-1 which correspond to hydroxyl group and presence of rare earth ions might significantly hydrogen bond, respectively. change the Te-O networking structure in Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42

unit through TeO3+1 intermediate coordination, this has been satisfied by Raman band shift at the certain region (Som and Karmakar, 2010).

3000

2500 C 2000 D 1500

Intensity (arb. unit) B 1000 A Figure 10: Raman spectra of (80-x) TeO2- 500 20Na2O-xSm2O3 glass system. 300 400 500 600 700 800 900 -1 theglasses(Plotnichenkoet al., 2000; Som and Raman Shift (cm ) Karmakar, 2010). TheRaman shift Figure 11: The de-convoluted Raman spectra corresponding to the band in the range of into Gaussian peak for sample TNS2. -1 465.11-473.45 cm is due to Te-O-Te Moreover, it was observed that the linkages vibration (Jaba et al., 2005). intensity of Raman peaks around 668.33- Meanwhile, the Raman peaks shift in the 684.12 cm-1 and peaks around 759.06-773.3 -1 range of 668.33-684.12 cm and 759.06- cm-1 are increased by the increasing of the -1 3+ 773.3 cm are corresponding to TeO3 bp unit concentration of Sm ions as shown in Figure and TeO4 tbp unit respectively. It can also be 10, This is may be due to the creation of TeO3 3+ observed that by adding the Sm ions from 0 tp unit by perturbation of TeO4. It is asserted to 1.5 mol % into the TNS glass will turn the that the addition of Sm3+ ions in TNS glasses glass structure to transform slightly creates more number of TeO3 tp units. byperturbation of TeO4 tbp unit into TeO3 tp

Table 5: Raman shift peaks position in cm-1 for (80-x)

TeO2-20Na2O-xSm2O3. -1 Sample % Raman Shifts/ cm Code Sm2O3 A B C D TNS1 0 284.34 473.17 671.8 759.06 TNS2 0.3 294.43 471.09 668.33 760.52 TNS3 0.6 289.74 473.45 671.01 767.81 TNS4 1 303.549 467.33 682.23 770.37 TNS5 1.2 306.63 465.11 684.12 773.3 TNS6 1.5 276.94 467.54 677.61 773.02

4. CONCLUSIONS a wide range of 2θ instead of high intensity In this study, glass formation range of narrower peaks obtained.The physical

(80-x) TeO2-20Na2O-xSm2O3 system parameters such as glass density, molar isprepared by melt quenching method.The volume and ionic packing density were found XRD results shows that all samples are to be (4.903-5.019) g cm-3, (28.359-28.919) amorphous innature since bump distributed in cm-3mol-1 and (0.4012-0.4092) respectively. Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 Thermal and structural properties are Fultz, B. and Howe, J. Transmission electron investigated by DTA, FTIR and Raman microscopy and diffractometry of materials. Springer. 2013. spectroscopies. The thermal characteristics Hager, I.Z. and El-Mallawany, R., 2010. Preparation reveal that the glass transition temperature and structural studies in the (70-x) TeO2-20WO3- and stability factor increases with the 10Li2O-xLn2O3 glasses. Journal of materials increasing of Sm2O3 mol%content. This is science, 45(4), pp.897-905. due to the increase in bond number per unit Hajer, S.S., Halimah, M.K., Azmi, Z. and Azlan, M.N., 2014. Optical properties of zinc-borotellurite doped volume which is an indication of change in samarium. Chalcogenide Letters, 11(11), pp.553- packing density in the structure.The 566. vibrational spectra of the glass system Jaba, N., Mermet, A., Duval, E. and Champagnon, B., suggested that the glass network consists of 2005. Raman spectroscopy studies of Er3+-doped zinc tellurite glasses. Journal of non-crystalline TeO4, TeO3/TeO3+1, Na2O and solids, 351(10), pp.833-837. Sm O units.Raman spectra for the (80-x) 2 3 kareem Ahmmad, S., Samee, M.A., Edukondalu, A. TeO2-20Na2O-xSm2O3 glasses showed that and Rahman, S., 2012. Physical and optical the TeO4 tbps convert to TeO3 tps with properties of zinc arsenic tellurite glasses. Results increasing of Sm2O3 % mol fraction.The in Physics, 2, pp.175-181. Raman shifts due to the structural units TeO4 Kavaklıoğlu, K.B., Aydin, S., Çelikbilek, M. and Ersundu, A.E., 2015. The TeO ‐Na O System: and TeO3 have almost equal to the intensities 2 2 Thermal Behavior, Structural Properties, and Phase in these glasses and overlapped to each other. Equilibria. International Journal of Applied Glass Science, 6(4), pp.406-418. Acknowledgments Kieffer, J., Johnson, J.A., Nickolayev, O. and Bass, The authors gratefully acknowledge the J.D., 2006. Structures and visco-elastic properties of potassium tellurite: glass versus melt. Journal of financial support from Ministry of Higher Physics: Condensed Matter, 18(3), p.903. Education, RMC, UTM and University of Murali, A., Chakradhar, R.S. and Rao, J.L., 2005. EPR Salahaddin/Ministry of Higher studies of Gd3+ ions in lithium tetra boro-tellurite Education/KRG through the research grant and lithium lead tetra boro-tellurite glasses. Physica (vote 4B182) are highly appreciated. B: Condensed Matter, 364(1), pp.142-149. Nazabal, V., Todoroki, S., Nukui, A., Matsumoto, T.,

Suehara, S., Hondo, T., Araki, T., Inoue, S., Rivero, References C. and Cardinal, T., 2003. Oxyfluoride tellurite Azmi, S.A.M., Sahar, M.R., Ghoshal, S.K. and Arifin, glasses doped by erbium: thermal analysis, R., 2015. Modification of structural and physical structural organization and spectral properties of samarium doped zinc phosphate properties. Journal of non-crystalline glasses due to the inclusion of nickel oxide solids, 325(1), pp.85-102. nanoparticles. Journal of Non-Crystalline Noran instruments. Energy dispersive x-ray Solids, 411, pp.53-58. microanalysis: Anintroduction. Kevex instruments, Bolundut, L., Culea, E., Borodi, G., Stefan, R., Inc., 1999. Munteanu, C. and Pascuta, P., 2015. Influence of Özen, G., Demirata, B., Öveçoğlu, M.L. and Genc, A., 3+ Sm : Ag codoping on structural and spectroscopic 2001. Thermal and optical properties of Tm3+ properties of lead tellurite glass ceramics. Ceramics doped tellurite glasses. Spectrochimica Acta Part International, 41(2), pp.2931-2939. A: Molecular and Biomolecular Çelikbilek, M., Ersundu, A.E., Solak, N. and Aydin, S., Spectroscopy, 57(2), pp.273-280. 2011. Investigation on thermal and microstructural Pal., M., Roy, B. and Pal, M. (2011). Structural characterization of the TeO2-WO3 system. Journal Characterization of Borate GlassesContaining Zinc of Alloys and Compounds, 509(18), pp.5646-5654. and Manganese oxides. J. Mod. Phys. 2, 1062 – El-Mallawany, R.A., 2011. Tellurite glasses handbook: 1066. physical properties and data. CRC press. Pan, Z., Morgan, S.H., Dyer, K., Ueda, A. and Liu, H., Emsley, J., 1989. The elements. Clarendon press. 1996. Host‐dependent optical transitions of Er3+ ions in lead–germanate and Mawlud S. et al./ZJPAS: 2017, 29(2): 32-42 lead‐tellurium‐germanate glasses. Journal of content. Journal of Applied Sciences, 6(2), pp.274- applied physics, 79(12), pp.8906-8913. 279. Pereira, C., Barbosa, J., Cassanjes, F.C., Gonçalves, Som, T. and Karmakar, B., 2010. Structure and R.R., Ribeiro, S.J.L. and Poirier, G., 2016. properties of low-phonon antimony glasses and

Thermal, structural and optical properties of new nano glass-ceramics in K2O-B2O3-Sb2O3

TeO2. Optical Materials, 62, pp.95-103. system. Journal of Non-Crystalline Solids, 356(20), Plotnichenko, V.G., Sokolov, V.O., Koltashev, V.V., pp.987-999. Dianov, E.M., Grishin, I.A. and Churbanov, M.F., Sun, H., Duan, Z., Zhou, G., Yu, C., Liao, M., Hu, L., 2005. Raman band intensities of tellurite Zhang, J. and Jiang, Z., 2006. Structural and up- glasses. Optics letters, 30(10), pp.1156-1158. conversion luminescence properties in Tm3+/Yb3+- Rada, S., Culea, E. and Rada, M., 2011. The codoped heavy metal oxide–halide experimental and theoretical investigations on the glasses. Spectrochimica Acta Part A: Molecular structure of the gadolinium–lead–tellurate and Biomolecular Spectroscopy, 63(1), pp.149-153. glasses. Materials Chemistry and Physics, 128(3), Upender, G., Chandra Mouli, V. and Sathe, V.G., pp.464-469. 2009. EPR, Raman, infrared and optical absorption 2+ Rada, S., Pascuta, P., Rada, M. and Culea, E., 2011. studies of Cu ions in 60TeO2-(40-x) WO3- xPbO Effects of samarium (III) oxide content on glasses. Physics and Chemistry of Glasses- structural investigations of the samarium– European Journal of Glass Science and Technology vanadate–tellurate glasses and glass Part B, 50(6), pp.399-406. ceramics. Journal of Non-Crystalline Xu, S., Fang, D., Zhang, Z. and Jiang, Z., 2005. Solids, 357(19), pp.3405-3409. Unconversion Luminescence and Mechanisms of Saddeek, Y.B., Shaaban, E.R., Abdel-Rahim, F.M. and Tm3+/Yb3+ co-doped oxyhalide tellurite Glasses. J. Mahmoud, K.H., 2008. Thermal analysis and Solid State Chem, 178, p.1817.

infrared study of Nb2O5-TeO2 Yusoff, N.M. and Sahar, M.R., 2015. Effect of silver glasses. Philosophical Magazine, 88(25), pp.3059- nanoparticles incorporated with samarium-doped 3073. magnesium tellurite glasses. Physica B: Condensed Sahar, M.R., Jehbu, A.K. and Karim, M.M., 1997. Matter, 456, pp.191-196. 3+ TeO2-ZnO-ZnCl2 glasses for IR Yusoff, N.M. and Sahar, M.R., 2016. Effect of Sm transmission. Journal of non-crystalline solids, 213, Concentration on Physical Properties of pp.164-167. Magnesium Tellurite Glasses Containing Silver Sahar, M.R., Sulhadi, K. and Rohani, M.S., 2007. Nanoparticles. In Materials Science Forum (Vol.

Spectroscopic studies of TeO2-ZnO-Er2O3 glass 846, pp. 107-114). Trans Tech Publications. system. Journal of materials science, 42(3), Yusoff, N.M., Sahar, M.R. and Ghoshal, S.K., 2015. pp.824-827. Sm3+: Ag NPs assisted modification in absorption Saritha, D., Markandeya, Y., Salagram, M., Vithal, M., features of magnesium tellurite glass. Journal of Singh, A.K. and Bhikshamaiah, G., 2008. Effect of Molecular Structure, 1079, pp.167-172. Bi2O3 on physical, optical and structural studies of

ZnO-Bi2O3-B2O3 glasses. Journal of Non- Crystalline Solids, 354(52), pp.5573-5579. Sidek, H.A.A., Halimah, M.K., Faizal, M.N., Daud, W.Y.W., Zaidan, A.W., Zainal, A.T. and Halim, S.A., 2006. Synthesis and elastic behaviour of borate glass doped with high tellurite

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 43-52 http://dx.doi.org/10.21271/ZJPAS.29.2.5

Assessment of natural radionuclide's in sediments of Darbandikhan Lake water resources at Kurdistan Region-Northeastern of Iraq.

Adeeb omer jafir1, Ali Hassan Ahmad1 and Wan Muhammad Saridan2

1- Department of physics, College of Science, Salahaddin University, Erbil, Kurdistan Region, Iraq.

2- Department of physic, university Technology Malaysia, Johor-Bahru, Malaysia

A R T I C L E I N F O A B S T R A C T

Article History: Abstract Received: 5/09/2016 A total of 25 of sediment samples were collected from Darbandikhan Lake and Accepted: 29/11/2016 Published: 07/06/2017 its different resources (spring, stream, and lake) during the summer season. The Keywords: activity concentration of primordial radionuclides and the concentration of major Radioactivity, elements were found using Energy Dispersive X-ray fluorescence (EDXRF) Sediments, Energy techniques. The average specific activity of 40K was found to be 202.27 Bq/kg, Dispersive X-ray while the activity concentration for both uranium and thorium was beyond the Fluorescence, detection limits. Statistics of multivariate analysis were applied to sediment Darbandikhan Lake. *Corresponding Author: samples, which shows that there is a strong positive correlation coefficient 40 40 Ali Hassan Ahmed between K and Ti, Mn and Fe and a weak negative correlation between K and [email protected] Mg, Si, P, Ca was observed.

1. INTRODUCTION different quantity of uranium, thorium and The radioactivity of the earth includes the potassium, their distributions are dependent on primordial radionuclides which have long half- the geological and geographical conditions. lives and they have survived during the The average concentration of uranium and creation of the earth and the cosmogentic thorium in the earth’s crust are about 2-3 and radionuclides which continuously produced 8-12 ppm, respectively [IAEA, 2003].One ppm due to bombardment of the atmosphere by of uranium in rocks is equivalent to 12.35 cosmic rays [UNSCEAR, 2000 report] Bq/kg, one ppm of thorium is equivalent to 4.06 Bq/kg and % of potassium is 313 Bq/kg The earth consists of major elements like [IAEA, 2003]. Ca, Fe, Cd, Pb, Mg, Mn, etc. and small 44 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

Sediments are small tiny particles that radionuclides and the major contain elements created due to erosion of the earth’s crust and of the earth. transported through fluid and any liquids and Study area finally deposited at the bottom of the water and Darbandikhan Lake is one of the major fluids [Sonon et al., 2007]. The radionuclides lakes among the three lakes in Kurdistan, are carried by soil, stream, and rivers, so the northern Iraq, 230 Km north-east of Baghdad lake sediments are considered as the main and 60 Km southeast of Sulaimani city on the source of radioactivity that contributes to road to the town of Darbandikhan, at altitude contamination of the aquatic living organisms. N35o8’41, and longitude E 45o45’18’ with an [IAEA,1989 Australia] altitude of 450- 578 m. Darbandikhan lake is one of the most It’s fed by two main tributaries: The important watersreservoir resources and the Tanjero River, which comes and flows in from sediments are one of the most important and the north/ northwest, and the Sirwan River, major mixing materials for building which flows from the east (Iran). The lake construction in Sulaimany governorate, so covers (according to the year) approximately detection and measurement of natural radiation 7,500 ha [Ararat K. et al., 2008; Evans, M.I., enable one to assess any possible radiological 1994]. hazard to mankind by the uses of such Many governorates in Iraq, especially in materials. Kurdistan, benefit from this lake as a source for Some previous natural radioactivity studies drinking and for irrigation agricultural lands have been carried out in sediment samples in around the lake. Darbandikhan Lake is different part of the world, such as done by currently at high risk due to working by Iran to Omale, P. E. et al., 2014; Ozmen H. et al., install Dam and pollution by sewage and 2004; Omoniyi et al., 2013 ; El-Bahi, S. M.et municipal wastes. al., 2013. The environment of the lake is surrounded

by hills covered with grass and small shrubs The aim of the present work was to and mountains (including Bashari, zmnako and determine the radioactivity concentration due zawally) that are covered in oak forests. The to natural radionuclides of 238U, 232Th and 40K rock filled embankment dam was constructed in Darbandikhan Lake sediments and the major between 1956 and 1961 for irrigation and elements in the sediments earth’s crust in power generation. summer seasons and also making the statistical correlations between the primordial 45 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

Water levels decline in summer after the spring (1). The map of Darbandikhan lake water with due to dam release and it rises again during their resources is shown in Figure (1). winter's rain .The land is used for field, especially wheat and barley [Evans, M.I., 1994].

The latitude, longitude and altitude recorded

from the GPS type (GPS72 GARMIN) at each

position the geological type and the height from the sea were recorded, as shown in Table

Table (1): Location and Geological Information of the Studied Sample Sites.

sample location Geology [Jassim, S.Z., Goff. JC, 2006] code name lontitude latitude altitude(m) S1 Jomarasi N 35O27,46.4" E 045O58,35.5" 1158 Slate and alluvial deposit qulqula S2 Hassan awa N 35O29,22.0" E 045O52,19.4" 735 Gness and state of metamorphic rock S3 Kelakawa N 35O23,48.5" E 045O53,20.3" 550.9 Alluvial deposite with grains of sand and chert S4 Zallmsarchawa N 35O19,01.9" E 046O05,26.6" 878.8 Marly limestone +chert and slope deposite of mixure of soil and pebbles Recent deposit, composed of mixture of carbonate soil and S5 Ganjan(khurmal) N 35O18,14.0" E 046O02,20.0" 569.2 sand with layers of limestone S6 Prdizalm N 35O18,24.6" E 045O58,15.8" 510.6 Alluvial deposit, composed of clay and silt. S7 Reshensarchawa N 35O21,49.0" E 045O58,45.5" 560.7 Qalqula formation (chert) with limestone of Avroman formation S8 Rechenshallma N 35O21,36.1" E 045O58,08.2" 532.7 Alluvial deposit , with grains of limestone and chert S9 Prdiqadafari N 35O20,16.3" E 045O57,09.5" 518.9 Alluvial deposit ,with mixture of sand silt and pebbles Marly limestone and slope deposit composed of mixture of clay S10 Sarchnar N 35O35,25.3" E 045O22,59.9" 763.2 and sand with pebbles S11 Prditanjaro N 35O28,45.3" E 045O25,39.4" 663.6 Alluvial deposit contain clay, sand and calcareous pebbles S12 Prdiqaragoll N 35O21,22.3" E 045O37,36.3" 557 Alluvial deposit with marl and marly limestone of Tanjero formation S13 Tapikaram N 35O20,19.95" E 045O45,07.37" 532 Alluvial deposit with marl and marly limestone of Tanjero formation S41 Awamarisaru N 35O05,08.3" E 046O04,46.2" 560 Marly limestone, marl and dolomitic limestone S15 Hana zhalla N 35O06,55.8" E 045O54,03.5" 480 Alluvial deposite S16 Xulami N 35O12,11.7" E 045O51,19.1" 481 Alluvial deposite Slope deposit mixed with pebbles of limestone with pebbles of S17 Xatitanjero N 35O16,30.31" E 045O51,05.5" 501 limestone and chert. S18 Prdikon N 35O17,12.2" E 045O35,07.0" 485 Marly limestone, marl and some layers of sandstone of tanjero formation S19 Awalellasirwan N 35O11,42.7" E 045O50,52.2" 479 Alluvial deposite S20 Plaspi N 35O11,57.5" E 045O48,14.0" 484 Dolomitic limestone with chert nodules S21 Shanisharaka N 35O09,32.63" E 045O47,25.01" 481 Red clay stone covered by alluvial deposit S22 Kani khan N 35O09,04.35" E 045O46,06.69" 480 Alluvial deposit composed of mixure of clay and low rate of humus S23 Ban qoin N 35O08,13.55" E 045O44,53.1" 482 Layers of limestone and marl covered by top soil O O Dolomitic limestone and chaky limestone with chert nodules covered S24 Darbanikhan N 35 07,18.29" E 045 43,28.49" 477 by top soil in some area. Dolomitic limestone and chaky limestone with chert nodules covered S25 Darbanikhan N 35O06,52.37" E 045O42,18.00" 480 by top soil in some area.

46 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

Figure (1): sample code location of Darbandikhan lake water with their resources.

2. MATERIALS AND METHODS homogeneous grains. About 3g of each sample 2.1 Sample collection and preparation for is pressed under the high pressure of making a XRF analysis capsule using hydraulic press and kept in a A total of 25 sediments samples were polythene bag until to analysis [Morikawa, collected from the Darbandikhan Lake with A.,2014]. their resources during the summer seasons in 2.2 X-Ray fluorescence analysis august 2014 in which six samples in each season from springs and the rest of the Energy dispersive X-ray fluorescence branches, streams and lakes were taken. spectrometer (EDXRF) types (Rigaku NEX CG) were used to measure the elemental The sediment samples were collected at the analysis of sediments as shown in Figure (2). . bottom of the lake, each sample of about 3Kg It’s a non-destructive, multi-elemental routine was kept in a thick plastic bag. The collected measurement used to determine the samples were brought to the laboratory; the concentration of 9 major elements present in 25 sediment samples were then oven dried at a sediment samples. It is capable of detecting temperature of 90° C until achieved constant wide range measurement from (11Na to 92U) weight. The sediment samples were pulverized from low part per million (ppm) levels in high into fine powder manually in order to obtain 47 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

weight percentages (%w) with high sensitivity Table (2): the specification of NEXCG spectrometer.

[Morikawa, A., 2014]. During the operation, the X-ray tube Pd target, air cooled semiconductor detector was thermoelectrically Tube power 50W:50Kv-2mA(max) cooled and no need to liquid nitrogen. Secondary targets 5 targets (max) Excitation is provided by a 50 watt Pd-anode end-window X-ray tube. A silicon drift Detector High performance SDD(Slicon detector) detector (SDD) affords extremely high count rate capability with excellent spectral Atmosphere Vacuum, Air, He resolution. This enables NEX CG to deliver the highest precision analytical results in the shortest possible measurement times. Secondary targets and polarized optics were used in NEX CG in order to provide the high peak to background ratio, which produces the higher sensitivity. Some specifications of the used detector are tabulated in table (2). The typical spectrum from XRF is shown in Figure (3).

Figure (3): The typical spectrum for sediment sample for RX9, Cu, and Mo secondary targets. Energy peaks for the various elements are indicated.

Figure (2): Rigaku EDXRF spectrometer NEXCG detector.

48 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

3. RESULTS AND DISCUSION with the standard value (400 Bq/kg) provided

by UNSCEAR, 2000 report for sediments. The Table 3 shows the ion concentrations of 40 higher value of K concentration may be sediment samples. The obtained data indicated attributed to the area around the lake which is that the main elements in all sediment samples used for agriculture purpose and for fertilizers are, Si, Mg ,Ca, Al, Fe ,Ti , Mn and Na. The +2 +2 +2 which used to enhance products and eventually major elements are Si , Fe and Ca . These leached to the water surface due to weathering elements represent about 90.5%. Generally, the and after that it deposited in the bottom of the concentrations of these elements were higher lake and causes contamination to the aquatic than the other metals in sediment samples. This environments. The average activity may be returned to the fact that these elements concentration of 40K is well below the are originated from the rock erosions. recommended values and there is no The range and average activity contribution to environmental hazards. While concentration of 40K were varied from 42.41 to 238 232 both U and Th concentration were beyond 473.68(202.27) Bq/kg. From Figure (4) its the detection limits see table (3). The same observed that only two positions have higher behavior was observed by [Omale, P. E. et al., potassium activity concentration compared 2014].

Table (3): Concentration of sediment sample (ppm) in summer seasons using the XRF technique.

Names Mg Al Si P K Ca Ti Mn Fe Th U Na S1 4400.00 15033.33 52666.67 131.67 8566.67 167000.00 3600.00 2110.00 79666.67 ND ND ND S2 3633.33 18200.00 57666.67 235.00 12033.33 143000.00 3666.67 2030.00 92666.67 ND ND ND S3 4400.00 14066.67 58666.67 97.33 9800.00 136333.33 3093.33 2586.67 104333.33 ND ND ND S4 1830.00 5066.67 34666.67 101.33 2416.67 257333.33 1256.67 1033.33 29766.67 ND ND ND S5 4966.67 14733.33 141000.00 346.67 2426.67 159000.00 826.67 313.67 9700.00 ND ND ND S6 3143.33 11200.00 185000.00 232.67 2020.00 121333.33 840.00 239.00 9200.00 ND ND ND S7 2693.33 6133.33 36333.33 203.00 2700.00 252666.67 1463.33 906.67 30400.00 ND ND ND S8 7233.33 10000.00 167000.00 333.33 1370.00 137666.67 766.67 178.67 8800.00 ND ND ND S9 4266.67 14100.00 210333.33 301.67 3003.33 89333.33 816.67 274.00 10933.33 ND ND ND S10 4900.00 12700.00 51666.67 222.33 6866.67 193000.00 2410.00 1870.00 60000.00 ND ND ND S11 5800.00 13333.33 57000.00 273.33 8566.67 175000.00 3400.00 1673.33 68666.67 ND ND ND S12 5766.67 12333.33 53333.33 159.67 7233.33 175666.67 2710.00 2050.00 74333.33 ND ND ND S13 15666.67 25200.00 131000.00 ND 6533.33 102666.67 2206.67 1236.67 48666.67 ND ND ND S14 3010.00 10100.00 37333.33 240.00 6433.33 226000.00 2693.33 1133.33 46333.33 ND ND ND S15 6766.67 20533.33 73333.33 174.00 15300.00 117000.00 5033.33 2026.67 89666.67 ND ND ND S16 6033.33 17266.67 176333.33 263.33 2783.33 118666.67 1040.00 326.33 10700.00 ND ND ND S17 4300.00 10133.33 45333.33 92.33 6333.33 190333.33 2293.33 1546.67 73000.00 ND ND 1703.33 S18 3933.33 13600.00 62333.33 133.33 9866.67 150000.00 3966.67 1593.33 86000.00 ND ND ND S19 8233.33 10933.33 48000.00 81.00 7566.67 139000.00 2706.67 2003.33 114666.67 ND ND ND S20 20100.00 7933.33 41000.00 36.00 3633.33 200333.33 1533.33 2173.33 57000.00 ND ND ND S21 5900.00 22233.33 181333.33 287.67 4600.00 96666.67 1640.00 340.00 12966.67 ND ND 3266.67 S22 6366.67 19500.00 62333.33 66.67 14200.00 107000.00 6400.00 2120.00 112000.00 ND ND ND S23 6866.67 13600.00 47333.33 72.33 7100.00 184333.33 2626.67 1456.67 70000.00 ND ND ND S24 26466.67 4800.00 34000.00 79.67 3316.67 221333.33 916.67 1540.00 41000.00 ND ND 826.67 S25 7233.33 11966.67 71000.00 19.67 8666.67 131000.00 2733.33 1413.33 98333.33 ND ND ND

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The kurtosis value is negative, which indicates that the peak distributions are flatness compared with the normal distributions. This indicates that there is an extra anthropogenic cause to sediment contamination rather than the natural sources. But the small values of skewness and kurtosis for 40 K tend the shape distribution to nearly normal distributions as shown in Figure (5). The same distribution for

40K was observed by [Omoniyi et al., 2013] Figure (4): 40K activity concentration across sample codes in summer seasons

Basic statistics

Descriptive statistics The descriptive statistics of the 40K primordial radionuclide for sediments during the spring season are given in Table (4).

Table 4: Descriptive statistics of activity concentration of 40K

Statistics 40K Bq/kg N valid 25 Minimum 42.41

Maximum 473.68 Figure (5): Frequency distributions of 40K activity Mean 202.27 concentration. Median 204.493

Std. Deviation 117.698 Variance 14167.903 Skewness 0.662 Kurtosis -0.081

Form Table (4), the skewness values for 40K radionuclides are positive and greater than zero, indicating the lake of normal distribution. 50 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

Pearson correlation P, Ca was observed. The strong positive

correlation between the 40K and Ti, Mn and Fe The Pearson correlation coefficients in sediment samples indicates that all four between 40K and the major elemental analysis elements come from the same source of are shown in Table (5).It indicates that there is contamination to the aquatic environments. a strong positive correlation coefficient And the negative correlation between 40 K and between 40K and Ti, Mn and Fe and a weak Mg, Si, P, Ca indicates that the variables are correlation between 40K and Al while a weak coming from different sources [Omoniyi et al., negative correlation between 40K and Mg, Si, 2013]

Table (5): Pearson correlation coefficients between K and other elemental concentrations

Variables K Mg Al Si P Ca Ti Mn Fe

K 1 Mg -.143 1 Al .495* -.115 1 Si -.425* -.128 .414* 1 P -.337 -.440* .070 .569** 1 Ca -.290 .071 -.777** -.690** -.142 1 Ti .958** -.187 .435* -.458* -.340 -.213 1 Mn .730** .182 .022 -.780** -.619** .163 .701** 1 Fe .851** -.008 .149 -.665** -.613** -.066 .820** .891** 1

*. Correlation is significant at the 0.05 level (2-tailed). **. Correlation is significant at the 0.01 level (2-tailed).

Cluster analysis Each object in the same cluster is most like

From Figure (6) it was observed that four in properties, but is dissimilar from different main groups (cluster) were formed. The first clusters. The Similarity is a measure of cluster contains the P, Mn, Ti and K. The distance between clusters relative to the largest second cluster contains Mg, Al and Fe. The distance between any two individual’s third and fourth clusters contain only Si and Ca variables. respectively.

51 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

Figure (6): Dendrogram shows the clustering of concentration of elemental variables.

40 Conclusions values of K activity concentration are well below the recommended values suggested By The concentration of all three primordial [UNSCEAR 2000]. Statistics of multivariate radionuclides of the Darbandikhan Lake water analysis of Pearson correlation, cluster analysis with their resources has been determined have been carried out. The positive coefficients during the summer season using the Energy of the 40K and Ti, Mn, Fe in sediment samples Dispersive X-ray Fluorescence technique. Only indicate that all four elements come from the two positions have higher value of 40K and the same source of contamination to the aquatic concentration for both 232Th and 238U are environments. beyond the detection limits. The average

52 Jafir, A. et al. /ZJPAS: 2016, 29(2): 43-52

REFERENCES Ararat, K., Mehdi, R.A., Falih, H.A., Maher, A.M. and THORIUM AND POTASSIUM IN WATER, Bachmann, A., 2008. DARBANDIKHAN LAKE SEDIMENTS AND ALGAE SAMPLES FROM POISONING EVENT. Nature. SELECTED COASTAL AREAS OF LAGOS, NIGERIA; USING ENERGY DISPERSIVE X- El-Bahi, S. M., Sroor, A. T., Arhoma, N. F., &Darwish, RAY FLOURESCENCE. Global Journal of Pure S. M. (2013).XRF Analysis of Heavy Metals for and Applied Chemistry Research, 2(1), 1-24. Surface Soil of Qarun Lake and Wadi El Rayan in Faiyum, Egypt.Open Journal of Metal, 3(02), 21. Omoniyi, I. M., Oludare, S. M., &Oluwaseyi, O. M. (2013). Determination of radionuclides and Evans, M.I., 1994. Important Bird Areas in the Middle elemental composition of clay soils by gamma-and East, BirdLife International Series, No X-ray spectrometry. Springer Plus, 2(1), 74. 2. Cambridge. UK, p.410. Özmen, H., Külahcı, F., Çukurovalı, A., &Doğru, M. IAEA (2003) International Atomic Energy Agency. (2004).Concentrations of heavy metal and Guidelines for radioelement mapping using gamma radioactivity in surface water and sediment of ray spectrometry data. IAEA-TECDOC-1363. Hazar Lake (Elazığ, Turkey).Chemosphere, 55(3), IAEA, Vienna, Austria 401-408. Jassim, S.Z., Goff. JC, 2006. Geology of Iraq. Sonon, L.S., Chappell M.A. and Evangelou V.P (2007): Morikawa, A.,(2014). Elemental analysis of PM2. 5 The history of Soil Chemistry. Journal. Science with energy dispersive X-ray fluorescence Total Environment 35, 2, 88-90. spectrometer NEX CG. United Nations Scientific Committee on the Effects of Omale, P. E., Okeniyi, S. O., Faruruwa, M. D., Atomic Radiation.(2000). UNSCEAR 2000 &Ngokat, A. B. (2014). DETERMINATION FOR report.Annex C: exposure to the public from man- LEVELS OF RADIONUCLIDES OF URANIUM, made sources of radiation.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 53-73 http://dx.doi.org/10.21271/ZJPAS.29.2.6

Species chick list of Bryophyte, Pteridophyta, Lichens and of Iraq and Kurdistan Region

1 2 Farhad Hasan Aziz and Basheer Al-Niama

1 Environment Department, College of Science, Salahaddin- Erbil University, Erbil, Iraq 2 Biology Department, College of Science, Mosull University

A R T I C L E I N F O A B S T R A C T

Article History: This is the first species check list of Iraqi lower plants and Kurdistan Received: 03/05/2016 especially from Erbil province. It is including 658 species. Hepatophyta with 18 Accepted: 01/12/2016 species in 1 class, 4 orders and, 9 families14 genus . Musci with 235 species in Published:07 /06/2017 1 class, 9 orders, 30 families and 80 genus. Pteridophyta with 27 species in 1 Keywords: class, 3 orders, 10 families, and 27 genus lichens with 224 species in 1 class, Check list, Hepatohpyta, 74 genus and Mushroom with 32 species in 1 class, 5 orders, 15 families and 19 Iraq, Kurdistan Lichnes, genus Musci, Mushroom, Pteridophyta *Corresponding Author: Farhad Hasan Aziz farhad.aziz @ su.edu.krd.com

. 1. INTRODUCTION (1975) recorded 54 genera and 149 species and Aziz (2010) identified 6 species of they referred in detail to old works on mosses hepatopsida (liver worts) of which four species collected from Mesopotamia, Iraq, Syria and were new records to Iraqi flora these are other Middle East countries e.g. Lebanon, Marchantia polymerpha in Zalm Sulaimani Phalstine, Persia and Afghanistan. Maulood Concephalum conicum in Sharansh, Duhok, and Rasheed (1994) recorded total number of Pellia epiphylla and Lophocolea cuspidata in 27 genera and 48 species in in Nineveh, Erbil Gali Ali-Beg valley, Shex Wassan village and and Duhok of which 4 genera and 9 species Nardia scalaris found near Faqyan village- were new records to Iraqi flora. However, Al- Doli Ikoyan, Erbil. Metezgeria furcata near Ni'ma (2003) identification 79 species (72 Shanadar cave and in Gali- Ali- Beg/ Erbil. mosses and 7 liverworts), covered 5 genus Guest (1966) in his book flora of Iraq among them 8 species was new records to represented most species of hepatophyta. Iraqi flora. He performed an excellent reference During an excursions of foreign workers to for bryophytes of Iraq, which has encouraged different parts of Iraq; Agnew and Vondracek authors of bryophytes (Schaffer, 1913, Frochlich, 1959 and Rechinger and Vondracek

54 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

1965).Aziz (2011) collected mosses in different Erbil province including Gwer and Dibaga parts of Erbil, Slemani, Duhok and Even districts. Among them 24 species are new Kirkuk. He recorded a total of 67 species in 32 records to Iraqi lichens flora. Forty two species genus, 16 families and 9 orders, among them arc of crustose, four of foliose and two of 17 species in 10 genus, two families frulicose forms. In other hand thirty four Schistogaceae and Ephemeraceae and the species found in rocks, while four species single order Schistostegales were new to Iraqi Collcniu spp., Diploschistes spp. Permelia, flora. The most rare species recorded in this Psora and Parinotrema were rare, scattered study was Schistostega pennato with fern-like and observed on soil. The recorded species are leaves inside Shanadar cave, Pottia wissia var. low due to habitat uniformity, dry conditions Crinata at the mouth of Ba-stoon cave, and the absence of old trees and forests in Ephemerum cristatum within Gali Ali-Beg studied area.. Qadir and Aziz (2015) recorded area. Al- Mashhadani and Al- Ni’ma( 2012) a total of 58 species of epilethic lichens belong collected mosses in 25 different areas, they to 33 genera in 20 families, 8 orders, I phylum identified 75 species of which 7 species and 1 ( Ascomytina) and 1 class (Ascomycetes) were genus Orthodonium was new record to Iraqi collected from north to extra south of Erbil flora. governorate. Among them 30 species are new In term of lichens and based on collections records to Iraq and Iraqi Kurdistan flora. made by Aziz ( 2005 ) within Erbil province Among various species, Caloplaca spp, from Safin mountain area and Rwandiz river Rhizocrbon spp., Lecanora spp, Physcia spp. path including Gali Ali-Beg, Jundian, and Verrucaria spp. are the most abundant. Kawlokan, Haji-Omaran and Kawshan, up to With respect to Mashroom and based on more than 2000 m.a.s.l. A total of 89 species in the collections made for mushroom between 37 genera of lichens were identified at the first 1996-2010 in mountain areas in Slemani and time in Iraq; sixty six (66) species are belong to Erbil provinces especially in Soran, Choman, crustose from ,19 species to foliose form , 3 Sedakan districts Qandil and Zalm areas up to species to squamilose form and 1 species to more than 3000 m.a s.l. A total of 34 species in fruticose forms. Aziz (2004) recorded seventy 23 genera, 17 families and 7 orders belong to seven (77) lichens species in 40 genera from woody and fleshy species were identified at Hasan Beg mountain area covering main road the first time in Iraq (Aziz and Tom, 2012). edge, Sari Bardi and it’s summit area in spring I hope that the present check list could be and summer season 2002. The Hasan Beg an additional contribution to the Bryophyta, lichens community relatively has no affinities ferns Lichnes and Mushroom of Iraq. with lichens community of Oak forest and up land rock outcrops excluding 26 species have been recorded elsewhere. While,51 species 2. METHODS encountered are new records for Iraqi The species are arranged alphabetically and flora.Lichens species was moderately of the lists were written independently started crustose form 60 species, followed by foliose from Bryophyta ended by Mushroom passing form 15 species then by fruiticose form 2 Lichens. For the former the species list and species. authors and place of recorded species are not In term of lichnes Aziz and Saeed (2006) changed as wrote by Al- Ni’ma, (2001) have been recorded a total of 50 species of because it is complicated. While, for the rest lichens flora in 24 genera arc reported fromm Qarajugh mountain and foothill area within

55 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73 lists and species the habitat ( place ) and Nineveh district…………………….. (FNI) authors are wrote directly as it’s. Kirkuk district………………………(FK1)

Erbil district ;………………………. (FAR) A. Authors and their Breviation (in part Central Alluvial plain district………(LCA) from Al-Ni’ma,2001) : Lower Jazira district……………….. (DLJ) Agnew ( 1973 )………………… . (Agn.) Basra Estuarine district…………….(LBA) Schiffner (1897)……………S18 Southern Marsh district' …………… (LSM) Agnew & Vondracek (1975 )…….( A and V) Qandil mountain……………………(QAN) Schffiner (1913)……………S19 These physiographic districts of Iraq were Long ( 1979 )……………………. ( Lon.) used throughout the Flora of Iraq by Guest Handel Mazz. (1914)………Han (1966). We prefer to use it here also rather than the distribution in this check list flora of Al- Ni'ma ( 1994 )………………. ( Aln.) Iraq, since it depends upon administrative Froilic(1959)……………….Fro units. (i.e.) Liwa or province. Names and borders of these unit,. ate probably subject for Vondracek ( 1965)……………….(Vond). changes with times as it was already took place Vandacek(1962)……………V62 (Al-Ni’ma,2001and Alkhay’at) with few addetions. Maulood and Rasheed (1998)……M and R) Vandacek(1962)……………V62

Aziz (2004, 2005, 2006, 2010, 2012)...(Aziz) 3. RESULTS

In this species check list of only in B.Physiographic districts and their Kurdistan within covering 658 species. List 1 abbreviations ( from Al-Ni’ma and covering Hepatophyta with 18 species of in 1 Alkhay’at, 2001) : class, 4 orders, 9 families, and 18 genus. List 2 covering Musci with 230 species in 1 class, 9 Amadiya district……………………..(MAM) orders, 30 families and 80 genus. List 3 Prsian Foothills district…………… (FPF) concerning Pteridophyta with 27 species in 1 class, 3 orders, 10 families, and 27 genus. List Rwandiz district:………………… (MRO) 4 deal with lichens with 224 species in 1 class, Ghurfa-Adhairn district…………….(DGA) 74 genus. And List 5 related to Mushroom with 32 species in 1 class, 5 orders, 15 families, and Sulaimainya district………………….(MSU) 19 genus. These observed species were found Western Desert district……………. (DWD) in different part of Iraq and Iraqi Kurdistan region as follows: Jabal Singar distric………………… (MJS) Southern Desert district…………… (DSD) List (1): Hepatophyta of Iraq and Iraqi Upper Jazira district………… ……... (FUJ) Kurdistan region. (Al-Ni’ma, 2001 and Aziz, 2010(MRO) Eastern Alluvial plain district:………LEA)

56 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Kingdome Plantae Lunaria cruciata (L.) Dum (Upper Jazera, Nineva district, And Aziz: Rwandiz (MRO) Division Hepatophyta- Liver worts (12 genera and 16 species):

Subdivision Hepaticae Family Ricciaceae

Class: Hepatopsida Riccia crytstalina (Aln. Mosul city) : Ali- Beg, Doli Malakan, Doli Ikoyan- Faqian ) Order: Sphyrocarpales (MRO)

Family: Sphyrocarpaceae Riccia frostii Chiffner Aziz: Rwandiz [ MRO] Sphyrocarpa michelil Bellrdi (Aln: Mosul city) R. frostrii var major Chiffner: (Western desert district) Order: Marchaniales R. sorcarpa Bisch: (Western desert Family: Targiolaceae district)

Targionia hypophylla L. ( Aziz: Rwandiz, Order: Jungermanniales Gali Ali- Beg- old road ) (MRO) Family: Fossommbroniceae

Fossommbronia caespitiformis De Not. Reccardia penguis (L.) Gray ( Aziz: Aziz from Rwandiz (MRO) (Rwandiz, Gali Ali- Beg - old road ) (MRO) Family: Pelliaceae:

Pellia epiphylla (L.) Corda ( Aziz, Family: Reboullaceae Rwandiz- Faqiyan[ MRO], Dum Upper Jazera, Nineva ) Reboullia hemisphaerica (L.) Radilic (Amadiya) P. endiviifolia (Dicks.) Dum. Aln. Dum Upper Jazera, Nineva Family: Marchantiaceae Riccardia pinguis (L.) Graya. Aziz from Marchantia polymorpha L. (Aziz: Rwandiz – Doli Ikoian/ Faqyan (MRO) Slemani: Zalm) Family: Southbyaceae Marchantia polymorpha var. alpestris Han( Al, Nima and Al- Khyyat) Family: Southbyaceae

Concephalum conicum (L.) Underw.(Aziz: Southbya nigrella (De Not ) Henriques(lon: Duhok, Zakho: Sharansh)[ Duhok]. jabal Hamrin, FKi / FPF)

Order Metzgeriales

57 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Family Metzgeriaceae Order Dicrinales

Metzgeria furcata (L.) Dum. Aziz: Family Ditrichaceae Rwandiz[ MRO - Doli Faqyan (MRO) Ditrichoideae Lophocolea cuspidate (Nees.) Limper. (Aziz from Doli Ikoyan/ Faqyan) (MRO) Ditrichum pusillum (Hedw.) Hampe.

Nardia scalaris (Schard.) Gray = Nardia D. heteromallum( Hedw.) E.G. Britton alicularia var. scalaris (Schard.) Corda (Aziz: Distchium capillaceum (Hedw.) B. S. G Rwandiz - Doli Faqiyan[ MRO] [A&V; MRO]

D.capillaceum var. compactum [Huben.)(FRO; Rementioned in A&V][FAR,ARO ]

List (2): Mosses (Musci) of Iraq and Cheilothela chloropus (Brid.) Lind. Kurdistan region (Al-Ni’ma, 2001and 2003; [A&V.,MRO] Al- Ni'ma & A.H.Khay'yat Aziz, 2011) (MRO) Family Dicranaceae

Sub family Dicranelloideae Class Musci ( Bryopsida) Anisothecium varium (Hedw.) Mitt. Order Fissidentales [A&V;MRO]

Family Fissidentaceae Dicranella varia (Hedw.) Schimp

Fissidens arnoldi Ruthe. [For: MAM; Dicranoweissia cirrata (Hedw) Mild. A&V: FAR, MSU, MANI] Campylopus schemperi (Mild) Husn. F. bryoides Hedw. [A&V: MSU] Family Leycobryceae F. crassipes Wils. [A&V: MAM] Leyucobryum glaucum (Hedw.) Angstr. F. crassipes var. submarginatus. Fleisch et Warnst. [S19: MJS; Han:; A&.MJS] Order Pottiales

F. mnevidis amann [A&V: MRO, FAR] Family Eucalyptaceae

F. persicus Ruthe et Milde [A&V: MJS, Encalypta intermedia Jur. [S19; FUJ-Han; MSU] Fro: MSU;A&VMSU,MRO,FUJ,MAM]

F. viridulus (Web. et Mohr) [A& V: E. rhadocarpa Swchwaegr. [A&V;MjS] MRO, MSU]

58 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

E. vulgaris Hedw. [A&V} B. trifiiria var. desertorum (Froehlich) S. MRO,FAR,MAM ,FNI ,MSU] Agnew Comb. Nov. [Fro: LEA ,FPF, LSM,

Family Pottiaceae LEA/LSM;A&V:Tib DGA, LEA, FPF, DWD, MRO, FKI , FUJ, FNI, MAM]. Didymodon revolutus (Cardot) R. S.Williams synonym Barbula rigidula var. desertorum. Syntrichia latifolia ( Bruch ex Hartm) Huebener B. unguiculata Hedw. [Fro: MSU, A&V: LEA, MRO, MSU, FNI] Timmiella crassinervis (Hampe) l. F. Koch B. uniqulata var. caspidata (Schultz) Brid Family Trichostomceae B. vienalis Brid. [S19: MAM, MJS, FUJ; Sub family Trichostomodeae Han: A&V: FPF Jebel

Barbula acuta (Brid.) 3rd. [Han: A and V: Diyala { Jabel Hindrian & Diyuluweire, Harnrin,LEA,MRO,DWD,FAR,MSU,MAM,F UJ,DLJ,MJS] B. fallax Hedw. [Fro; A&V:MSU] B. vienalis var. cylindrica Boul. [A&V: B. Hornschuchiana Schultz [Han.; A and V MRO, FNI, MAM, MSU] :FAR,MRO,MAM,FNI] Hydrogoniurn ehrenbergii (Lorentz) Jager B.Hornschuchiana var. pseudorevoluta et Sauerb. [Han: A&V: MRO, MAM,] Reim. [A and V:FPF (Jabel Hamrin)] synonym Didymodon ehrenbergii. B. icmadophila Schimp [A&V:MRO] Streblotrichum convolutum (Hedw.) P. Barbula revoluta Brid. [Han.; Beauv. [A&V: MAM] A&V:MRO,MSU] Hymenostylium recurvirostrum (Hedw.) B. rigidula (9Hedw.) Mitt. [S19: MAM, Dix. [A&V: MRO] Han.; synonyme Didymodon rigidulus Hedw. Anoectangium aestivum (Hedw.) B. S. G. B. tophaceae (Brid.) Mitt. [Fro: FKI; A&V: [A and V: MSU] LEA, FAR, MRO, MSU] the synonym A. handelii Schiffn [Han.*; A&V: MAM, Didymodon tophaceae. Aziz Aziz. MSU] Ruwandiz[ MRO] Eucladium verticillatum (Brid.) B. S. G.[Fro: B. tophaceae f. Lingulata Moenkm. [A&V: MSMRV62, MRO, A&V, MRO, FPF, FNI] LEA, MRO] E. verticillatum var. angustifolium Jur. [A,&V: B.trifaria (Hedw.) Mitt. [V62: MRO] MRO]

59 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Hymenostornurn tortile (Schwaegr.) B. S. G. Subfamily Pottieae [S19: MJS; Han; A&V: MRO, MSU, FNI, MJS] Acaulon triquetrum (Spruce) C. Mull [ A&V: LEA] Weissia controversa var amblydon (Brid.) C. Jens. [V62: MRO A&V]. Pteryouneurum ovatum (Hedw.) Dix .[Han: A&V: FM, DGA LEA, DWD, LCA, MSU] It seems that both authors referred to the same specimen since they were collected it from synonyme P. cavifolium.

Halgurd mountain, but the variety was Pottia commutata Limp [Han: A&V: LCA, mentioned only in (A&V). (Baghdad) LEA, N4SU, FNI]

W. crispata (Nees & Hornsch.) C. Mull. [Han] P. davalliana (Smith) Broth. [A&V: LCA, LEA (Baghdad). MSU, MAM] W. fallax Sehlm. [A&V: MRO, MSU, MAM] P. lanceolata (Hedw.) C. Mull. [Han: A&V: Gymnostmum aeruginosum Smith [A&V: M MRO, MAM] RO, DLJ, MSU] P. mutica ven [S19: Fill; Han: A&V: FM, G. calcareurm Nees & Hornsch [V62: MRO; MSU, DLJ, FUJ]; A&V: FKI, MSU, FUJ] A&V: MRO, FK1, MSU] P. recta (Sm.) Mitt.[A&V: LCA/LEA G. mosis (Lor) Jur. at Milde [A&V: FPE (Jebel (Baghdad)] Hamrin),MRO,FKI,MSU,DLJ,FNI,MAM,DSD ] P. strakeana (Hedw.) C. Mull. [A&V: DLJ] B.A. Al- Ni'ma & A. H. Al Kharyat G. rupestra Schleich [Han.V62:MRO] P. truncata (Hedw) Furnr. Aziz: [ Gyroweisia tenuis (Hedw.) Schimp. [S19: Rawandiz- Jundian, MRO] MAM; Han. A&V: LEA, FP (Diyala P. wilsoni var. crinata (Br. Eur.) Warnts.( weir), LBA, DWD, MSU, MAM] Aziz, Sulaimani- Jabal Qandil, MAU

Tirmmiella harbuloides (Brid.) Moenk. [S19: Phascum curvicolla Hedw

FUJ,MJS;Han: A&V: MRO, FKI, MSU, P. cuspidatum Hedw. [Lon: FPF] MAM, FNI, FUJ, MJS] P. cspidatum var. piliferum Han Trichostomum crispulurn var. elatum Schimp. [A&V: MRO, MSU, MAM] Aloina ambigua (B,S.G) Limpr [A&V: DSD, FPF, MRO, FKI, MSU, DLJ, FNI, MAM] Tortella tortuosa (Hedw.) Limpr. [V62: MRO; A&V: MRO, MAM, MSU] A. rigida (Hedw.) Kindb. [Fro: FPF, A&V: LEA, DWD, DLJ, FUJ] Pleurochezete .stquarrosa (Brid.) Lindb. [A&V; MSU, MAM]

60 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

A. rigida var. pilifera, B.S.G. [A&V: LCA, river, DGA, LEA, FPF, DWD, DU, LCA, LEA (Baghdad), DGA, FPF, DWD, DLJ, LCA, FIC1, FUJ] FKI, T. handelii Schiffn. Han. Aziz Choman, A. stellata Han. Aziz: [RMO] Sedakan, Ruwandiz [MRO]

Crossidiutn chloronotus (Brid.) Limpr. [Han: T. linermis (Brid.) Mont. [S19: FM, N. A&V: LEA] Griseum Jur [S19: MJS; Han] Kurdistan 250-1 100m; Han: ]

C. squamigerum (Viv.) Jur. [Han: A&V: Tip T. marginata (B.S G.) Spruce [A&V: MRO, river FPF/LEA/LSM, DWD, FKI] FNI, Msu]

C. squatnigerum var. pottioideum (De Not.) T.montana (Nees) Lndbg. [Han. Fro: Moenkm. [A&V: DSD, FPF, Diyala weir, MANI] DWD, T. muralis Hedw. ( A&V): MSU, MAM] LCA, WS, FNI, MAM,MSU] T. muralis var aestiva (P. Beauv) Brid. [Han: Tortulla alpina (B.S.G.) Bruch [S19: FUJ; ; A&V: MRO, MAM] synonyme Tortula Han.] aestivia

T. richostomopsis aaronis (Lor.) S. Agnew T. muralis f. brevifolia (Sehiffn.) Podp. [S19. & Townsend [A&V: DGA, LEA, FPF, DWD, NUS; A&V: MTh FM] the synonyrne MRO, T.aestive var.

DLJ, MAM, FUJ, DWD] brevifolia

T. Haussknechtii (Jur. Et Milde) S. Agnew T. princes De Not. [Frp: MAM] & Towsend [A&V: LEA (Diyala), FM] T. rurals (Hedw.) Gaertn [Han.] (Aziz T. atrovlrens (Smith) Lindb. [A&V: DSD, Rawandiz, Gali Ali- Beg ( MRO) LEA, MSU, FNI] T. subulata Hedw. [Han.] T. brevissitna (Schiffn.) [S19: Fuj; Han: A&V: A&V: DSD, LCA/LEA (Baghdad), T. tortuosa (Hedow )Limp.Laubm (Aziz, LEA, FPF, Ruwandiz, Gali Ali - Beg and Kawlokan

LCA, DWD, HU, FUJ, DLJ, Mosul] T .vahlianas (Schultz) Mont. [Lon: FPF]

T. desertorum Broth.= T. Bronmulleri Tortulla sp. Aziz: Kawlokan [RMO] Schiffn. [S19; FUJ, MJS; Han.] Syntrichia alpina (. S. G.) Jur. [V62: MRO ] Fioroo (Vent.) Roth. [S19: FUJ, MJS, Han.; Fm: Tib river FPF/LEATLSWI, FPF; A&V: S. desetorum (Broth.) Amann [A&V: FPF, Tib DWD, MRO, FKI, FUJ, MJS]

S. hadacii Vonderacek [V65: DLJ; A&V: DLJ]

61 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

S. handelii (Schiffn.) Podp. [A&V: MRO, Encalypta streptocarpa Hedow MAM, MSU] Order Crimmiatales S. inermis (Mont.) Huben [A&V: MRO, MSU, FUJ, MAM] Family Crimmiaceae

S. laevipila Brid [A&V: MRO, MAM, MSU] Coscindon cribrosus (Hedw.) Spruce [Han:*]

S. montana Nees et Esneb [V62: MRO, MJS, Schistidium apocarpum var. atrofuscum MAM, MSU] (Schimp.) Husnot [S19: NJS; Han.;V62: MRO.; A&V: S. montana var. calva (Dur. Et Sag.) Amann ST nd [A&V: MSU] MRO, MSU, MJS, MAM]. The 1 & 2 synonym Grimmia singarensis. S. papillosissima (Coppey) Loeske [A&V: MRO] Grimmia anodort B. S. G. (S19: MTh; Han. A&V: MRO, MIS, MSU] S. princeps (De Not.) Mitt. [A&V: MRO, MSU, MAM, FUJ, DWD] G. apiculata Hornsch. [A&V: MR0] Aziz. Shaqlawa S. pseudodesertorum Froehlich [A&V: FPF, DWD, FKI, DU, FNI] G. apocarpa Hedw [Han;]

S. pseudohandelii Froehlich [V65:MSU; A&V: G. campstris Hook. [Han] MRO, FM, FNI, FUJ, DLJ, MSU]. synonym S. G. commutata Hub. (Han; Fro: MSU, V62: MRO; A&V: MRO, MSU] handelii var. pseudodesertorum. G. crinita Brid. [Fro: Tib river FPF,LEA,LSM, S. pulvinata (Jur.) Jur. [A&V: M SU] DSD; A&V: EFT, HB.A. Al- Ni'ma & A. H. Al

S.ruralis Brid. [A&V: MRO, MAM, MSU] Khay'yat; Aziz. Jabal Qandil Aziz, Shaqlawa G. gibbosa S. Agnew [Agn.; FKI; Subfamily Cinnlidoteae Rementioned in A&V} (Tuz khurmatil bridge over Lesser zab Cinclidotus fontinaloides (Hedw)p. Beauv. [A and V ; MRO, MAM, MSU] river and in Ain Dibbis). Note: Altone Kopri is located on lesser zab not Tuz khurmatil as the C. nigricans (Brid.) loeske [A&V: MAM]. author mentioned. C. riparius Amott. [Han.] G. laevigata (Brid.) Brid. [A&V: MRO ] Order: Encalyptales G. mesopotamica Schiffn. [S19: DWD; Han.; Family: Encalyptaceae A&V: FPF, Diala weir, DWD, LCA, FPF]

62 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

G. orbicularis Bruch [S19: at 400-1250 m; P.patens var. marginate Vondraccek [A&V: Fm: MAM; A&V: FPF, MRO; FKI, MAM, LSM] FNI, Entosithodon.angustifithus Jur. et Milde FUJ, DLJ, MAM, MSU] [A&V: FKI, 'MIS]

G. orbicularis var. persica Han. ( Aziz, E.handelii Schiffn. [S19: synonym Funaria Choman -Haji Omaran)] andelii on calcareous rock in North East

G. ovalis var. simplex Vondracek [V65: MRO; Mesopotamia and Kurdistan 250. 1800 m; A&V: MRO] Han: .FUJ; A&V: MRO, JEW, MAM, FNI,

G. pulvinata (Hedw.) Sm. Schiffn. [S19:DWD, E. templetoni (Smith) Schwaegr. [A&V: MRO, FUJ,MJS; [Han.; A&V: MRO, MSU, MAIM] FUJ, MAMH]

G. subcaespitica Schiffn. [Han.; A&V: MRO] Steppomitra hadacii Vondracek [V65: 'FLU, (A&V)] G. lergestina Tomm. (Han.; A&V• MRO, MJS, FNI, MSU] Funaria hygrometrica Hedw. [Han. ; A&V: LCA .(Baghdad), MRO, MAM, FUJ, MSU] G. trichophylla Grey. [Fro. MSU; A&V] F. mediterranea Lindb. [Ham.; A&V: MRO, Racomitrium affine ( Wib Hedw. and Mohr.) FNI, FUJ] Lindb. (Alni’ma) Family Splachnaceac Funariales Tayloria lingulata var. acutijblia Han. Ham.; Family Funariaceae A&V: MRO, FNI, FUJ]

Funaria hygomatrica Order Eubryales

Family Ephermeraceae Bratramiacea

Ephemerum cristatum (Hook) F. Wils. Family Bryaceae

Chistostegales Aginiobriutn albicans (Wahib.) Lmpr . [S19 MJS; Han.; A&V: LCA (Baghdad), MRO Family Chistostegaceae OSU)

Schistostega pennata (Hedw) Web and Mohr Mniobrium delicatrulum (Hedw.) Dix (A&V: (Aziz, Amadyea MAM and Ruwandiz, RMO LCA, MRO, MAM, MSU, FPF, MJS] ) M. latifoliutm Schiffn. [Han.; A&V: MRO] Physcomitrella patens (Hedw.) B. S. G. [V65: Aziz, Shaqlawa LSM; A&V: ,LEA (Baghdad)] Pahilia crudes (Hedw.) Lindb. [A&V: MRO]

63 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Bryum sp. Sterile specimen [Han.] B. pseudotriquetum (Hedw.) Schwaegr. [V62: MRO; A&V: MRO] Bryum sp. [Fm: DSD] B. schleicheri Schwaegr. [A&V: MRO, MSU] B. . alpinurn Brid. [Fro: MSU; A&V: MRO, MAM, MSU] B. syriacum Lor. [Han.; Fro: MRO; A&V]

B. argentum Hedw [A and V: MRO, MSU] B. vent-rico Han.

B.argentum var. lanatum (P. Beauv.) B.S.G. B. rubens Mitt. (Aziz, Ruwandiz [MRO] [Fro: MSU; A&V: FKI, MSU] B. uliginosum (Grid.) Rohl. B. bicolor Dicks [Lon: FPF] Rhodobryum roseum ( Hedw.) Limper. B. badium Batch ex :Ruthe [Han.; A&V: FAR, MA M, MSU]

B. caespiticum Hedw. [Han.; Fro: MAM; Family Mniaceae A&V: MAM, MSU] Mnium longirostrum Brid. [V62: MRO; A and B capillare Hedw. [Han.; A&V: MRO, MAM, V : MRO] FUJ, MSU] Plagiominum rostratum (Schard.) kop. Aziz B. capillare f. flaccidum B.S.G. [A&V: MSU] [RMO]

B.capillare var. torquescens (B.S.G.) Husn. Plagiothecium denticulatum (Hedw.) Br. Eur. [S18: MRO; Fro: NISU; A&V: MRO, MAM Aziz [MRO] MSU] Isoptergiopsis taxiphyllum (Schimp.) Wats. synonyme Bryum torquescens Aziz [MRO]

B. cirratum Hoppe et Hornsch. [A&V: MRO] Family Bartamiaceae

B. donianum Grev. [A&V: MSU] Anacolina webbii (Mont.) Schimp. [A&V: MRO] B. funkii Schwaegr. [Han.; V62: MRO; A&V: LBA, LCA (Baghdad), DWD, FNI, MSU, Philonotis caespitosa Wits. [A&V: MRO, LEA] MAM]

B. gemmiparum De not Upper plain and P. calcaera (B. S. G.) Schimp. [Han.; foothlls V62:MRO; A&V: .MRO,MAM]

B. pallens (Grid.) Rohl. [A&V: MRO] P. fontana (Hedw.) Brid. [Fro: MRO; A&V: MRO, MSU] B. pallescens SchIeich. [V62: MRO; A&V: MSU, NIRO, FPF, DWD, LCA] P. fontana f. laxifolia Moenk. ap. Loeske [A&V: MRO]

64 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

P. marchia (Hedw.) Brid. [Han.] MRO; A&V: Family Leucodontaceae MRO] Antitrichia breidleriana Schiffn.[Han.; A&V: P, seriata (Mitt.) Lindb. [Fro: MAM and MRO] A&V] Order Hypnobryales P.tomentella Mol. [Han.; V62: MRO; A&V: MRO] Family Fabroniaceae

Family Orthodentaceae Fabronia pusilla Radi [A& V: MRO, MAM]

Orthodontum lineare Schwagre Family Hypnaceae

Order Isobryales Subfamily Amblystegiadeae

Family Fontinalacese Cratoneuron commutatum (Hedw.) Roth. [Han; A&V: MRO, MAM] Fontinalis mesopotamica Han. Commutatum m var. suicatum (Lindb.) Monk. Family Orthotrichaccae [V62: MRO]

Orthotirichum affine Brid. [A&V: MRO, C. decipivar. falcatum (Bride) Moenkm [Fro; MAM, MSU] MRO; V62: MRO; A&V: MRO,MSU]

O.cupulanon Brid. [Fro: MAM; A&V: MRO, C. commutatuens (De not.) Loeske Han V62: MAM,MSU] MRO; A&V: MRO]

O. cupulatum var. papaillsum Gronv. C. decipiens var. napaeforme Han [A&V:MRO, MSU] C. filicinum ( Hedw. ) Roth . [Fro : MSU; O. cupulatum var. bistratosum Han. A&V:MRO, MAM,MSU]

O. lyellii Hook et Tayl. [A&V: MRO, MAM, Plagiominum rostratum (Schard.) Kop. MSU] Amblystegium juratzkanum Schimp. [A&V: O. octoblephare [V62: MRO] MRO]. Smith (1978) treated this taxon as synonym of O. rupestre Schleich [Han. ; V62: MRO; A&V: MRO] A. serpens as it is quite impossible to separate the two taxa. O. schimperi Hammar [A&V: MRO, MAM, MSU] A. kurdicum [Han]

O. soeciosum Nees [A&V: MSU] A. serpens (Hedw.) B. S. G. [A&V: MAM]

O. strumii Han

65 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

A. tenax (Hedw.) C. jens = B.rivulare (Bruck) B.S.G. [V62: MRO; A&V: Hygroamblystegium irriguum [Han} synonym MRO, MAM, MSU] Hygroamly stegium B. rutabulum (Hedw.) Br. Eur. [Alni’ma] irrguum but Smith (1978) following Nyholm (1954-69) included Hygrownbly stegium B. salebtaosum Web. Et Mohr B.S.G. [A&V: MRO. MAM] and use the new name A. tenax. B. trachypodium Han. A. varium (Hedge) Lindb. [A&V: MRO, MSU] B. Euryhynchium confertum (Dicks.) MiIde Amblystegiella jungermanniaides (Brid.) [A&V: MRO Giacomini [A&V: MRO] Eyrhynchium paralongum var. paralongum A. spruci (Brach) Loeske [V62: MRO] (Hedw.) Br. Eur.

Leptodictyum riparium (Hedw.) Warnst. E. reipariodes (Hedw.) P.W. Richards [A&V. [A&V: MSU] MRO, MAM, MSU]

Drepanockaus aduncus (Iledw.) Moenkm. E. speciosum (Bride) Milde [A&V: MA M] jA&V: MRO] Rhynchostgiella curviseta (Brid.) [A&V: Acrocladium cuspidatum (Hedw.) Lindb. [AIM MAM] MRO] Hypnaceae Calliergon cuspidatum =Calliergonella cuspidata [V62: MRO], after Smith (1978). Hypnoideae

Subfamily Brachytheciaceae Rhytidiaelphus loreus Warnst.

Homalothecium philippeanum (Spruce) B.S.G. List (3): Pteridophyta (Ferns) Iraq and [Han.; A&V: MRO,MAM] Kurdistan region (from Guest, 1966 and Aziz,2015). H.seriaceum (Hedw.) B.S.G. [Han.; A&V: MRO, MSU] Kingdome Plantae

Scorpiurum aircinnatum (Brill,) Fleisch [Han:] Pteriodphyta F. Ballard

Camptothecium lutescns (Hedw.) B.S.G. [Fro: Eequisetales MAM, MRO; A and V] Equisetaceae F. Ballard Brachythecium collinnum (Schleich.) B.S.G. [Han.; A&V: MRO, MAM, MSU] Equisetum arvense L. Erbil _

B.olympicum Han E.. Ramosissimum Desf, FL. Atlant, Aziz , Bastora – Hanara village

66 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Filicales Phyllitis scolopendruium (L.) Newm Jabal Al Khayat, Pramagron Marsileaceae F.Ballard Cystopteris . fragilis (L.) Bernh Marsilea L. capensis A.Br. C. regia…( Aziz, Choman- Doli Salviniaceae F. Ballard Balaiyan - Wassan village)

Salvinia natans (L.) All. Flor. Pedum Aspidiaceae F. Ballard

Adiantaceae F. Ballard Polystichum setiferum (Forssk) Woyne Aziz, Sulaimani- Ahmad Iwa- Zalm village Adiantum capillus- veneris L.Aziz, Gali Ali –Beq, Sperrnatophyta

Anogramma leptophylla (L.) Link. Gymnospermae Hawraman Ephedraceae R.A. Blakelock and J.B Cheilanthes fragrans (L.) Sw. Jabal Gillett Bawaji , Gali Ali- Beg Ephedra alata Decne syname Gnetales C. margirata (L.) Mick alata Decne.

C. persica (Bory ) Melt ex lkuhn , E. transitoria Riedl Aziz, Choman - Haji Omaran Coniferales Ceratopteris Brongn Family Cupressaceae R.A Blaeklock C. thalictriodes (L.) Brongn. Janipperus polycarpos L. Koch in Aspelinaceae F. Ballard linnaae...... Erbil and Duhok

Aspleninum trichomonas L. Aziz, Cupressus L Sulaimani-Ahmad Iwa C. arizonica Greene A. virid Huds. C.semperrivens L. A. husskaechii Godett Reater Thuja ovientalis L. A. ceterach Garsault Aziz, Erbil - Gali Ali Beg Family Pinaceae

A. officinarum DC. Pinus . halepensis L (Snobar in Kurdish Duhok, Zawita) Athyriaceae F. Ballard p. halepensis var. brutia (Ten) Henry ex Elwes and Henry

67 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

List(4) : Lichenes of Kurdistan mountian areas, C. feracissima.H.Magn. Iraq (Aziz,2004, 2005, 2006; Kostly all of C. flavorubescence (Huds.)J.R. Laundon them are widely distributed). C. holocarpa (Hoffm. ex Ach.), M.Wade Class Ascomycetes (Ascolichenes). C. epithallina Lyng. Subclass Ascomycetidae. C. ignea Arup Acarospora hilaris (Dufour) Hue. C.ochracea (Schaer.) Flagey lieppina A. fuscata (Schrader)Arnold (Muell.Arg.) Zahlbr

A. Htitblicata Bagl. C. luteominia var. bolanderi (Tuck.) Aurp.

A. strigata (Nyl.) Jutta C. pellodella. (Nyl.) Hasse

Aspicilia calcarea (L.) Mudd. C. thallincola (Wedd.) Du Rietz

A. candida (Anzi) Hue. C. variabilis (Pers.) Mull. Arg.

A. cinerea (L.) Korber C . velana.(A.Massal.).Du Rietz

A. contorta (Hoffm.) Kremb C. verruculiferi (Vainio) Zahlbr.

Aspicilia sp. Candelariella aurella.(Hoffm.)Zahlbr.

Bellemerea aplina (Somm.) Clauz. & Roux. C. vitellina.(Hoffm.) Mull. and Arg.

B. cinereorufescens (Ach.) Clauz. and Roux. Citrysotlirix candelaria (L.) J. R. Laundon

Bellemerea sp. (Aziz. 2003) Coccocarpia palmicola (Sprengel) Arr.&D.J.Galloway Biotora vernalis (L.) Fr. C. erthroxyli (Sprengel) B . disciformis (Fr.)Mudd. Collema cristatum (L.)F.H.Wigg B. spuria (Schaerer)Anzi. C. flaccidum (Ach.)Ach. B. stigmaea Tuck. C. tenax (Sw.)Ach. Caloplaca aurantia (Pers.) Hellbom Coccotrema urceolatum (Ach.) Tuck. C. citrine (Hoffm.) Th. Fr. Dermatacarpon miniatum (L.)W.Mann C. bolaacina.(Tuck.) Herre Dermatocarpon sp.

68 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Dimelaena oreina (Ach.) Norman. L. cinereofusca var. appalachensis H. Magn.

Diploschistes caesioplumbeus (Nyl.) Vain. L. circumborealis. Brodo and Vitic.

Diploschistes ocellatus (DC.) Norman. L. dispersa (L.) Sommerf.

D. muscru. (Scop.) R.Sant L. garovaglii (Korber) Zahlbr.

D. scruposus (Schreb.) Norman Syn.: L. muralis (Schreb.) Rabenh. Urcelaria L. mutabilis (Ach.) Nyl. Dirina catalinarie Hasse L. novomexicana.H.Magn. Endocarpon pusillum. Hedwig L. polytropa.(Hoffm.) Rabenh. Fulgensia fulgens (Sm.) Elenkin L. pruinosa Chaub. F. subbracteata (Nyl.) Poelt. L. hybocarpa (Tuck.)Brodo Graphis elegans (Borrer ex Sm.) Ach. L. cupressi Tuck. Graphina peplophora M.Wirth & Hale L. xylophila Hue. Gypsoplaca macrophylla Lecanora sp. Fink H. Magn Haematomma ventosum (L.) A. Massal. L. wargiitata Shaerer Hartel & Rambold Heterodermia crocea R.C. Harris Lecanora sp. H. diademata. (Taylor)D.D.Awasthi Lecanora sp. Fink H. Magn Heteroplacedium sp Lecidea atrobrunnea (Ramond ex Lam.&DC.)Schaerer Hypotrachyna livida.(Taylor) Hale L. acropora var, subplicata Zahlbr Hypogymnia austerodes (Nyl.)Rasanen Syn.:Parmelia austerodes L. cythoides (Weber) Ach. Kaernefeltia merrillii (Du Rietz.) Thell.& Goward Syn. Cetraria merrillii L. fuscoatra (L.) Ach.

Lecanactis abietina (Ach) Korbe Lecidella picida.(Nyl.)Hertel and Leuckert L. stigmata (Ach.)Hertel &Leuckert syn.:Lecidea micacea L. cinereofiisca var. appalachensis Brodo Lecidella sp. L. argopholis (Ach.) Ach.

69 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Lepraria incana (L.) Ach. P. tinctina (Mah.)Gill

Leptotrema wightii (Taylor) Mull. and Arg. Parmelia sp.

Leptotrema sp. P. quercina (Willd.) Hal

Lobothallia praeradiosa (Nyl.) Hafellner Parmotrema chinense (Osbeck) Hale and Ahti =Parmelia (Hudson.) Ach. Eproloma vouauxii (Hue)J.R. Laundon P.perforatum (Jacq) A.Massal.syn.Physcia perforata (Ach Megaspora verrucosa (Ach.) Hafellner &M.Wirth syn.: Parmotrema sp Pachyospora Verrucosa Peltigera sp. Melanelia disjucta (Frichsen) Essl. Peltula obscurans (Nyl.)Gyelnik M. panniformis (Nyl.)Essl.syn.:Parmdia punniformis Peltula richardsii (Herre) Wetmore Mycoblastus affinis (Schaerer)Schauer Pertusaria aspergilla (Ach.) J.R. Laundon Neofuscelia pulla (Ach.) Essl. P. flavicunda Tuck. Normandina pulchella (Borrer) Nyl. P. paratuverculifera Dibben Ochrolechia frigida (Sw.) Lynge P. flavicunda Tuck. O. pallescens (L.) A. Massal P. subambigens Dibben O. tartarea Gudbear P. texana Mull. & Arg. Opegrapha sp. P. trachythallina Erichsen Orphniospora moriopsis. (A.Massal.)D.Hawksw P. lactea Erichsen lacidium lacinulatum (Ach.) Breuss P. macoumii (Lamb) Dibben Pannaria rubiginosa var. canoplea P.subpertusa (L.) Tuck. Parmelia acetabulum (L.) Ach. P. rubefacta Erichsen P. caperata (L.) Ach. (Ach.) Bory P. velata (Furner) nyl. P. conspersa.(Ehrh. ex Ach. )Ach. Physcia aipolia (Ehrh. ex Hump.) Furnr. P. saxatilis (L.)Ach. P. biziana (A.Massal) Zahlbr.

70 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

P. caesia (Hoffm.) Furnr. R. subdiscrepans (Nyl.)R.Sant.

P. simpinnata (L.) Nyl. Rhizoplaca sp.

P. pulverulenta Schreber) Furner Rinodina atrocinerea (Hook.) Korb.

Physconia distorta =P.pulverulacea Schreber) Furner R. ascociscana Tuck.

P. perisidiosa (Flarke) Moberg =P. grisea Schreber) FurnerR. bolanderi H. Magn.

P. thamsonii Ess R. populicola H.Magn

P. pulverulacea Moberg. Rinodina sp.

Propidia flavocaerulescens (Hornem.)Hertel and A.J. SchwabRoccellina conformis Tehler

Psora decipiens (Hedwig) Hoffm. Staurothele diffractella (Nyl.) Tuck.

Pyrenula nitida (Flarke) Mull. and Arg. Squmarnia cartilagnea (With.) P. James

P . pseudobufonia (Rehm) R.C. Harris S. crassa (Hudson) Poelt

Rhizocarpon calcareum (from Alvin Kershaw , 1963) S. stellata -petrea Poelt

R. chioneum (Norman) Th. Er. Tephromela grumosa (Pers.) Hafellner & Cl. Roux

R. chionphilum (Norman) Th. Er. Thelomma californicum (Tuck.) Tibell

R. disporum (Naegeli ex Hepp.) Mull. And Arg. Tonina alutacea (Anzi) Latta

R. hochstetteri (Korb.) Vain. T. candida (Weber)Th.Fr.=T.Alutacea

R. georaphicum (L.) DC. T. sedifolia (Scop.)Timdal

R. macrosporum Rasanen Tonina sp. (Aziz , 2003)

R. obscuratuni (Ach) A. Massal Trapelia involuta (Tylor) Hertel

R. richardii (Nyl.) Zahlbr T. placodioides Coppins & P. James

R. umblicatum (Ramond) Flagey Trapeliopsis wallorothii

R. marginalis (Hass.) W.A.Weber Theilidium pyrenohorum (Ach) Mudd ( Florke) Hertel& G

Rhizoplaca melanophthalma (DC.)Leuckert &Poelt Trapelopsis wallorothii (Ach.) Mu

71 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Umbilicaria americana (Poelt & T. Nash) A. campestri ( L. ) Fr.

Verrucaria amphibia Clemente Macrolepiota sp

V. baldensis A. Massal. Order: Aphyllophorales

V. calsiceda DC. Family: Corticiaceae

V. marmorea (Scop.) Arnold Chondrostereum purpureum

V. maura Wahlenb Family: Stereaceae

V. nigrescence Pers. Stereum rugosum Pers

Xanthoria elegans (Link) Th. Fr. Family: Hymenochaetaceae

Phellinus igniarius ( L.Fr.) Quel. s.l.

Family: Fomitaceae X. fallax (Hepp.)Arnold Bjerkandera adusta X. fulva (Hoffm.) Poelt. and Petut Family: Fomitopsidaceae X.parietina (L.) Th. Fr. Fomes fomentarius ( L.Fr.) Kicky Xanthoparmelia plittii (Gyeln.) Hall. Family: Polyporaceae List (5): Classification of identified species of Mushroom (Aziz and Toma, 2012, mostly they found Fomitopsis pincola in Ruwandiz, Joman, Jabal Qandil- Asha- Qulka village, Fomitopsis Ahmad Iwa pincola- Zalm village ) Trametes ochracea Kingdom: Fungi T. versecolor (L.,Fr.) Pilat Phylum : Basidiomycota Family: Paxillaceae Order: Agricales Paxilus corrugatus Family: Agricaceae Order: Cortinariales Agricus arvensis Sch. Family: Cortinariaceae A. bernardii Sch. Crepidotus variabilis (Pers.,Fr.) Kummer A. bisporus ( L.) Fr.

72 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Family: Inocybaceae Pleurotus ostreatus (Jacq Kummer

Inocybe godeyi (Bull,Fr,) Kummer. Family: Corihaceae

Family: Strophariaceae Panaeolus papilionaceus var. papilionaccus

Hypholoma fosciculare (Huds) ex Fr. Kumme (Bull) Quel.

Order: Entolomatales Panaeolus semiovatus var. semiovatus

Family: Entolomataceae (Sowrerby) S. Lundell ,Nannf.

Entoloma rhodopolium (Fr.) Kummer

Entoloma serrulatum (Fr.) Hesler

Order: Tricholomatales

Family; Tricholomataceae

Clitocybe metachora

C. nebularis (Batch) Quel.

C. odora Bull.ex Fr.) Quel.

Cystoderma amianthinum (Scop) Konrad , Marbl.

Micronphale foetidum

Familly; Mycenaceae

Mycena arcangeliana

Russula aeruginea Fr.

Ochrolechyia tartaria (Pers.)Fries

Lactarius vellerus (Fr.) Fr

Family: Tricholomataceae

Tricholoma sejunctum

Family: Pleurataceae

73 Aziz F and Niama B /ZJPAS: 2016, 29(2): 53-73

Aziz, F. H. (2010). Six new records of Hepatophyta REFERENCES (Liverworts) to Iraqi flora. Sci. J. Duhok Univ. 13 (1): Agnew S. (1973). A new Middile Eastern Grimmia j. 86 - 98 Bryol., 7:339-342. Aziz, F. H. (2011). Seventeen spp. New records for the Agnew, S., & Townsend, C.C.( 1970). Trichostornopsis mosses flora of Iraq. Phyton Card., A moss genus new to Asia Israel Box., 19: International J. of Exprimental Botany. 254-259. Argentina . 80: 35-46. Agnew, S. & Voudracek, M. (1975). Moss Flora if Iraq. Aziz, F. H. and Toma Fareed H. (2012). First attempt Feddes Repertorium, 86: for collection and identification of mashroom in 341489. Kurdistan Iraq. Journal advanced laboratory. 3(2):330-350 Al-Nima, B.A. B. 1994 New records of Liverworts from Mosul -Iraq. J. of Educe & Long, D.G. (1979). Some Additions to the Bryophyte Flora of Iraq. Rev. Bryol. Lichen., Sc., 20:36-44. 45:103-105. Al-Nima, B.A. B and Al-Khaiyat A (2001). Check list of Schiffner, V. (1897). Musci Bronrnuelleriani. Osterr. Iraqi Bryophyta. Bull. Iraq. Bolt Z., 47:125-132. Nat Hist. Mus. 3 (9) 7-18 Schiffner, V.( 1913). Bryophyta aus Mesopotamiem und Kurdistan, Sowie, Rhodos, Al- Naqshbandi M.A. and Al-Nima, B.A. B. (2012 ). New record of seven Mosses Mytilini und Prinkipo. Ann. Naturhist., illus., Wien, 27:1-34. species for Iraqi Bryflora ( un published.) Qadir, S. B.and Aziz F. H. (2015). Thirty new records Erbil-province Iraqi of epelithic Kurdistan region, Iraq. 2- In Hassan - Beg mountain lichens m within Erbil governorate, Kurdistan area. Zanco. The Sci. J. of Pure and region M.Sc. Thesis near main Aziz, F. H. (2005). Observation in lichens of roads from north to south part of Erbil Governorate, mountainous area within Erbil-province Kurdistan Region, Iraq

Iraqi Kurdistan region, Iraq. 1- In Safm, Jundian, Kawlokan and Haji Omaran areas, Qadir, S. B. and Aziz, F. H. (2015). Lichens as a bioindecators for air pollution mountain area. Zanco, The Sci. J. of Pure and Appl. assessmen College Of Science, Salahaddin Sci. Salahaddin Univ.-Erbil, Iraq. Univ.- Erbil, Kurdistan, Iraq 16 (5): 1-19. (un published). Aziz, F. H. (2004). Observation in lichens of Vondracek, M. 1962 New Bryophyte for the Iraqi Flora. mountainous area within Erbil-province Bull. Iraq. Nat. Hist. Inst., Iraqi Kurdistan region, Iraq. 2- In Hassan - Beg 2: 9-10. mountain area. Zanco. The Sci. J. of Pure Vondracek, M. 1965 Some New Mosses from Iraq. and Appl. Sci. Salahaddin Univ.-Erbil, Iraq. 17 Collected by E. Hadae. Bull. Soc. Amis. Sci. Lettres Poznan, Ser. D., 6:117-122. (2): 89-117.

Aziz, F. H. and Saeed, J.F. (2006). Observation in lichens flora of mountainous area within Erbil-province Iraqi Kurdistan region, Iraq. 3- In Karajugh mountain and foothill area. Sci. J. of Anbar Univ. 3 (3): 32 - 54.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 74-77 http://dx.doi.org/10.21271/ZJPAS.29.2.7

New species of the genus, Protaetia Burmeister, 1842 from Iraq

(Coleoptera: Scarabaeidae :Cetoniinae)

Hozan Q. Hammamurad, Nabeel A. Mawlood and Banaz S. Abdulla

College of Agriculture, Salahaddin University-Erbil

A R T I C L E I N F O A B S T R A C T

Article History: The new species Protaetia kurdistanica sp. nov. are described Received: 20/07/2016 and illustrated from Iraq.The differences between the species and Accepted: 01/12/2016 closely related species is discussed. Diagnostic characters of the Published: 07/06/2017 Keywords: new species is figured. The materials examined are deposited in ,Scarabaeidae . New species the Museum of plant protection department. College of ,Protaetia kurdistanica sp. Agriculture ,Salahaddin University –Erbil-Iraq. nov., Erbil Kurdistan . region- Iraq.

*Corresponding Author: Hozan Q. Hammamurad [email protected]

1. INTRODUCTION white grubs caused damage to the roots of Protaetia is a genus of beetles of the family cereal, legumes, small fruit plants, shrubs thin Scarabaeidae and subfamily Cetoniinae of caused damage to field crops and fruit trees superfamily Scarabaeoidea, the family number (Mehta et al., 2010). The classification of this exceed 30,000 species of beetles worldwide family is fairly unstable with numerous often called Scarabs or Scarab beetles and then competing theories, many of subfamilies listed genus Protaetia occurring primarily in Asia probably will not be recognized very much and containing over 300 species (Mittal, 2000). linger.Some of scarab beetles are used in the Ratcliffe (1991) study the key of genus biological control of dung and dung flies Protaetia in Floridae and there are five genera (Machatschke, 1972). Lawrence and Britton in United state, Canada and Northern Mexico. (1991) indicated the classification of Thomas (1998) mention the 250 species of superfamily. Arnetts (1968) mention the genus Protaetia in the Oriental Australian and hierarchical level of families and subfamilies. Palearctic region. The adults of Cetoniinae feed In Iraq 10speciesin six genera of the family on flower and fruits, thin popularly referred to listed by Derwesh (1965),and Al-Ali (1977) as flower beetles, the larvae scarab beetles recorded six species.

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2. Type material: (♂) (Holotype) Iraq- the middle impunctate , the anterior margin Kurdistan region: Erbil- Rania, 360 Km N moderately concave, posterior margin convex Baghdad, 18-May.2015 from Milk thistle at the middle, the anterior angle slightly acute , Silybum marianum L., Hozan Q. Hammamurad posterior angle rounded. Scutellum grassy leg., Paratype (8 ♂♂7 ♀♀): from same locality green, triangular ,apex obtusely rounded , and date, the holotype is kept in the insect surface impunctate and bare . procoxal cavity museum of College Agricultural- Erbil, close, prosternum dark brown, surface Kurdistan region- Iraq. randomly irregular of fine punctures , anterior margin of prosternum strongly concave

,densely yellow setose, prosternal process 3. RESULTS AND DISCUSSION nearly globular densely yellow setose.. Elytra Protaetia kurdistanica sp. nov. metallic green, simply punctures, bare, 1/4 of outer margin moderately concave .Epiplural Body:Oval expanded, Metallic green reddish. dark brown, sparsely fine punctate , yellow Length 16.1-20.5 mm, width 7.8-11.1mm. setose. Hind wing brown, veins dark brown. Forelegs dark green, outer margin of fore tibia Head:Parallel sides, elongated. Dark grassy (Fig. 1e) triedenticate, apical part with single green completely covered with Tomentum long spur; tarsus five segmented, 1st- 4th .Eyes black, rounded. Vertex brightly green, segments cup shaped, 2nd segment 1.3 times as flat, with low dense of fine punctures. Coronal long as 1st segment, 2-4 segments same in suture present. Frons densely punctured. length, 5th segment tubular, 1.3 times as long as Clypeus flat, rectangular, laterally wrinkled, 4th segment, apical part with short process; middle part simply punctured. Anterior margin claws long simple moderately curved. Mid legs of clypeus with shallow, narrow impression resemble forelegs except the, mid tibia with along entire margin. Labrum (Fig. 1a) nearly single denticle at the middle, apical part globular , pale yellow, sparsely pale yellow tridenticate, with two spurs. Hind legs resemble setose, anterior margin moderately concave. forelegs except, coxa plate shaped, outer Mandible (Fig. 1b) dark brown, high margin of hindtibia with single denticle, apical sclerotized, apical part bidenticles, inner part with two short spurs. denticles shorter than the outer. Maxilla (Fig. 1c) dark brown, cardo triangular , sparsely Abdomen: metallic grassy green, oval, with yellow setose, distal part of galea rectangular, six segments , surface sparsely yellow setose moderately sclerotized, apical part densely and randomly irregular punctures, 2nd -5th pale brown setose, lacinia membranous , apical abdominal sternites same in length.6th nd part densely pale brown setose,2 segment of abdominal sternite nearly cup shaped, anterior maxillary palp square shaped 2 times as long as margin convex, posterior margin rounded, st th 1 segment, 4 segment oval elongated, 1.5 surface sparsely yellow setose, . 6thtergite dark rd times as long as 3 segment. Antenna (Fig. 1d) brown, cup shaped, anterior margin nearly lamellate, dark brown, surface yellow setose,1- straight, posterior slightly concave. Spiculum th 4 segment cup shaped, 5-8 segments nearly gaster absent. equal in size, 9-11 segment lamellate, 11th segment 1.1 times as long as 8th segment. Male genitalia:Aedeagus (Fig. 1g,h) brown, moderately curved, basal hood pale brown Thorax:Pronotum metallic grassy green, .Length 0.6-0.7 mm, apical part low sclerotized surface randomly irregular punctures laterally ,

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nearly hook shaped. Tegmen (Fig. 1f) pale identification. We deeply express my gratitude brown, nearly Y- shaped, highly sclerotized. to Pro. Dr. Mohammed S. Abdul Rassoul in Division of Entomology, Natural History Diagnosis:Protaetia kurdistanica sp. nov. this Research Center – University of Baghdad / Iraq species differs from closely related species , for his kind help and continuous Protaetia maxwelli Jakl by the following encouragement to this work characters :Body length 16.-20.5 mm. Middle parte of pronotum impunctate and bare. Elytra bare .Fore tibia triedenticate .Aedeagus pale brown-yellow, moderately curved, apical part nearly hook shaped.

Acknowledgements We sincerely thank the specialist in German museum of technology who confirmed the

Figure:1 Protaetia kurdistanica sp.nov.

a. Labrum b. Mandibll c. Maxilla d. Antenna e. Foretibiaf. Tegmen g. Male genitalia lateral view h. Male genitalia dorsal view.

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REFERENCES

Al-Ali, A.S.(1977). Phytophagous and Ratcliffe, B.C.(1991). The Scarab beetles of entomophagous insects and mites of Iraqi Nebraska. Bulletin of the Univiersity of Natural History Research center, Nebraska State Museum, 12:1-333 pp. publishing,No. 33-142pp. Ritcher, P.O.(1958). Biology of scarabaeidae. Arnetts, R.H.,J.R.(1968). The beetles of the Ann. Rev. Ento., 3:311-334. Unite states. Amanual for identification. Thomas, M. (1998). A flower beetle, Euphoria Amer. Entomo., Ann Ardor, IM., 1-112pp. sepuleralis (Fabricius). In florida Derwesh, A.I. (1965). A preliminary list of (Coleoptera: identified insects and arachnids of Iraq. Scarabaeidae). Florida Department of Direct. Gen. Agr.Res. Proj. Baghdad. Bull., Agriculture and Consumer services, No. 121:123pp. Entomology circular, No. 386:1-2. Mehta, P.K.; Chandel, R.S. and Mathur, Lawrence, J.F. and Britton, E.B. (1991). Y.S.(2010). Status of whitegrubs in North Coleoptera. The insects of Australia, Melbo. Western Himalaya, Jour. Inse. Sci., 23:1- Univ. Carlton, 2nd ed., Vol., 1:543-683pp. 14.

Mittal, I.C.(2000). Survey of scarabaeid (Coleoptera) fauna of Himanchal pradesh (India). Jour. Ento., 24:133-141.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 78-87 http://dx.doi.org/10.21271/ZJPAS.29.2.8

Using Proposed Nonparametric Regression Models for Clustered Data (A simulation study)

Taha H.A. Alzubaydi Department of Statistics, College of Administration and Economics, Salahaddin University, Erbil, Kurdistan Region, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: A nonparametric model is introduced to account varying impacts of factors Received: 8/11/2016 over clusters using proposed models in comparison with some classical models. It Accepted: 2/12/2016 achieves the parsimony of parameterization and allows the explorations of Published:07/06/2017 nonlinear interactions. The random effect in the nonparametric model also accounts Keywords: within-cluster correlation. Local, linear-based estimation procedure is proposed for Nonparametric Regression, estimating functional coefficients, residual variance and within-cluster correlation matrix for three cases (the autoregressive, the exchangeable and the unstructured). Cluster data, Kernel method, Simulation studies are carried out to demonstrate the methodological power of the Efficient estimation and proposed methods in the finite sample, Using MATLAB language program Nonlinear model. designed for this purpose. *Corresponding Author:

Taha H.A Email: [email protected] 1. INTRODUCTION Nonparametric methods try to avoid subject correlation to improve the efficiency of assumptions about the probability distributions estimation through three correlation structures in order to generate methods that can be used correspond to correlation ρ , (Silverman, B. in settings where regular parametric W., 1984): the autoregressive case with r=0·6, assumptions do not work (Lin, X. & Carroll, the exchangeable case with r=0·6 and the R. J., 2000). Although applicable in more unstructured case with r = r = 0.8 and general circumstances, nonparametric models 12 23 = can lead to very complex mathematics in all r13 0.5 correlation matrices. Clustered data but the simplest models by using seemingly arises from many applications, including unrelated kernel estimator method. ophthalmologic studies, rodent teratology experiments, dental research, family-based In clustered data, it is clear the data that genetic studies, and community intervention are collected from the same subject at different studies, etc. times are correlated and those observations from different subjects are often independent. 2: Methodology: Therefore, it is of great interest to estimate the regression function incorporating within- 2.1: Nonparametric Regression for Clustered data: 79 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

T Consider data from n clusters with mi Y = (Y1, Y2 ,, Yn ) , and Ti ,T and are observations in the ith cluster (i = 1,2,,n) . θ (T) similarly defined. th th The j observation ( j =1,2,,mi ) in the i −1 Define: K h (s) = h K(s / h), where K(.) cluster consists of an outcome variable Yij and is a zero-mean kernel function and h is a a single covariate Tij whose values vary within bandwidth, where: the cluster. For longitudinal data, a cluster refers (−1 5).sd (x) to a subject and within-cluster observations refer h = (1.06).m  (2) to repeated measures over time, and Tij is a Where x = Tij is (n × m) matrix and K(.) time-varying covariate or time; for familial data, computed from the following (Wang, N., 2003): a cluster refers to a family and within-cluster observations refer to different family members 1 2 and T is a member specific covariate. For K = exp{− ui / 2}/ h  (3) ij 2π simplicity, we assume the number of observations per cluster takes the same value Where ui = (xij − xis )/ h where (s=1,2,…,m) m in all clusters, although the results hold when and K(.) = diag(K ) cluster sizes vary. The outcome Yij depends on the covariate Tij through (Xihong Lin and et al., Let V be a working covariance matrix 2004). (Liang, K. Y. & Zeger, S. L.,1986):

Yij = θ (Tij )+ ε ij  (1) V = si .ρ.si

Where θ (Tij ) is an unknown smooth Where (si ) is the standard deviation for T function, and the errors ε ij = (ε11 ,,ε1m ) are all clusters, and we have the three correlation independent with mean zero vector and true structures corresponding to ρ matrix, the covariance matrix Σ . We assume in our autoregressive case with r=0·6, the asymptotic study that the cluster size m is exchangeable case with r=0·6 and the finite but the number of clusters n goes to unstructured case with r12 = r23 = 0.8 and infinity. r13 = 0.5 correlation matrices, respectively, and Nonparametric estimation of θ (t) can they are as follows: proceed using kernel method. It is of interest to 1 .6 .36 1 .6 .6 1 .8 .5 construct nonparametric estimators of θ (t) that       ρ =  1 .6  , ρ =  1 .6 , ρ =  1 .8  (4) account for the within-cluster correlation  1   1  1 (Wang, Y., 1998). Let Y be the dependent variable matrix Define: by dimension (n,m) for several models (Xihong T Yi = (Yi1, Yi2 ,, Yim ) , Lin and et al., 2004):

T θ (Ti ) = {θ (Ti1 ),θ (Ti2 ),,θ (Tim )} Model − (1) Y = θ (xis ) = sin(xis )  (5)

Model − (2) Y = θ (xis ) = exp(xis )  (6) 80 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

−1 Model − (3) Y = θ (xis ) = sin(2xis )  (7) n m  ij  K wh (xis ) = ∑∑ Kh (xij − xis )v  Model − (4) Y = θ (x ) = sqrt(z *(1− z))∗  i =1 j =1  is −3 / 5 −3 / 5 −1 T sin(2π (1+ 2 ) *(z + 2 ) )  (8) ,{Kh (x11 − xis ),, Kh (xnm − xis )} is an nm ×1 vector, Where z = (xis + 2)/ 4 =  T The proposed models that have been used in this K w {K wh (x11 ), , K wh (xnm )} is an nm × nm ~ research are as follows: matrix, V d = diag(V d ,,V d ) and V d = diag(V −1 ). Model − (5) Y = θ (xis ) = sin(exp(2xis ))  (9)

θˆ Model − (6) Y = θ (xis ) = cos(2xis )  (10) Let K (x) be an (nm×1) vector containing the ˆ evaluations of θK (x) at the vector of all the Model − (7) Y = θ (xis ) = cos(π sin(xis ))  (11) design points x, which is (Welsh, A. H., Lin, X.

Model − (8) Y = θ (xis ) = sin(cos(xis ))  (12) & Carroll, R. J., 2002):

Consider a qth-order polynomial kernel ˆ ˆ ˆ θ K (x) = (θ K (x11 ),,θ K (xnm )) estimator (Zhang,D., Lin, X., Raz, J. & Sowers, th Then M., 1998), we have θ (xis ) is estimated at the l (l ) − iteration by θˆ (x ), one updatesθ (x )at the ˆ ~ −1 ~ d 1 ~ −1 K is is θ K (x) = {I + K w (V −V )} K wV Y  (15) (l+1)th iteration byθˆ(l+1) (x ) = αˆ , where K is 0 Where I be an (nm×nm) identity matrix, for T αˆ = (α 0 ,α1 ,,α q ) solves the qth-order polynomial seemingly unrelated

kernel estimator, one modifies K wh (x) in (7) n m T −1 T ∑∑ K h (xij − xis )Bij (xis ) V {Yi − µi( j ) (xis )}= 0  (13) i=1 j=1 to K wh (x) where In which B (x ) is an m×(q+1) matrix of zeros ij is − T T ~ T ~ d ~ 1 th K (x) = δ {x(x ) K (x )V x(x )} ∗ except that the j row is wh 1 is dh is is ~ T x(xis ) K dh (xis )  (16) q T [1 , (xij − xis ) ,  , (xij − xis ) ] And

T T ~ θˆ (l )  θˆ (l )  Whereδ1 = (1,0,,0) , x(xis ) is an  K (xi1 ), , K (xi, j −1 ),  q µi( j ) (xis ) =    k ˆ (l ) ˆ (l )  nm×(q+1) matrix with {(n−1)i+j}th row given  ∑α k (xij − xis ) ,θ K (xi, j +1 ),,θ K (xim )  k = 0  q by {1,(xij − xis ),,(xij − xis ) }, and The final kernel estimator at convergence is called the seemingly unrelated K dh (xis ) = diag{K h (x11 − xis ),, K h (xnm − xis )}. kernel estimator of θ (x ) and is denoted is 2.2: Measurement of Performance: ˆ byθ K (xis ) is given by Mean squares error (MSE) is an efficient

~ − ~ −1 ~ − criterion used in this research and given by θˆ (x) = K T (x ){I + (V 1 −V d )K } V 1Y  (14) K wh is w (Green, P. J. & Silverman, B. W., 1994): Where 81 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

T −1 MSE = e vy e / df / m  (17) e is an (nm×1) vector containing the ˆ evaluation of θ K (x)− Y .

v y is an (nm×1) vector containing the evaluations of S y .ρ.S y and df is degrees of freedom and equal to

−1 −1 −1 T {1− trace((I + K w (v y − vw ) ).K w .v y .Y )}, −1 where vw = diag(v y )

3: Application side: In this section, we are presenting simulation results which compare the finite sample efficiency of the several models for a researcher (Xihong lin and et al, 2004) and the proposed models using MATLAB language program designed for this purpose (Appendix). We assumed in the simulation process that the number of clusters is n=50 and n=100, and the cluster size is m=3. The covariate xij was generated independently from Uniform distribution [−2, 2]. The outcome Yij for formula (1) with θ (xis ) specified by eight models for formulas (5-11) and depending on the three cases, the correlation matrices as in the formula (4), by using the final kernel estimator of θ (x ) and is denoted byθˆ (x ) which is is K is given by formula (15) with values Y (For the first implementation of the program) illustrated in the following figure:

82 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

Through Figure 1 shows that the four models for researchers (Xihong lin and et al, 2004) and the proposed four models may be suitable for nonparametric regression. To apply the proposed models and compared them with some classical models. and the simulation was repeated 100 times (Appendix) for the various correlation matrices (1-the autoregressive case with r=0·6, 2- the exchangeable case with r=0·6, 3-the unstructured case with r12 = r23 = 0.8 and

r13 = 0.5 ), the number of clusters and constant size cluster equal to (3) and estimates the average of (MSE), are presented in the following table: Table 1.Simulated relative (MSE) efficiencies for eight models Model Correlation Average (MSE) Average (MSE)

matrices when n = 50 when n = 100 1 1 0.1979928566 0.1978854409

1 2 0.1841472635 0.1836087996

1 3 0.3388164937 0.3394399230

2 1 0.6181976333 0.6180748045

2 2 0.5999275949 0.5991284199

2 3 0.8832032833 0.8870484324

3 1 0.1839746494 0.1820016702

3 2 0.1772850018 0.1749359576

3 3 0.3094399909 0.3086228664

4 1 0.4742110433 0.4747155109

4 2 0.4644110384 0.4647012081

4 3 0.4051703109 0.4054840370

5 1 0.1773526586 0.1737244334

5 2 0.1728166669 0.1688910795

5 3 0.2620699431 0.2600647566 ˆ 6 1 0.1989420567 0.1983955033 Fig. (1): Values of Y and θ K (xis ) for eight models when n=100, m=3, the autoregressive 6 2 0.1896013825 0.1886204909 case with r=0·6 83 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

6 3 0.3503713517 0.3503368354 1. Applying the proposed models, especially the eighth model with correlation matrix (the 7 1 0.2317351071 0.2302940121 exchangeable case with r=0·6). 7 2 0.2211896886 0.2193551186 2. Comparison of the proposed models between 7 3 0.3984642780 0.3980704645 seemingly unrelated kernel estimator and spline 8 1 0.1497015227 0.1472124237 method.

8 2 0.1413271547 0.1386288225 3. A comparison between the nonparametric regression and ridge regression with some 8 3 0.2412455434 0.2401688833 transformations. From table (1), we note that the best model 5: References: is the eighth one of the proposed model and the matrix of the second correlation (the Green, P. J. & Silverman, B. W. (1994). exchangeable case with r=0·6), because it has Nonparametric Regression and Generalized the least value of MSE which is equal to Linear Models: A Roughness Penalty Approach. (0.1413271547 and 0.1386288225). The number London: Chapman and Hall. of the clusters (n) by increasing it leads to a Liang, K. Y. & Zeger, S. L. (1986). Longitudinal better model appropriate to the data for all data analysis using generalized linear models. models and cases. Correlation matrix of the Biometrika 73, 13–22. second (the exchangeable case with r=0·6) is the best, followed by the first matrix (the Lin, X. & Carroll, R. J. (2000). Nonparametric autoregressive case with r=0·6) and finally the function estimation for clustered data when the third matrix (the unstructured case with predictor is measured without/with error. J. Am. Statist. Assoc. 95, 520–534. r12 = r23 = 0.8 and r13 = 0.5 ). Silverman, B. W. (1984). Spline smoothing: the 4: Conclusions and Recommendations: equivalent variable kernel method. Ann. Statist. 12, 898–916.

Through this simulation study we reached Wang, N. (2003). Marginal nonparametric kernel to the following Conclusions and regression ccounting for within-subject Recommendations. correlation. Biometrika 90, 43–52.

Wang, Y. (1998). Mixed effects smoothing spline analysis of variance. J. R. Statist. Soc. B 60, 159– 174. 4.1: Conclusions: Welsh, A. H., Lin, X. & Carroll, R. J. (2002). 1. The four proposed models can be applicable Marginal longitudinal nonparametric regression: in the nonparametric regression for cluster data. Locality and efficiency of spline and kernel methods. J. Am. Statist. Assoc. 97, 482–493. 2. The proposed eighth model had its preference in the appropriate cluster data with a correlation Xihong Lin, Naisyin Wang, Alan H. Welsh and Raymond J. Carroll, (2004). Equivalent kernels matrix (the exchangeable case with r=0·6), of smoothing splines in nonparametric regression followed by (the autoregressive case with for clustered/longitudinal data. Biometrika 91,1, r=0·6). pp.177-193.

3. Increasing the number of clusters leads to an Zhang,D., Lin, X., Raz, J. & Sowers, M. (1998). Semiparametric stochastic mixed models for increase in the estimation accuracy of longitudinal data. J. Am. Statist. Assoc. 93, 710– nonparametric regression models. 699.

4.2: Recommendations: 84 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

Appendix case 4 z=(x+2)/4; N=100 y=sqrt(z.*(1- for L=1:N z)).*sin(2*pi*(1+2^(-3/5))*(z+2^(- n=100; model=1; cor=1; m=3; a=-2 ; 3/5)).^(-1)); b=2;ss=1;n1=n; case 5 switch cor y=sin(exp(2*x)); case 1 case 6 co=[1 .6 .6^2;.6 1 .6;.6^2 .6 1] ; y=cos(2*x); case 2 case 7 co=[1 .6 .6;.6 1 .6;.6 .6 1]; y=cos(pi*sin(x)); case 3 case 8 co=[1 .8 .5;.8 1 .8;.5 .8 1]; y=sin(cos(x)); end end while n >= 1 sy=std(y'); v=diag(inv(sy*co*sy)); x=unifrnd(a,b,1,m); sx=std(x'); p=1; h=(1.06)*m^(-.2)*sx; p=1; s=1; for i= 1:m for i =1:m for j=1:m for j=1:m v(p)=v(j); p=p+1; u(p) = (x(s,j)-x(i))/h; q(p) = (x(s,j)-x(i)); end k(p)=((1/sqrt(2*pi))*exp(- end u(p)^2/2))/h; p=p+1; vw=diag(v); delta=[1 0 0]; end kw=delta*(inv(x1'*kdh*vw*x1))*x1'*kd h; p=1; end for i =1:m k=k'; kdh=diag(k); x1=[ones(m^2,1) q' q'.^2]; for j=1:m switch model kw1(i,j)=kw(p); p=p+1; case 1 end y=sin(x); end case 2 kw1; vy=sy*co*sy; vy=diag(vy); vy=diag(vy); vw1=inv(sy*co*sy); y=exp(x); vw1=diag(vw1); vw1=diag(vw1); case 3 y=sin(2*x); 85 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

theta=((eye(m)+kw1*(inv(vy)- y=sqrt(z.*(1- vw1))^(-1))*kw1*inv(vy)*y'; z)).*sin(2*pi*(1+2^(-3/5))*(z+2^(- df=1-trace(((eye(m)+kw1*(inv(vy)- 3/5)).^(-1)); vw1))^(-1))*kw1*inv(vy)); case 5 e=theta-y'; mse=e'*(inv(vy))*e/df/m; y=sin(exp(2*x11(t,:))); h1(ss)=mse; x11(ss,:)=x; case 6 theta=theta'; theta11(ss,:) =theta; y=cos(2*x11(t,:)); ss=ss+1; n=n-1; case 7 end y=cos(pi*sin(x11(t,:))); n=n1; h1; xc=x11; theta11; ss=1; case 8 while n > 1 y=sin(cos(x11(t,:))); h1; [ma no]=max(h1); h1(no)=[] ; x11(no,:)=[]; n=n-1; ss=1; end for t=1:n; sy=std(y'); v=diag(inv(sy*co*sy)); p=1; p=1; for i= 1:m for i =1:m for j=1:m for j=1:m v(p)=v(j); p=p+1; u(p) = (x11(t,j)-x11(t,i))/h1(t); q(p) = x11(t,j)-x11(t,i); end k(p)=((1/sqrt(2*pi))*exp(- end u(p)^2/2))/h1(t); p=p+1; vw=diag(v); delta=[1 0 0 ]; end kw=delta*(inv(x1'*kdh*vw*x1))*x1'*kd h; p=1; end for i =1:m k=k'; kdh=diag(k); x1=[ones(m^2,1) q' q'.^2 ]; for j=1:m switch model kw1(i,j)=kw(p); p=p+1; case 1 end y=sin(x11(t,:)); end case 2 kw1; vy=sy*co*sy; vy=diag(vy); vy=diag(vy); y=exp(x11(t,:)); vw1=inv(sy*co*sy); case 3 vw1=diag(vw1); y=sin(2*x11(t,:)); vw1=diag(vw1); case 4 theta=((eye(m)+kw1*(inv(vy)- z=(x11(t,:)+2)/4; vw1))^(-1))*kw1*inv(vy)*y'; 86 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

df=1- y=sin(exp(2*xc(s,:))); trace(((eye(m)+kw1*(inv(vy)-vw1))^(- case 6 1))*kw1*inv(vy)); y=cos(2*xc(s,:)); e=theta-y'; mse=e'*(inv(vy))*e/df/m; h1(ss)=mse; case 7 ss=ss+1; y=cos(pi*sin(xc(s,:))); end case 8 end y=sin(cos(xc(s,:))); n=n1; xc; ss=1; end while s <= n sy=std(y'); v=diag(inv(sy*co*sy)); p=1; p=1; for i =1:m for i= 1:m for j=1:m for j=1:m u(p) = (xc(s,j)-xc(s,i))/h1; v(p)=v(j); p=p+1; q(p) = xc(s,j)-xc(s,i); end k(p)=((1/sqrt(2*pi))*exp(- end u(p)^2/2))/h1; p=p+1; vw=diag(v); delta=[1 0 0]; end kw=delta*(inv(x1'*kdh*vw*x1))*x1'*kd end h; p=1; k=k'; kdh=diag(k); x1=[ones(m^2,1) for i =1:m q' q'.^2 ]; for j=1:m switch model kw1(i,j)=kw(p); p=p+1; case 1 end y=sin(xc(s,:)); end case 2 kw1; vy=sy*co*sy; vy=diag(vy); y=exp(xc(s,:)); vy=diag(vy); vw1=inv(sy*co*sy); case 3 vw1=diag(vw1); vw1=diag(vw1); y=sin(2*xc(s,:)); theta=((eye(m)+kw1*(inv(vy)- vw1))^(-1))*kw1*inv(vy)*y'; case 4 theta111(ss,:) =theta; ss=ss+1; s=s+1; z=(xc(s,:)+2)/4; end y=sqrt(z.*(1- z)).*sin(2*pi*(1+2^(-3/5))*(z+2^(- the=theta111*5; 3/5)).^(-1)); switch model case 5 case 1 87 Alzubaydi T./ZJPAS: 2017, 29(2): 78-87

y=sin(xc); case 2 y=exp(xc); case 3 y=sin(2*xc); case 4 z=(xc+2)/4; y=sqrt(z.*(1- z)).*sin(2*pi*(1+2^(-3/5))*(z+2^(- 3/5)).^(-1)); case 5 y=sin(exp(2*xc)); case 6 y=cos(2*xc); case 7 y=cos(pi*sin(xc)); case 8 y=sin(cos(xc)); end MAE(L)=sum(sum(abs(the-y)))/(n*m); end MAE; AMAE=sum(MAE)/N plot(xc,y,'.',xc,the,'.');

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 88-95 http://dx.doi.org/10.21271/ZJPAS.29.2.9

Petroleum System Modeling of Jabal Kand Oil Field, Northern Iraq

Rzger A. Abdula Department of petroleum Geosciences, Faculty of Science, Soran University, Soran, Kurdistan Region, Iraq

A R T I C L E I N F O A B S T R A C T

Article History: The petroleum system of Jabal Kand Oil Field shows that the formations Received: 06/06/2016 such as Tertiary Kolosh, Cretaceous Shiranish, and Jurassic Sargelu are Accepted: 08/12/2016 immature and have not generated any oil Ro< 0.55%. They are neglected as Published: 07/06/2017 compared to formations below them which are also source rocks. The Kurra Keywords: Chine Formation is mature with Ro> 0.55%. Other formations such as Gele PetroMode Khana and other Triassic formations are with high maturity with Ro≥ 1.3% and Hydrocarbon generation are within wet and dry gas window while older formations are either within dry Jabal Kand gas zone or completely generated hydrocarbon and depleted after hydrocarbon Petroleum system was expelled and migrated to reservoir rock of structure traps. Northern Iraq. *Corresponding Author: Rzger A. Abdula [email protected] 1. INTRODUCTION development and migration of the axis to the The Jabal Kand-1 Well is located 30 km to SW direction occurred during Lower the north of Mosul city (coordination latitude: Cretaceous-Miocene (North Oil Company, 36º 39' 52.8'' and longitude: 43º 01' 36.8''). The 1983). The well was completed in 1983 (Jassim ground level elevation is 398.4 m and Rotary and Goff, 2006). Table Kelly Bushing (R.T.K.B.) elevation is A petroleum system includes a mature 406 m. The well was drilled to the depth of source rock, reservoir rock, cap rock, and 5848 m R.T.K.B. and penetrated Paleozoic overburden rock. In addition, it includes the Chia Zairi and Harur formations (North Oil processes such as stratigraphic or structural Company, 1983). The Jabal Kand structure is trap formation and the generation-migration- 33 km long and 5 km wide (Jassim and Goff, accumulation of petroleum. In order for 2006). This structure is a long, twisting petroleum accumulation to be present, all structure with a minimum of three peaks on top required elements and processes should be of the Lower Fars (Fatha) Formation. The well within a specific time and place (Magoon and is located on the middle dome (North Oil Dow, 1994). Company, 1983). The presence of structural The study tries to determine the burial complication features was not verified by any history, the thermal history, and the maturity indicators from the Dipmeter, but a NW-SE history of the source rocks of the basin to axial trend migration of the axis to the NE reduce petroleum exploration risk. direction during the Carboniferous-Upper 2. MATERIALS AND METHODS Jurassic can be inferred. Additional structural The studied well was modeled using PetroMod 1-D modeling software (one of the 89 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

most famous commercial modeling software) Beduh, Gele Khana, Kurra Chine, Baluti, developed by Integrated Exploration System Butmah, Adaiyah, Mus, Alan, Sargelu, Gotnia, GmbH. The 1-D burial history models are point Garagu, Sarmord, Qamchuqa, Aqra, Shiranish, locations, mainly wells. Kolosh, Khurmala, Gercus, Pila Spi, Lower For chronostratigraphic divisions, the time Fars (Fatha) formations (Fig. 1). scale of the Lexique Stratigraphique The results of the model indicate that peak International (Bellen et al., 1959) and petroleum generation from the Paleozoic Harur International Commission on Stratigraphy Formation oil- and gas-prone source rock in the (2008) was used. The input data include deepest parts of the basin occurred and the thickness, lithology, heat flow and absolute accumulation and preservation happened from ages for each formation and each episode. The Mid Triassic (Fig. 2). The Jurassic Sargelu 1-D model includes 23 formations from the Formation is supposed to be more mature than base of the Lower Carboniferous Harur it is but the absence of Upper Jurassic Najmah Formation to the Middle Miocene Lower Fars and Chia Gara formations and comparatively (Fatha) Formation and is based on the UTM low thickness of overburden rocks (2107 m) Zone 38 (Northern Hemisphere) coordinate have not contributed to increase the system using the WGS 84 datum. The temperature to cook Sargelu. The Mid Sargelu stratigraphic units, their ages, and lithologies Formation oil and gas-prone source rock not are shown in Table 1. The compositional entered the oil window in the Miocene and it is mixtures or lithology characterized as end still not within the oil window at the present member rock types was assigned to the facies time (Fig. 2). The Cretaceous source rock has in each formation. The thermal conductivities no significance in the study area because of and heat capacities with their thermal tectonic activity (obduction) and non- properties of different rock types are either user deposition of Oligocene-Lower Miocene and defined or software default values. The Tmax erosion of Upper Miocene-Pleistocene values and their mathematically determined sediments. Also the relatively reduced Ro% equivalent, obtained by Rock-Eval thickness of the Middle Miocene sediments pyrolysis, were used for calibration. (some hundred meters) and the erosion or non- deposition of Lower Bakhtiary, Upper 3. RESULTS AND DISCUSSIONS Bakhtiary, and Alluvial during Pliocene- Basin modeling combines several Pleistocene time seems to be relevant for geological parameters to assess the formation hydrocarbon maturity (Fig. 3). and evolution of sedimentary basins to help evaluation of prospective hydrocarbon 3.2. Temperature and Heat Flow Analysis reserves. The scale of the model ranges in size The goal of heat-flow analysis is from a single well to a whole basin. temperature calculation, a prerequisite for determining geochemical reaction rates. The 3.1. Burial History and Thermal Maturation provided bottom hole temperature data from Modeling well logs and final geologic reports for Jabal Burial history, thermal maturity, and timing Kand-1 Well (Fig. 4) were used to estimate the of petroleum generation were modeled for present heat flow in Mosul area. several key source-rock horizons at Jabal Kand-1. The formations from the oldest to youngest are the Harur, Chia Zairi, Mirga Mir, 90 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

Table 1: Data used to generate burial -history curves in well Jabal Kand- 1 in Mosul area, Northern Iraq. Depo. Depo. Eroded Eroded HI (mg Top Base Thickness Eroded TOC Formation From to From to Lithology PSE HC/g (m) (m) (m) (m) (wt.%) [Ma} [Ma] [Ma] [Ma] TOC) Lower Fars -398 -242 156 250 13.7 11.6 11.6 0.1 Evap. shaly Seal Rock Pila Spi -242 177 419 100 40.4 33.0 33.0 13.7 Lime. Dolom. Reservoir Rock Gercus 177 413 236 48.6 40.4 Shale & sand Seal Rock Khurmala 413 606 193 55.8 48.6 Limestone (shaly) Reservoir Rock Kolosh 606 911 305 63.6 55.8 Shle. & Lime. Source Rock Shiranish 911 1013 102 75.0 63.6 Shale calc. Reservoir Rock Aqra 1013 1054 41 89.8 75.0 Limestone (micrite) Reservoir Rock Qamchuqa 1054 1242 188 100 113.0 93.9 93.9 89.8 Lime. dolom Reservoir Rock Sarmord 1242 1275 33 133.9 113.0 LimestoneE Reservoir Rock Garagu 1275 1360 85 140.2 133.9 Lime. sandy Reservoir Rock Gotnia 1360 1677 317 250 159.0 149.0 149.0 140.2 Lime. & Evap. Seal Rock Sargelu 1677 1890 213 150 177.2 164.7 164.7 159.0 Lime. marly Source Rock 3.93 444 Alan 1890 1991 101 180.0 177.2 Lime. & Evap. Seal Rock Mus 1991 2047 56 186.0 180.0 Lime. marly Reservoir Rock Adiyah 2047 2085 38 190.5 186.0 Lime. & Evap. Reservoir Rock Butmah 2085 2479 394 199.6 190.5 Lime. dolom Reservoir Rock Baluti 2479 2535 56 202.0 199.6 Evap. shaly Seal Rock Kurra Chine 2535 3682 1147 170 227.3 205.0 205.0 202.0 Shale carb. Reservoir Rock Gele Khana 3682 4463 781 239.0 227.3 Shale carb Source Rock 0.79 144 Beduh 4463 4530 67 241.0 239.0 Limestone (shaly) Reservoir Rock Mirga Mir 4530 4695 165 247.0 241.0 Dolomite Reservoir Rock Chia Zairi 4695 5325 630 270.6 247.0 Limestone Reservoir Rock Harur 5325 5848 523 110 359.2 340.3 340.3 270.6 Limestone (shaly) Source Rock

Figure 1: seismic crosses the plunge of and the ends of Jabals Kand and Bashiqa (Kent, 2010).

91 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

Figure 2: Calculated vitrinite time profile of well Jabal Kand-1 in Mosul area, Northern Iraq. The figure shows that Harur Formation entered oil window in the Mid Triassic and entered gas window in the Early Jurassic. The Sargelu Formation has not entered oil window and it is still not within oil window at the present time.

Figure 3: Burial history with vitrinite reflectance (Ro %) of well Jabal Kand-1 in Mosul area, Northern Iraq.

The temperature- versus- depth curve temperature between Gotnia and Baluti clearly shows intervals of steep and low formations (Fig. 4). Also the heat flow from the increases, which is due to the difference in base upward does not remain constant, because thermal conductivity of rocks (Fig. 5). The changing paleoheat flow caused an increase in figure clearly shows a steep increase in pressure and compaction. An important 92 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

Figure 4: Bottom hole temperature variation with depth of well Jabal Kand-1 in Mosul area, Northern Iraq. The figure shows that temperature rapidly increases between Gotnia and Baluti formations.

Figure 5: 1D model of the calculated and measured temperature (blue line) and thermal conductivity (vertical lines) versus depth of well Jabal Kand-1 in Mosul area, Northern Iraq. 93 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

consequence of this long period of relative As Tmax values are reliable, the maturity of the stability, with lower and constant rates of source rocks was evaluated on the Tmax basis subsidence, is that the heat flow can be where Tmax could be measured from cuttings assumed to be constant through time. Based on (Table 1). In the middle part of Jurassic this assumption and in agreement with the heat sequence the maturity is indicated by Tmax. The flow values, 42- 80 milliwatt/square meter measured Tmax values range between 427ºC (mW/m²) considered for foreland basins by (0.53 Ro%) and 436ºC (0.69 Ro%) at depths of Allen and Allen (2005), constant heat flow 2110 m and 2134 m, respectively in well Jabal values were considered for modeled wells. In Kand-1. This range corresponds to immature to order to investigate the accuracy of the early oil-window because generally, the early calibrated thermal and maturity models, the oil window is defined by a vitrinite reflectance thickness of overburden, timing and duration of of Ro=0.55%, the main oil window by a hiatus and unconformities and surface erosion reflectance of Ro=0.70% and the late oil intensity, a sensitivity analysis was performed. window by a vitrinite reflectance of Ro=1.00% A good fit between calculated and measured (Sweeney and Burnham, 1990). More than temperature values was attained (Fig. 5) using 1700 m erosion can be estimated due to the estimated heat flow value equal to (42 mW/m²) Lower and Upper Permian, Upper Triassic, in the studied area, assuming a mean surface Upper Jurassic, Middle Cretaceous, Oligocene, temperature of (25ºC) through the region. Lower Miocene, and Upper Miocene- Pleistocene uplifts, respectively. This huge 3.3. Thermal Maturation amount of eroded and/or non-deposited The Tmax showed systematically normal sediments is responsible for the organic maturity, due to the non-contaminated samples. matters’ low thermal maturity (Fig. 6).

Figure 6: Calculated vitrinite-depth profile with measured values (squares) of well Jabal Kand-1 in Mosul area, Northern Iraq. 94 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

3.4. Generic Events Chart immature (Al-Habba, 1988). The Early Jurassic The petroleum system in well Jabal Kand-1 sediments (Alan and Mus formations) though indicates that oil has not started to generate in thermally mature, have a low hydrocarbon Sargelu Formation although a trap has formed yield potential (Al-Habba, 1988), even though since Miocene. The Harur Formation started to there are Triassic (mature) and Palaeozoic generate hydrocarbon 207 Ma ago (Fig. 2). (either within late gas zone or postmature) Most of the generated oil migrated, resulting in source rocks. major upward migration and oil accumulations The earlier study on crude oils in Tawke-3 since Late Jurassic and the critical moment and Tawke-4 showed that oils belong to started 110 Ma ago (Fig. 3). The uplift and Jurassic source rocks and they are within the non-deposition during Upper Jurassic and equilibrium phase (Abdula, 2015). collision caused migrated oil to be lost. Furthermore, the same study showed that Therefore, the well Jabal Kand -1 is not a Middle Jurassic source rock is not totally productive well. mature in Tawke-15 Well. The maturity of source rocks in well Tawke-15 occurs below 3.5. Burial History the depth of 2,880 m and the depth of expelled One-dimensional modeling of burial oil in TA-15 Well is 2,910 m (Abdula, 2015) history and thermal maturity was performed on which supports immaturity of Jurassic source well Jabal Kand-1 by using PetroMod 2012.2 rocks. (Fig. 3). The profile as shown in figure 3 for Jabal Kand Oil Field demonstrates the effects 3.6. Porosity for Rock Types of continuous burial on source rocks The model showed the present porosity for temperature within stratigraphic section. At the different rock types and compaction effect present time, the basin is reaching a maximum (Fig. 7). The lowest porosity was recorded for burial temperature of 180ºC-190ºC at 5840 m Chia Zairi Formation (10%) and the highest underground. The profile for this well shows was recorded for Adaiyah Formation (32%). that the temperature of source rocks of Paleozoic age represents maximum burial 4. CONCLUSIONS temperature due to burial and tectonic Based on the PetroMod burial history and subsidence through the time of the sedimentary petroleum generation renovation in the area, basin. As expected, the extensive petroleum the Sargelu Formation has not started to generation from Jurassic Sargelu Formation generate oil yet. The Harur source rock started has not occurred because of the small to generate oil in the Late Triassic (207 Ma) overburden rock thickness and not being and the generation lasted until 130 million deeply buried (the overburden rocks are mostly years ago. The Gele Khana Formation is within eroded or not deposited). wet gas zone. The formations younger than A thermal maturation depth in Jabal Kand- Gele Khana are either within oil window or 1 is around 3000 m according to geochemical immature while formations older than Gele data (Al-Habba, 1988). The Sargelu Formation Khana are either within dry gas zone or is shallower than that depth (2107 m) while it postmature. is of high hydrocarbon potential (the primary, pre-expulsion potential; S2 is around 17.8 ACKNOWLEDGMENTS milligram hydrocarbon per gram rock) and The author thanks the Iraqi Ministry of Oil reaches a good thickness (213 m) and it is in Baghdad, Iraq and North Oil Company in 95 Abdula R. /ZJPAS: 2017, 29 (2): 88-95

Kirkuk, Iraq for their generous help by samples. providing necessary information and cutting

Figure 7: Calculated porosity depth profile for different rock types of well Jabal Kand-1 in Mosul area, Northern Iraq.

REFERENCES Abdula, R. (2015) ‘Hydrocarbon potential of Sargelu Formation and oil-source correlation, Iraqi Jassim, S.Z. (2006) Geology of Iraq. Edited by J. C. Kurdistan’, Arabian Journal of Geosciences, Goff. Brno: Dolin, Prague and Moravian 8(8), pp. 5845–5868. Museum. Al-Habba, Y.K. (1988) Possible petroleum source rocks Kent, W.N. (2010, April). Structures of northern Iraq in the well Kand-1. Baghdad: Oil Exploration and Syria, and their implications for Company Archives. Unpublished report in interpretation of the region’s stratigraphy. New Arabic Orleans, Louisiana. doi:Search and Discovery Allen, P.A. and Allen, J.R. (2005) Basin analysis. Article # 40623 (2010) second edn. Blackwell Publishing. Magoon, L.B. and Dow, W.G. (1994) The petroleum Bellen, R.C. van, Dunnington, H.V., Wetzel, R. and system - From source to trap. (60 Vols). Morton, D.M. (1959) Lexique stratigraphic American Association of Petroleum Geologists. international. (Fascicule 10 a Vols). Paris: North Oil Company (1983). Final well report of Jabal CNRS and Congres Geologique international, Kand-1. Kirkuk: Iraqi Ministry of Oil in Commision de Stratigraphie. Baghdad. International Commission on Stratigraphy (2008) A Sweeney, J.J. and Burnham, A.K. (1990) ‘Evaluation of concise geologic timescale. Edited by J. G. a simple model of vitrinite reflectance based on Ogg, G. Ogg, and F. M. Gradstein. Cambridge chemical kinetics’, American Association of University Press. Petroleum Geologists, 74(10), pp. 1559–1570.

ZANCO Journal of Pure and Applied Sciences The official scientific journal of Salahaddin University-Erbil

ZJPAS (2017), 29 (2); 96-105 http://dx.doi.org/10.21271/ZJPAS.29.2.10

Theoretical, Numerical, and Experimental Analysis of Composite Double-Cracked Cantilever Beams with Various Fibers Volume Fraction and Angles

Nazhad A. Hussein1 Sardar S. Abdullah 2 1,2Department of Mechanics, College of Engineering,Salahaddin University-Erbil

A R T I C L E I N F O A B S T R A C T

Article History: Crack changes the dynamic characteristics of the vibrating body such as the Received: 31/07/2016 natural frequencies and stiffness of the system. Now a day many researchers are Accepted: 10/12/2016 studying on the cracks in the structures made of composite material because are being used more than past due to their great mechanical properties such as their Published:07/06/2017 high strength to weight ratio. This study presents theoretical, numerical (FEM), Keywords: and experimental analysis of a cantilever composite beam with double FEM, Dynamic Analysis, transverse crack. Carbon fiber- Epoxy has been taken as the material for this Crack, Composite Beams, study. Several factors play grate and important rules in vibration response and Natural Frequency natural frequencies of the cracked composite beams. This work presents *Corresponding Author: dynamic responses of double-cracked composite beams at different fiber Email: [email protected] volume fraction and angles. The numerical results were found in good agreement with experimental and analytical results. The study concludes that

the existence of double crack in composite structure with different fiber volume fraction and angles can be diagnosed by using vibration signatures, and it useful

for monitoring the health of the composite structures.

a vibrating beam and plate which are made of INTRODUCTION graphite-fiber reinforced polyimide. They also developed a new method to calculate the Vibration is one of the most important aspects additional flexibility induced by the crack. It of dynamic which is difficult and vital to has been shown that when the angle of fibers is analyze during designing of mechanical 45 degrees, the crack surfaces intercept the members and machine parts, because the material principle planes. M.Krawczuk and stiffness and damping properties of most W.M.Ostachowicz [1991] presented a paper vibrating parts lead to behave non-linear and which analyzed the effects of the cracks on the will change but usually vibrating parts are natural frequencies of a cantilever beam. They assumed to behave linearly. Mechanical parts presented a method to analyze the effect of two may expose to some defects such as flows, open cracks on the vibration of the beam. They cracks due to having motion during operations. considered two types of cracks in which one of As the result of these defects, the parts may them was a double-sided crack and another was lead to break down and fail. Cracks in vibrating a single-sided crack. It was assumed that the parts can reduce natural frequencies of the cracks have occurred in the first mode of vibrating system resulting in large amplitudes fracture. They found out that the position of the of vibration causing failure of the structure. cracks in relation to each other can have a great K.Nikpur and A.Dimarogonas [1986] presented role in changing the natural frequencies if both a paper to investigate the effect of the crack on 97 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105 cracks have the same relative depth. perpendicular to the fiber direction, there will Manivasagam and Chadrasekaran [1992] tried be the highest decrease in the natural frequency to investigate experimentally the effects of and also when the angle of fibers increase there damage in the form of cracks on the reduction will be a reducing in the changes of the first of the fundamental frequency of layered frequency. Murat Kisa and M.ArifGurel [2006] composite materials. M.Krawczuk [1993] proposed a new numerical model combining Presented a new finite element method for the finite element and component mode static and dynamic analysis of the cracked synthesis method for the modal analysis of composite beam. He assumed a beam with a beam having circular cross-section area and single non-propagating one-edge open crack. multiple non-propagating cracks. They The crack was in the mid-length of the beam. theoretically investigated the effects of location He concluded that the crack in a cantilever and depth of the cracks on the natural composite beam causes an increase of static frequencies and mode shapes of three beams deflection and reduce of the first bending that were cantilever and simply supported with natural frequency. M.Krawczuk and multiple cracks. They concluded that mode W.M.Ostachowicz [1995] presented two shapes and natural frequencies are dependent models for a cantilever composite beam having on the cracks depth and location. K.Oruganti, a transverse non-propagating one-edge open M.Mehdizadeh, S.john, I.Herszberg [2009] crack. The first model was discrete-continuous presented a paper that highlighted the which was based on the concept of an utilization of vibration based testing on equivalent linear spring, for which the composite beams made of Carbon/Epoxy for flexibility was calculated according to the detecting damage. The analytical relationship Castiglione’s theorem and the basis of fracture was developed based on Euler-Bernoulli beam mechanics. The second model was based on theory. They used stiffness loss parameter at finite element model. By virtue of beam finite the location of damage (EId) instead of (EIo) elements, the undamaged parts of the beam in Euler-Bernoulli formula. A.Ranjbaran were modeled. They investigated the Eigen [2010] derived a general and a new governing frequencies of a cantilever beam made of of differential equation for obtaining the graphite-fiber reinforced polyimide with natural frequencies of cracked members. He transverse crack. Ghoneam [1995] investigated worked on lateral free vibration of cracked theoretically and experimentally the dynamic beams and axial vibration of multi-cracked characteristics of laminated composite beams bars. Ranjbaran solved the proposed standard having fibers with various orientations and ordinary differential equations and determined different boundary conditions with and without the exact analytical solution for eigen values cracks. Ghoneam studied on the effects of and mode shapes of the members. M.Rezaee number of layers of laminated composite, and H.fekrmandi [2010] investigated different crack depths and locations and theoretically and experimentally free vibration boundary conditions on the dynamic behavior of a cantilever beam having a characteristics of laminated composite beam. breathing (opening and closing) crack. They The experimental and theoretical results were assumed that the stiffness changes with time as close to each other. Murat Kisa [2003] worked a harmonic function because of opening and theoretically on the effects of cracks on the closing the crack duration vibration and natural e frequencies of a cantilever composite operation. They used Zwick/Roll of model beam made of graphite fiber reinforced Amsler, HA250 instrument to create the cracks polyamide. He denoted that when the crack is on the beams. They observed a decreasing in 98 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105 the natural frequencies and having larger The natural frequencies of beams for various amplitudes due to the cracks. boundary conditions in radian/unit time are PragyanSaraswatiBisi [2011] investigated given as: vibration and buckling analysis of cracked composite beam. The main aim of his working (3) was to work out a composite beam finite element with a non-propagating one-edge open Figure (1) shows the chosen model which is crack. He wanted to analyze the effects of a cantilever composite beam having a uniform cracks on a cantilever composite beam and also cross-section area (A) and also having several the influence of the volume of fibers, open edge transverse cracks with different magnitude and location of the crack and angle depths at different distancesfrom the fixed side. of fibers on the natural frequencies of the Dimensions of the beam are defined by the cracked composite beam. Bisi concluded that length (L), height (H) and width (B). The angle natural frequencies are not only functions of by which the fibers are arranged or angle crack location and crack depths but also they between the fibers and axis of the beam is’ α are functions of fiber volume and fiber angels. ‘as shown in the figure Pankaj Ch.Jena, dayal R.P Goutam P. [2012] (1). worked out fault detection in a beam consisting of a single transverse crack. Theoretical and Experimental analysis were done to identify the location and the depth of the crack in the beam with single transverse crack. A few more flexibility produced due to the presence of the crack examined by applying the strain energy function.

VIBRATION ANALYSIS OF Fig. A Cracked Beam Scheme COMPOSITE CRACKEDBEAM [N] Matrix is used to obtain the warping The equations are governed for vibration displacement. analysis of non-cracked composite beam. For the case of cracked beam, additional flexibility matrix is added to the flexibility of non- cracked beam to obtain the total flexibility and [N] * (4) consequently the total stiffness matrix of the cracked composite beam.

Fourth –order differential equation Here [N] is a matrix which is called shape function matrix. (1) We use boundary conditions to obtain N matrix = f(x) (2) as: (5) Where b = (6) 99 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

(7)

(8) (13) Where is a matrix, which is called strain (9) nodal displacements relation matrix. (10) Mass matrix for both cracked and non- cracked beam is assumed to be the same so Where q, and both are representing the only mass matrix is derived once and is used displacements (transverse and rotational for both cases of cracked and non-cracked displacements). because it is assumed that the crack does not Now the shape of above equations must be change the mass of the beam. changed into a new matrix as: (14) Where (i,j=1,2,3,4,5,6)

Mass matrix elements are as following:

, = = *

, (11)

Matrix) will be obtained by taking the inverse of the middle matrix. To obtain (shape function matrix), is used and by rearranging the formulas finally it will be: ,

(12)

By taking the same fashion we can obtain linear corresponding strains as: ,

, 100 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

Where ρ is the density of mass of the element constants and will be given in Appendix A. and Le is the length of the element. Crack influences on the beam and results in an additional strain energy. The best way to find Stiffness matrix for each element of non- cracked composite beam element stiffness cracked beam element with three nodes and matrix is to calculate the total flexibility matrix two degree of freedom for each of the nodes and then obtain its inverse. Due to crack, there θ with ∂={w, } is obtained by following will be two parts for the total flexibility matrix. formulas where ∂ is displacement vector. The first part is original flexibility matrix for non-cracked composite beam, and the second (15) part is the additional flexibility matrix created Where (i,j=1,2,3,4,5,6) by the crack leading to energy release, additional deformation, and lower stiffness of the vibrating system or structure. Then, the elements of the stiffness matrix for non-cracked element will be as following: In the region close to the crack the stress field is affected by the crack. Crack causes an , additional strain energy which includes flexibility coefficients expressed by stress , intensity factors obtained and derived by Castiglione’s theorem. From the strain energy , release rate, the compliance coefficients of the flexibility matrix can be obtained.

The strain energy of the cracked beam is obtained by following relation: , U= + , + (16)

+ + (17)

, Where =the strain energy release rate

A= Area of the crack section

are stress intensity factors for fracture modes of opening and , sliding crack types and crack evaluation models, and are coefficients , and can be obtained by following formulas:

) ,

Where Le, B, H are dimensions of the beam , element and and are the stress-strain 101 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

(18) Applying Castiglione’s theorem will give the overall additional flexibility induced by the The coefficients are given crack to the beam element. appendix A. The term ‘Im’ means imaginary part of the expression because the (27) expression ) will be a complex number.

Stress intensity factors can be obtained from bellow equation: (28) (19)

Where is the stress for fracture mode, is the correction factor for the anisotropic (29) material is the correction factor for the For the case of determining the flexibility finite specimen size , and both , matrix of the non-cracked element arised from the lack of ( , it is required to take the symmetry and the deformation at the free edges inverse of the force-displacement equation. of the beam .They are taken from the investigations of Krawczuk and Ostachowicz (1991 and 1993).

(30)

Total Flexibility Matrix for the Cracked (20) element of the composite beam is:

(31)

(21) Stiffness Matrix for a Cracked Element Where (22) is:

(Relative crack depth) (23) (32)

(24) EXPERIMENTAL PROCEDURE

=1 ( 25) The beams are assumed to be made of unidirectional laminates of carbon fibers Where (26) reinforced by Epoxy matrix. The type of carbon fibers is T300. The epoxy type is Bisphenol-F type epoxy resin. Tables 1and 2 (The material constants are show the properties of carbon fiber T300 and given in Appendix A). Bisphenol - F type epoxy resin, respectively. Accelerometers and data acquisition system 102 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

(type B&K frame 3560) were used to record Fig.2.A double cracked beam and analyze. Figure (2) will show a double Fig. 3. Experimental Measurement Scheme cracked beam ready to test and figure (3) shows the vibration testing components. RESULTS AND DISCUSSION

Table1 Elastic Properties of Carbon Fiber (T300) The first three natural frequencies of the

Properties Value composite beams with various fiber angles and volume fraction of fibers are determined and Modulus of Elasticity in Ef1 230 GPa the results are presented for all specimens. longitudinal direction Theoretical, numerical (FEM), experimental Modulus of Elasticity in Ef2 13.9 GPa methods are used to determine the natural transverse direction frequencies of the double-cracked composite

Modulus of Rigidity in Gf1 12.5 GPa beams. Finite element analysis ANSYS was longitudinal direction used to extract the natural frequencies and Poisson Ratio in (1-2) plane results compared with experimental and νf12 0.2 analytical methods. Tables 3,4, and 5 show the Poisson Ratio in (2-3) plane νf23 0.25 results obtained from analytical method, ANSYS program, and experimental study, Mass Density ρ 1760 kg/m3 f respectively. The results of all methods were

satisfactory and showed a good agreement. The effect of fiber angles for different fraction volume are shown in the figures 4,5, and 6. As Table2 Elastic Properties of Matrix (Bisphenol F type) the fiber angle increased the stiffness and natural frequencies decreased while the Properties Value flexibility of the beam will be increased. It is

Modulus of Elasticity Em 2.9 GPa observed that the slope of the curve is more significant between 15o and 75o of fiber angles

Modulus of Rigidity Gm 1.23 GPa and indicating a steep fall in frequency. There is no significant effect on the natural frequency Poisson Ratio o νm 0.43 for the fiber angle lower than 15 and higher than75o. The highest natural frequency is Mass Density 1160 kg/m3 ρm obtained when fiber angle is zero and on the contrary the lowest natural frequency is obtained when the fibers are arranged with angle 90º. The results showed the high drop in natural frequency is when the fiber volume fraction changed from the 53% to 40% and the fiber angle was below the 75o. The beams are stronger and stiffer, if the angle between the fibers and longitudinal axis of the beam is lower.

Table 3 First three natural frequencies obtained by theoretical method for Double cracked beams (a/H= 0.4 at L/8, & a/H= 0.4 at 3L/8). 103 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

Fiber Fiber Volume Fraction Fiber Volume Fraction Fiber Fiber Volume Fiber Volume Fraction

angle =0.4 =0.53 angle Fraction =0.4 =0.53 (deg.) (deg.) ω1 ω2 ω3 ω1 (Hz) ω2 (Hz) ω3 (Hz) ω1 ω2 ω3 ω1 ω2 ω3 (Hz) (Hz) (Hz) (Hz) (Hz) (Hz) (Hz) (Hz) (Hz) 0 0 89.407 586.09 1452.8 82.3808 525.45 1642.6 92.3 587.91 1419.4 83.18 532.26 1565.14 15 85.940 559.65 1402.0 78.936 514.05 1580.9 15 88.76 563.68 1389.07 78.80 509.06 1533.69 30 73.046 471.25 1188.4 65.135 420.30 1332.7 30 73.98 469.92 1176.69 65.40 423.97 1287 45 50.941 324.27 872.83 44.579 302.52 906.40 45 60 53.93 342.90 847.95 47.2 310.47 937.28 34.879 224.22 582.55 32.088 206.32 633.20 60 75 37.18 234.7 595.46 32.82 214.5 652.26 29.747 191.73 475.74 26.160 168.61 541.03 75 90 30.60 190.57 487.26 27.15 175.20 528.61 28.042 181.05 455.18 24.981 161.25 511.13 90 29.28 187.25 478.78 26.82 172.11 517.26

Table 4 First three natural frequencies obtained by ANSYS software for Double cracked beams (a/H= 0.4 at L/8, & a/H= 0.4 at 3L/8).

Table 5 First three natural frequencies obtained experimentally for Double cracked beams (a/H= 0.4 at L/8, & a/H= 0.4 at 3L/8). Fig.4.Firstnatural frequency of double-cracked beam as Fiber Fiber Volume Fraction Fiber Volume Fraction a function of fiber angle.

angle =0.4 =0.53 (deg.) ω1 ω2 ω3 ω1 ω2 ω3 (Hz) (Hz) (Hz) (Hz) (Hz) (Hz) 0 90 587.5 1424 82.5 523.5 1588 15 88.84 562.9 1382.5 77 500 1526.3 30 73 471 1162 66 426.9 1291 45 54 339 837.5 47 302.5 925 60 35.63 225 583.13 31 211.5 638.88 75 29 181 490 27.5 173.5 541 90 28 176 473.75 24.88 165.6 518

104 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

Fig.5.Secondnatural frequency of double-cracked beam 5. A high drop in natural frequency was occurred when the fiber volume fraction changed from the 53% to 40% for fiber angle below the 75o.

REFERENCES 1. Ghoneam S. M. (1995). Dynamic analysis of open cracked laminated composite beams. Composite Structures 32 3-11. 2. Jena P. Parhi D. Pohit G. (2012) Faults detections of a single cracked beam by theoretical and experimental analysis using vibration signatures. Odisha: Orissa Engineering College. IOSR Journal of Mechanical and Civil Engineering (IOSR-JMCE)ISSN: 2278-1684 Volume 4, Issue 3 PP 01-18. 3. Kisa M. Gurel M. (2006) Modal analysis of multi- cracked beams with circular cross section. Sanliurfa: Harram University. Engineering Fracture Mechanics 73 as a function of fiber angle. 963–977 4. Kisa Murat (2003) Free vibration analysis of a Fig.6.Thirdnatural frequency of double-cracked beam cantilever composite beam with multiple cracks. Composites Science and Technology 64 1391–1402. as a function of fiber angle 5. Krawczuk M, (1993). A new finite element for the static and dynamic analysis of cracked composite beams. CONCLUSIONS Composite & Structures Vol. 52. No. 3, pp. 551-561. 6. Krawczuk M., and Ostachowicz W.M., (1995). 1. Natural frequencies of double-cracked Modelling and Vibration Analysis Of a Cantilever beam are functions of the fibers angles Composite Beam with a Transverse Open Crack. Journal of Sound and Vibration 183(1), 69-89. and fiber volume fraction. 7. Manivasagam S. &Chandrasekharan K. (1992). 2. Presence of double cracks will increase Characterization of damage progression in layered the total flexibility and consequently composites. Journal of Sound and Vibration 152, 177- 179. decreases the total stiffness and natural 8. Nikpour K. and Dimarogonas A.D. (1988). Local frequencies of the cracked composite compliance of composite cracked bodies. Journal of beam. Composite Science and Technology 32,209-223. 9. Oruganti Ranjbaran A. (2010) Analysis of cracked 3. The flexibility of the cracked composite members the governing equations and exact solutions. beam is directly related to the angle Shiraz: University of Shiraz. Iranian Journal of Science & Technology, Transaction B: Engineering, Vol. 34, No. between the fibers when the fiber angle B4, pp 407-417, Printed in The Islamic Republic of o o variation between 15 and 75 . Thus, Iran. when the fiber angles reach lower than 10. Ostachowicz W.M. and Krawczuk M (1991). Analysis o o of the effect of cracks on the natural frequencies of a 15 or higher than 75 , the effect of cantilever beam. Journal of Sound and Vibration cracks on the fundamental natural 150(2),191-201 frequency especially will be too small. 11. PragyanSaraswatiBisi (2011) “Vibration and buckling analysis of cracked composite beam”, Msc. Thesis, 4. Angle of crack plane with respect to the Department of Civil Engineering National Institute of fibers has great effects on the natural Technology Rourkela. 12. Rezaee M. Fekrmandi H. (2010) A theoretical and frequencies. There will be a highest experimental investigation of free vibration behavior of a reducing in the fundamental and other cantilever beam with a breathing crack. Tabriz: natural frequencies when the crack is University of Tabriz. Journal of aerodynamic and mechanic of Iran, Vol. 6, No.3. perpendicular to the fibers orientations (i.e. when fiber angle is zero). Appendix A 105 Hussein N Abdullah S/ZJPAS: 2017, 29 (2): 96-105

different roots but only those which possess positive imaginary part are taken for the calculations.

The constants can be obtained from the following

relations: The following terms are the elements of the stiffness matrix (note that ).

Where and and the constant

terms of can be calculated:

And consequently D

Engineering constants are calculated from transformed compliance matrix as:

And are the roots of the following characteristic equation:

The roots could not be real numbers and they are either complex numbers or pure imaginary. There will be four ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (1); 106-116 http://dx.doi.org/10.21271/ZJPAS.29.2.11

Statistical Probability Distributions of the Noble Quran

Delshad Shaker Ismael Botani Department of Statistics, College of Administration and Economics,SalahaddinUniversity, Erbil, Kurdistan Region, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: Classification of raw data through a frequency distribution is very important to Received:20/11/2016 determine the nature of the data distribution (probability distribution) and their Accepted: 22/12/2016 structures. This paper describes the classifications of the number of verses (Ayas), Published: 07/06/2017 words and letters in the chapters (Sura) of the Noble Quran using frequency Keywords: distributions (tables) and then drawing histograms for each of the three types in Noble Quran order to find their structures. The main objective of this paper is to test and Classification compare the frequency distributions of verses, words and letters of the Noble Chapter (Sura) Quran with the common theoretical probability distributions using appropriate Verse (Aya) statistical methods. The results showed that the probability distributions for the number of verses and words per Quranic chapter are Exponential and Gamma Probability Distribution. respectively. The software which had been using to obtain data was QuranCode *Corresponding Author: software created by Adams, and Excel, Statgraphics Centurion XV, and EasyFit Delshad Shaker Ismael 5.5 programs used for the data analyses. Botani [email protected]

there should be very important things in Quran like mathematical or statistical models to save 1. INTRODUCTION the whole Quran from corruption or distortion. Too many miracles of Noble Quran have been Therefore, mathematicians and statisticians are revealed from the time of revelation till now. trying to find these hidden models. From all over the world scientists trying to Al-Dargazelli (2004) had used three conduct researches in order to discover these different schemes to classify the Quranic miracles in different fields, such as: Biology, chapters based on verses. The first Chemistry, Physics, Astronomy, Psychology, classification was grouping the number of Medicine, Economy, Geology, Mathematics, verses per chapter into Makki and Madani and and so forth. But unfortunately till now there then she computed frequency distribution and are few research studies in the field of Statistics some descriptive statistics with scatter plots for concerning the miracles of Noble Quran. each group. Al-Dargazelli (2004) used Allah said in the chapter of Al-Hijr – verse sequential scheme in the second classification ْ ُ Verily, We, it is by placing consecutive chapters that are all" (إِﻧﱠﺎﻧَ ْﺤﻨُﻨَ ﱠﺰﻟﻨَ ﱢﺎاﻟﺬ ْﻛ َﺮ َوإِﻧﱠﺎﻟَﮭُﻠَ َﺤﺎﻓِﻈ َﻮن ) :9 We Who have sent down the Dhikr (Quran) either Makki or Madani together and made 25 and surely, We will guard it (from corruption)", classes. Concerning the third classification she 107 Botani D /ZJPAS: 2017, 29(2): 106-116

used the classification scheme suggested by Finding the probability distribution Mir (1999) which contained 7 classes. Dost and function of any phenomena is very important to Ahmed (2008) constructed a new classification know its characteristics and describing how using frequency distribution of chapters over likely we will obtain the different possible verses sizes by words. The distribution values of the random variable. In this paper consisted of seven classes. Also, in their paper, two important probability distribution functions the symmetry of Makki and Madani chapters will be used to define the empirical distribution had been discussed using the shape of function of the verses and words of Quranic skewness and kurtosis. The study of Akour et chapters. These two functions called Gamma al. (2014) was presented an approach and Exponential distribution functions. measuring of Quranic verses similarity and sura classification using N-gram for retrieving 2.1. Gamma and Exponential Probability the most similar verses in comparison with a Distribution Function user input verse as a query. The work reported here is concerned with The Gamma probability distribution has simple statistical classification methods for found applications in various fields. It can be verses, words, and letters. After that trying to describe the gamma function before answer the question: are there any similarities introducing the gamma probability distribution. between the empirical frequency distributions The gamma function, denoted by , is of the Quranic chapters and the theoretical defined as (Ramachandran &Tsokos, 2009): probability distributions?

A continuous random variable X has a Gamma 2. THEORETICAL PART distribution if its probability distribution The process of collecting the data is to function is given by: describe through some tables and graphs in order to visualize the most important information, then trying to use statistical methods to analyze it and making decisions Where: and are parameters of Gamma depending on the outputs. The most important distribution and they are positive integers (i.e. descriptive statistics used in this paper are , >0). measures of central tendency, measure of The most important properties of Gamma dispersion, frequency distributions and distribution are: histogram. A frequency distribution is a table , and containing two columns, one of them consists of classes and the other composed the frequencies of each class. Also, we can If in the gamma distribution =1, then the p.d.f. describe this table by a graph that is called specializes to the exponential distribution: histogram, which is a chart plotting values of observations on the horizontal axis, with a bar showing how many times each value occurred in the data set. Frequency distributions can be Where; very useful for assessing properties of the distribution of scores (Field, 2013). 108 Botani D /ZJPAS: 2017, 29(2): 106-116

, and > median > mode for all of the three groups (the number of verses, words, and letters). Also, the skewnesses of all these groups are positive. This means that the data distributions of these three groups are not symmetric and skewed to the right. On the other hand, the above table shows that the three groups are leptokurtic because the value of 3. PRACTICAL PART kurtosis is greater than zero. In order to have more The data that has been using in this paper are information about these three groups, it is better to obtained from QuranCode software created by draw the scatter plots for all of them without Adams (2016). This software is genius making any sorts for the chapters, i.e., starting from Al-Fatiha chapter until the last Quranic chapter software for all researchers, who attempting to which is Al-Nas chapter (see graph 1 & 2). conduct researches in Quranic numbers and systems. In this paper 29 Arabic letters take Table 1: Descriptive statistics of the number of (ء) into consideration (with accounting Hamza as a letter). Also, the starting verse of each verses, words, and letters in the Quranic chapter (In the name of Allah, Most Gracious, chapters Second Most Merciful) considered as a verse in whole First group Third group Quran. For this reason, the number of Quranic group Statistics No. of No. of verses is equal to 6348 verses In most of verses No. of letters words literatures, the number of verses is equal to (No. of Aia) 6236 verses because of non-accounting 112 N 114 114 114 starting verses as a Quranic verse (In most of Range 283 6106 25823 Minimum 4 14 61 literatures, the number of verses is equal to Maximum 287 6120 25884 6236 verses because of non-accounting 112 Sum 6348 77878 327792 starting verses as a Quranic verse.), number of Mean 55.68 683.14 2875.37 words is equal to 77878 words, and number of 9.00 27.00 90.00 letters is equal to 327792 letters. Most of Mode statistical analyses are computed using Excel, Median 40.00 348.00 1455.00 First 15.75 93.50 388.00 Statgraphics Centurion XV, and EasyFit 5.5 Percentile Second programs. 40.00 348.00 1455.00 Percentile Third 79.00 889.50 3838.75 Percentile 3.1. Descriptive Statistics of Raw Data in Standard 53.21 931.14 3933.69 Quranic Chapters Deviation In this section, some important statistical Variance 2831.21 867018.9 15473954.6 measurements of verses, words, and letters of Skewness 1.74 2.88 2.91 Quranic chapters are computed for raw data Kurtosis 3.59 11.22 11.42 (ungrouped data presented in the appendix) as Standard Error of 4.98 87.21 368.42 described in table 1 (Found by author). Mean Table 1 shows some initial information about the pattern nature of the number of verses, words, and letters in the chapters. It is clear that the mean 109 Botani D /ZJPAS: 2017, 29(2): XX-XX

Figure 1: Scatter plot of the number of verses per Quranic chapter (Unsorted chapters)

Figure 2: Scatter plot of the number of words per Quranic chapter (Unsorted chapters)

Figure 1 and 2 illustrate that the number of chapter which contains highest number of verses, verses and words per Quranic chapter are after that the second chapter which contains the exponentially declining and their trends also second highest verses, and so forth (see figure 3). are exponential (The scatter plot for the The same thing is done for the number of words per Quranic chapter (see figure 4). number of letters approximately is the same as the number of words, for this reason did not Figure 3 and 4 are giving additional plotted). evidences that the distribution of the number of It can be draw figures 1 and 2 in another way verses and words per Quranic chapter by sorting them descendingly, i.e., starting from exponentially distributed. 110 Botani D /ZJPAS: 2017, 29(2): XX-XX

Figure 3: Scatter plot of the number of verses per Quranic chapter (sorted chapters descendingly)

Figure 4: Scatter plot of the number of words per Quranic chapter (sorted chapters descendingly)

In the third section, the classification of the distribution. Simple statistical formulas are verses, words, and letters of Quranic chapters used to find the frequency distributions of the will be discussed. number of verses, words, and letters per Quranic chapter. The number of classes for 3.1. Classification of Quranic Chapters each group (verses, words, and letters) using The main reason of data classifications and Sturges or Yule's formulas are equal to 8 drawing histograms of the resulting frequency classes (see table 2a – 2c). distributions (tables) is to specify the nature of

111 Botani D /ZJPAS: 2017, 29(2): XX-XX

Table 2: Frequency distributions for the number of verses, words, and letters per Quranic chapter Table 2a Table 2b Table 2c Classes of verses Classes of Frequency Frequency Classes of letters Frequency (Aia) words 4 - 39 57 14 - 777 77 61 – 3288 78

40 - 75 25 778 - 1541 24 3289 – 6516 24

76 - 111 16 1542 - 2305 6 6517 – 9744 5

112 – 147 9 2306 - 3069 3 9745 – 12972 3

148 – 183 3 3070 - 3833 3 12973 – 16200 3

184 – 219 2 3834 - 4597 0 16201 – 19428 0

220 – 255 1 4598 - 5361 0 19429 – 22656 0

256 – 291 1 5362 - 6125 1 22657 – 25884 1

Total 114 Total 114 Total 114

As shown in table 2a, 2b, and 2c, it is obvious the number of verses exponentially distributed that half or more than half of the Quranic as the same as the scatter plot of its raw data chapters lay under the first class. Also, it is (figure 1 & 3). clear that the frequencies of the three In figure 6, the frequency distribution of mentioned tables are decreasing exponentially. the number of words is also exponentially The frequencies of the table 2b and 2c are distributed. Therefore, it is very important to similar to each other because the number of find the probability distributions of the letters in each chapter depends on the number frequency tables and testing them. of words. Therefore, only the histograms of the first and second frequency tables will be discussed. Figure 5 and 6 illustrate the histogram of the frequency tables of the number of verses and words per Quranic chapters. Figure 5 demonstrates how the frequency distribution of 112 Botani D /ZJPAS: 2017, 29(2): XX-XX

Figure 5 Histogram of the number of verses per Quranic chapter (Table 2a)

Figure 6 Histogram of the number of words per Quranic chapter (Table 2b)

3.3. Probability Distribution of the Data two main statistical tests for the goodness of fit In this section the researcher is comparing the distribution have been used: the empirical distribution of the verses and  Chi-Square; words of Quranic chapters with the theoretical  Kolmogorov Smirnov. statistical probability distributions (fitting of Using EasyFit program, the frequency the distribution). As described in section 2 and tables of the number of verses and words per 3 by demonstrating the raw and grouped data Quranic chapter (table 2a & 2b) are compared graphically, it is apparent that data are with more than 50 probability distributions. exponentially declined (even for raw data, the Depending on the mentioned two tests, the best trends are exponential). Therefore, in this paper appropriate probability distributions fits the number of verses and words per Quranic 113 Botani D /ZJPAS: 2017, 29(2): XX-XX

chapter are EXPONENTIOAL distribution Table 3 shows that P-value amongst the tests with parameter λ = 0.01795 and GAMMA performed is greater than or equal to 0.05, i.e. distribution with parameters α = 0.538 and β = that the null hypothesis cannot be rejected and 1269.9 (see table 3). the number of verses and words per Quranic chapter come from exponential family Table 3: Goodness of fit tests of the number of (Exponential and Gamma distributions). verses and words per Quranic chapter The probability distribution of Quranic Test Number Number verses is as follows: of verses of words (λ = (α = 0.538 0.01795) and β = 1269.9) Kolmogorov Statistic 0.06089 0.10471 Smirnov P-Value 0.76847 0.15283 The probability distribution of Quranic d.f. 7 7 words is as follows: Chi-Squared Statistic 0.57498 2.5577 P-Value 0.9968 0.86196

4. CONCLUSIONS ters/2014/a105705-605.pdf Al-Dargazelli, S. 2004. A Statistical Analysis of The miracles of Noble Quran will remain Noble Quran. [Online] Available: until the day of doom. Therefore, each of us http://quranicstudies.com/articles/miscellany/stati from his/her place and specialty must try to stical-analysis-of-the-Noble-quran.html discover all those miracles. The results showed Al-Quran Al-karim, Sura Al-Hijr 15:9. that each of the verses, words, and letters per Dost, M. K. and Ahmed, M. 2008. Statistical Profile of Noble Quran and Symmetry of Makki and Quranic chapter classified into 8 classes. The MadniSurras, Pakistan Journal of Commerce and frequency distribution of words and letters are Social Sciences, Volume 1. approximately the same. Therefore, just the Field, A. 2013. Discovering Statistics Using IBM probability distributions of the number of SPSS Statistics, 4th ed., Sage: Thousand Oaks, verses and words have been found. The CA. Mir, M. 1999. Is the Quran a shapeless book? probability distributions of these two groups Renaissance, Volume 9, No. 8. [Online] are Exponential and Gamma respectively. Available: http://www.islamic- awareness.org/Quran/Q_Studies/Mirshape.html REFERENCES Ramachandran, K. M., Tsokos, C. P. 2009. Adams, A. 2016. QuranCode Software.. [Online] Mathematical Statistics with applications, Available: http://www.heliwave.com/ Elsevier Academic Press, USA. Akour, M., Alsmadi, I. and Alazzam, I. 2014. MQVC: Measuring Quranic Verses Similarity and Sura Classification Using N-gram, WSEAS TRANSACTIONS on COMPUTERS, Volume 13, pp. 485-49. [Online] Available: http://www.wseas.org/multimedia/journals/compu

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Appendix Name of Chapters in Arabic Name of Chapter Verses (Without Bismilah) Words Letters Chapters al-Fatihah 1 7 29 139 اﻟﻔﺎﺗﺤﺔ al-Baqarah 2 287 6120 25884 اﻟﺒﻘﺮة Al-Imran 3 201 3485 14757 آل ﻋﻤﺮان an-Nisa' 4 177 3751 16082 اﻟﻨﺴﺎء al-Ma'idah 5 121 2808 12034 اﻟﻤﺎﺋﺪة al-Anàm 6 166 3054 12573 اﻷﻧﻌﺎم al-A`raf 7 207 3324 14232 اﻷﻋﺮاف al-Anfal 8 76 1237 5361 اﻷﻧﻔﺎل at-Taubah 9 129 2498 10940 اﻟﺘﻮﺑﺔ Yunus 10 110 1837 7525 ﯾﻮﻧﺲ Hud 11 124 1921 7733 ھﻮد Yusuf 12 112 1781 7210 ﯾﻮﺳﻒ ar-Ra`d 13 44 857 3514 اﻟﺮﻋﺪ Ibrahim 14 53 834 3513 اﺑﺮاھﯿﻢ al-Hijr 15 100 659 2845 اﻟﺤﺠﺮ an-Nahl 16 129 1848 7728 اﻟﻨﺤﻞ Al-Isra 17 112 1560 6574 اﻹﺳﺮاء al-Kahf 18 111 1583 6499 اﻟﻜﮭﻒ Maryam 19 99 965 3880 ﻣﺮﯾﻢ Ta Ha 20 136 1339 5348 طﮫ al-Anbiya' 21 113 1173 4988 اﻷﻧﺒﯿﺎء al-Hajj 22 79 1278 5251 اﻟﺤﺞ al-Mu'minun 23 119 1054 4409 اﻟﻤﺆﻣﻨﻮن an-Nur 24 65 1320 5674 اﻟﻨﻮر al-Furqan 25 78 897 3837 اﻟﻔﺮﻗﺎن ash-Shuàra' 26 228 1322 5583 اﻟﺸﻌﺮاء an-Naml 27 94 1155 4761 اﻟﻨﻤﻞ al-Qasas 28 89 1434 5873 اﻟﻘﺼﺺ al-Ànkabut 29 70 980 4268 اﻟﻌﻨﻜﺒﻮت ar-Rum 30 61 821 3447 اﻟﺮوم Luqman 31 35 550 2151 ﻟﻘﻤﺎن as-Sajdah 32 31 376 1557 اﻟﺴﺠﺪة al-Ahzab 33 74 1291 5683 اﻷﺣﺰاب Saba' 34 55 887 3565 ﺳﺒﺈ Fatir 35 46 779 3202 ﻓﺎطﺮ Ya Sin 36 84 729 3034 ﯾﺲ as-Saffat 37 183 865 3844 اﻟﺼﺎﻓﺎت Sad 38 89 737 3030 ص az-Zumar 39 76 1176 4800 اﻟﺰﻣﺮ Ghafir 40 86 1223 5052 ﻏﺎﻓﺮ Fussilat 41 55 798 3349 ﻓﺼﻠﺖ ash-Shura 42 54 864 3488 اﻟﺸﻮرى az-Zukhruf 43 90 834 3565 اﻟﺰﺧﺮف ad-Dukhan 44 60 350 1472 اﻟﺪﺧﺎن al-Jathiyah 45 38 492 2062 اﻟﺠﺎﺛﯿﺔ al-Ahqaf 46 36 647 2640 اﻷﺣﻘﺎف 115 Botani D /ZJPAS: 2017, 29(2): XX-XX

Muhammad 47 39 543 2404 ﻣﺤﻤﺪ al-Fath 48 30 564 2493 اﻟﻔﺘﺢ al-Hujurat 49 19 351 1526 اﻟﺤﺠﺮات Qaf 50 46 377 1507 ق ad-Dhariyat 51 61 364 1541 اﻟﺬارﯾﺎت at-Tur 52 50 316 1320 اﻟﻄﻮر an-Najm 53 63 364 1438 اﻟﻨﺠﻢ al-Qamar 54 56 346 1479 اﻟﻘﻤﺮ ar-Rahman 55 79 355 1671 اﻟﺮﺣﻤﻦ al-Waqiàh 56 97 383 1733 اﻟﻮاﻗﻌﺔ al-Hadid 57 30 578 2522 اﻟﺤﺪﯾﺪ al-Mujadilah 58 23 476 2027 اﻟﻤﺠﺎدﻟﺔ al-Hashr 59 25 449 1950 اﻟﺤﺸﺮ al- 60 14 352 1557 اﻟﻤﻤﺘﺤﻨﺔ Mumtahanah as-Saff 61 15 225 962 اﻟﺼﻒ al-Jumuàh 62 12 179 773 اﻟﺠﻤﻌﺔ al- 63 12 184 806 اﻟﻤﻨﺎﻓﻘﻮن Munafiqun at-Taghabun 64 19 245 1088 اﻟﺘﻐﺎﺑﻦ at-Talaq, 65 13 291 1199 اﻟﻄﻼق at-Tahrim 66 13 253 1091 اﻟﺘﺤﺮﯾﻢ al-Mulk 67 31 337 1347 اﻟﻤﻠﻚ al-Qalam 68 53 304 1282 اﻟﻘﻠﻢ al-Haqqah 69 53 262 1130 اﻟﺤﺎﻗﺔ al-Maàrij 70 45 221 968 اﻟﻤﻌﺎرج Nuh 71 29 230 971 ﻧﻮح al-Jinn 72 29 289 1114 اﻟﺠﻦ al- 73 21 203 868 اﻟﻤﺰﻣﻞ Muzammil al-Mudathir 74 57 259 1043 اﻟﻤﺪﺛﺮ al-Qiyamah 75 41 168 686 اﻟﻘﯿﺎﻣﺔ al-Insane 76 32 247 1094 اﻻﻧﺴﺎن al-Mursalat 77 51 185 839 اﻟﻤﺮﺳﻼت an-Naba' 78 41 177 794 اﻟﻨﺒﺈ an-Naziàt 79 47 183 790 اﻟﻨﺎزﻋﺎت Abasa 80 43 137 565 ﻋﺒﺲ at-Takwir 81 30 108 450 اﻟﺘﻜﻮﯾﺮ al-Infitar 82 20 84 347 اﻹﻧﻔﻄﺎر Al- 83 37 173 763 اﻟﻤﻄﻔﻔﯿﻦ Mutaffifeen al-Inshiqaq 84 26 111 459 اﻹﻧﺸﻘﺎق al-Buruj 85 23 113 482 اﻟﺒﺮوج at-Tariq 86 18 65 271 اﻟﻄﺎرق al-A`la 87 20 76 315 اﻷﻋﻠﻰ al-Ghashiya 88 27 96 399 اﻟﻐﺎﺷﯿﺔ al-Fajr 89 31 141 594 اﻟﻔﺠﺮ al-Balad 90 21 86 355 اﻟﺒﻠﺪ ash-Shams 91 16 58 269 اﻟﺸﻤﺲ 116 Botani D /ZJPAS: 2017, 29(2): XX-XX

al-Layl 92 22 75 333 اﻟﻠﯿﻞ ad-Duha 93 12 44 184 اﻟﻀﺤﻰ ash-Sharh 94 9 31 121 اﻟﺸﺮح at-Tin 95 9 38 176 اﻟﺘﯿﻦ al-Àlaq 96 20 76 304 اﻟﻌﻠﻖ al-qadr 97 6 34 131 اﻟﻘﺪر al-Bayyinah 98 9 98 416 اﻟﺒﯿﻨﺔ Az-Zalzala 99 9 40 175 اﻟﺰﻟﺰﻟﺔ al-Àdiyat 100 12 44 183 اﻟﻌﺎدﯾﺎت al-Qariàh 101 12 40 177 اﻟﻘﺎرﻋﺔ at-Takathur 102 9 32 141 اﻟﺘﻜﺎﺛﺮ al-Àsr 103 4 18 90 اﻟﻌﺼﺮ al-Humazah 104 10 37 152 اﻟﮭﻤﺰة al-Fil 105 6 27 115 اﻟﻔﯿﻞ al-Quraish 106 5 21 94 ﻗﺮﯾﺶ al-Maùn 107 8 29 133 اﻟﻤﺎﻋﻮن al-Kauthar 108 4 14 61 اﻟﻜﻮﺛﺮ al-Kafirun 109 7 30 114 اﻟﻜﺎﻓﺮون an-Nasr 110 4 23 99 اﻟﻨﺼﺮ Al-Masad 111 6 27 100 اﻟﻤﺴﺪ al-Ikhlas 112 5 19 66 اﻹﺧﻼص al-Falaq 113 6 27 90 اﻟﻔﻠﻖ an-Nas 114 7 24 99 اﻟﻨﺎس

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 117-125 http://dx.doi.org/10.21271/ZJPAS.29.2.12

Development of Mobile Application for Android Platform: Medical Guide

1 1 2 Salar Kheder Shaikhah , Ibrahim Shamal Abdulkhalieq , Jamal A. Hassan

1 Department of Information System Engineering, Erbil Technical Engineering College, Erbil Polytechnic University, Erbil- Iraq

2Department of Electricity, College of Engineering, Salahaddin University-Erbil, Erbil-Iraq

A R T I C L E I N F O A B S T R A C T

Article History: Abstract Received: 23/05/2016 Developing smartphones leads to increase demands on verity of Accepted: 24/12/2016 applications. As the Android operating system is getting more popular, the Published: 07/06/2017 application based on Android attracts much more attention especially Android is Keywords: more flexible for designers and users than other mobile phone operating systems. Android Technology, This paper presents an Android mobile phone application that developed to help System Architecture, patients to get information about the health issues in Kurdistan Region of Iraq with Open Source Platform, Kurdish Language. The software works as a simple and efficient health directory to system Implementing present what patients are needed. The application is offline and it can be connected with the online website for extra information. The user can check information via *Corresponding Author: viewing the text information and finding the geographic places with an online map, Jamal A. Hassan besides that, the user can give rates for the parts of software. The rate that users [email protected] give to the participants re-appeared for other users in order the best participant (e.g. Doctor, Pharmacy, etc…) can be chosen via rates of users. The data is classified to some groups to facilitating the search.

1. INTRODUCTION people of our society are not familiar with Nowadays, huge numbers of health using website. organizations causes difficulty to find what you Therefore; mobile applications are the best want. Thousands of doctors, hundreds of choice to be used as health directory, because hospitals and pharmacies are located in mobile applications are user friend. Many web different geographical places, therefore, it takes sites were implemented to work as business time and money to search for them in directory and rarely these sites focus on health traditional way like searching by car, asking even if they have sub-parts in this field but they from relatives and friends don't lead to good do not fulfill the demand and do not have result, as well as websites are not efficient to enough information, while most peoples use use us directory in most cases, because many 118 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

mobile applications due to simplicity to use Rate), working hours and user current body and they do not need extra device to access the conditions (i.e. Body Temperature, Heart rate services. Recently many applications were and SPO2 via Sensors). Decision-Tree is being developed for the Kurdistan Region market, used to make all suggestions. The application even some of them were applications of health supports continuous monitoring of user health. field but no one focused on this field as a guide The proposed system is scalable for all line to direct the patients to correct target Android Based Mobile Devices [2]. In Hopeful easily. hearts side of health issue is covered but it doesn't consider as a guide. A health system is proposed for pregnant women in [1]. The proposed system An emergency mobile application works based on mobile Geographic system is proposed in [3] with support of GIS, Information System (GIS) to select closest care and GPRS networks, but the problems of Centre or hospital maternity on Google map for network connectivity also is ignored for the pregnant woman [1]. But due to problems emergency case. of accessibility for the General Packet Radio In this paper, as a solution for many emergency Service (GPRS) or data network online cases and to direct the patients to right target; applications have weak points. Hopeful hearts an offline mobile application is proposed for is proposed in [2]. Authers have used mobile as the health guide under the name Medical a platform for a healthcare, so that people can Guide. The application contains many efficient get factual information about their health and features for searching, and the application is can have command on their health. It will help connected with a website for getting extra them to learn about their health and understand information. Each participant of the application their illness. In this paper Mobile based can has its own user and he/she can update its healthcare application `Hopeful Hearts' has information beside that the doctors can access been proposed. Application which will suggest their accounts in the program and see their diet and physical activity based on six input activities with patients. The application is in parameters. The input parameters are BMI Kurdish Language and it is designed to be user (Body Mass Index), BMR (Basal Metabolic friendly

2. Android Technology the Linux operating system and developed by Android is a software platform and Google and the Open Handset Alliance [4]. It operating system for mobile devices based on allows developers to write managed code in a 119 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

Java-like language that utilizes Google- Runtime, the framework layer and on top of all developed Java libraries [4]. Open source the applications [6]. Figure 1 outlines the software is currently one of the most debated current (layered) Android Architecture. phenomena in the Software industry, both The modified Linux kernel operates as the theoretically and empirically. At the most basic Hardware Abstraction Layer (HAL), and level, the term open source software simply provides device driver, memory management, means software for which the source code is process management, as well as networking open and available. Android is such an functionalities, respectively. The library layer operating system for low powered devices, that is interfaced through Java (which deviates from on battery and are full of hardware like Global the traditional Linux design). It is in this layer Positioning System (GPS) receivers, cameras, that the Android specific libc (Bionic) is light and orientation sensors, WiFi and located. The surface manager handles the user Universal Mobile Telecommunication System interface (UI) windows. The Android runtime (UMTS) connectivity and a touch screen. Like layer holds the Dalvik Virtual Machine (DVM) all operating systems, Android enables and the core libraries (such as Java or IO). applications to make use of the hardware Most of the functionalities available in Android features through abstraction and provide a are provided via the core libraries [5, 6]. defined environment for applications [5]. To summarize, the Android operating environment can be labeled as [6, 7]: 1- An open platform for mobile development 2- A hardware reference design for mobile devices 3- A system powered by a modified Linux 2.6 kernel 4- A run time environment 5- An application and user interface (UI) framework. The application framework houses the API interface. In this layer, the activity 3.Android System Architecture manager governs the application life cycle. The The Android software stack can be content providers enable applications to either subdivided into five layers: The kernel and low access data from other applications or to share level tools, native libraries, the Android their own data. The resource manager provides 120 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

access to non-code resources (such as “Anyone who contributes to the open Source graphics), while the notification manager project is an open source developer.” such as a enables applications to display custom alerts. User of the software, a developer who develops On top of the application framework are the the Software, a debugger or hobbyist who likes built-in, as well as the user applications, spending time on open source, or a promoter respectively. It has to be pointed out that a user who funds such a Development [4]. Eric states application can replace a built-in application, that developers are attracted towards open and that each Android application runs in its source development because that gives them an own process space, within its own DVM opportunity to demonstrate their ability. So instance. Most of these major Android they voluntarily select a project and start components are further discussed (in more contributing. Open source developers are detail) in the next few sections [5, 6]. involved in a variety of activities such as designing, coding, debugging and utilizing.

Each activity occurs simultaneously. Parallel

development and debugging is the key to open Figure 1: Android system architecture source success, users also play a vital role in 4. Open Source Platform the debugging process by reporting bugs to Open source software development developers or sometimes fixing it themselves. represents a fundamentally new concept in the Developers are well aware that users are the field of software engineering. Open source best testers [7,8]. development and delivery occurs over the 5. System Design for application Internet. Developers are not confined to a geographic area. They work voluntarily on a The diagram for the overall system of project of their choice. As new requirements medical guide and explanation of the relation emerge, the software is enhanced by the between website and the android application user/developers. In this paper we show a software is showed in figure 2. Also, the comparative study of open source and closed relation between internal and external source software development approaches and databases is explained. Two different database present a software life cycle model for open sources are used in the application; offline source software development [4]. database and online database. Each database Bruce Perens defines that Open Source is a has its own function on the application. Any Specification of what is permissible in a mobile application without database considered software license for that software to be referred as static and its information is not editable. to as Open Source. Developing done by Medical guide application has its own database 121 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

that can be edited by the administrator. An Doctors) in the list due to rates, likes and internal database is placed on the application visitors of pages, as well as records the which is SQLITE file. The application reads notifications that come from the installation of SQLITE file to get information about the the application by any device which be helpful content of the all branches (Doctors, to know the application is installed by how Pharmacies, Hospitals, ect.). This internal many devices. All the dynamic information are database gives ability to the application to stored on external database that is connected work offline which is one of the most with the PHP script on the server and the server important features of the application due to low is connected with MYSQL database.The accessibility of internet in Kurdistan Region. external database also contains the updates So the user can access the data of the about the new participants, when the devices application without needs for the internet. that the application is installed on it is connected to the internet the internal database The second database is external and the users fetches the new information to the application, of application can get benefits in online. The by this process the internal database is adjusted external database has many functions and they when the device connected to the internet fulfill the application to become one of the most power full application. 5. System Implementing and testing

The medical guide system consists of web site and mobile application software. Both, website and mobile application are implemented and tested in real time with all the features of the system. Figure3 show the activities and pages of the mobile application. For simplicity; three levels of pages are designed and the health parts are classified

within these three levels. Additional to the

health parts some other pages are added like; Figure 2: Overall system of Medical Guide application About us, Contact us, Help, Registration, and website page. User can access the web in the The external database sends notifications and Website page that is linked to the homepage of attentions for the users about any subject the site or within the information of any related to the application program. The external participant (e.g. a Doctor) user can access the database sorts the name of the participants (e.g. 122 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

site by clicking the site link which is linked to A- Web site Implementation the page of Doctor in the website. The web site is created using PHP Scripts. The To show content of any page click its button, if website is dynamic using MYQSL database. the page contains sub groups they will be The website database is a copy of the appeared otherwise the list of participants of application database addition to some extra this group will be showed. The diagram in information and subjects. The user can get figure3. is showed by English language to be same information of the application in the understandable while the application program website, as well as its database should be daily works in Kurdish Language. Here, we see that adjustable with the application. As explained in most the parts of the application software are previus section, inside the page of any three levels. In the main level which is the particiapant there is abutton that directs the main parts that are shown in the home page of user to the web site in case he/she want to get the program after opening are (Doctors, more information Hospitals, Emergency, Website, Registeration Form, Help, About Us, and Contact Us). In the sencond level the user perhaps find the information that he/she want or the part is classified to more groups are is "Doctors" we see in second level classification of Doctors. In third level which is mostly last level of the hierarchical the information of the particiapnts (e.g. Doctors) are showed. Beside that, a button is dedicated to forward the user to map as well Figure 4: Home page of Medical Guide website as to the web site of the software program. New participants of the application can send their request via a form in the website with all necessary information and GPS information as shown in figure5

Figure 3: Mobile application, Medical Guide Application Architecture 123 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

Doctors, Pharmacies, Laboratories, dentists, x- ray centers, beauty centers, and eyes centers. Each type contains subgroups. For example the Doctors page contains all the specialist types of doctors.

When a sub-group is opened (for example Doctors, as shown in figure8) a new window is opened which contains a list of specialist doctors by clicking the button of each specialist the new list be opened that all Doctors' name are listed. The names are sorted from A to Z

alphabetic for easy eye search. The last page is Figure5 Registration form of Medical Guide subscriber page; it contains the information about the subscriber (for example Doctor), contact information and detail about the specialization as shown in figure9. Also, this A- Mobile Application Implementation page contain a button of map by clicking it the Android application usually created by java map to be opened and the geographical place of class code and xml language for design. The the subscriber is determined by detecting the Medical Guide application is implemented longitude and latitude of the place as shown in using android Studio. Internal database that is figure 10. Also, inside the same page the user offline database is implemented using SQLITE can contact with the website, by clicking the which is a standard database for android and website button the application directs the user IOS applications. to the page of the same subscriber in the

Figure6 shows the main page of the mobile website; this is used in case the user needs for application. There are three health groups and information about the subscriber. The website four other pages that support the program, is the support part for the mobile application additional to the page of website. The health because when all information is added to the page groups contain the list of most fields of application the size of the application to health. Additional page can be added to the becoms huge and it will be not interested program easily. When the first group/page is opened a list of different health needs to be opened as shown in figure7. The list contains 124 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

Figure 6: Main page of application Figure 9: Page of participant Doctor in App

Figure 7: Page of Doctors in application Figure 10:asample of map in app

Figure 8: specialist list of Doctors in application 125 Salar K. et al. /ZJPAS: 2017, 29(2): 117-125

6. Conclusion

Medical Guide can be considered as one of International Conference on Contemporary the most powerfull applications. It can be used Computing (IC3), 2014. Ayad Gh. Ismaeel, " An Emergency System for online and offline. The offline features of the Succoring Children using Mobile GIS", (IJACSA) application are enough for the necessary International Journal of Advanced Computer Science requirements of user while the online features and Applications, Vol. 3, No. 9, 2012. make the application to be unique in Kurdistan Ed Burnette, "Hello, Android Introducing Google’s Region. Medical Guide can be used as a Mobile Development Platform", 3rd Edition. 2010. Stefan Brahler, "Analysis of the Android Architecture ", directory, or as first aid application and even Thesis, 2 Jun. 2010– 6 Oct. 2010. can be a reference for getting medical Dominique A. Heger, "Mobile Devices - An Introduction information. Its internal and external databases to the Android Operating Environment. -. Design, give ability to the application to be dynamic. Architecture, and Performance Implications", DH Also, the website of the application will be Technology, 2011. Vidyasagar Potdar, Elizabeth Chang, "Open Source and another support for the program. Closed Source Software Development Medical Guide is designed in a way to be Methodologies", ICSE 2004: Twenty Sixth International Conference on Software Engineering friendly and very flexible in using, also many (with) Collaboration Conflict and Control: icons are used to help the persons who cannot Proceedings of the Fourth Workshop on Open Source read, so everybody can use Medical Guide Software Engineering, May 1 2004, pp. 105-109. without facing any problem. Munish Saini and Kuljit Kaur, "A Review of Open Source Software Development Life Cycle Models", Acknowledgement: International Journal of Software Engineering and Its Applications, Vol.8, No.3 (2014), pp.417-434. We appreciate the contribution of the following students in this research; Muhamad Azad Hamad, Nura Najmadden Othman, and Zina Gaylani Hatam

7. References Ayad Gh. Ismaeel and Nur G. Hamead " Mobile GIS and Open Source Platform Based on Android: Technology for System Pregnant Women", International Journal of Scientific & Engineering Research, Vol. 5, Issue 2, February-2014. Nirwal, N., Sardana, N. and Bhatt, A.J., " Hopeful hearts: A mobile health care application", Seventh ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2016), 28 (5); 126-135 http://dx.doi.org/10.21271/ZJPAS.29.2.13

Natural Convection in a Trapezoidal Cavity Filled With Cu–Water

Nanofluid and Heated From Its Bottom Wall

1Ahmed W. Mustafa and 2Omar M. Ahmed

1Department of Mechanical Engineering, Al-Nahrain University, Baghdad

2Department of Civil and environmental Engineering, Samarra University, Salah Al-Din

A R T I C L E I N F O A B S T R A C T

Article History: Received: 03/10/2016 Accepted: 24/12/2016 Natural convection in a trapezoidal enclosure heated from below and filled Published: 07/06/2017 Keywords: with Cu-water nanofluid has investigated numerically. The lower wall is Natural convection; maintained at constant high temperature, the side walls are maintained at Trapezoidal enclosure; constant low temperature, and the upper wall is thermally insulated. Flow Nanofluid; Finite Volume *Corresponding Author: within the enclosure is steady, two-dimensional, and laminar. The pure fluid 1 Ahmed W. Mustafa molecules (water) and the basic nanoparticles (Cu) are in thermal equilibrium, [email protected] and there is no sliding between them. A finite volume method with collocated grid is used to discretize mass, momentum and energy equations. Grid generation method is employed to generate the coordinate system. SIMPLE algorithm is used to link the velocity and pressure fields. The range of Rayleigh number is ) , the tilt angles of the side walls

are (θ = 0°, 30°, and 45°) and the range of solid volume fraction is (0 ≤ φ ≤ 0.2).The results show that the highest average Nusselt number occurs at (θ = 0°) for both pure fluid and nanofluid, and the average Nusselt number at (θ = 30°) is almost equal to the average Nusselt number at (θ = 45°) for both pure fluid and nanofluid. .

1. INTRODUCTION the copper (Cu) has a thermal conductivity 700 The low thermal conductivity of conventional time greater than the water. Since the fluids such as water is a primary limitation in nanoparticles have small sizes and very large enhancing the heat transfer. Solid has a higher specific surface areas, nanofluids have superior thermal conductivity than liquid. For instance, properties like high thermal conductivity, 127 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135 minimal clogging in flow passages, long term dissipation is required. This study focuses on stability, and homogeneity. Thus, nanofluids the heat transfer by natural convection in a can be used for a wide range of applications trapezoidal enclosure heated from below and like electronics, heat exchanger where filled with Cu-water nanofluid. improved heat transfer or efficient heat

2.Literature Review of the side walls were (45o; 60o and 90o (square)). The range of Rayleigh number was Studies of natural convection in square or (103 ≤ Ra ≤ 105) and Prandtl number was rectangular enclosures filled with nanofluids (0.015 ≤ Pr ≤ 1000). The lower wall was are widely available in the literature for both uniformly heated and top wall was insulated. side heating and bottom heating, for example They found that at low Ra (Ra =103) the heat (Khanafer et al., 2003), and (Ogut, 2008). transfer mode is conduction. At Ra = 105, and Studies of natural convection in trapezoidal for linearly heated side walls, the fluid flow enclosure filled with nanofluids are limited to and heat flow patterns were symmetrical. It side heating. (Natarajan et al.,2008)studied the was found that, less intense circulations natural convection in a trapezoidal enclosure. occurred in square cavity compared to other The bottom wall was either at constant hot cavities. In case of linearly heated left side wall temperature or sinusoidal temperature. The two and cold right side wall, the cold right side wall vertical walls were maintained at constant low received greater amount of heat from bottom temperature and the top wall was adiabatic. wall in compared to that of linearly heated left The range of Rayleigh number (Ra) was (103 ≤ 5 side wall. (Salah et al., 2011) investigated the Ra ≤ 10 ) and Prandtl number (Pr) was (0.07 ≤ natural convection in a differentially heated Pr ≤ 100). The side wall inclination angle was trapezoidal enclosure filled with Cu-water and (30o).They found that heat transfer rate at the Al2O3-water nanofluids. They found that the center of the lower wall in the sinusoidal Cu-water nanofluid and the acute sloping wall temperature case was greater than the constant of the cavity were effective to enhance the heat temperature case for all Rayleigh numbers but transfer rate.(Hasanuzzaman et al., average Nusselt number in the sinusoidal 2012)investigated MHD natural convection in temperature was lower than the constant a trapezoidal enclosure. The bottom wall was temperature. (Basak et al.,2009) studied the kept at constant hot temperature while the two heat flow for natural convection in a vertical walls were kept at constant cold trapezoidal enclosure for constant and temperature and the top wall was insulated. sinusoidal hot temperatures of the lower wall at The inclination angles of the side walls were various inclination angles of the side walls, o o o o o o o (0 ; 30 , 45 and 60 ). The range of Rayleigh (45 ; 30 and 0 (square)). The range of 3 6 3 5 number was (10 ≤ Ra ≤ 10 ) and Hartmann Rayleigh number was (Ra) (10 ≤ Ra ≤ 10) number (Ha) was (0 ≤ Ha ≤ 50). They found and Prandtl number (Pr) was (0.026 ≤ Pr ≤ that the heat transfer decreased as the 1000). They found that average Nusselt inclination angle increased, and heat transfer number does not change significantly with the decreased as Hartman number inclination angles for non-uniform case. (Basak increased.(Nasrin and Pravin, 2012) et al.,2011) investigated the natural convection investigated the natural convection in a flow in a trapezoidal enclosure for linearly differentially heated trapezoidal cavity filled heated side walls and for linearly heated left with Cu-water nanofluid. The Rayleigh wall and cold right wall. The inclination angles number and solid volume fraction were fixed at 128 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

105 and 0.05 respectively. They found that both 3.Mathematical Formulation Prandtl number and aspect ratio affect the heat transfer and fluid flow in the cavity. Consider a trapezoidal enclosure with base (Ramakrishna et al., 2013)investigated the length (L) equals to the height (H). The side entropy generation for natural convection in walls are inclined at an angel (θ) with y – axis differentially heated trapezoidal cavity. They as shown in figure 1.The enclosure is filled found that the best shape of the trapezoidal with (Cu – water) nanofluid. The pure fluid cavity was at (θ= 60°) and (Pr = 0.015) molecules (water) and the nanoparticles (Cu) according to lower total entropy generation and are in thermal equilibrium, and there is no higher average Nusselt number. (Mahmoudi et sliding between them. All thermophysical al.,2013) investigated the MHD natural properties of the nanofluid except density are convection and entropy generation in a assumed to be constant. Boussinesq trapezoidal enclosure filled with Cu –water approximation is used in the body force term in nanofluid. They used a two dimensional the y-momentum equation to calculate the trapezoidal cavity with the left vertical wall variation of density. The flow is assumed to be and the inclined right wall maintained in a low steady, laminar and two-dimensional.Under the constant temperature and a constant heat flux above assumptions the governing equations can heat source placed on the lower wall of the be written as:- cavity. They found that at Ra = 104 and 105 and in the presence of nanofluid the Nusselt number increased with the Hartman number, (1) but at higher Rayleigh number, a reduction had been seen. Also the entropy generation is decreased in the presence of nanofluid but (2) increased in the presence of magnetic field. (Esfe et al., 2016) investigated the natural convection for trapezoidal enclosure filled with carbon-nanotube-EG- water nanofluid (3) numerically. The bottom wall of the enclosure was kept at constant hot temperature while the (4) top wall of the enclosure was kept at constant cold temperature. The sides of the enclosure Whereu and v are the velocity components in were insulated. They used the finite volume the x and y directions, respectively.p is the method to solve the governing equations. The pressure, T is the temperature, and β is the 3 6 range of Rayleigh number was 10 -10 , and the thermal expansion coefficient. By using the solid volume fractions were 0.0015, 0.03, and following dimensionless variables 0.045. They concluded that the average Nusselt number decreases as the inclination angle increasing at low Rayleigh number (Ra ≤ 104) for all solid volume fractions. The present (5) study deals with the natural convection nanofluid flow within a trapezoidal enclosure, The Prandtl number (Pr) and Rayleigh number heated isothermally from below, cooled (Ra) are defined as: isothermally from the sides, and insulatedfrom the top. 129 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

(6) The thermal expansion coefficient of the nanofluid can be calculated by The governing equations can be written in non- dimensional form as:

(15) (7) The effective viscosity of the nanofluidcan be

calculated based onBrinkman model (Brinkman, 1952) as

(8)

(16)

(9) The thermophysical properties of the water and (10) Cu-particle are given in Table 1. (Basak and Chamkha, 2012).

The thermophysical properties of the nanofluid The boundary conditions for governing are obtained from the following relations. equations in the dimensionless form are given (Basak and Chamkha, 2012). by

The densityof the nanofluid can be calculated as Top wall ,

Right and left walls

(11) Bottom wall , =1

The thermal conductivity of the nanofluid can be calculated as (Maxwell model) The local Nusselt number on the bottom wall can be calculated from the following relation

(12) (17)

Thermal diffusivity of the nanofluid can be calculated as: The average Nusselt Number on the bottom wall is calculated from

(13)

The heat capacity of the nanofluid can be (18) calculated as The streamfunctions can be obtained from the (14) velocity components as 130 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

(19)

4. Numerical Procedure, Grid Independence (22) Test, and Validation

A FORTRAN computer code is written to solve the governing equations.The set of conservation equations (7-10) can be written in general form in Cartesian coordinates as The transferred equation (21) is integrated over

the control volume in the computation domain. The convective terms are discretized by using (20) hybrid scheme, while the diffusion terms are discretized by central scheme. SIMPLE algorithm on a collocated nonorthogonal grid is Where is the effective diffusion coefficient, used to adjust the velocity field to satisfy the is the general dependent variable, is the conservation of mass. Since all variables are source term. The grid generation scheme based stored in the center of the control volume, the on elliptic partial differential equations is used interpolation method is used in the pressure in the present study to generate the curvilinear correction equation to avoid the decoupling coordinates. Equation (20) can be transformed between velocity and pressure as in (Rhie and from physical domain to computational domain Chow, 1983). In order to consider the effect of according to the following the cross derivatives and to avoid solving a transformation , nine diagonal matrix of the pressure-correction equation, the cross derivatives are calculated the final form of the transformed equation can by the approximate method of (Wang and be written as:- Komori, 2000). The resulting set of discretization equations are solved iteratively using the line-by-line procedure which uses the (21) Tri-Diagonal Matrix Algorithm (TDMA). The convergence criterion is that the maximum residuals in all equations fall below 10-4. For Where and are the contravariant velocity further information, numerical details can be components, is the Jacobian of the found in (Ferziger and Peric, 1996). The transformation, on the computational plane, numerical investigation requires grid and , are the coefficients of independency test, to analyze the grid transformation. They are expressed as sensitivity; Table 2 shows that an accuracy test of grid fineness is made for grids (40 × 40 ), (60 × 60 ), (80 × 80 ), (100 × 100 ), (120 × 120 ) and (140 × 140 ) control volumes for the trapezoidal enclosure with inclination angle (θ = 30°) filled by nanofluid ( Cu – Water ) and 131 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135 volume fraction of nanoparticle (φ = 0.1) at Ra anticlockwise directions inside the cavity as =105 . To reduce the effect of the temperature indicated by signs of stream functions. For discontinuity at the edges of the bottom wall, square enclosure (θ = 0°), the values of stream average temperature of the two walls at corner function for pure fluid and nanofluid are is assumed. This method is suggested by considerably lower and the heat transfer is (Ganzarolli and Milanez, 1995). All of the purely due to conduction as shown in figure simulation results presented in this paper are 2,note that (|ψ* max | = 0.1474) for pure fluid based on (140 × 140) grid because have while(|ψ* max | =0.1189) at φ =0.1. For (pure minimum change in average Nusselt number fluid and nanofluid) the isotherms ( ) (1.8%) and minimum change in stream are symmetrical in vicinity of the side walls of function (0.055%) as shown in Table 2. the enclosure, and the other isotherms The present numerical results are validated by ( takes place smoothly and comparing with the solution of (Hussain and symmetrically with respect to the vertical line Hussein, 2014) for the average Nusselt number as shown in figure 2. For trapezoidal enclosure in natural convection flow in a differentially at (θ = 30°), the magnitudes of stream function heated square cavity filled with Cu-water are larger than the square enclosure (θ = 0°) for nanofluid at Ra=105. Comparison is given in both pure and nanofluid as shown in figure3, table (3) and it is observed a good agreement. note that (|ψ* max | = 0.4329) for pure fluid and (|ψ* max | = 0.3428) for nanofluid at φ = 0.1. 5. Results and Discussion The isotherms for (pure fluid and nanofluid) In this section, the numerical results for with ( are symmetrical in vicinity of streamlines and isotherms are presented for the side walls of the enclosure, and the other various Ra , inclination isotherm ( ) occur smoothly and angles of side walls (θ =0°,30°, 45°) and solid symmetrically with respect to the vertical line volume fraction of ( Cu – Water) nanofulid (0 of the enclosure as shown infigure 3. As the ≤ φ ≤ 0.2) . inclination angle increases (θ = 45°) the magnitude of stream function increase as

shown in figure, note (|ψ* max | = 0.7107) for 5.1 Effect of Rayleigh Number (Ra) and pure fluid and (|ψ* max| = 0.515) for nanofluid θ Inclination Angle ( ) on Stream function at φ =0.1. The isotherms for both (pure fluid and Isotherms and nanofluid) with ( are

symmetrical in vicinity of the side walls of the Figures (2, 3, and 4) illustrate the stream enclosure. The other isotherms with function and isotherm for Rayleigh number ( occur smoothly and symmetrically (Ra=103), pure and nanofluid (φ =0.1 and φ with respect to the vertical line of the enclosure =0.2), and for inclination angles (θ = 0°, 30°, as shown in figure 4.As Rayleigh number 5 and45°) respectively. Note that the solid lines increases to (Ra =10 ), the effect of buoyancy represent the nanofluid while the dashed lines force is stronger compared to the viscous force represent the pure fluid. Since the vertical side and the intensity of fluid motion has been walls are cold, fluids (pure and nanofluid) rise increased as indicated by greater magnitudes of from the mid part of the bottom wall and stream functions for both pure and nanofluid as o o descend along the side vertical walls creating shown in figs. (5, 6, and 7) for (θ = 0 , 30 , and o o two symmetric vortices rotate clockwise and 45 ), respectively. For the three angles (θ = 0 , 132 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

30o, and 45o), and for pure and nanofluid, the (5. b), the thickness of the thermal boundary isotherms for (pure fluid and nanofluid) with layer increases with increases (φ) value. Also ( are symmetrical in vicinity of the for Ra=105 and for trapezoidal enclosure (θ = side walls of the enclosure, and the other 30o and 45o), as (φ) increases from 0.1 to 0.2, temperature contours with ( are the isotherms ( ≤ 0.5) in the upper part of the squeezed towards the vertical side. It is enclosure approach to the centerline of the interesting to note that the stronger circulation enclosure, this can be shown in figures (6b and occurs for (θ =30o and 45o), the top half of the 7b) in which the isotherm ( = 0.5) crosses the enclosure attains the largest temperature. At Ra line of the pure fluid (solid line) near the top 5 = 10 , the isotherms are strongly squeezed wall, this gives indication that the thickness of towards the top part of the sidewalls due to the thermal boundary layer increases near the higher temperature gradient within the thermal side walls as (φ) increases. boundary layer. It is seen that the thermal boundary layer thickness at the upper part of 5.3 AverageNusselt Number the both side walls is reduced for Ra=105 as compared to Ra=103. Figure (8a, b) shows the influence the inclination angle of side walls on the average Nusselt number for pure and nanofluid (φ = 0, 5.2 Effect of Solid Volume Fraction (φ) on and 0.2). The figures show that the highest Stream function and Isotherms value of the average Nusselt number occurs at

(θ = 0 °) for all values of Rayleigh (Ra) and for

pure and nanoflud (φ = 0, and 0.2), this is As the volume fraction (φ) increases, the because when increase the inclination angle of circulation of flow decreases for all Rayleigh side walls the thermal boundary layer will be numbers and for all inclination angles as shown thicker compared with the angle (θ = 0°), from the values of (ψ*) in figures (2, 3, 4, 5, 6, which leads to a decrease in the rate of heat and 7),this is due to that the viscous effect transfer, and this is evident from the large increases with increasing (φ) and resulting in deformation that gets to the temperature lines less fluid motion. Note that at Ra=103in figure (compression lines toward the side walls) (2a), |ψ* | = 0.1189 at (φ = 0.1) whereas |ψ* max because of increasing inclination angel (θ) . | = 0.0904 at (φ =0.2). At Ra =103 and (θ = max Also it is important to note that the rate of heat 0o), the thickness of the thermal boundary layer transfer at (θ = 30°) is almost equal the rate at at the upper part of side walls is greater for (θ =45°), for all values of (Ra) and (φ = 0, and nanofluid and increasing with solid fractions 0.2). (φ). The isotherms are identical adjacent the bottom wall of the enclosure, and it is observed 6. Conclusions that isotherms with (T*≥ 0.5) are not affected by the presence of nanofluid for the whole Through the results of the numerical study can range ofφ.At Ra=105 and for square enclosure be drawn the following conclusions: (θ = 0o), the isotherms corresponding to ( = 1- The stream function (intensity of 0.3 & 0.4) for pure fluid (water) coincide with circulation) increases as the inclination the isotherms ( = 0.2 & 0.3), respectively for angle of the side walls increases to (θ = 30 (Cu + water) nanofluid at (φ = 0.2) near the °, and 45°) for both pure fluid and nanofluid upper parts of the side walls as observed in fig. 133 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

at all the range of Rayleigh concept,International Journal of Heat and number( ). Mass Transfer, 52 (11), 2471-2483. 2- For trapezoidal enclosure at (θ = 30°, 45 °), Basak, T., Ramakrishna, D., Roy, S., Matta, A. the upper half of the enclosure be at higher and Pop, I. 2011. A comprehensive heatline temperature than the square enclosure (θ = 0 based approach for natural convection flows °) for both pure fluid and nanofluid due to in trapezoidal enclosures: Effect of various increasing the intensity of circulation with walls heating,International Journal of increasing angle. Thermal Sciences, 50 (8), 1385-1404. Saleh, H., Roslan, R. and Hashim, I. 2011. 3- Average Nusselt number at (θ = 30°) is Natural convection heat transfer in a almost equal Average Nusselt number at (θ nanofluid-filled trapezoidal = 45°) for both pure fluid and nanofluid. enclosure,International Journal of Heat and 4- The highest value of the average Nusselt Mass Transfer, 54 (1), 194-201. number occurs at (θ = 0°) regardless of the Hasanuzzaman, M., Öztop, H. F., Rahman, M., type of fluid (nanofluid and pure) and the Rahim, N., Saidur, R. and Varol, Y. 2012. value of (Ra). Magnetohydrodynamic natural convection 5- The average Nusselt number increases as (φ) in trapezoidal cavities,International increases for square and trapezoidal Communications in Heat and Mass enclosures and for Rayleigh number Transfer, 39 (9), 1384-1394. ( ). Nasrin, R. and Parvin, S. 2012. Investigation of 6- The flow circulation intensity increases as buoyancy-driven flow and heat transfer in a the angle on the enclosure increases for both trapezoidal cavity filled with water–Cu pure fluid and nanofluid. nanofluid,International Communications in Heat and Mass Transfer, 39 (2), 270-274. References Ramakrishna, D., Basak, T. and Roy, S. 2013. Analysis of heatlines and entropy generation Khanafer, K., Vafai, K. and Lightstone, M. during free convection within trapezoidal 2003. Buoyancy-driven heat transfer cavities, International Communications in enhancement in a two-dimensional Heat and Mass Transfer, 45, 32-40. enclosure utilizing nanofluids,International Mahmoudi, A. H., Pop, I., Shahi, M. and Journal of Heat and Mass Transfer, 46 (19), Talebi, F. 2013. MHD natural convection 3639-3653. and entropy generation in a trapezoidal Öğut, E. B. 2009. Natural convection of water- enclosure using Cu–water nanofluid, based nanofluids in an inclined enclosure Computers & Fluids, 72, 46-62. with a heat source. International Journal of Esfe, M. H., Arani, A. A. A., Yan, W.-M., Thermal Sciences, 48 (11), 2063-2073. Ehteram, H., Aghaie, A. and Afrand, M. Natarajan, E., Basak, T. and Roy, S. 2008. 2016. Natural convection in a trapezoidal Natural convection flows in a trapezoidal enclosure filled with carbon nanotube–EG– enclosure with uniform and non-uniform water nanofluid,International Journal of heating of bottom wall,International Heat and Mass Transfer, 92, 76-82. Journal of Heat and Mass Transfer, 51 (3), Basak, T. and Chamkha, A. J. 2012. Heatline 747-756. analysis on natural convection for Basak, T., Roy, S. and Pop, I. 2009. Heat flow nanofluids confined within square cavities analysis for natural convection within with various thermal boundary trapezoidal enclosures based on heatline 134 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

conditions,International Journal of Heat NuNusselt number = hL/k and Mass Transfer, 55 (21), 5526-5543. P Pressure, Pa Brinkman, H. 1952. The viscosity of PrPrandtl number, Cp μ/k concentrated suspensions and solutions. The Ra Rayleigh number Journal of Chemical Physics, 20 (4), 571- 571. Greek symbols α 2 -1 Rhie, C. and Chow, W. 1983. Numerical study Thermal diffusivity, m s β Volume expansion coefficient, K-1 of the turbulent flow past an airfoil with γ, δ, ε Transformation parameters trailing edge separation,AIAA journal, 21 ζ ,η Curvilinear coordinates (11), 1525-1532. θ Inclination angle Wang, Y. and Komori, S. 2000. On the 2 -1 improvement of the SIMPLE-like method Dynamic viscosity, m s -3 for flows with complex geometry,Heat and Density, kg m Mass Transfer, 36 (1), 71-78. Volume fraction of nanofluid Ferziger, J. H. and Peric, M. 2012, Φ Computational methods for fluid dynamics, Dependent variable Springer Science & Business Media, USA. ψ Stream function m2/s Ganzarolli, M. M. and Milanez, L. F. 1995. Natural convection in rectangular enclosures Subscripts f pure fluid heated from below and symmetrically nfnanofluid cooled from the sides,International Journal p solid particles of Heat and Mass Transfer, 38 (6), 1063- 1073. h hot Hussain, S. H. and Hussein, A. K. 2014. c cold Natural convection heat transfer enhancement in a differentially heated av average parallelogrammic enclosure filled with S Source term copper-water nanofluid, Journal of Heat Transfer, 136 (8), 082502. Superscript

* Dimensionless quantity Nomenclature x,y Space coordinates in Cartesian system , m u, v Velocity components in the x and y directions , m/s Table1 The thermophysical properties of the T Temperature, K base fluid (water) and the nanoparticles (Cu) at 2 300 K. (Basak and Chamkha, 2012) g gravitational acceleration, m/s H Enclosure height, m Properties Water Cu Particle -1 -1 Cp(J.kg k ) 4179 385 L Enclosure width, m k(w.m-1k-1) 0.613 401 -3 k Thermal conductivity, W/m K (kg.m ) 997.1 8933 -5 -5 -1 1.67*10 21*10 -1 -1 ( K ) Cp Specific heat, J kg K 135 Mustafa A and Ahmed O/ZJPAS: 2017, 29(2): 126-135

0 4.82 4.719 2.14 0.1 5.29 5.383 1.7 Table 2 Grid independency test for trapezoidal 0.2 5.66 5.935 4.6 enclosure (θ = 30°) filed by nanofluid (Cu –

Water) at (φ = 0.1) and (Ra = 105).

Number Nu ψ* Error Error av max of (Nu %) (ψ av max control %)

volumes

in x*-y*

40x40 9.721138 18.01 ------

60x60 10.30422 18.11 5.99 0.555

80x80 10.70939 18.15 3.932 0.22

100x100 11.01833 18.16 2.884 0.055

120x120 11.26773 18.17 2.263 0.055

140x140 11.47658 18.18 1.853 0.055

Table 3 Comparison of the present average Nusselt number with (Hussain and Hussein, 2014) for natural convection in differentially heated square enclosure filled with Cu-water nanofluid at Ra=105

φ Present (Salam and Error % Ahmed, 2014)

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 136-143 http://dx.doi.org/10.21271/ZJPAS.29.2.14

Improve differentiation of Breast mass using fuzzy segmentation method

1Heamn N. Abduljabbara*, 1 Haidar J. Ismailb and 2 Sardar Y. Perxdra

1Department of Physics, College of Education-Shaqlawa, Salahaddin University, Iraq

2Department of Physics, College of Education, Salahaddin University, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: Breast cancer is one of the almost public types of cancer in women. Breast Received: 09/08/2016 masses generally classified to cystic and solid masses and in both, there are many Accepted: 26/12/2016 subtypes. So that understanding exact types of them is useful for better treatment Published: 07/06/2017 Keywords: of the patient. There are clinic invasive techniques for that but image processing Breast mass, Cyst, usually seems helpful to get same or better results. Furthermore, an intelligent Fibroid, Image computer-aided diagnosis system or proper algorithm can be very helpful for enhancement, Fuzzy Edge radiologist in detecting and diagnosing abnormal cases earlier and faster than detection. typical screening methods. One of the most important image processing is Edge . detection which targets towards image understanding. This study tried to improve

the early detection of breast masses (cystic/solid) from 2D ultrasound scanning, *Corresponding Author: by running the resulted images of the abnormal cases in image enhancement, edge Heamn N. Abduljabbara [email protected] detection, furthermore comparing between the resulted 2D images by 3D images, Elastography, and then thermal detection of breast mass images. Four cases of different abnormalities taken from 783 patients had been scanned in Harer hospital by 2D ultrasound B- Mode Linear probe with 7.2 MHz frequency, 47 of them diagnosed as breast mass. The images were enhanced by adaptive histogram equalization (AHE) which usually given proper contrast enhancement. Then appropriate conditions were chosen for Fuzzy set theory to give us proper edge detection. The result was the obtained 2D images are much more clear for diagnosis after running into image processing, the mass easily can be detected and classified into the correct type without using 3D high-cost ultrasound. .

1. INTRODUCTION called Complicated cysts [Cha et al, 2005]. The

The lesions that have echogenic (solid) first type must use percutaneous biopsy and/or and anechoic (cystic)components known as surgical ablation to get histological Complex cystic masses while those contain just verification. So, according to results it may be echogenic fluid which imitates a solid lesion benign or malignant. Histopathological 137 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143 correlation, which will be done through biopsy, (cells that storing fat). The fat placed in the is so important toconfirm the situation of the down of the breast due to the effect of estrogen samples, and not to fail to diagnose high risk or hormone. Generally, the breast has three layers malignant lesions which requiring different which are the fatty layer, lactic (nodules), and management[Zhi et al., 2007]. muscular layer that makes the base wall of the breast as shown in Figure 1. While performing an ultrasound check, the utmost commonly appearance are Cysts that are usually asymptomatic and found accidentally. The BIRADS lexicon is used to categorize the Cystic lesionsto three types. Simple cysts (termed ACR2) are strictly anechoic content, imperceptible wall,posterior acoustic enhancement, andprobably benign.The second type called Complicated cysts (termed ACR3)which havehomogeneous hypoechoic content or withmore or less sloping fluid/fluid Figure 1: Breast anatomy levels, imperceptible wall, with posteriorenhancementor without it. The last 1.2 Breast Imaging modalities typeis Complex cysts of indeterminate nature (termed ACR4)contain both cystic and solid There are severalkinds of breast imaging components, thick wall or internal techniques such as Magnetic Resonance septum/septa. The distinguishing between a Imaging (MRI), Computed Tomography (CT) complicated cyst and a complex cystic mass is scan, Ultrasound (US) scanning,Nuclear the challenge for the radiologist.When a solid Medicine, Mammography, component is appeared, even if discreet, andThermography.Each modality used for thelesion comes into the category ACR4, different purposes, and parameters, but which has Positive Predictive Values (PPV) ultrasound scanning is the relatively accurate, between 2-95%,with a biopsy indicated for low cost, safe, and comfortable one for diagnostic purposes [Athanasiou et al., 2014]. distinguishing breast lesions.

1.1 Anatomy 1.3 Ultrasound The breast is situated in the forepart of the Ultrasound is applied widely to scan the chest and contains the mammary gland which non-lactating breast to find abnormality cases produces milk. It is made mainly of fat cells (e.g. cysts, fibroadenomas and malignant) from 138 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143 normal structures (e.g. milk ducts, lymph from cyst walls) so that posterior ultrasound nodes, glandular and adipose tissue) [Stavros et variations are seen better. Compound mode al., 1995]. Furthermore, the capability of enhances the signal/noise ratio by reducing ultrasound increased due to recent background noise and speckle artifact technological advances to determine very small optimizes analysis of the margin of the lesion structures for example ducts small as 0.5 mm and the internal echo structure of masses. It [Sohn et al., 1999]. also enables better finding of intralesional calcifications [Doshi at el., 2007]. On the other 1.4 Examination techniques hand, posterior ultrasound modifications are As for any imaging examination, all the reduced [Candelaria et al., 2013]. Doppler clinical and radiological data is important mode (color and/or power) ought to be before doing and interpreting a breast systematic. It presents hints guiding diagnosis: ultrasound examination. The ultrasound perilesional hyperemia if lesions are technique (B mode) should meet the following inflammatory (cysts, abscesses). Doppler box criteria: linear probes of frequencies between size can be changed to improve sensitivity and 7.2 and 20 MHz (more often 12-14 MHz) decrease flow artifacts. Power Doppler is more should be used. The frequency must be altered sensitive to slow flows but is also more to the breast volume and the location of lesion sensitive to artifacts. It must be remembered in the breast (small frequency for deep lesions, that the lake of a Doppler signal does not mean large frequency for superficial lesions); total that the solid nature of a lesion can be omitted. gain and TGC must use to get proper and Elastography can help to differentiate homogeneous signal from the skin to the depth complicated cysts by revealing the fluid of the pectoral muscle; the focal zone must be component (appear trilaminar or bull's eye in adjusted in depth according to the lesion; the static mode and signal void in shear mode). lesion should be examined at least in two Likewise, if the lesion is found to be very hard, planes: transverse and longitudinal. The this help to improve identification of complex another mode useful to characterize the lesion; masses and guide percutaneous biopsies the radiologist needs to know their main (improving the histological characterization of characteristics as well as their respective the lesion) [Youk et al., 2013]. advantages and disadvantages to getting an optimize use of them. 1.5 Ultrasound signs of complicated cysts

Harmonic mode increases spatial Complicated cysts show all the aspects of resolution and contrast of the lesion and simple cysts except for the content, which is reduces artifacts (e.g. reverberation artifacts excellently echogenic. They can show a fluid 139 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143 level or internal echoes that correspond to combination used because basic techniques for debris and which are shifted gradually with edge detection (Sobel, Prewitt, Roberts) suffer changes in the patient's position. The types of from improper smooth and unclear edge due to breast masses illustrated in Figure 2. noise and steep light alterations of medical .images

Anand et al. 2015 segment the input image and then sort tumor within the breast images and normal breast images using a hybrid of Fuzzy c-means and Self-organizing map

(SOM) algorithm. In another work, Aroquiaraj and Thangavel 2013 proposed better algorithm Figure 2: show types of breast mass which improves the detection of edges by using Ultrasound images suffer from low fuzzy rules. The weights of each fuzzy rule resolution, so the interpretation of the image give good results to achieve edge detection of greatly depends on the skill of the operators. the mammogram images. The results show the Since image processing has a significant role to higher quality of the extracted edges compared enhance true positive results. One of the most to the basic techniques of edge detection such extensive and effectivetechniques of image as Sobel, Robert, and Prewitt. processing is fuzzy logic techniquethat used in In the present work,enhance technique and different types of medical imaging. proper fuzzy edge detection algorithm will El-Khamy et el. (2000) propose a modified apply on four cases of breast ultrasound fuzzy Sobel method for edge detection and imaging and investigate range of their benefits differentiation of metastases, meningioma, to help operator to make correct diagnosis. gliomas and brain astrocytoma with respectable 2. Materials and Methods accuracy. Another researcher, prefer a modified fuzzy method (MFCM) to be used for marking Tow ultrasound images that represented and diagnosis of brain tumors for their less for different cases of breast taken by the first sensitive to the noise [Dasgupta, 2012]. author and predicted as simple cyst, and complex cyst, respectively. The input images A combination of fuzzy c-means with which are gray level images cropped manually watershed algorithm was used by Hoseyni et al. to obtain better results for edge detection with 2014, to reduce the error in the process of dimensions about 500x400 pixels then image segmentation and to improve edge enhanced byAdaptive Histogram Equalization detection in MRI of brain tumor. This (AHE).It is a method of contrast enhancement 140 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143

that is different from ordinary histogram Table 1: Fuzzy sets for input and output equalization. In adaptive method, many variables histograms are computed where each histogram Fuzzy Range MF type corresponds to a different section of image. sets Hence, AHE improves the local contrast of an P1_input [ 0.1 0] Gaussian image and more details can be observed.Figure P2_input [ 0.1 0] Gaussian 3 shows the main steps of applying fuzzy edge White [0.1 1 1] Triangular detection. Poutput Black [0 0 0.7]

3. Results and Discussion Figure 3: shows flow chart of main steps of 3.1 Simple Breast cyst applying fuzzy edge detection Simple breast cyst defined in the 2D 2.1 Fuzzy Logic edge detection ultrasound in the original image as shown in As known, the fuzzy algorithm has three Figure 5a having thin regular wall with clear

main steps. Two-dimension Gradient Gx and fluid filled while Figure 5b shows the same

Gy computed and fuzzified by two Gaussian image after using image enhancement Tanique membership functions. The rules that modify in image processing which improves the image membership values is to be white color for both quality as or close to 3D ultrasound image. two gradients with zero value else black color The same image after using edge detection, if one of them don’t zero. Lastly, the resulted which shown in Figure 5c, by using Fuzz edge defuzzified by triangular membership function. detection technique. The cyst is clearer and can Table 1 shows fuzzy sets for input and output be defined even better than infra-red IR or variables and Figure 4 illustrate the main steps thermal detection of breast mass as the image of fuzzy algorithm. quality is much better than IR (see Figure 5d).

Fuzzy Rule 3.2 Complex breast cyst

The complex breast cyst is another type of Input Fuzzificat Decisio Defuzzifica breast cysts it can be recognized by ultrasound scanning as it has the thick irregular outline Membership Function and acoustic shadows as shown in Figure 6a Figure 4: shows flowchart of fuzzy algorithm also the fluid inside it is thick fluid, not clear echogenicity. While Figure 6b shows the same 141 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143 cyst after running the image through image 5. Acknowledgements processing software by making image The authors would like to express their enhancement which gives us more information acknowledgment to Salahaddin University for about the cyst from Figure 6c, moreover we supporting them with available tools. If anyone can see the intensity of the wall thickness who needs the program, please contact the clearly after using fuzzy edge detection for the second author for any additional help. same image it helps also to detect the severity of the cyst by defining the outline and the acoustic shadow as shown in Figure 6d below. It is clear that the image quality is higher and better after using Fuzzy edge detection to detect complex breast cyst than Elastography as shown in Figure 12.

4. Conclusion

The importance of early accurate diagnosis of breast masses in early stages resulted in making this study so that four breast ultrasound images were segmented through fuzzy edge detection method and contrast enhanced. All images were obtained from the correspondent author from his privet clinic (ultrasound scanning clinic in Erbil). The fuzzy algorithm with our proper definitions for all main steps capable of determining edges of all cases precisely but it suffer from low contrast. They were contrast enhanced as the second step. According to our results, fuzzy edge detection is a good choice for sonologists to have a correct decision about suspicious cases related to breast mass as it is a low-cost method to increase the image quality of 2D ultrasound.

142 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143

Figure 5:(a) simple breast cyst. (b) simple breast cyst after making image enhancement. (c) explains the using of Fuzzy Logic Edge detection way which shows the cyst much more clear. (d) shows breast mass by IR infra-red imaging the arrow pointing the breast mass.

Figure 6:(a) shows the cyst with thick irregular outline and has multiple acoustic shadows. (b)complex breast cyst shows wall thickness the red arrow and thick fluid the blue arrow better. (c) the wall thickness clearly defines the severity of the cyst and the intensity of the cyst outline clearly shows the rate of the outline's solidity and compatibility. (d) complex breast cyst by using Elastography techniqueZhi H et al (2007).

143 Heamn N. et al. /ZJPAS: 2017, 29(5): 136-143

References Science Conference, 2000. 17th NRSC'2000. Seventeenth National (pp. C32-1). IEEE. Anand, S., Vinod, V. and Rampure, A., 2015, Hoseyni, F.A.R.N.A.Z., Haghipour, S.I.A.M.A.K. and Application of Fuzzy c-means and Neural networks Sorkhabi, A., 2014. Improvement of segmentation to categorize tumor affected breast MR Images. on MRI images using fuzzy clustering C-means and International Journal of Applied Engineering watershed marker control algorithm. Indian J. Sci. Research, 10(64), p.274-281. Res, 4(3), pp.447-451. Aroquiaraj, I.L. and Thangavel, K., 2013. Mammogram Sohn, C., Blohmer, J.U. and Hamper, U., 1999. Breast Edge Detection Using Hybrid Soft Computing ultrasound: a systematic approach to technique and Methods. arXiv preprint arXiv:1307.4516. image interpretation. Thieme. Athanasiou, A., Aubert, E., Salomon, A.V. and Stavros, A.T., Thickman, D., Rapp, C.L., Dennis, M.A., Tardivon, A., 2014. Complex cystic breast masses Parker, S.H. and Sisney, G.A., 1995. Solid breast in ultrasound examination. Diagnostic and nodules: use of sonography to distinguish between interventional imaging, 95(2), pp.169-179. benign and malignant lesions. Radiology, 196(1), Candelaria, R.P., Hwang, L., Bouchard, R.R. and pp.123-134. Whitman, G.J., 2013, June. Breast ultrasound: Youk, J.H., Gweon, H.M., Son, E.J., Han, K.H. and current concepts. In Seminars in Ultrasound, CT Kim, J.A., 2013. Diagnostic value of commercially and MRI (Vol. 34, No. 3, pp. 213-225). WB available shear-wave elastography for breast Saunders. cancers: integration into BI-RADS classification Cha, J.H., Moon, W.K., Cho, N., Chung, S.Y., Park, with subcategories of category 4. European S.H., Park, J.M., Han, B.K., Choe, Y.H., Cho, G. radiology, 23(10), pp.2695-2704. and Im, J.G., 2005. Differentiation of Benign from Zhi, H., Ou, B., Luo, B.M., Feng, X., Wen, Y.L. and Malignant Solid Breast Masses: Conventional US Yang, H.Y., 2007. Comparison of ultrasound versus Spatial Compound Imaging elastography, mammography, and sonography in 1. Radiology, 237(3), pp.841-846. the diagnosis of solid breast lesions. Journal of Dasgupta, A., 2012. Demarcation of brain tumor using ultrasound in medicine, 26(6), pp.807-815. modified fuzzy C-means. International Journal of

Engineering Research and Applications, 2(4), pp.529-533.

Doshi, D.J., March, D.E., Crisi, G.M. and Coughlin, B.F., 2007. Complex Cystic Breast Masses:

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El-Khamy, S.E., Lotfy, M. and El-Yamany, N., 2000. A modified fuzzy Sobel edge detector. In Radio

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 144-150 http://dx.doi.org/10.21271/ZJPAS.29.2.15

Effect of pitfall trap size on the abundance and diversity of ground dwelling

insects in an arable land within Erbil Province- Kurdistan region-Iraq

Khalid Qadir Khidher, Karzan Sabah D.Ahmed and Nawzad Bawakir Kadir Department of Plant Protection, College of Agriculture, Salahaddin University–Erbil, Erbil, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: The abundance and diversity of ground dwelling insects in an arable Received: 14/08/2016 land within Erbil Province- Kurdistan region-Iraq were investigated using Accepted: 28/12/2016 four different pitfall trap sizes (10 cm, 13cm, 16cm and 19 cm diameter Published: 07/06/2017 respectively). Five insect orders were reported with fourteen insect Keywords: families. The order Diptera was the most abundant insect taxa recovered Below ground (372.9) followed by orders Hymenoptera (328.8), Coleoptera (268.4), Pitfall trap Lepidoptera (26.7) and Hemiptera (6.4). The size of pitfall trap affected Soil fauna the abundance and diversity of the taxa. The highest number (450.7) of Soil insects soil dwelling insects was observed in 19 cm diameter pitfall traps Soil biodiversity followed by 16cm (231.2), 13cm (198.4) and 10cm (123) respectively; suggesting that the 19cm diameter pitfall trap size may be an effective *Corresponding Author: method for sampling and monitoring soil dwelling insects of arable lands Khalid Qadir Khidher in our region mainly field crops. [email protected]

1. INTRODUCTION least one stage of their life cycle in the Soil is known as one of the richest habitat soil(Imam et al., 2016; Klein, 1988); for various kinds of terrestrial organisms, influencing the diversity of plant communities, considering the habitats like vertebrate faeces, competitive interactions among plants and the decaying wood, epiphytic soils and yield of agricultural systems(Hunter, 2001).All forest/agricultural or domestic litter (Imam et of the major winged insect orders—the al., 2016). The community in the soil has been Coleoptera (beetles), Lepidoptera (butterflies described as ‘poor man's tropical rainforest’ as and moths), Hymenoptera (bees, wasps and a result of several factors such as their ants), and Diptera (flies)—include soil- remarkable biodiversity and undescribed dwelling species. The Isoptera (termites) are species they contain, and many research gap on essentially soil insects and are saprophages. their community structure and dynamics The Homoptera (aphids, cicadas), Orthoptera (Giller, 1996). Soil biodiversity includes (grasshoppers and crickets), and minor orders various kinds of terrestrial insects including such as the Dermaptera (earwigs) contain soil- many ground dwelling insects which spend at dwelling species or life history stages. Indeed, 145 Khidher Q. et al. /ZJPAS: 2017, 29(2): 144-150

of the 26 pterygote insect orders, all but seven et al., 1999)however, little is known about the contain at least some species that are involved effect of pitfall trap size on the abundance and in soil food webs in one way or another diversity of ground dwelling insects in arable (Greenslade, 1985).Some soil insects are lands and such studies are lacking in our phytophagous and feeding on plant roots and/or region. This is particularly important for soil movers; thus having economic importance monitoring and integrated pest management of as crop feeders such asthe order Homoptera, pest species in soils of field crops such as cicadas, aphids, and others (Callahamet al., wheat and barley in our region. Therefore, the 2000), Coleoptera (wireworms, wheat ground current study was undertaken to: beetle etc.) (Bassett, 1978 and Milosavljevićet 1- Detect the ground dwelling insects available al., 2016), and Lepidoptera larvae (cutworms) at Grdarasha arable lands (pest and none pest (Lemicet al., 2016). Conversely, some others species). are acting as biological control agents such as 2- Determine the effect of different pitfall trap many coleopteran carabid and rove beetles size on species biodiversity and richness at the (Lang et al., 1999; Josephet al., 2015; selected study site. Kulkarniet al., 2015and Saito, T. & 2. MATERIALS AND METHODS Brownbridge, M. 2016). The use of pitfall trapping is known to be a The survey was initiated at Grdarasha field very effective and useful method for sampling station-Erbil from the beginning of February and monitoring soil insects (both pest and none 2016 to the beginning of May2016 using pitfall pest species) since they are economical, eco- traps. The sampling station was selected using friendly and easy to use in the field (Schauff, Randomized Complete Block Design (RCBD) 2001). They have been used for monitoring and using four different sized pitfall traps (10cm, population study of various arthropods in 13cm, 16cm and 19 cm diameter) each with different ecosystems for example forest three replicates (blocks) to provide an even ecosystems (Bury and Corn, 1987; Majer, 1978 coverage of the study area of the arable lands. andOlson, 1991), grasslands and winter wheat In each block the four different sized pitfall fields (French and Elliott, 1999;Soppet al., traps were installed, these comprised of plastic 1987 and Standen, 2000), horticulture cups set side by side with a distance of 5 (Audisio, 1990 and Ester and Van Rozen, meters between them over which a square of 2005) and vegetated margins of different arable transparent plastic was supported on metal tent fields (Thomas and Marshall, 1999).Despite pegs (Figure 1) in order to prevent flooding of their wide use in the ecological study of soil the traps by the irrigation system, protection dwelling arthropods, the pitfall trap catches from rain and predation by other animals (e.g. may be affected by several factors for example birds).The cups were half full of water with the the use of baits and pheromones associated addition of some alcohol (ethanol 25%) which with pitfall traps are known to affect pitfall trap acts as a bactericide and thus prevents decay of catches (Ester and Van Rozen, 2005; the catch. It is also nontoxic to mammals and Greensladed̊ , 1971),pitfall trap spacing (Larsen thus was not a hazard to visitors. The pitfall and Forsyth, 2005 and Ward et al., 2001), the traps were emptied every 7 days over the study shape of pitfall trap (Luff, 1975) and habitat period. Samples were kept in 70% ethanol structure (Melbourne, 1999). Despite the (both mature and immature stages) and then limited studies on the effect of pitfall trap size transported and kept in laboratory for on certain arthropods such as spiders (Brennan identification. Insects were identified to family 146 Khidher Q. et al. /ZJPAS: 2017, 29(2): 144-150

level using the keys available and online followed by 16cm, 13cm and 10cm information. respectively (Figure 4a). The Family Syrphidae was the second most abundant insect family recorded during the study which comprised of 311.7 individuals in general. The greatest number of Syrphidae was observed during the study at 19cm and 13cm pitfall trap followed by 16cm and 10cm trap diameter respectively (Figure 4a).The family Chironomidaewas found in much lower numbers than Formicidae and Syrphidae but comprised the third abundant taxa when compared with the other taxa. The composition of Chironimidea was affected by increase in trap size similar to Forficidae and Syrphidae. The family Figure 1: The pitfall trap design and the study area. Carabidae and Staphylinidae were found nearly in similar numbers (56.3 and 53.7respectively). 3. RESULTS AND DISCUSSION Although both families were found in greater In total, 1003.3 insects were collected numbers at 19cm and 16cm trap diameter belonging to five Insect orders and fourteen respectively, however, in contrast to the Family insect families. The order Diptera was the most Staphylinidae, the 10cm trap size collected abundant insect taxa recovered comprising more numbers of Carabidae than the 13cm trap about 37% of the collected insect taxa followed size. The composition of the family Anthicidae by the orders Hymenoptera (33%), Coleoptera was relatively higher than the lower remained (27%), Lepidoptera (3%) and Hemiptyera (0.0%) respectively (Figure 2). Although the taxa which was 46.1 individuals and were number of Coleopteran insects was lower when affected by trap size similar to Formicidae. compared with Diptera and Hymenoptera, Both families Curculionidae and Scarabidae however; the greatest family diversity was were found nearly in similar numbers (33.1 and observed in the order Coleoptera which 30.2 respectively). Their abundance affected by comprised 69% of the collected insects increasing the trap size which were higher at followed by Diptera (13%), and similar family 19cm trap size and lower at 10 cm trap size. diversity for the orders Hymenoptera, Lepidoptera and Hemiptera (6%) (Figure 3). The composition of other insect taxa was generally low and all were affected by increase The pitfall trap size affected the abundance of in trap size (Figure 4a). Since the family each insect family throughout the study period. Formicidae and Syrphidae were found in much The greatest insect number was found in the higher numbers when compared with the other 19cm diameter pitfall trap in general insect taxa, therefore their peak is much higher (450.7individuals) followed by 16cm than the other studied taxa in Figure 4a. To (231.2individuals), 13cm (198.4individuals) give a more detailed and clarified image of and 10cm (123 individuals). The family other studied taxa, these two families were Formicidae was the most abundant insect excluded and the effect of pitfall trap size on family observed during the study comprising of other lower taxa have been demonstrated in 328.9 individuals. The greatest number of Figure 4b. Formicidae was found in the 19cm pitfall trap 147 Khidher Q. et al. /ZJPAS: 2017, 29(2): 144-150

Figure 4b: Total number of each insect family except Formicidae and Syrphidae collected during the study period for the four different trap sizes used (T1-T4).

DISCUSSION:

The current study shows that the abundance and diversity of soil insects is related to pitfall trap diameter with higher numbers at larger trap sizes which was found for almost all taxa in this study (Figure 4a and 4b). The high Figure 2: % Abundance of each taxon during the study period numbers of Formicidae found in this study could be related to their social behaviour and nesting site as they live in colonies and are active throughout the season. Their high numbers at 19cm trap size could be due to the fact that at larger trap sizes, rare species of ants are fallen to the trap as such studies have been conducted in a semi-arid eucalypt woodland by Abensperg‐Traunand Steven, (1995) who found that 52% of rare ant species are caught at larger trap sizes. Similar to Formicidae high numbers of Syrphidae found in this study Figure 3: % Species diversity of each taxon during particularly at larger trap size (19cm). the study period Although there has been no studies on the use of pitfall traps for monitoring Syrphidae larvae but their occurrence in the traps are likely due to their adult oviposion behaviour and predation on their prey (aphids). This study area has been cultivated with wheat and barley for several years and is infested by cereal aphids annually. Therefore, as a natural enemy adult syrphids lay as much eggs as possible (egg clusters) on these infested plants with Figure 4a: Total number of each insect family collected during the study period for the four aphids. When these eggs hatch, the emerged different trap sizes used (T1-T4). larvae feed on aphids but many of them may fall to the ground due to the wind and rain; and as they move they fall into the pitfall traps. Their high numbers at 19 cm trap size could be due to the larger surface area of the trap than the 16cm, 13cm and 10cm trap sizes respectively. `The Chironomidae were similarly affected by trap size but their abundance was lower than Syrphidae and

Formicidae. Many chironomid larvae are 148 Khidher Q. et al. /ZJPAS: 2017, 29(2): 144-150

aquatic and detritophages (Henriques-Oliveira family Carabidae was the most abundant et al., 2003) and only few chironimid larvae are coleopteran taxa whereas Cerambycidae was known as pests of field crops such as rice the least. This is in agreement with Purvis and (Ferrarese, 1992) therefore, their population is Fadl, (2002) who found that theCarabidground generally low in arable lands. The low beetles are among the more familiar insects abundance and diversity of Lepidoptera caught in pitfall traps or active on the soil (Noctuidae) is due to the fact that these are surface of agroecosystems. Similarly, the sporadic pests. Although the Noctuidae larvae Staphylinid rove beetles are mostly predacious may cause significant damage to crop roots; and adults are agile runners which are often but they are often affected by environmental caught in pitfall traps(Coleman et al., 2004) as factors such as rain and predation by ants found in this study. The composition of other which feed on eggs and larvae of some species coleopteran insects was generally low (Figure (López and Potter, 2000). Only few numbers 4a and 4b), particularly for Elateridae larvae on Hemiptere (Cydnidae) was found in this which are known as important soil pests but study especially at 19cm trap size. These insect numbers were increased by trap size which orders are mostly living on vegetative part of were higher at 19cm trap diameter. Therefore plants and there have been no reports on the the majority of the insect taxa in this study damage of Cydnidae in our region; thus have were found in higher numbers at larger trap not a significant economic importance as crop sizes; indicating the importance of trap size pests. The higher diversity of Coleptera found when sampling and monitoring soil dwelling in this study in comparison other insect orders insects in arable lands. refer to their high global diversity and they are the most abundant animals on the planet. The diameter) at the species level and in different field crops for the economically important soil 4. CONCLUSIONS insect pests in arable lands of our region and The current study shows that the populations of their natural enemies. soil dwelling insects could be affected by changes in the size of sampling unit (trap sizes) Conflict of Interest with higher population sizes at larger sampling This research was conducted in the absence of units. This has implications for monitoring and any commercial or financial relationships that integrated pest management of economically could be construed as a potential conflict of important soil insect pests in arable lands. interest. Therefore, future research should focus on the use of suitable pitfall traps (here 19cm AUDISIO, P. 1990. First records in Italy of REFERENCES Glischrochilusquadrisignatus on horticultural ABENSPERG‐TRAUN, M. &STEVEN, D. 1995. and fruit crops. InformatoreFitopatologico, 40, The effects of pitfall trap diameter on ant 27-28. species richness (Hymenoptera: Formicidae) and BASSETT, P. 1978. Damage to winter cereals by species composition of the catch in a semi‐arid Zabrustenebrioides (Goeze)(Coleoptera: eucalypt woodland. Australian Journal of Carabidae). Plant Pathology, 27, 48. Ecology, 20, 282-287. BRENNAN, K. E., MAJER, J. D. &REYGAERT, N. 1999. Determination of an optimal pitfall trap 149 Khidher Q. et al. /ZJPAS: 2017, 29(2): XX-XX

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ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 151-156 http://dx.doi.org/10.21271/ZJPAS.29.2.16

Sero-prevalence of TORCH among pregnant and non- pregnant women by ELISA and One step TORCH assay in

Erbil city of Kurdistan region, Iraq

Hemdad Hawez Mawlood1, Wijdan Mohammed Salih Mero1, Ronak Ali Ismail2 Abdallah Mohamad Isa3

1 Department of Biolo gy, Faculty of Science, University of Zakho- Kurdistan region/Iraq 2Erbil Maternity Teaching Hospital

3Department of Biological Science, School of Life and Physical Sciences, Tennessee State University, USA

A B S T R A C T A R T I C L E I N F O

Article History: The present study was conducted to detect the sero-prevalence of anti- Received: 15/08/2016 TORCH antibodies (Toxoplasma gondii, Rubella virus, Cytomegalovirus, Accepted: 28/12/2016 Herpes simplex virus type-II) among pregnant and non-pregnant women from Published: 07/06/2017 different ages (18≥48 years) in Erbil city and their relation with age and Keywords: infertility, by using ELISA (Enzyme linked immunosorbent assay) and One- step TORCH assay. A total of 313 sera samples (150 pregnant and 90 women TORCH, were suffering from infertility and 73 fertile non-pregnant) were enrolled in the Pregnancy, study. In the age group 18-27 years showed the highest seropositive IgG by Infertility ELISA test, were 21, 20, 17 and 13% for Rubella, CMV, HSV-II and Toxoplasma gondii, respectively. The seropositive for ELISA TORCH –IgM test/seropositive for one step TORCH- IgM test was 45/14% The comparison *Corresponding Author: of ELISA test with one-step TORCH test for detection acute TORCH infections Hemdad H. Mawlood was significant. Hence, it could be concluded that ELISA test is more [email protected] efficacious than One-step TORCH test and There are no significant differences among ages with the TORCH infection. Also, in infertility cases high rate of T. gondii was observed among other TORCH groups.

1. INTRODUCTION The TORCH infection is the major cause of Bad Obstetric history (BOD) which implies TORCH group includes T. gondii, others previous unfavorable fetal outcome in terms of such as; Coxsakievirus, Syphilis, Varicella- two or more consecutive spontaneous Zoster virus, HIV, etc. then Rubella, abortions, intrauterine growth retardations, Cytomegalovirus and Herpes simplex virus congenital anomalies and maternal infections type I and type II (Franca and Mugayar, 2004). transmissible in utero at various stages of These agents gain access to the fetal blood gestation lead to recurrent pregnancy wastage stream transplacentally via the chorionic villi. (Cabe and Remington, 1988). TORCH Hematogenous transmission may occur at any infection usually occurs before the woman time during gestation or occasionally at the realizes that she is pregnant or seeks medical time of delivery via maternal- to-Fetal attention. The primary infection is likely to transfusion (Kumar et al., 2009). have more important effect on fetus than 152 Mawlood H. et al. /ZJPAS: 2017, 29 (2): 151-156

recurrent infection While each of congenital centrifuge at 3000 rpm for 5 minutes, and then infection possesses distinct clinical stored at -20Ċ until used for serological testing. manifestation some of these infections share 2.3 Methods certain characteristics, therefore, it is important 1-ELISA IgG and IgM: to know the effect of each of them. (Maruyama All the serum samples collected were tested for et al., 2007). In Iraq, few serological studies T. gondii, CMV, Rubella, and HSV-II, IgG and have been carried out on TORCH infection. A IgM antibodies using commercial ELISA kits study in Kirkuk city showed that the rate of (Bio Check, Inc., USA) which proofed by TORCH infection was 71.82%. The federal drug administration and International contribution of CMV, T. gondii, Rubella, and standards organization (ISO) HSV-II in this rate were 34.92, 26.68, 21.03, and 16.06% respectively (Mohammad and The results were calculated by ELISA reader Salman, 2014), In Erbil city (Amin et.al.2012), and they were interpreted as positive, equivocal showed that T. gondii was a major parameter or negative by determining the among TORCH groups. immunoglobulin index. IgG or IgM indexes values <0.9, 0.9-0.99 and >1.0 were suggestive In Duhok city, a study by (Amedi,2013) for negative, equivocal and positive, indicated that seropositivity of TORCH respectively. infections was significantly higher in women 2-One Step TORCH IgM: with BOH than normal pregnant women with previous normal full term deliveries. All sero-positive IgM samples of T. gondii, CMV, Rubella, and HSV-II were tested by This attempt was carried out to correlate one-step TORCH Panel IgM test, (Health- TORCH infection during pregnancy and their CHEM Diagnostics LLC, USA) the kit was relation with age and infertility among proofed by Federal drug administration pregnant and non-pregnant women by using (FDA).and International standards organization ELISA and one step TORCH assay in Erbil (ISO) The results were interpreted as city capital of Kurdistan region /Iraq. following: 2. Subjects, Materials and Methods Positive: Rose-pink color band in the Control 2.1 Study subjects region(C) and in the test region (T) This study was carried out from October 2013 Negative: Rose-Pink color band in Control to October 2014 in Erbil city/Kurdistan region only. region/Iraq, 313 Blood samples were collected Invalid: No Rose-pink color band in the from women (150 pregnant, and 90 women Control region. were suffering from infertility and 73 fertile 2.4 Statistical Analysis non-pregnant) of different ages (18 to > 48) A Chi-square (and Fisher’s exact) test was years. Each woman participated in this study used to analyze the differences of Torch sero- requested to fill out a questionnaire form prevalence by graph pad prism v.5.01Pakage related with the age, primary and secondary between the tested groups. infertility. 2.2 Sample collection Results The results presented in (Table 1 and Table Five ml of venous blood was drawn aseptically 2) by ELISA regarding age group there were from both groups. The sera were separated by no significant differences among ages with the 153 Mawlood H. et al. /ZJPAS: 2017, 29 (2): 151-156

TORCH infection for both IgG and IgM. The According to the distribution of TORCH highest seropositivity of TORCH IgG in age 18 positives among 90 infertility cases in current to 27 years were recorded 21, 20, 17 and 13%. study The TORCH IgG and IgM positives were For Rubella, CMV, HSV-II and T. gondii high among secondary infertility cases more respectively(Table.1). The highest than primary infertility cases also, T. gondii seropositvitly for TORCH IgM in age 28 to 37 IgG was the highest one among TORCH years was recorded 5.4, 5, 3 and 2.6% for T. infection in primary and secondary infertility gondii, CMV, HSV-2 and Rubella respectively cases. The previous research of lab animals (Table .2). recorded that infection with T. gondii could be The occurrences of TORCH IgG infection a cause of infertility in experimental mice among secondary infertility were recorded as (Stahl et al., 1994; Terpsidis et al., 2009). 27, 7, 5 and 5% for T. gondii, Rubella, HSV-II In current study recorded a causative relation and CMV respectively. T. gondii IgG in between chronic toxoplasmosis and infertility, secondary infertility cases (27%) was higher this is similar to each of (Li et al., 2011) in than T. gondii (13%) in primary infertility China and (EL-Tantawy et al., 2014) in Egypt. cases. Also T. gondii IgM (8%) in secondary In our finding chronic toxoplasmosis and acute infertility cases was higher than T. gondii IgM toxoplasmosis in secondary infertility were (3%) in primary infertility cases. higher than primary infertility. these results can Considering the role of immunological be explained by the hypothesis that in women techniques for detecting IgM antibodies for during toxoplasmosis the proliferate TORCH infection (Table 3), the rate of ELISA tachyzoites may invade female reproductive TORCH IgM (45%) was higher than One-step organ specially the oviducts, subsequently TORCH IgM (14%). evoke tissue cysts formation in it, that may produce tubule dysfunctions, and leads to 4. Discussion: hormonal abnormalities which give rises into The highest chronic TORCH infection secondary infertility sequels (Salman,2014). occurred among youngest aged when compared Also, toxoplasmosis leads to low level of anti- with other ages. (Table 1 and Table 2) This Mullerian hormone (AMH) in women, this outcome due to the fact that this group was hormone seems to be the best endocrine marker most exposure to risk infection sources that for growth follicles also it has a potential lead to chronic infection especially for ability to predict future reproductive life span Toxoplasmosis (Srirup et al., 2011). This result (Guyton and Hall, 2006). disagrees with the study in Duhok (Amedi, In Babylon city in Iraq (Areej, 2012) stated 2013) who had recorded low infection of that CMV and Rubella were higher than T. TORCH among young aged group. gondii among secondary infertility cases and The highest acute TORCH infection occurred this is in disagreement with recent study. among age group 28 to 37 and the T. gondii Considering role of immunological techniques was highest whereas Rubella was lowest when for detecting acute TORCH infection the compared with other age groups. (Table 2) ELISA efficacy higher than one step TORCH, According to T. gondii infection rate, the it could be explaining that ELISA method has current results for T. gondii IgG and IgM are in high affinity reaction occurs between TORCH accordance with (Hamad, 2009) in Erbil city/ antibodies and coated antigen in the bottom of Iraq ELISA well than the reaction between antigen coated on immobilized antibodies in one step 154 Mawlood H. et al. /ZJPAS: 2017, 29 (2): 151-156

TORCH device because the antibodies which is TORCH infection especially T. gondii they used in ELISA is monoclonal antibodies need further study in Erbil to find out relation Otherwise, the antibodies in one step TORCH between female reproductive hormones is polyclonal antibody. This finding agrees especially anti-mullerian hormone(AMH)and with (Mohammad and Salman, 2014) which seropositive of T.gondii among secondary recorded that ELISA method has highest infertility cases. In addition, one-step TORCH efficacy than one step test. is not very accuracy technique for clinical lab. 5. Conclusion Hence it is urgent issue for future about In conclusion, this study revealed high genotyping study to find out virulent strain of T seropositivity of IgG among TORCH group gondii among congenital cases in Kurdistan and it is estimated that Rubella IgG positives region/Iraq. wasn’t real result because most of Kurdish Acknowledgement people in Iraq they were vaccinated by Rubella, Thanks to all participants /patients also private otherwise TORCH IgM has not high clinical laboratories and Laboratory staff in percentage, it due to few acute infection Hawler Maternity Teaching Hospital. present among both groups .On the other hand, relation between infertility in women and Table 1 Sero-Positive of TORCH IgG by ELISA. There are no significant differences among ages with the TORCH IgG. by using Chi Square (Fisher's Exact) Test. Toxo IgG CMV IgG Rubella IgG HSV-2 IgG

Total= n= Positive Negative P Positive Negative P Positive Negative P Positive Negative P 313 value value value value

(18-27) 132 41(13%) 91(29%) NS 64(20%) 68(22%) NS 67(21%) 65(21%) 54(17%) 78(25%)

(28-37) 98 38(12%) 60(19%) 57(18%) 41(13%) 48(15%) 50(16%) N.S 40(13%) 58(18%) N.S

(38-47) 51 19(6%) 32(10%) 26(8%) 25(8%) 21(7%) 30(10%) 18(6%) 33(10%)

(>=48) 32 9(3%) 23(7%) 14(4%) 18(6%) 12(4%) 20(6%) 10(3%) 22(7%)

Table.2 Sero-Positive of TORCH IgM by ELISA. There are no significant differences among ages with the TORCH IgM. by using Chi Square (Fisher's Exact) Test.

Total n Toxo -ve P. CMV -ve P. Rubell -ve P. HSV-II IgM P = 313 IgM val IgM val a IgM val val ue ue ue -ve +ve ue

(18-27) 132 9(3%) 123(39 10(3%) 122(39 6(2.0%) 126(40 10(3.0%) 122(39 %) %) %) %)

(28-37) 98 17(5%) 81(26%) N.S 16(5%) 82(26%) N.S 8(3%) 90(29%) N.S 9(3.0%) 89(28% N.S )

(38-47) 51 6(2%) 45(14%) 4(1%) 47(15%) 1(0%) 50(16%) 3(1%) 48(15% )

(>=48) 32 2(1%) 30(9%) 1(0%) 31(10%) 1(0%) 31(10%) 1(0%) 31(10% ) 155 Mawlood H. et al. /ZJPAS: 2017, 29 (2): 151-156

Table 3 Comparison between ELISA TORCH IgM and One step TORCH IgM by Chi Square (Fisher's Exact)

Test.ELISA technique more efficacious (significant) than One-step TORCH test.

Total Sample no = 313 Positive % Negative p value

% ELISA Toxo IgM 44 14% 269 86% 0.001 One Step Toxo IgM 16 5% 297 95% ELISA CMV IgM 43 14% 270 86% 0.001 One Step CMV IgM 17 5% 296 94%

ELISA Rubella IgM 21 7% 292 93% 0.001 One Step Rubella IgM 4 1% 309 99%

ELISA HSV-2 IgM 33 11% 280 89% 0.001 One Step HSV-2 IgM 8 3% 305 97% Total ELISA TORCH IgM 141 45% 172 55% 0.001

Total One Step TORCH IgM 45 14% 268 86%

References: Hamad, N.R. (2009). Epidemiology and comparison between the efficacy of different techniques for Amedi A. H. 2013. Serological screening for TORCH diagnosis of Trichomonas vaginalis and Toxoplasma infections among pregnant women in gondii among women in Erbil Province-Iraqi Duhok. M.Sc. thesis. College of Medicine, Kurdistan. PhD. Sc. Dissertation, collage of science, University of Duhok. University of Salahaddin. Amin, KY, Taher HJ and Rasul MH (2012) Screening Kumar V, Abbas AK, Fausto N, Aster J, 2009. IgM and IgG against cytomegalovirus, rubella and Robbins &Cot ran, Pathologic Basis of Disease (8th toxoplasma infections among spontaneous Edition). Philadelphia PA: Elsevier, p. 480. miscarriages in Maternity Teaching Hospital- Li S, Cui L, Zhao J, Dai P, Zong S, Zuo W, Chen C, Jin Erbil province.3rd International conference for H, Gao H, Liu Q (2011). Seroprevalence of Medical sciences proceeding Book vol.(I) Toxoplasma gondii infection in female sterility Areej-A-Jabbar. (2012) Positive serological markers patients in china. The journal of parasitology ,97, associated with infertility. Across sectional study on 529-530. 50 couples. Journal of Babylon university .3(20):931- Maruyama Y, Sameshima H, Kamitomo M, Ibara S, 414-El-Tantawy, N., Taman, A.and Shalaby, H. Kaneko M, Ikenoue T, (2007): Fetal manifestations (2014) “Toxoplasmosis and female Infertility: Is and poor outcomes of congenital cytomegaloviruses there a Co-Relation?” American Journal of infection: possible candidates for intrauterine Epidemiology and Infectious Disease, Vol. 2, no. 1: antiviral treatments. J Obest Gynae.; 33:619-3. 29-30.doi: 10.12691/ajeid-2-1-6. Cabe R, Remington JS. (1988) Toxoplasmosis: the time Franca CM, Mugayar LR (2004). “Intrauterine has come. N Eng1 J Med; 318:313 infections: a literature review”. Spec Care Dentist Mohammad, EA, Salman, YJ (2014). Study of TORCH 24(5):250-3. infections in women with bad obstetric history, Int.J. Guyton, A.C., Hall, J. E (.2006). Textbook of Medical Curr. Microbiol.App.sci; 3(10)700-709. Physiology, 11 th edn.W. B Saunders Company, Salman, J.Y(2014). Correlation between Toxoplasma Philadelphia: Pp.1011-1026 gondii and anti-mullerian hormone levels in sera of 156 Mawlood H. et al. /ZJPAS: 2017, 29 (2): 151-156

women in Kirkuk city using Elisa method. Int.J. Terpsidis, K.I, Papazahariadou, M.G.; Taitzoglou, I.A.; Curr.App. Sci 3(10)85-9 Papaioannou, N.G.; Georgiadis, M.P. and Srirup, A. Pal; Nibedita, Das and Pal, D., (2011). Sero- Theodoridis, I.Th.(2009) Toxoplasma gondii: Prevalence and risk factors of T. gondii in pregnant Reproductive parameters in experimentally infected women in Kolkata, India. Journal of recent advance male rats.EXP. Parasitol., 121:238-241. in applied science (JRAAS) V. (26): Pp.27-33 Stahl W, Kaneda Y, Noguchi T. (1994) Reproductive failure in mice chronically infected with Toxoplasma gondii. Parasitology research, 22-28.

1 ZANCO Journal Hasan D etof al./ZJPAS: Pure and 2017, Applied 29 (2): Sciences 157-165 The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 157-165

http://dx.doi.org/10.21271/ZJPAS.29.2.17

Real-time data acquire from multiple Accelerometers and IMU to calculate 3-direction angles and relative orientation

1Dler Salih Hasan, 2Carl Crane III, 3Ibrahim Isamel Hamarash 1 Department of Mechanical Engineering, College of Engineering, Salahaddin University-Erbil, Kurdistan, Iraq 2Department of Mechanical and Aerospace Engineering, College of Engineering, University of Florida, Florida, USA

3Department of Electrical Engineering, College of Engineering, Salahaddin Uiversity- Erbil, Kurdistan, Iraq

A R T I C L E I N F O A B S T R A C T

Article History: Measuring human body kinematics using inertial measurement unit Received: 25/10/2016 (IMU) has increased in popularity as its flexibility, cheap and ease of use, Accepted: 28/12/2016 compared to alternative strategies. In this work estimation of Elbow joint Published: 07/06/2017 angles was done in three directions based on 9-DOF IMU and three ADXL- Keywords: 345 accelerometers. A special wearable sensor system was designed that Robotics, can be mounted on the human body to obtain information on human arm Inertial Sensors movement, the firmware was developed to capture accurate data using Kalman Filter Arduino UNO.As the outcome data is huge a program has been developed Joint Angles using C# to capture the data from two links. A mathematical model was Rotational Matrix devloped and coded with Matlab software to estimate three direction angles and relative orientation based on the data collected from the sensors. The *Corresponding Author: Kalman filter is applied to the IMU data and adapted to work with the Dler S. Hasan circuit adequately .Also, low pass filters applied to the Accelerometers data. Three directions joint angle has been estimated and rotational matrix [email protected] for the model is formulated.

attempt to develop intelligent machines that can 1. INTRODUCTION easily be integrated into the environment (Jiang The use of robots as intelligent providers & Deng, 2014). In the other way, the use of of support for humans is not a new concept as it sensors has transformed robots into machines is widely apply in varietiessectors in industrial that can easily interact with humans in the real- technology and daily life. Technological life situation. As such, studies indicate that advancements have led to expansive research understanding robot operation system is a and development in the robotic sector in an 158 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165 significant aspect of understanding the measurements of the direction of the Earth’s mechanical manipulation of such systems. In magnetic field. (Yadav and Bleakley, 2014) addition, understanding aspects such as In a research study by (Kanjanapas, movement of robot joint has contributed to the 2014) an upper extremity motion capture system development of knowledge regarding human is proposed based on inertial sensing. The IMU movement and other complex tasks perfumed sensor is used to obtain raw sensing data of by the human body (Luinge, 2002). The most triaxial acceleration, Magnetometer, and beneficial results in understanding human Gyroscope. To discard the noise in movement is the possible improvements in accelerometers, drift in gyroscopes, and methods of treatment in terms of improving the magnetic distortion in magnetometers, a time- mobility of individuals with motor functions varying complimentary filter is proposed. A ‘problems, and developing a technique for research by (Bae and Jung, 2014) applied the improving athletes’ performance. Study compensation method for an accelerometer to conducted by (Wieser M., 2009) contributed to calculate acceleration data precisely when a the ambitious goal to develop service robots that robot manipulator in slow motion. Although the autonomously accomplish complex tasks in accelerometer works good when a robot mainly unrestricted environments. The purpose manipulator is in fast motion, Accelerometers of service robots is actually to help humans in provide relatively inaccurate acceleration data recurring and tedious ordinary tasks. under slow movements. Inertial measurements is a method Research by (Vikas and Crane, 2011). designed to measure the joint angles and angular indicates that techniques used in estimating acceleration of a body without the requirement orientation provide the angular velocities of a of an external reference. (Lawrence, 1998). joint. Such findings are obtained using Inertial Measurement Units (IMUs) are a Inclinometer (VDI) which is non-contact combinations of different inertial sensor sensors. The use of a sensor that arranges the technologies, including accelerometers, accelerometers’ and gyroscopes symmetrically gyroscopes and sometimes magnetometers, to and measures all the joint parameters deliver an precise estimation of Parameters. instantaneously eliminates the use of filtering Gyroscopes provide estimation of the angular techniques as they do not have integration error velocity applied to the body and thus an accumulation. In this study, the constraint estimation of the rotated angle and actual eliminated by the instantaneous measurement of orientation Since gyroscopes have different joint parameters using gyroscopes and sources of dynamic drift, the estimation of accelerometers’ data enables the researcher to orientation deteriorates with time. To correct measure the angular acceleration and angular these effects, accelerometers and velocity of a joint without the use of any magnetometers are added to the sensor through filtering technique. data fusion algorithms so that external references are provided for drift correction. To improve the accurate of the IMU Accelerometers measures the direction of the sensor, several scholars had developed some gravity vector, and magnetometers provide filtering approaches such as a complementary 159 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165 filter and extended Kalman filter (EKF), They are always in a standby mode in a small however, most of the preceding research works profile package to detect shake, tap, orientation, focused on filtering algorithm design, but few double tap and also to measure acceleration and researchers proposed how to practically tilt. They detect high accurate motion for calibrate the IMU sensor leading to one of the augmented e-readers, medical, smartphones and challenging points facing IMU sensor also the portable navigation devices. After the (Kanjanapas, K. 2014), (Vladimir K. and design of the circuit board. The Arduino sketch Michal R. 2012). was developed to read data from both links simultaneously and all data present is filtered. 2- SYSTEM DESIGN AND Two types of filters are used in the Arduino IMPLEMENTATION sketch, the Kalman filter and the low pass filter. In this research circuitry system and an algorithm have been designed and implemented. The aim of the circuit board is to derive and read data from both the human body and the robotic links comprising of double links. The proposed system can be worn as shown in fig. 1. For each link, one Arduino microcontroller is used with three 3-axis 345 ADXL Adafruit accelerometers and one nine degrees Adafruit IMU. Current Arduino microcontrollers are not capable of reading three accelerometers at the same time. Thus, four channel I2C Multiplexer (MUX) is introduced which extend the The Kalman filter also referred to as the Linear capability of the Arduino microcontroller to Quadratic Estimation (LQE) is an algorithm, address four devices that have the same address. designed with a series of measurements Since there are six accelerometers which are observed overtime that contain statistical data using the same address two MUX are needed. which gives more precise estimates, of The designated board used two Arduinos. Each unidentified variables than those provided by a MUX is therefore directed to each link and single measurement (Arasaratnam, I., & Haykin, connected to it the three accelerometers on that S. 2008). link. Also, two IMU was used which are Figure 2: Low Pass Filter Applied on Accelerometer connected directly to the Arduino Data. microcontroller each one for a link. The Whereas the low pass filter is used in functional block diagram of proposed system is passing signals with a lower frequency than of shown in Appendix 1. the stipulated cutoff frequency. The fig. 2 shows Figure 1: wearable sensor system to capture data a sample of the accelerometer data from our The accelerometers have fast time system filtered with low pass filter in three axis response routines and operate on low voltages. x, y and z. The design of the low-pass filter is 160 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165 among the factors that determine the amount of 3. Mathematical model attenuation allocated to each frequency (Baselli Consider two rigid bodies that share a et al., 2001). common point Q as shown in Fig.1.Such a situation will exist if the two bodies are Hence the low pass filter is applied in connected by a ball-and-socket joint, a Hooke the accelerometers and the Kalman filter is joint, or a revolute joint. applied in the inertia measurement units as programmed with the Arduino sketch. The two The orientation relationship between Arduino were then connected together, one to coordinate systems and as represented by a act as the master and the other one to act as a real matrix let as say . slave microcontroller, they were then connected to the PC with a serial port. Assume that a is a coordinate system This method is failed due to huge with respect to the global coordinate amounts of data transfer in real time. There are system. It is described by transformation matrix 27 data in each link, involved in the transfer processes between the PC and the Arduino in each time-step, where both Arduino are connected using two serial ports. The method would have been a success but after a computer program was developed using C#to capture huge data simultaneously in real time.

Figure. 3: shows three3-axis accelerometers and one 9 DOF IMU attached to each body.

Similarly, assume that the orientation of the coordinate system with respect to the global coordinate system is described by transformation matrix .

A vector with components in the system has global components s,

161 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165

A positive pitch angle is defined to be The global components of vector , can be clockwise rotation about the positive Y-axis. transformed in terms of the coordinate system as follows:

Note that: After transformation: If and

then Or it may be written as: If and

then

Where Heading: Rotation around the Z-axis

The product or is the transformation A positive heading angle is defined to be clockwise rotation about the positive Z-axis. matrix from to coordinate system.

One method for determining the nine direction cosines that describe the orientation of a body-fixed coordinate system with respect to the reference coordinate is to use Joint angles. The output data from the sensors are used If, then the elements of the transformation together with the mathematical model above, matrix can be computed, we can calculate the the results of the Roll, Pitch and Heading for the joint angles of both coordinate systems. body A are shown in Fig.4.

The orientation based on accelerometer The average results of the body A are and magnetometer data for the Roll, Pitch and Heading is calculated as follows: i. roll angle is 174.20 degree. ii. pitch angle is -25.44 degree. Roll: Rotation around the X-axis iii. heading angle is 168.42 degree.

A positive roll angle is defined to be clockwise rotation about the positive X-axis.

where: , are returned value from accelerometer sensor.

Pitch: Rotation around the Y-axis 162 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165

And the Rotation Matrix is given by: Figure 4: Joint angles for Body A.

The output data from the sensors are used together with the mathematical model above, the results of the Roll, Pitch and Heading for the The above matrices are calculated for bodies A body B are shown in Fig.5. and B as follows: Body A

On average rotation matrix for body A is:

Figure 5: Joint angles for Body B The average results of the body B are

i. roll angle is -86.01 degree. ii. pitch angle is 39.02 degree. iii. heading angle is 157.88 degree.

The Joint angles rotational matrix for Roll, Pitch and Headings are as follows:

163 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165

Body B sensors (four sensors in each link). The data fusion of these sensors contributes to increase of On average rotation matrix for body B is: accuracy of the data thus the accurate estimation of the results.The real-timereading hardware model designed is wearable for both human body and robot manipulator also it is easy to use. Simultaneous results from the designed application also is very precious as it depends on the multiple accelerometers and IMU. The developed technique uses direct angles measurement and relative orientation bypassing the use ofmathematical integrations. Also, Three accelerometers and one IMU have been implemented that attached to the links. The model critically evaluates the robotic phenomenon. The model is also avoiding the use of mathematical derivatives of sensed data which reduces the effect of sensor noise on the calculations critically.

REFERENCES: Arasaratnam, I., &Haykin, S. (2008). Square-root quadrature Kalman filtering. Signal Processing, IEEE Transactions on, 56(6), 2589-2593 Finally, the orientation matrix from B to A Bae, Y. and Jung, S. (2014). Compensation for Position coordinate system is given as: Control of a Robot Manipulator Using a Modified Disturbance Observer (DOB) based on an Accelerometer.Journal of Institute of Control, Robotics and Systems, 20(6), pp.651-656. Dierks, T., Thumati, B. T., &Jagannathan, S. T. (2010). Fault Tolerant Control of Nonholonomic Mobile Robot Formations. In Rigatos G. (ed) Intelligent Industrial Systems: Modeling, Automation and Adaptive Behavior. Harshely, PA: IGI Global. Ghassemi, F., Tafazoli, S., Lawrence, P., &Hashtrudi- Zaad, K., (2007). ‘Design and calibration of an integration free accelerometer-based joint- anglesensor’ .IEEE Transactionson Instrumentation and Measurement, New York, USA: IEEE press57(1), 4. CONCLUSION pp. 150–159. The existing gap regarding the calculation of Jiang, L., & Deng, M. (2014). Support Vector Machine robotic parameters and understanding Based Mobile Robot Motion Control and Obstacle kinematics and dynamics in robotic motion will Avoidance. Robotics: Concepts, Methodologies, be filled by using a multiple instantaneous Tools, and Applications , Hershey PA: IGI Global 164 Hasan D et al./ZJPAS: 2017, 29 (2): 157-165

Kanjanapas, K. (2014). Human Mechatronics Wieser, M. (2009). Hierarchical Memory Organization of Considerations of Sensing and Actuation Systems for Multimodal Robot Skills for Plan-based Robot Rehabilitation Application. Ph.D. Berkeley, CA. Control. Ph.D. Hamburg. Luinge, H. (2002). Inertial Sensing Of Human Movement. Vladimir K. and Michal R.. (2012) “Complementary PhD. Twente University. filtering approach to orientation estimation using inertial sensors only”. Robotics and Automation Lawrence, A. (1998). Modern inertial technology. New (ICRA), 2012 IEEE International Conference on. York: Springer. IEEE. pp.599–605. Vikas, V., & Crane, C. D., (2011). ‘Inclination parameter Yadav, N. and Bleakley, C. (2014). Accurate Orientation estimation for manipulator and humanoid robot links’ Estimation Using AHRS under Conditions of .In ASME International Design Engineering Technical Magnetic Distortion. Sensors, 14(11), pp.20008- Conference, ASME. San Diego, USA: ASME. pp. 20024. 1177-1183

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Appendix 1 : The Functional Block Diagram of the Proposed System

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2016), 28 (5); 166-176 http://dx.doi.org/10.21271/ZJPAS.29.2.18

Pelvic organ prolapse at Maternity Teaching Hospital in Erbil city, its prevalence

and risk factors 1 2 Suzan K. Younus and Serwa R. Al-Dabakh 1 Department of Gynecology and Obstetrics, Maternity Teaching Hospital, Erbil-Iraq. 2Department of Gynecology and Obstetrics, College of Medicine, Hawler Medical University, Erbil- Iraq

A R T I C L E I N F O A B S T R A C T

Article History: Abstract Received: 01/09/2016 The present study is carried out to describe the prevalence rate of pelvic Accepted: 02/01/2017 Published: 07/06/2017 organ prolapse (POP) among women in Erbil city, to compare the prevalence Keywords: between normal vaginal delivery and cesarean section and to find out the risk Pelvic organ prolapse factors associated with POP. This study is a cross-sectional observational study (POP), POP-Q, Risk factors, carried out in Maternity Teaching Hospital in Erbil city, Kurdistan region, Erbil. north of Iraq from 1st April 2015 to 1st April 2016. It includes 510 married *Corresponding Author: Suzan K. Younus1 women aged between 15-80 years both nulliparous and multiparous, excluding [email protected] pregnant women and those in perpurium period in addition to those who underwent previous POP surgery. The data collected by using standardized Pelvic Organ Prolapsed - Quantitification system (POP-Q system) and the results were analyzed using SPSS computer software version 23.0, Chi-square test; the results were considered significant at p<0.05. The prevalence of POP was 90.2% in general. The prevalence among those who have vaginal births were 92.1%, while those who had caesarean sections were 77.3%. Generally among those 90.2% of the cases, who have prolapse, nearly half of the cases (52.9%) have both anterior and posterior vaginal wall prolapse and the 2nd stage was found to be the most common stage (39.2%). Findings of the study showed that POP is very common among women and is more so among those women who delivered vaginally than those delivered by cesarean section; those who delivered by cesarean section have a fewer degree of prolapse. The most important risk factors were . age, a high number of vaginal deliveries, occupation, history of an overweight baby, short birth gap space, history of chronic diseases and low social economic state

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1. INTRODUCTION predisposition and connective tissue disorders Pelvic organ prolapse (POP) is a may play a role in it (Buchsbaum et al., 2006; common health problem that affects hundreds Twiss et al., 2007). Factors attributing to the of women in different age groups worldwide. It development of POP includes: multiparity, affects quality of life by limiting physical, advancing age, menopause obesity, high body- social, psychological, and sexual functions to a mass index (BMI), instrumental delivery, degree that living with severe types of prolapse lifting heavy things, increasing intra-abdominal can be a challenge both physically and pressure conditions like chronic constipation, emotionally (Monga and Dobbs, 2011; chronic cough and chronic diarrhea, in addition Paudyal, 2006; Detollenaere et al., 2011; Bump to genetic predisposing factors (Buchsbaum et and Norton, 1998; Dietz et al., 2002). al., 2006; Twiss et al., 2007; Bai et al., 2002; POP is regarded as a reason for Mant et al., 1997) and connective tissue significant gynecological operations with a disorders (Bump and Norton, 1998; Thapa et high failure rate and the reoperation incidence al., 2013; Jelovesk et al. (2007). However, is about 30% (Olsen et al., 1997). In the USA vaginal delivery and aging process are regarded billions of dollars are spent annually for the as the most common risk factors according to treatment of this condition (Bump and Norton, Garshabi et al. (2006), and Dietz (2008). 1998) and regarded as the 3rd most common Although the majority of POP cases were indication for hysterectomy in menopausal asymptomatic, symptoms can be recorded only women (Pearce et al., 2008; Wilcox et al., by 10-20% of them (Sushma and Dudley, 1994). POP defined as protrusion or descent of 2010), and even when the symptoms are one or more of female pelvic organs out of present, it has no correlation with the prolapse their normal anatomical position into or out of stages and its severity. vagina (Thapa et al., 2013), including the In this research because of the lack of bladder, uterus, rectus, post-hysterectomy previously published data about prevalence of vaginal cuff, and the small bowel, causing POP among women in Erbil city an attempt urethrocele, cystocele, rectocele, enterocele and was done to report the cases, finding the utero vaginal prolapsed (Munir'deen et al., associated factors and determining the stages 2012) by using standardized POP-Q system. It is a POP may occur in up to 50% of parous new system approved by International women (Maher et al., 2010). However, Continence Society (ICS) (Bump and Norton, nulliparous women cannot be excluded from 1998). It is validated by inter-system developing this disease in which genetic association and an inter-examiner agreement in 168 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

a small-scale study by Swift et al. (2006). This to deal with such conditions and finding better study was done to report the findings in a ways of management to increase the quality of standardized fashion, help the health carriers to life of affected women both physically and find better plans about how to handle this issue emotionally. 2. Methods overweight baby and birth gap space), and 3rd part include extra questions (family history of This study is a cross-sectional the same conditions, history of chronic disease observational study conducted in Maternity and history of lifting heavy things). Teaching Hospital in Erbil city, Kurdistan region, North of Iraq from 1st April 2015 to 1st After filling the questioner, an April 2016. The study included all married examination was followed by the researchers women both nulliparous and multiparous aged for the subjects by measuring BMI and between 15-80 years who visited the thorough vaginal examination done in dorsal gynecological outpatient department for position after evaluation of urinary routine health examination. Pregnant women, incontinence. Assessment of prolapse is done women in purpurium and those who underwent by using a standard POP-Q (prolapse previous POP surgery are excluded. The quantitative examination) system, which is sample size of this study was 510 (n) women. approved by International Continence Society (ICS) in 1996. Data collected by using close-ended questioner which is designed by the According to this system, nine points researchers in a face to face interview after were measured by using wooden spatula taking permission from the subjects and giving measured in 1 cm interval and sterile assurance that the confidentiality is kept disassembled bivalve speculum after throughout the study by using code for each performing maximal valsaval effort except for individual. In addition of explaining for them the total vaginal length. For the classification that the research is only for academic of POP, Bump et al. (1996) was used (Fig. 1). purposes. Based on the obtained 9 points results, the stages of POP were determined as follow: The questioner consists of three parts: 1st part include demographic data (name, age, Stage 0: No prolapse; anterior and posterior BMI, occupation, education level and social points are all −3 and C (cervix) or D (posterior status), 2nd part include obstetric history (age at fornix) is between −TVL (total vaginal length) first pregnancy, parity, mode of delivery, place and − (TVL − 2) cm. of birth, complications during labor, history of 169 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

Stage 2: The most distal prolapse is between 1 cm above and 1 cm below the hymeneal ring (at least one point is −1, 0, or +1). Stage 3: The most distal prolapse is > 1 cm below the hymeneal ring but no further than 2 cm less than TVL.

A point on the The most Most distal edge Stage 4: Represents complete vault eversion; anterior vaginal dependent point of cervix or the the most distal prolapse protrudes to at least wall, 3 cm of the upper leading edge of (TVL − 2) cm. proximal to the anterior vaginal vaginal cuff 3. Results: external wall; from C During the period of the study, 510 urethral meatus vaginal fornix Aa to Point Aa women examined for the presence of POP, 460 Ba women have some degree of prolapse, giving A point at The most A point represents the prevalence of 90.2%. Table 1 shows the posterior dependent point the location of the frequency of POP according to the type of vaginal wall, 3 of the upper posterior fornix child births. The result showed that the cm proximal to posterior the hymen vaginal wall; D frequency was greatest among those who had from vaginal vaginal births (80.87%) than those who had Ap fornix to point caesarean deliveries (14.78 %), while it was the Ap least among nulliparous women (4.35%). Bp Table 1. Frequency of POP for the Middle of the Posterior The greatest external margin of the depth of the present study urethral meatus genital hiatus to vagina to the posterior the midanal Table 1. Frequency of POP for the present study midline hymen opening Type of Delivery Prolaps No Prolaps Total tv1 gh Vaginal delivery 372 20 392 pb Cesarean section 68 20 88 Nulliparous 20 10 30 Figure 1. Convenient scheme for determining Total 460 (90.2%) 50 (9.8%) 510 the nine points (Bump et al., 1996), abbreviations as shown in the table Stage 1: The criteria for stage 0 are not met, and the most distal prolapse is > 1 cm above the level of the hymen (< −1 cm). 170 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

Generally among those 90.2% of the while the least one was posterior vaginal wall cases who have prolapse, the most frequent prolapsed (2%) as shown in Table (2). type of POP was combined anterior and cesarean section could not be regarded as a posterior vaginal prolapsed (52.9%) , followed protective factor by anterior vaginal wall prolapsed (32.9%),

Table 2. Type of prolapse for the present study

Anterior Posterior All Anterior and Total No Types of prolapse posterior Prolapse Present study 168 (32.9%) 10 (2%) 12 (2.4%) 270 (52.9%) 460 (90.2%) 50 (9.8%) 4. Discussion The obtained results for other risk factors are The obtained data from the present shown in the table (3). The mean age of women study showed that 90.2% of the populations of in this study was 38.1±11.8 years. In this study Erbil city have some degree of prolapse. This the factors which had significant relationship result is consistent with that of Swift et al. with POP were age, occupation, number of (2003) in which the prevalence rate of POP vaginal delivery, low social economic state, was 92.6%. This result is also supported by the number of caesarean section, history of results obtained by Nygaard et al. (2008) overweight baby, short birth gap space and (97.9%), Swift (2000) (93.6%) and Direkvand- history of chronic diseases. Age regarded a Moghadam et al. (2014) (80.8%). strong risk factor which showed that whenever Vaginal delivery is one of the causative it increases the frequency increases (p<0.006). agents of POP (Dietz and Korda, 2005). POP Whenever the number of vaginal delivery shows to be more common among women who increases the rate of POP will increase delivered by normal vaginal delivery than those especially in those who had more than four delivered by cesarean section which are also deliveries (p<0.001). supported by the study results of Patel et al. The history of overweight baby also (2006). Although those who delivered by was regarded as a causative agent in addition to cesarean also having a degree of prolapse, but complications during delivery. Smoking is in lower frequency, and that is why cesarean regarded as a non-causative agent, while delivery could not be regarded as a protective factor as proved by Brazilian study done by Rodrigues (2009). In addition, 66.67% of . nulliparous women of the present study had 175 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

POP. Dietz et al. (2004) declared a significant congenital contribution in these cases. This study showed that nearly half of the examined women have both anterior and posterior type of prolapse at the same time.

This is supported by a study done in Ethiop by (2000), Swift et al. (2001; 2005), Dietz and Akmel and Segani (2012). Our results showed Korda (2005), Garshabi et al. (2006), Kim et that the anterior vaginal wall prolapse was al. (2007), Lemack et al. (2007), Onowhakpor more common than the posterior type of et al. (2005), Akmel and Segani (2012) and prolapse which agrees with data obtained by Direkvand-Moghadam et al. (2014); Neuman and Lavy (2007) and Scherf et al. meanwhile, Dietz (2008) demonstrated that the (2002). age has a limited role in developing POP. Among those 90.2% of the cases who Stanton (1999) and Campbell and Monga have prolapse, 26.3% have the 1st stage (2000) stated that estrogen deficiency in prolapse, 39.2% have the 2nd stage prolapse, menopause women which results fascia and 1.2% have the 3rd stage prolapse, 2.4% have connective tissue weakness and collagen loss, the 4th stage prolapse and 21.2% have is also a potential factor for POP. Menopause combined stage of prolapse (Table 4). The was found to be a potent risk factor for this latter represent the women who have both study (n=84). This is also proved by Lukman anterior and posterior vaginal wall prolapse at (1995), Onowhakpor et al. (2005), Garshabi et the same time. Stage 2 was found to be the al. (2006) and Kim et al. (2007). POP found to most common stage of prolapse (39.2%) (Fig. be more common in reproductive age group 2). This result is supported by similar results (20-35 years) than other age groups (Fig. 2). reached by Swift (2000) and Norton et al. The most important risk factor for (2014). developing POP was found to be pregnancy, Age is regarded as an accusative agent parity and the number of vaginal deliveries in developing POP and is accepted to be an (Mant et al., 1997; Samuelson et al., 1999; established risk factor (Jelovsek et al., 2007). Sajan and Fikree, 1999; Swift, 2000; Dietz and This is statistically proved by our data and Korda, 2005; Patel et al., 2006; Garshabi et al., agreed with many studies done by Swift 2006 and Direkvand-Moghadam et al., 2014)

in which there will be more weakness in pelvic Figure 2. Stages of POP associated organ support due to damage to the nerve, with different age groups for the present fascia and muscle of the pelvic floor as the study 176 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

number of vaginal deliveries increase (Allen et an extra extension of pelvic fascia and al., 1990; Gurel and Gurel, 1999; Kim et al., weakening of supportive ligaments. This is in 2007). It appears that the women with greater consistent with the results of Gurel and Gurel parity and more vaginal deliveries have higher (1999), Swift (2000) and Garshabi et al. POP stage. Our data shows a strong (2006). relationship between these factors and POP and Statistically, the history of chronic its ratio showed to be doubled (64.5%) in those diseases (e.g., cough, constipation and who had more than four deliveries comparing diarrhea) shows a significant relationship with to those who had <4 vaginal deliveries POP (P<0.04). This agrees with the results of (35.5%). an Iranian study done by Arya et al. (2005) and Occupation is one of the analyzed data Direkvand-Moghadam et al. (2006). that have a positive relationship with POP. A negative association was observed However, most of the women in this study between smoking and POP in the present study. were unemployed (housewives) which is in This is consistent with the results of Swift et al. agreement with the results of Swift et al. (2005). This is also proven by Bump (1993) (2005) and Akmel and Segani (2012). They meanwhile; Miedel (2009) proposed that stated that house wives are more prone to smoking correlate positively with POP. develop the disease and statistically it was Studied POP found that 57.27% were significant (p<0.001) due to the nature of heavy their first pregnancy under the age of 20 years, working styles and large size family numbers which agrees with the results of a study done in in this area. The same results also obtained by Nepal by Thapa et al. (2013). studies done in Sweden by Samuelson et al. Operative vaginal delivery discussed by (1999) and Nepal by Thapa et al. (2013). other studies is not practiced in this study due A study done in Serbia by Mladenovic- unavailable data and limited use of forceps and Segadi (2010) proposed that overweight vacuum in our working field. especially those who have BMI > 30 have Swift et al. (2005) described the risk of higher risk POP. The same results accepted by jobs involving a lot of lifting with POP. They Swift et al. (2003) and Iranian study done by found that those employees who are heavy Garshabi et al. (2006). The current study shows lifters including housewives and laborers are that 52.61% of those with BMI >30 have POP. more likely to undergo correction operation. Another risk factor that also found to Heavy working also has a positive association have a positive relationship is the weight of the as proven by Thapa et al. (2013). Heavy baby. Deliveries with babies more than 4 kg working during pregnancy and perpartum weight have a higher degree of prolapse due to proved to be strongly associated with POP in a 177 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

study done by Bonder-Adler et al. (2007). He require stronger strategies of managements to found that 84% of women with prolapse are provide a better quality of life for women and heavy workers during pregnancy and 87% of to help clinician about how to determine them during the postpartum period. The same consistent frequency of POP and to define the results are proven by Nigerian study done by true pathological conditions. Onowhakpor et al. (2005). The present study This high POP rate in our community is data shows that 85.65% of those lifting heavy due to high parity, short birth space, and low things have POP. educational level as the majority of candidates Complications during delivery (prolong were illiterate, with few of high school or labor pain, heavy bleeding, difficulty during university level education and most of them placenta delivery and birth injury) showed were housewives with poor economic state and positive relationships with POP in this study; without personal outcome. Effective plan is the same results were obtained by Onowhakpor needed for increasing health education leading et al. (2005), Akmel and Segani (2012) and to decreasing the family size by using Thapa et al. (2013). contraceptive; which is better to be cost free for Home delivery showed by many studies every woman as is the case in developed as an added factor for POP (Gurel and Gurel, countries. In addition to that improving the 1999; Garshabi et al., 2006; Akmel and Segani, quality of life is essential through good 2012). In this study the relation shows to be nutrition, regular exercise and avoiding heavy significant. This is not related to the place of works. It is also recommended to increase the delivery, but is directly related to the lack of quality of services in delivery centers which the hand-skilled trainer at home. will help to decrease the rate of POP. It is worth noticing that the present work is explaining the distribution of POP in our population depend on correlations between physical findings with POP without consideration of symptomatic state of the object. 5. Conclusions and Recommendations The POP rate for women who delivered vaginally is nearly six times more compared to those who delivered by caesarean section operation and 86.7% of the subjects had stage 1 or/and 2 prolapse. These surprising results 178 Younus S and Al-Dabakh S /ZJPAS: 2016, 28(5): 166-176

Table 3. Various risk factors for pelvic organic prolapsed for the present study (n=510) Risk factor Prolapse No prolapse P value Age group <20 12 (2.61%) 2 (4%) 0.006 20-35 182 (40.63%) 30 (60%) 36-45 132 (49.62%) 14 (28%) >45 134 (29.13%) 4 (8%) BMI <18.5 2 (0.43%) 0 (0%) 0.064 18.5-24.9 50 (10.87%) 10 (20%) 25-29.9 166 (36.09) 10 (20%) ≥ 30 242 (52.61%) 30 (60%) Educational level Illiterate 220 (47.83%) 16 (32%) 0.213 Read and write 66 (14.35%) 8 (16%) Primary 82 (17.83%) 10 (20%) Secondary 66 (14.35%) 12 (24%) University 26 (5.65%) 4 (8%) Occupation Employed 44 (9.57%) 12 (24%) 0.001 Unemployed 416 (90.43%) 36 (72%) Retired 0 (0%) 2 (4%) Social economic state High 2 (0.43%) 2 (4%) 0.015 Medium 120 (26.09%) 16 (32%) Low 338 (73.48%) 32 (64%) Smoking habit Smoker 52 (11.3%) 6 (12%) 0.883 Non smoker 408 (88.7%) 44 (88%) No. of viginal delivery 0 20 (5.1%) 10 (33.33%) 0.001 1 to 4 132 (33.67%) 14 (46.67%) 5 to 8 140 (35.71%) 6 (20%) >8 100 (25.51%) 0 (0%) No. of caesarean section 1 18 (26.47%) 4 (20%) 0.018 2 34 (50%) 4 (20%) 3 6 (8.82%) 4 (20%) >3 10 (14.71%) 8 (40%) Place of birth Hospital 268 (60.91%) 34 (85%) 0.003 Home 172 (39.09%) 6 (15%)

Complications during delivery Yes 88 (20%) 10 (25%) 0.453 No 352 (80%) 30 (75%) Types of complications Prolong labor pain 26 (28.89%) 0 (0%) 0.068 Heavy bleeding 38 (42.22%) 8 (80%) Difficulty of placental delivery 12 (13.33%) 0 (0%) Birth injury 14 (15.56%) 2 (20%) History of overweight baby Yes 144 (32.73%) 6 (15%) 0.021 No 296 (67.27%) 34 (85%) Birth gap space < 2 years 288 (65.45%) 10 (25%) 0.001 ≥2 152 (34.55%) 30 (75%) History of lifting heavy things Yes 394 (85.65%) 40 (80%) 0.286 No 66 (14.35%) 10 (20%) History of chronic disease No disease 208 (45.22%) 22 (44%) 0.046 Cough 2 (0.43%) 2 (4%) Constipation 244 (53.04%) 26 (52%) Diarrhea 6 (1.3%) 0 (0%) Age at first pregnancy <20 252 (57.27%) 24 (60%) 0.256 20-35 186 (42.27%) 16 (40%) 36-45 2 (0.45%) 0 (0%)

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Table 4. Stage of prolapse for the present study compared to other studies Stage of prolapse 1st 2nd 3rd 4th Combined* No Prolapse Present Study 134 200 6 12 108 (21.2%) 50 (n=460) (26.3%) (39.2%) (1.2%) (2.4%) (9.8%) Swift (2000), (n= 43.3% 47.7% 2.6% 0% 6.4% 497) Swift et al. (2005), 38% 35% 2% 0% 24% (n= 1004) Garshabi et al. 23.1% 18.3% 11.6% 47% (2006), (n= 3730) * Those who have both anterior and posterior prolapse in stage 1 and 2.

Acknowledgments tissue abnormalities in Korean women, Journal of Reproductive Medicine, 47, 231-234.

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Pathophysiology of pelvic organ prolaps and (eds.), Obstetrics and Gynecology: an evidence stress urinary incontinence, Indian Journal of based text for MRCOG, Britain Arnold, British, Urology, 22, 310-316. pp. 725-734. Paudyal S., 2006. Prevalence of Uterine prolapse Swift S., Woodman P., O'Boyle A., Kahn M., among married women in Slum area at Valley M., Bland D., Wang W. and Schaffer J., Thapathali, Kathmandu. Master thesis, 2005. Pelvic Organ Support Study (POSST): the Tribhuvan University. distribution, clinical definition, and Pearce M., Swift S. and Goodnight W., 2008. epidemiologic condition of pelvic organ support Pelvic organ prolapse: is there a difference in defects, American Journal of Obstetrics and POPQ exam results based on time of day, Gynecology, 192(3): 795-806. morning or afternoon? American Journal of Swift S.E., 2000. The distribution of pelvic organ Obstetrics and Gynecology, 199: 200.e1-5. support in a population of female subjects seen Rodrigues A.M., de Oliveira L.M., Martins Kde F., for routine gynecologic health care, American Del Roy C.A., Sartori MG, Girao M.J. and Journal of Obstetrics and Gynecology, 183(2), Castro Rde A., 2009. Risk factors for genital 277-285. prolapse in a Brazilian population, The Revista Swift S.E., Pound T. and Dias J.K., 2001. Case- Brasileira de Ginecologia e Obstetrícia, 31(1), control study of etiologic factors in the 17-21. development of severe pelvic organ prolapsed, Sajan F. and Fikree F.F., 1999. Perceived International Urogynecology Journal and Pelvic gynecological morbidity among young ever- Floor Dysfunction, 12(3), 187-92. married women living in squatter settlements of Swift S.E., Tate S.B. and Nicholas J., 2003. Karachi-Pakistan, Journal of the Pakistan Correlation of symptoms with degree of pelvic Medical Association, 49, 92-97. organ support in a general population of women: Samuelsson E.C., Victor F.T.A., Tibblin G. and what is pelvic organ prolapsed? American Svardsudd K.F., 1999. Signs of genital prolapse Journal of Obstetrics and Gynecology, 189, in a Swedish population of women 20 to 59 372-377. years of age and possible related factors, Thapa S., Angdembe M., Chauhan D. and Joshi R., American Journal of Obstetrics and 2013. Determinants of pelvic organ prolapse Gynecology, 180, 299-305. among the women of the western part of Nepal: Scherf C., Morison L., Fiander A., Ekpo C. and A case-control study, Journal of Obstetrics and Walraven G., 2002. Epidemiology of pelvic Gynecology Research, 40(2), 515-520. organ prolapse in rural Gambia-West Africa, Twiss C., Triaca V. and Rodriguez L.V., 2007. British Journal of Obstetrics and Gynecology, Familial transmission of urogenital prolapse and 109 (4), 431-436. incontinence, Current Opinion in Obstetrics and Stanton S. L., 1999. Vaginal prolapse. In: Edmonds Gynecology, 19, 464-468. D.K. (ed.), Dewhurst's Textbook of Obstetrics Wilcox L.A., Koonin L.M., Pokras R., Strauss L.T., and Gynecology for Postgraduates, 6th edition, Xia Z. and Peterson H.B., 1994. Hysterectomy Blackwell Sciences, pp. 462-473. in the United States, 1988-1990, Obstetrics and Sushma S. and Dudley R., 2010. Urogenital Gynecology, 83, 549-555. Prolapse. In Luesley D.M. and Baker P.N.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 177-195 http://dx.doi.org/10.21271/ZJPAS.29.2.19

Operation Analysis and Capacity Improvement of Signalized Intersections Using TRANSYT-7F-Case Study

Shamil A. Flamarz

Building and Construction Engineering Department, University of Garmian, Kalar, Sulaimaniya, Kurdistan Region, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: Signalized intersection operation performance evaluation provides Received: 04/12/2016 important and valuable knowledge about the performance of the city Accepted: 19/01/2017 transportation network or system, where signalized intersections are major elements and critical points within the city transportation network. Published: 07/06/2017 The capacity and operation performance of signalized intersections as Keywords: part of the transportation network is very important and more significant Capacity improvement because the signalized intersections often control the ability of the city Optimization run streets and transportation network to accommodate the traffic volumes. The objective of the present study is operation analysis and capacity Signalized intersection improvement of Shahid Hama Rash and Sherai Naqib signalized TRANSYT-7F intersections in Kalar City by suggesting number of intersection capacity improvement scenarios, and investigates the proper scenario among the suggested scenarios to improve the traffic capacity. The required data for *Corresponding Author: the study purposes like existing geometric design (using field Shamil A. Flamarz observation) and traffic volumes (using video records through the cameras installed at both intersections) were collected. The results of this [email protected] study revealed that Shahid Hama Rash and Sherai Naqib signalized intersections currently operating under congested and low performance conditions, and the suggested intersection capacity improvement scenarios provide reasonable and proper solutions to improve the capacity of the selected signalized intersections. The combination the first and second improvements has a significant impact on increasing the capacity and improving the quality of operation for both intersections, where the degree of saturation for Shahid Hama Rash reduced from 124% to 83% and the intersection level of service (LOS) changed from F to level of service (LOS) C, and the degree of saturation for Sherai Naqib intersection reduced from 126% to 66% and the intersection level of service (LOS) changed from F to level of service (LOS) D.

1. INTRODUCTION governed by intersection capacity. The lack of Signalized intersections are critical surface space for roads in cities and the elements of an urban road transportation continuously increasing traffic demand, both system and maintaining these control systems are challenging traffic engineers towards all at their optimal performance for different type of improvements in traffic management to demand conditions has been the primary make existing infrastructure more efficient concern of the traffic engineers (Borkloe, (Tovar, et al., 2010). 2013). Urban traffic networks are highly 178 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Capacity of a road is represented by the signalized intersection. Control delay includes maximum rate at which vehicles can pass initial deceleration delay, queue move-up time, through a given point in an hour under stopped delay, and final acceleration delay prevailing operational conditions. The number (TRB, 2000). and width of lanes, grades, and lane use allocations, as well as signalization conditions ascertains the capacity of the road. The 2. OBJECTIVES OF THE STUDY measures of effectiveness, which are The objectives of this study are evaluating the commonly used to evaluate the signalized traffic operation performance in the selected intersection operations, are Capacity and congested signalized intersections through the volume-to-capacity ratio, delay, and queue estimation of the existing level of service behavior of the vehicles. Intersection capacity (LOS) using TRASYT-7F software, then or volume-to capacity ratio is one of the propose number of improvements on the signal operational measures of effectiveness used in timing and geometric design of the selected measuring signalized intersection LOS signalized intersections and measure the (Kumar, et al., 2013). influences of the improvements on its The level of service at any intersection on a capacities by re-evaluating the traffic operation highway has a significant effect on the overall performance using TRASYT-7F software. operating performance of that highway. Thus, The objectives of the present study can be improvement of the level of service at each achieved through the following steps: intersection usually results in an improvement 1- Operation analysis of two congested of the overall operating performance of the signalized intersections in Kalar City. highway. An analysis procedure that provides This can be achieved by the estimation for the determination of capacity or level of of the existing LOS using TRASYT-7F service at intersections is therefore an software for the selected signalized important tool for designers, operation intersections as a case study. personnel, and policy makers. Factors that affect the level of service at intersections 2- Evaluation of the traffic operation include the flow and distribution of traffic, the performance in the selected congested geometric characteristics, and the signalization signalized intersections. system (Garber, et al., 2009). 3- Proposing number of improvements on the signal timing and geometric design The Highway Capacity Manual of the selected signalized intersections methodology addresses the capacity, level of and measure the influences of the service (LOS), and other performance improvements on its capacities by re- measures for lane groups and intersection evaluating the traffic operation approaches and the level of service (LOS) for performance using TRASYT-7F the intersection as a whole. Capacity is software. evaluated in terms of the ratio of demand flow rate to capacity (v/c ratio), whereas level of service (LOS) is evaluated on the basis of 3. STUDY AREA control delay vehicle (in second per vehicle). Kalar city is the center of Kalar District located Control delay is the portion of the total delay in northeast of Iraq lies on Sirwan (Diyala) river, attributed to traffic signal operation for and it is one of Sulaimaniya Governorate Districts. 179 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Currently Kalar city is the center of Garmian Area • Shahid Hama Rash signalized intersection Administration, the population of Kalar City is is located on a very important commercial (197,230 persons) which represent (74%) of Kalar route that connects three governorates; District population. Diyala, Sulaimaniya and Salah Al-Din in Kalar now is in a continuous progression addition to two official border points with toward further urban expansion, infrastructural Iran. growth and economic booming, due to its location • Sherai Naqib signalized intersection is which connects Iraq, Iran and Kurdistan together, located in center of Kalar in center of Kalar can be considered as one of the most number of very important government expensive place in the entire region, economists facilities and departments such as; Sherai have classified Kalar's properties as more expensive Naqib Maternity Governmental Hospital, than many other advanced countries including Saya Private Hospital and Passports USA. The rapid increase of Kalar City population is Department. the main cause of the increasing demand for Figure. 1 is map of the city locating the transportation and mobility. This may create major operation problems especially during the peak two intersections, and for the operation periods. analysis for both Shahid Hama Rash and Sherai Naqib intersections, it is very important to As a case study two congested signalized specify the number of lanes in addition to the intersections (Shahid Hama Rash and Sherai Naqib intersections) were selected. Both intersections direction of each movement. Figures. 2, 3 have congested traffic and represent significant demonstrate the existing geometric layout for traffic facilities in Kalar City traffic system due to both intersections. the following reasons:

Figure 1: Map of the city locating the two intersections (Google Maps)

180 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Figure 2: Shahid Hama Rash signalized intersection existing geometric design (field measurements and drawing by Auto CAD)

Figure 3: Sherai Naqib signalized intersection existing geometric design (field measurements and drawing by Auto CAD)

181 Flamarz S./ZJPAS: 2017, 29(5): 177-195

4. ANALYSIS OF SIGNALIZIED The current version of TRANSYT-7F INTERSECTION USING TRANSYT-7F Release 11 (January 2008) is dimensioned to SOFTWARE RELEASE 11 accommodate a maximum of 99 intersections TRANSYT-7F is a traffic simulation and per data file. Although many cities contain signal timing optimization program. The more than 99 coordinated intersections, they primary application of TRANSYT-7F is signal are typically subdivided into much smaller timing design and optimization. TRANSYT-7F coordinated sections, with small groups (or features genetic algorithm optimization of "clusters") of intersections coordinated with cycle length, phasing sequence, splits, and one another. The software can analyze a offsets. TRANSYT-7F is the only software maximum of 7 "single-ring" signal phases per package available that combines a state-of-the- intersection, which is sufficient for modeling art optimization process (including genetic virtually any pre-timed or traffic-actuated algorithm, multi-period, and CORSIM control plan (McTrans 2008). optimization) with a state-of-the-art TRANSYT-7F is considered an "offline" macroscopic simulation model (including optimizer because the signal timing plan is queue spillback, platoon dispersion, and developed in the engineer's office, well in actuated control simulation) (McTrans 2008). advance of field implementation. Before The primary qualities of the underlying performing any optimization, a certain amount macroscopic traffic model within TRANSYT- of engineering expertise and judgment are 7F include detailed simulation of platoon required for 1) coding the input data, and 2) dispersion, queue spillback, queue spillover, calibrating the model. For a retiming project, traffic-actuated control, and the flexibility to signal timing programs should ideally be made perform lane-by-lane analysis. In addition, to reasonably replicate existing conditions in while other models are limited to analyzing 4 the field before proceeding with any or 5 intersection approaches, there is no optimization. If the model cannot reasonably practical limitation to the number of replicate existing conditions in the field, approaches that can be simulated by optimization results become less reliable. TRANSYT-7F. Explicit handling of both right- Software packages are not smart enough to hand and left-hand driving, as well as both code their own input data, and are not smart English and metric units, allow TRANSYT-7F enough to calibrate themselves to match field to be used worldwide (McTrans 2008). conditions (McTrans 2008). The primary qualities of the TRANSYT- 7F optimization process include the availability 5. DATA COLLECTION of multiple search techniques (hill-climb and genetic algorithm), numerous optimization Field observation including traffic objective functions (e.g., involving volumes, geometric data and other required combinations of progression opportunities, data was collected. The data collection is done delay, stops, fuel consumption, throughput, and manually and using video records on queuing), extensive ability to customize the workdays, in which the highest congestion and optimization process, and the ability to inefficient use of transportation system occur at optimize all signal settings (cycle length, peak hours. phasing sequence, splits, and offsets) (McTrans 2008).

182 Flamarz S./ZJPAS: 2017, 29(5): 177-195

5.1. Traffic Volume highest recording traffic volume in each The traffic volume count was carried out at direction is recorded to be used in the analysis Shahid Hama Rash intersection from (7:45 a.m of the present study. to 8:45 a.m) and Sherai Naqib intersection The period of the volume counting is divided from (7:55 a.m to 8:55 a.m) using video into 15 minutes intervals; Table 1 shows the records (see Figures. 4, 5) during the workdays total volume for all approaches each one hour of the week on 5th of October 2015 and the at both intersections.

Figure 4: Shahid Hama Rash signalized intersection- traffic volume count (video record)

Figure 5: Sherai Naqib signalized intersection- traffic volume count (video record) 183 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Table 1: Traffic volume, Peak Hour Factor (PHF), and signal timing at Shahid Hama Rash and Sherai Naqib Intersections for all approaches in the peak hour period Collected Data NB SB EB WB TH L TH L TH L TH L Movement No. 101 102 103 104 105 106 107 108 7:45-8:00 a.m - - - 110 - 160 106 31

8:00-8:15 a.m - - - 139 - 135 94 30

olume 8:15-8:30 a.m - - - 148 - 138 108 40 8:30-8:45 a.m - - - 133 - 117 109 40 - - - 530 - 550 417 141 7:45-8:45 a.m Traffic V Traffic - - - 3% HV - 11% HV 0% HV 2% HV

PHF - - - 0.90 - 0.86 0.96 0.88

G=30 Y=5 G=25 Y=5 G=25 Y=5 Signal Timing (sec) -

Shahid Hama Rash intersection y=5 ar=0 y=5 ar=0 y=5 ar=0

7:55-8:10 a.m 20 83 42 12 63 16 110 67

8:10-8:25 a.m 29 85 60 22 87 28 108 77 ion

olume 8:25-8:40 a.m 26 73 41 22 51 23 102 65 8:40-8:55 a.m 46 73 41 11 71 28 68 58 121 314 184 67 272 95 388 267 7:55-8:55 a.m Traffic V Traffic 0% HV 3% HV 1% HV 1% HV 10% HV 0% HV 8% HV 0% HV PHF 0.66 0.92 0.77 0.76 0.78 0.85 0.88 0.87 G=20 Y=7 G=20 Y=7 G=30 G=35 Y=7 Signal Timing (sec) Sherai Naqib intersect Y=7 y=5 ar=2 y=5 ar=2 y=5 ar=2 TH= Through movement, R= Right movement, L= Left movement, % HV=Percent5 of2 Heavy Vehicles, NB=North Bond, SB=South Bond, EB=East Bond and WB=West Bond

6. REAULTS AND DISCUSSION • Shahid Hama Rash signalized 6.1. Operation Analysis for the Existing intersection: the major result of the Conditions for Shahid Hama Rash and simulation run for this intersection were; Sherai Naqib signalized intersections the degree of saturation is 124%, the level of service (LOS) is F, fuel A simulation run used for the operation consumption 236 liter and disutility analysis for both Shahid Hama Rash and Sherai index is 57. Naqib intersections using TRANSYT-7F Software Release 11. The major output results • Sherai Naqib signalized intersection: the of the simulation runs are summarized in Table major result of the simulation run for 2. this intersection were; the degree of saturation is 126%, the level of service The major output results of the simulation (LOS) is F, fuel consumption 314 liter runs of both intersections were as in the and disutility index is 71. following:

184 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Table 2: Operation analysis (a simulation run) major output results for Shahid Hama Rash and Sherai Naqib Intersections (data analyzed using TRANSYT-7F Software Release 11) Operation Analysis NB SB EB WB Outputs TH L TH L TH L TH L Degree of 124 56 92 34 Uniform 13.2 2.4 4.1 1.2 Random 20.6 0.1 2.7 0.0 Total Delay 33.9 2.5 6.8 1.2 Average 207 28 56 28 Fuel 140 29 51 14 LOS F C E C Intersection 124 Uniform 21 Random 23.5 Total Delay 44.5 Average 106 Shahid Hama Rash intersection Fuel 236 Disutility 57 Intersection F Degree of 68 126 88 33 86 28 93 65 Uniform 2.7 13 3.6 1.2 4.8 1.3 5.8 3.7 Random 0.3 13.5 1.8 0.0 1.6 0.0 3.1 0.2

Total Delay 3 26.6 5.4 1.2 6.4 1.3 8.9 3.9

on Average 60 280 82 51 66 42 73 46 Fuel 22 100 33 9 44 11 58 33 LOS E F F D E D E D Intersection 126 Uniform 36.3 Random 20.7 Total Delay 57 Sherai Naqib intersecti Average 99 Fuel 314 Disutility 71 Intersection F

6.2. Evaluation of the Existing Conditions intersections are operating under level of for Shahid Hama Rash and Sherai Naqib service F which is the worse operating signalized intersections condition thus the fuel consumption (236 liter The output results show that both and 314 liter respectively) and disutility (57 intersections are operating under congested and 71 respectively) are big. conditions, where the degree of saturation for Shahid Hama Rash and Sherai Naqib signalized intersections is Higher than 100% (124% and 126% respectively) which mean that they are over saturated. Also both 185 Flamarz S./ZJPAS: 2017, 29(5): 177-195

6.3. The Suggested Capacity Improvement fuel consumption and performance index Scenarios (disutility index). 6.3.1. Signal Timing Optimization For the purposes of double check simulation Optimization runs applied for the signal runs applied using TRANSYT-7F Software timing optimization for Shahid Hama Rash and Release 11 for Shahid Hama Rash and Sherai Sherai Naqib signalized intersections using Naqib intersections using the optimum cycle TRANSYT-7F Software Release 11. The major lengths which resulted from the cycle length output results and the percentages of the optimization using TRANSYT-7F Software improvement of the optimization runs are Release 11 and the results of the simulation summarized in Tables 3, 4 and 5. runs are summarized in Table 6. The impacts of the signal timing optimization The simulation run results for both on the both intersections were as in the intersections shows that the optimum cycle following: lengths for both intersections resulted from the optimization of the signal timing has • Shahid Hama Rash signalized significant impact on the improving the quality intersection: as a result of the of both intersections operation, where the optimization run an optimum cycle degree of saturation for Shahid Hama Rash length has been selected by the software reduced from 124% to 102% and the (the old cycle length = 95 sec and the intersection level of service (LOS) changed optimum cycle length = 80 sec) and the from F which is the worse operating condition control delay reduced from 108 sec/veh to level of service (LOS) D which is good to 52.6 sec/veh thus very good operating condition, and the degree of improvement in all other performance saturation for Sherai Naqib intersection indicators including the fuel reduced from 126% to 98% and the intersection consumption and performance index level of service (LOS) changed from F which is (disutility index). the worse operating condition to level of • Sherai Naqib signalized intersection: as service (LOS) E which is one step better a result of the optimization run an operating condition than level of service (LOS) optimum cycle length has been selected F. by the software (the old cycle length = 133 sec and the optimum cycle length = 140 sec) and the control delay reduced from 103 sec/veh to 78.8 sec/veh thus good improvement in all other performance indicators including the

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Table 3: Signal timing optimization major output results for Shahid Hama Rash Intersection (optimization done using TRANSYT-7F Software Release 11) Optimization Results SB EB WB Green=30 Green=25 Green=25 Initial signal timing (sec) Yellow=5 Yellow=5 Yellow=5 Green=29 Green=14 Green=22 Optimized signal timing (sec) Yellow=5 Yellow=5 Yellow=5 Initial cycle length (sec) 95 Optimized cycle length (sec) 80 Initial control delay (sec/veh) 108 Optimized control delay (sec/veh) 52.6 Initial total stop (%) 138 Optimized total stop (%) 120 Initial fuel consumption (lit/hr) 238 Optimized fuel consumption (lit/hr) 173 Shahid Hama Rash Intersection Initial travel time (veh-hr/hr) 54 Optimized travel time (veh-hr/hr) 30 Initial performance index 58.68 Optimized performance index 38.25

Table 4: Signal timing optimization major output results for Sherai Naqib Intersection (optimization done using TRANSYT-7F Software Release 11)

Optimization Results NB SB EB WB Green=20 Green=20 Green=30 Green=35

Initial signal timing (sec) Yellow=5 Yellow=5 Yellow=5 Yellow=5

All Red=2 All Red=2 All Red=2 All Red=2 Green=28 Green=19 Green=29 Green=36

Optimized signal timing (sec) Yellow=5 Yellow=5 Yellow=5 Yellow=5

All Red=2 All Red=2 All Red=2 All Red=2 Initial cycle length (sec) 133 Optimized cycle length (sec) 140 Initial control delay (sec/veh) 103 Optimized control delay (sec/veh) 78.8 Initial total stop (%) 118

Sherai Naqib Intersection Naqib Sherai Optimized total stop (%) 112 Initial fuel consumption (lit/hr) 319 Optimized fuel consumption (lit/hr) 281 Initial travel time (veh-hr/hr) 70 Optimized travel time (veh-hr/hr) 57 Initial performance index 72.88 Optimized performance index 61.27 187 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Table 5: Percentages of improvement in the major output results for Shahid Hama Rash and Sherai Naqib Intersections resulted from the signal timing optimization (optimization done using TRANSYT-7F Software Release 11) Major Output Results Initial Condition Optimization Results % of Improvement in the Results (Reduction)

Control delay (sec/veh) 108 52.6 51.29 Total stop (%) 138 120 13.04 ama ama Fuel consumption (lit/hr) 238 173 27.31 Travel time (veh-hr/hr) 54 30 44.44 Shahid H

Rash Intersection Rash Performance index 58.68 38.25 34.81 Control delay (sec/veh) 103 78.8 23.49

Total stop (%) 118 112 5.08 Fuel consumption (lit/hr) 319 281 11.91 Travel time (veh-hr/hr) 70 57 18.57 Intersection Sherai Naqib Performance index 72.88 61.27 15.93

Table 6: Operation analysis (a simulation run) major output results for Shahid Hama Rash and Sherai Naqib Intersections using the optimum cycle length resulted from the optimization run (data analyzed using TRANSYT- 7F Software Release 11) Operation Analysis Outputs NB SB EB WB TH L TH L TH L TH L Degree of Saturation (%) 90 102 88 32

Uniform Delay (veh-h) 3.9 3.3 3.3 1 Random Delay (veh-h) 2.9 4.9 2.3 0 Total Delay (veh-h) 6.9 8.3 5.6 1.1 Average Delay (sec/veh) 42 93 46 24 Fuel Consumption (Liter) 62 48 48 13 LOS D F D C Intersection Degree of 102 Uniform Delay (veh -h) 11.6 Random Delay (veh-h) 10.3 Total Delay (veh-h) 22 Average Delay (sec/veh) 52 Fuel Consumption (Liter) 172

Shahid Hama Rash intersection Disutility Index 38 Intersection LOS D Degree of Saturation (%) 51 95 98 36 94 30 95 66 Uniform Delay (veh-h) 2.5 5.2 4 1.3 5.2 1.4 6.2 3.9 Random Delay (veh-h) 0.2 3.4 3.4 0.1 3.2 0 3.8 0.6

ion Total Delay (veh-h) 2.7 8.6 7.4 1.4 8.4 1.5 10.1 4.6 Average Delay (sec/veh) 54 91 112 59 87 49 82 53 Fuel Consumption (Liter) 21 49 39 10 50 12 62 35 LOS D F F E F D F D Intersection Degree of 98 Uniform Delay (veh -h) 30.1 Random Delay (veh-h) 14.9 Total Delay (veh-h) 45.1 Average Delay (sec/veh) 78 Sherai Naqib intersect Fuel Consumption (Liter) 280 Disutility Index 61 Intersection LOS E

187 Flamarz S./ZJPAS: 2017, 29(5): 177-195

significant impact on increasing the capacity 6.3.2. Improving the Existing Geometric and improving the quality of both intersections Design operation, where the degree of saturation for Improving the existing geometric design Shahid Hama Rash reduced from 124% to 87% of Shahid Hama Rash and Sherai Naqib and the intersection level of service (LOS) intersections can be achieved by re allocating changed from F which is the worse operating of the exiting lanes and increasing the number condition to level of service (LOS) D which is of the lanes (this improvement involve good operating condition, and the degree of widening the sides of approaches and re- saturation for Sherai Naqib intersection painting them) in the targeted approaches. It is reduced from 126% to 76% and the intersection noticed from the operation analysis (simulation level of service (LOS) changed from F which is run) for the existing conditions for Shahid the worse operating condition to level of Hama Rash and Sherai Naqib signalized service (LOS) D which is good operating intersections that most of the lane groups are condition. operating under the level of service (LOS) E and F which are congested and poor operation The impact of improving the existing condition in addition to that the level of service geometric design on both intersection lane for both intersections Shahid Hama Rash and groups was as following: Sherai Naqib is F which is the worse operation • Shahid Hama Rash signalized intersection: condition. a. The impact of this improvement on the Based on what mentioned above the lane groups degree of saturation were; number of lanes for the congested lane groups South Bond (SB) Left turn (L) the degree are increased by re allocating the existing lanes of saturation changed from 124% to 71%, or increasing the number of lanes in the East Bond (EB) Left Turn (L) the degree targeted approaches in both intersections of saturation changed from 56% to 33%, Shahid Hama Rash and Sherai Naqib to reduce West Bond (WB) Through (TH) the the delay caused by the congested lane groups degree of saturation changed from 92% to and improve its operation quality and as a final 87% and West Bond (WB) Left Turn (L) result improve the overall operation quality for the degree of saturation changed from both intersections. 34% to 38%. For the purposes of measuring the impact b. The impact of this improvement on the of improving the existing geometric design on lane groups level of service (LOS) were; the operation quality of Shahid Hama Rash and South Bond (SB) Left turn (L) the level Sherai Naqib intersections a simulation run has of service (LOS) changed from F to D, applied using TRANSYT-7F Software Release East Bond (EB) Left Turn (L) the level of 11 on each of the two intersections after re service (LOS) remained C, West Bond allocating the existing lanes or increasing the (WB) Through (TH) the level of service number of lanes in the targeted approaches for (LOS) changed from E to D and West both intersections. The results of the simulation Bond (WB) Left Turn (L) the level of runs are summarized in Table 7. service (LOS) remained C. The simulation run results for both c. The impact of this improvement on the intersections shows that improving the existing lane groups fuel consumption were; geometric design of both intersections has a South Bond (SB) Left turn (L) the fuel 188 Flamarz S./ZJPAS: 2017, 29(5): 177-195

consumption changed from 140 liter to 59 (NB) Left Turn (L) the level of service liter, East Bond (EB) Left Turn (L) the (LOS) changed from F to E, South Bond fuel consumption changed from 29 liter (SB) Through (TH) the level of service to 27 liter, West Bond (WB) Through (LOS) changed from F to D, South Bond (TH) the fuel consumption changed from (SB) Left turn (L) the level of service 51 liter to 49 liter and West Bond (WB) (LOS) remained D, East Bond (EB) Left Turn (L) the fuel consumption Through (TH) the level of service (LOS) remained 14 liter. changed from E to D, East Bond (EB) Left Turn (L) the level of service (LOS) • Sherai Naqib signalized intersection: remained D, West Bond (WB) Through a. The impact of this improvement on the (TH) the level of service (LOS) changed lane groups degree of saturation were; from E to D and West Bond (WB) Left North Bond (NB) Through (TH) the Turn (L) the level of service (LOS) degree of saturation changed from 68% remained D. to 62%, Bond (NB) Left Turn (L) the c. The impact of this improvement on the degree of saturation changed from 126% lane groups fuel consumption were; to 76%, South Bond (SB) Through (TH) North Bond (NB) Through (TH) the fuel the degree of saturation changed from consumption remained 22 liters, Bond 88% to 40%, South Bond (SB) Left turn (NB) Left Turn (L) the fuel consumption (L) the degree of saturation changed changed from 100 liters to 43 liters, from 33% to 15%, East Bond (EB) South Bond (SB) Through (TH) the fuel Through (TH) the degree of saturation consumption changed from 33 liters to changed from 88% to 39%, East Bond 26 liters, South Bond (SB) Left turn (L) (EB) Left Turn (L) the degree of the fuel consumption remained 9 liters, saturation changed from 28% to 25%, East Bond (EB) Through (TH) the fuel West Bond (WB) Through (TH) the consumption changed from 44 liters to degree of saturation changed from 93% 34 liters, East Bond (EB) Left Turn (L) to 42% and West Bond (WB) Left Turn the fuel consumption changed from 11 (L) the degree of saturation changed liters to 10 liters, West Bond (WB) from 65% to 59%. Through (TH) the fuel consumption b. The impact of this improvement on the changed from 58 liters to 42 liters and lane groups level of Service (LOS) were; West Bond (WB) Left Turn (L) the fuel North Bond (NB) Through (TH) the consumption changed from 33 liters to level of service (LOS) remained E, Bond 31 liters.

189 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Table 7: Operation analysis (a simulation run) major output results for Shahid Hama Rash and Sherai Naqib Intersections after improving the existing geometric design (data analyzed using TRANSYT-7F Software Release 11) Operation Analysis Outputs NB SB EB WB TH L TH L TH L TH L Degree of Saturation (%) 71 33 87 38 Uniform Delay (veh-h) 5.1 2.2 4 1.2

Random Delay (veh-h) 0.8 0 2.1 0.1 Total Delay (veh-h) 6 2.3 6.2 1.3 Average Delay (sec/veh) 36 25 51 31 Fuel Consumption (Liter) 59 27 49 14 LOS D C D C Intersection Degree of 87 Uniform Delay (veh -h) 12.7 Random Delay (veh-h) 3.2 Total Delay (veh-h) 15.9 Average Delay (sec/veh) 38 Shahid Hama Rash intersection Fuel Consumption (Liter) 151 Disutility Index 29 Intersection LOS D Degree of Saturation (%) 62 76 40 15 39 25 42 59 Uniform Delay (veh-h) 2.7 5.1 3 1 3.6 1.1 4.2 3.1 Random Delay (veh-h) 0.4 1.1 0.1 0 0.1 0 0.1 0.4

Total Delay (veh-h) 3.1 6.2 3.1 1 3.8 1.1 4.4 3.5 Average Delay (sec/veh) 62 66 47 43 39 37 36 41 Fuel Consumption (Liter) 22 43 26 9 34 10 42 31 LOS E E D D D D D D Intersection Degree of 76 Uniform Delay (veh -h) 24.1 Random Delay (veh-h) 2.4 Total Delay (veh-h) 26.6 Sherai Naqib intersection Average Delay (sec/veh) 46 Fuel Consumption (Liter) 221 Disutility Index 42 Intersection LOS D

improving the existing geometric design) in 6.3.3. The Combination of Signal Timing order to find out if the combination of signal Optimization and Improving the Existing timing optimization and improving the existing Geometric Design geometric design gives better results than each The third capacity improvement scenario of the suggested capacity improving scenarios is a combination of signal timing optimization in above or not, which will help the decision and improving the existing geometric design. maker to decide later which capacity improving The idea behind this capacity improving scenario is the best option to increase the scenario is to measure the combined effect of capacity and improve the quality of operation the first and second capacity improving for Shahid Hama Rash and Sherai Naqib scenarios (signal timing optimization and signalized intersections. 190 Flamarz S./ZJPAS: 2017, 29(5): 177-195

To measure the impact of the third the degree of saturation changed from capacity scenario (the combination of signal 34% to 36%. timing optimization and improving the existing b. The impact of this improvement on the geometric design) on the capacity and lane groups level of service (LOS) were; operation quality of Shahid Hama Rash and South Bond (SB) Left turn (L) the level Sherai Naqib intersections a simulation run has of service (LOS) changed from F to C, applied using TRANSYT-7F Software Release East Bond (EB) Left Turn (L) the level of 11 on each of the two intersections. The results service (LOS) changed from C to D, of the simulation runs are summarized in Table West Bond (WB) Through (TH) the level 8. of service (LOS) changed from E to D The simulation runs results for both and West Bond (WB) Left Turn (L) the intersections shows that the combination of level of service (LOS) remained C. signal timing optimization and improving the c. The impact of this improvement on the existing geometric design for both intersections lane groups fuel consumption were; has very significant impact on increasing the South Bond (SB) Left turn (L) the fuel capacity and improving the quality of operation consumption changed from 140 liter to 49 for both intersections, where the degree of liter, East Bond (EB) Left Turn (L) the saturation for Shahid Hama Rash reduced from fuel consumption changed from 29 liter 124% to 83% and the intersection level of to 32 liter, West Bond (WB) Through service (LOS) changed from F which is the (TH) the fuel consumption changed from worse operating condition to level of service 51 liter to 45 liter and West Bond (WB) (LOS) C which is very good operating Left Turn (L) the fuel consumption condition, and the degree of saturation for remained 14 liter. Sherai Naqib intersection reduced from 126% to 66% and the intersection level of service • Sherai Naqib signalized intersection: (LOS) changed from F which is the worse a. The impact of this improvement on the operating condition to level of service (LOS) D lane groups degree of saturation were; which is good operating condition. North Bond (NB) Through (TH) the The impact combination of signal timing degree of saturation changed from 68% to optimization and improving the existing 25%, Bond (NB) Left Turn (L) the degree geometric design on both intersection lane of saturation changed from 126% to 32%, groups was as following: South Bond (SB) Through (TH) the degree of saturation changed from 88% to • Shahid Hama Rash signalized intersection: 49%, South Bond (SB) Left turn (L) the a. The impact of this improvement on the degree of saturation changed from 33% to lane groups degree of saturation were; 18%, East Bond (EB) Through (TH) the South Bond (SB) Left turn (L) the degree degree of saturation changed from 88% to of saturation changed from 124% to 51%, 47%, East Bond (EB) Left Turn (L) the East Bond (EB) Left Turn (L) the degree degree of saturation changed from 28% of saturation changed from 56% to 60%, to 30%, West Bond (WB) Through (TH) West Bond (WB) Through (TH) the the degree of saturation changed from degree of saturation changed from 92% to 93% to 48% and West Bond (WB) Left 83% and West Bond (WB) Left Turn (L) 191 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Turn (L) the degree of saturation changed c. The impact of this improvement on the from 65% to 66%. lane groups fuel consumption were; North Bond (NB) Through (TH) the fuel b. The impact of this improvement on the lane groups level of Service (LOS) were; consumption changed from 22 liters to 19 North Bond (NB) Through (TH) the level liters, Bond (NB) Left Turn (L) the fuel of service (LOS) changed from E to D, consumption changed from 100 liters to Bond (NB) Left Turn (L) the level of 37 liters, South Bond (SB) Through (TH) service (LOS) changed from F to D, the fuel consumption changed from 33 South Bond (SB) Through (TH) the level liters to 28 liters, South Bond (SB) Left of service (LOS) changed from F to E, turn (L) the fuel consumption changed South Bond (SB) Left turn (L) the level from 9 liters to 10 liters, East Bond (EB) of service (LOS) remained D, East Bond Through (TH) the fuel consumption (EB) Through (TH) the level of service changed from 44 liters to 38 liters, East (LOS) changed from E to D, East Bond Bond (EB) Left Turn (L) the fuel (EB) Left Turn (L) the level of service consumption changed from 11 liters to (LOS) remained D, West Bond (WB) 12 liters, West Bond (WB) Through (TH) Through (TH) the level of service (LOS) the fuel consumption changed from 58 changed from E to D and West Bond liters to 46 liters and West Bond (WB) (WB) Left Turn (L) the level of service Left Turn (L) the fuel consumption (LOS) remained D. changed from 33 liters to 35 liters.

Table 8: Operation analysis (a simulation run) major output results for Shahid Hama Rash and Sherai Naqib Intersections after the third improvement scenario- the combination of signal timing optimization and improving the existing geometric design (data analyzed using TRANSYT-7F Software Release 11) Operation Analysis Outputs NB SB EB WB TH L TH L TH L TH L

Degree of Saturation (%) 51 60 83 36 51 Uniform Delay (veh-h) 3.2 2.7 3.2 1 3.2 Random Delay (veh-h) 0.2 0.4 1.7 0.1 0.2 Total Delay (veh-h) 3.5 3.1 5 1.1 3.5 Average Delay (sec/veh) 21 35 41 25 21 Fuel Consumption (Liter) 49 32 45 14 49 LOS C D D C C Intersection Degree of Saturation 83 Uniform Delay (veh-h) 10.3 Random Delay (veh-h) 2.5 Total Delay (veh-h) 12.8 Average Delay (sec/veh) 30 Fuel Consumption (Liter) 141

Shahid Hama Rash intersection Disutility Index 26 Intersection LOS C Degree of Saturation (%) 25 32 49 18 47 30 48 66 Uniform Delay (veh-h) 2.4 4.5 3.7 1.3 4.7 1.4 5.3 3.9

Random Delay (veh-h) 0 0 0.2 0 0.2 0 0.2 0.6 Total Delay (veh-h) 2.4 4.6 3.9 1.3 4.9 1.5 5.6 4.6 Average Delay (sec/veh) 48 48 59 54 50 49 45 53 Fuel Consumption (Liter) 19 37 28 10 38 12 46 35 LOS D D E D D D D D Intersection Degree of Saturation 66 Uniform Delay (veh-h) 27.5 Random Delay (veh-h) 1.4 Total Delay (veh-h) 28.9 Average Delay (sec/veh) 50

Sherai Naqib intersection Fuel Consumption (Liter) 228 Disutility Index 43 Intersection LOS D 192 Flamarz S./ZJPAS: 2017, 29(5): 177-195

fuel consumption, disutility index and level 6.4. A Comparison between the Suggested of service) which are summarized and Capacity Improvement Scenarios Results explained in Table 9 for the existing The goal of this comparison is to identify conditions and the three suggested which of the three intersection capacity intersection capacity improvement improvement scenarios gave the best results in scenarios applied on Sherai Naqib term of increasing the intersection capacity and intersection the best capacity improvement improving the quality of operation. Depending scenario is the second and third intersection on the simulation runs for the existing capacity improvement scenarios, where in conditions and the three suggested intersection terms of intersection; delay, fuel capacity improvement scenarios applied to consumption and disutility index the results Shahid Hama Rash and Sherai Naqib of the second capacity improvement signalized intersections using TRANSYT-7F scenario (improving the existing geometric Software Release 11, it can be decided which design) is better and in term of intersection of the three capacity improvement scenarios degree of saturation the result of the third gave the best results as it is explained in the capacity improvement scenario following: (combination of signal timing optimization • Shahid Hama Rash Signalized Intersection: and improving the existing geometric from the simulation runs major results design) is better. Regarding the intersection (Intersection; degree of saturation, delay, level of service (LOS), both capacity fuel consumption, disutility index and level improvement scenarios resulted intersection of service) which are summarized and level of service D which is good operation explained in Table 9 for the existing quality condition. But in the second conditions and the three suggested intersection capacity improvement scenario intersection capacity improvement the level of service for the through and left scenarios applied on Shahid Hama Rash movements of the North Bond is E and it is intersection it is easily recognized that the D for all other movements (see Table 7), best capacity improvement scenario is the where in the third intersection capacity third intersection capacity improvement improvement scenario the level of service scenario (combination of signal timing is E only for the through movement of the optimization and improving the existing South Bond and it is D for all other geometric design). movements (see Table 8). • Sherai Naqib Signalized Intersection: from the simulation runs major results (Intersection; degree of saturation, delay,

193 Flamarz S./ZJPAS: 2017, 29(5): 177-195

Table 9: Simulation runs major output results for Shahid Hama Rash and Sherai Naqib Signalized Intersections existing conditions and the applied three suggested intersection capacity improvement scenarios using TRANSYT-7F Software Release 11

Intersection Operation Analysis Major Output Results Design) Improveme Optimization) (Signal Timing nd Initial Conditions 2 Geometric Design) Geometric Design) Improvement Scenario

Improvement Scenario (Combination of Signal st rd Scenario (Improving the Timing Optimization and 1 (Improving the Geometric the (Improving 3 Intersection Degree of Saturation (%) 124 102 87 83 Uniform Delay (veh-h) 21 11.6 12.7 10.3 Random Delay (veh-h) 23.5 10.3 3.2 2.5 Total Delay (veh-h) 44.5 22 15.9 12.8 Average Delay (sec/veh) 106 52 38 30

Intersection Fuel Consumption (Liter) 236 172 151 141 57 38 29 26

Shahid Hama Rash Disutility Index Intersection LOS F D D C Intersection Degree of Saturation (%) 126 98 76 66 Uniform Delay (veh-h) 36.3 30.1 24.1 27.5 Random Delay (veh-h) 20.7 14.9 2.4 1.4 Total Delay (veh-h) 57 45.1 26.6 28.9 Average Delay (sec/veh) 99 78 46 50

Intersection Fuel Consumption (Liter) 314 280 221 228 Sherai Naqib Disutility Index 71 61 42 43 Intersection LOS F E D D

intersections. TRANSYT-7F release 11 7. CONCLUSION used in applying the suggested three 1- The operation analysis results using intersection capacity improvement TRANSYT-7F Software Release 11 of scenarios on Shahid Hama Rash and Sherai Shahid Hama Rash and Sherai Naqib Naqib signalized intersections as in the signalized intersections which were following: selected as a case study for this study clearly explained that both intersections are A. First intersection capacity improvement operating under congested operating scenario (signal timing optimization): An conditions with level of service (LOS) F Optimization run applied for the signal which is the worse operating conditions. timing optimization for each of Shahid Hama Rash and Sherai Naqib intersections 2- A strategy consists of three intersection using TRANSYT-7F Software Release 11 capacity improvement scenarios are and the results of the optimization run were selected to increase the capacity and an optimum cycle length has been selected improve the operation quality of Shahid by the software for each of the selected Hama Rash and Sherai Naqib signalized 194 Flamarz S./ZJPAS: 2017, 29(5): 177-195

intersection with a significant improvements improvement scenarios applied on Shahid in all intersection performance indicators. Hama Rash intersection it is clearly recognized that the best capacity B. Second intersection capacity improvement scenario (improving the existing geometric improvement scenario is the third scenario design): The simulation runs results for the (combination of signal timing optimization selected intersections shows that improving and improving the existing geometric the existing intersections geometric design design). have a significant impact on the increasing B. Sherai Naqib Signalized Intersection: from the capacity and improving the quality of the simulation runs major results selected intersections operation. (Intersection; degree of saturation, delay, fuel consumption, disutility index and level C. Third intersection capacity improvement scenario (the combination of signal timing of service) for the existing conditions and optimization and improving the existing the three suggested intersection capacity geometric design): the simulation runs improvement scenarios applied on Sherai results for the selected intersections shows Naqib intersection the best capacity that the combination of signal timing improvement scenarios are the second and optimization and improving the existing third scenarios, where in term of geometric design has very significant impact intersection; delay, fuel consumption and on the increasing the capacity and disutility index the results of the second improving the quality of both intersections capacity improvement scenario (improving operation. the existing geometric design) is better and in term of intersection degree of saturation 3- Depending on the simulation runs for the the result of the third capacity improvement existing conditions and the three suggested scenario (combination of signal timing intersection capacity improvement optimization and improving the existing scenarios applied on Shahid Hama Rash geometric design) is better. Regarding the and Sherai Naqib signalized intersections intersection level of service (LOS), both using TRANSYT-7F Software Release 11, capacity improvement scenarios resulted it can be decided which of the three intersection level of service D which is good capacity improvement scenarios gave the operation quality condition. But in the best results as it is explained in the second intersection capacity improvement following: scenario the level of service for the through A. Shahid Hama Rash Signalized Intersection: and left movements of the North Bond is E from the simulation runs major results and it is D for all other movements, where in (Intersection; degree of saturation, delay, the third intersection capacity improvement fuel consumption, disutility index and level scenario the level of service is E only for the of service) for the existing conditions and through movement of the South Bond and it the three suggested intersection capacity is D for all other movements. Conflict of Interest There is no conflict of interest.

195 Flamarz S./ZJPAS: 2017, 29(5): 177-195

REFERENCES Borkloe, J. K., Nyantakyi , E. K ., Mohammed, G.A., 2013. Capacity Analysis of Selected Intersections on Mampong Road, Kumasi- Ghana Using Micro Simulation Model. International Journal of Structural and Civil Engineering Research (IJSCER), 2(3), pp.39–61.

Garber, N.J., Hoel, L.A., 2009. Traffic and Highway Engineering 4th ed., Cengage Learning.

Kumar, S., Ranjitha, J., 2013. Improvement Of Traffic Operations In Congested Signalized Intersections - A Case Study In Bangalore City. International Journal of Engineering Research and Technology (IJERT), 2(7), pp.2284–2291.

McTrans, 2008. TRANSYT-7F User’s Guide 11th ed., University of Florida.

Tovar, S. R., Alvaro, R. V., 2010. Effect of Phase Sequence in Capacity Signalized Intersections. Wolrd Conference on Transport Research (WCTR), 12(7), pp.1–17.

Transportation Research Board (TRP), 2000. Highway capacity manual, National Academy of Sciences.

ZANCO Journal of Pure and Applied Sciences

The official scientific journal of Salahaddin University-Erbil ZJPAS (2017), 29 (2); 196-207 http://dx.doi.org/10.21271/ZJPAS.29.2.20

SYBR Green Real Time PCR Assay for Quantitative Detection of Escherichia coli Directly from Clinical Samples

Ari Q. Nabi* * Department of Biology, College of Science, Salahaddin University, Erbil, Kurdistan Region, Iraq.

A R T I C L E I N F O A B S T R A C T

Article History: Diagnosis of bloodstream bacterial infection in its early stages are key steps Received: 04/10/2016 for its treatment, however because of the brutal effects of sepsis and the necessity Accepted: 25/02/2017 of its immediate treatment, many physicians don’t wait for the conventional Published: 07/06/2017 microbiological diagnosis and start prescribing antimicrobial drugs. Therefore designing a fast, accurate and economic quantitative real-time PCR method (qR- PCR) to quantify the total number of Escherichia coli and to detect pathogenic Keywords: strains of the bacterium from blood and clinical samples is a crucial step for early SYBR Green I diagnosis and treatment of the problem. In this study, SYBR Green I used as inexpensive indicator to reduce the costs in comparison with probe based methods Quantitative PCR and is compatible with conventional microbiological methods. UspA gene which Blood infection. encodes for the universal regulator stress protein has been selected as a target gene which is the most suitable candidate to detect the presence of any E. coli, while eae gene which encodes for the outer membrane protein intimin was targeted in order *Corresponding Author: to evaluate the presence of virulence strains among positive samples. The Dr. Ari Q. Nabi suitability and utility of the quantitative SGR-PCR assay for detection of E. coli in different samples sources has been evaluated by artificial inoculation of healthy [email protected] blood with type strains of E. coli used for designing a quantitative standard curve. The protocol was then applied on blood and some clinical samples collected from suspected patients with sepsis. Using this method and despite of a relatively low positive data when testing the blood samples, both sets of primers showed to be useful for the detection of E. coli and the strains that harbor virulence genes. The developed standard curves confirmed that this method is a quantitative in a detection range of 102 to 108 cells mL-1, and that the qSG R-PCR assay can be used as a new and successful molecular tool to detect and quantify all and pathogenic E. coli directly from clinical samples without pre-enrichment steps, when presenting at concentrations greater than 102 cells mL-1.

1. INTRODUCTION up to 5 days or more to rule in or rule out the The most important limitation of blood cultures presence of a pathogen in the blood for diagnosis of infection is the time required sample(Gilbert DN et al., 2004). Some from blood sampling to reporting results back information on whether culture bottles are to the treating clinician. Culture based infection showing a detectable growth will usually be diagnosis is a multistep process that can take available with 1-2 days but this is still slow when it is taken into account that antibiotic 197 Nabi A./ZJPAS: 2017, 29 (2): 196-207 therapy has to be administered very quickly to expression of intimin, an outer-membrane patients who have clinical evidence of protein encoded by the eae gene that is part of infection. Inadequate antimicrobial treatment the locus of enterocyte effacement (Sharma, has a major impact on mortality in these 2002).The popularity of using SYBR Green I patients and a recent study of patients with assays with R- PCRs users is due to three severe sepsis demonstrated that each hour factors: 1) low cost for the dye; 2) ease of assay delay of administration of an effective development, only a pair of primers is required; antibiotic therapy is associated with an 8% and 3) the same detection mechanism can be increase in mortality (Kumar et al., 2006, used for every assay (Dorak, 2007, John M. Gilbert DN et al., 2004). Walker and Rapley, 2008). The most recent The most common bacterial pathogens advances in qR-PCR methods are focused on frequently isolated in association with the reduction of the limits of detection and quantification, on the discrimination between bloodstream infection, particularly in critical care, are Enterobacteriaceae including E.coli, dead and live cells or the simultaneous Klebsiella species, Serratia and Proteus detection of different foodborne pathogens. species. E.coli and Proteus species are mostly The performances of these methods were, in isolated with urinary tract infection but also some cases, successfully compared with the reported as vascular line-associated infections official protocols or with diagnostic (Livermore et al., 2008).Blood culture, which commercial kits (Pasquale Russo et al., 2014, is the traditional method for bacterial Elizaquivel and Aznar, 2008, Dorak, 2007). identification, takes 2-3 days (Dark et al., The aim of this work was development a PCR 2009). There has been great interest in the assay that would allow a rapid and direct development of new diagnostic methods able to detection and quantification of the pathogen in speed up the process of determining presence blood samples without pre-enrichment step of infection and identification of the pathogen. before DNA extraction, to ensure an effective PCR can detect and identify pathogen DNA treatment of patients with blood stream present in small amounts (Cursons et al., bacterial infections. 1999).

Quantitative real-time PCR has enhanced the sensitivity and specificity of PCR-based assay 2. MATERIALS AND METHODS in the detection of pathogenic microorganisms 2.1. Samples in food and the environment, allowing A total of forty-five blood samples were quantitative analysis and avoiding the use of collected from suspected patients for blood time-consuming and cost-effective infection during the period from January to electrophoresis (Beneduce et al., 2007). August 2016 from 2 local hospitals located in UspA gene which encodes for the universal Erbil city. During the sampling period, 2 to 6 stress protein has been identified and samples were collected from each hospital characterized in E. coli K-12 strain W3110 according to the case coincidences. Specimens (Nyström and Neidhardt, 1992), was found to (blood samples) were aseptically collected into be highly specific for E. coli differentiating it Brain Heart Infusion Medium bottles (Oxoid, from other Gram-negative bacteria (Chen and UK), according to laboratory-defined standard Griffiths, 1998, Siegele, 2005). The production operating procedures, and then prepared for of attaching-and-effacing lesions requires the genomic DNA extraction. Each specimen was 198 Nabi A./ZJPAS: 2017, 29 (2): 196-207 aseptically transferred in an ice box and 2.4. Artificial inoculation of control strains, transported to the DNA extraction laboratory quantification and DNA extraction within maximum of 2 hrs. After culturing and incubation of the control type strains of E. coli EDL933 and HB101 in 2.2. Reaction controls TSB broth (Oxoid, UK) until reaching mid exponential phase, then artificially inoculated Escherichia coliHB101 and the pathogenic into healthy bloods in tenfold dilution from 101 strain EDL933 from previous work (Beneduce to 108 bacterial cells mL-1according to a et al., 2008) used as positive controls for the modified procedure by Beneduce et al. (2007). presence of uspA and eae genes respectively in Positive control E. coli cells were quantified all PCR reactions. Pseudomonas aeruginosa using BLAUBRAND counting hemocytometer ATCC 9027 provided by Media Clinical (BRAND, Wertheim, Germany) for bacterial Centre, has been used as negative control to the cell quantification. Counting of bacteria started presence E. coli. All strains were routinely after 1-3 minutes so that the movement of the cultured at 37°C in TSB broth (Oxoid, cells in the sample comes to a halt. Total E. Hampshire, UK) until reaching mid coli counts performed by multiplying the exponential phase then subjected for DNA average number of E.coli counts in the main isolations. A none-template control NTC which chambers of the slide (volume 0.004µL, area is a blank master mix with no DNA template 0.04mm2, depth 0.0025mm2) by their dilution added for each experiment. Each sample was factors (DF), using this formula “Cells in 1mL analyzed in duplicate in the same q SGR-PCR = cells in 1µL(DF.1) x 1000 (DF.2)”.Then reaction. DNA from the inoculated and diluted blood samples (known cell counts) were extracted in 2.3. DNA isolation duplicates to prepare the quantitative standard curve using aforementioned DNA isolation kit A bacterial specific DNA extracting kit (Geneaid, Taiwan). (Presto™ Mini gDNA, Geneaid Biotech, Thaiwan) have been used to isolate total genomic DNA from any bacteria in blood samples according to the manufacture 2.5. Primers instructions. DNA was then extracted from In order to identify E. coli from our DNA artificially inoculated healthy bloods with the sources, we had to select two sets of primers bacterial control strains. Moreover, bacterial from our previous work (Beneduce et al., DNA from patients’ blood samples in BHI 2008). The first set of primers; uspA selected bottles was isolated for the possible detection to amplify uspA gene that encodes the and quantification of the pathogen. The regulatory universal stress protein which is qualities and quantities of isolated DNAs were present in all strains of E. coli while the second determined using spectrophotometric analysis set of primers; eae selected to target the eae method of DNA with Nano-Drop (ND- 1000, gene which encodes for gamma intimin outer- USA) by measuring the A260/A280 and the membrane protein which is present in all A260/230 ratios. Both extracted DNAs from enteropathogenic E. coli (Touchon et al., 2009, the control bacterial strains and blood samples Sharma, 2002).The primer sequences and their were stored in -20°C until further experiments targets are illustrated in Table (1). were conducted. 199 Nabi A./ZJPAS: 2017, 29 (2): 196-207

Table 1. List of oligonucleotide primer sequences and Initial denaturation at 95°C for 3 min; 10 their targets used for the real time PCR assays for cycles of denaturation at 95°C for 15 annealing detection and quantification of E. coli from different at 68 to 59°C(-1°Cper cycle) for 25 s, and samples. extension at 72°C for 50 s; followed by 30 cycles of denaturation at 95°C for 15 s,

annealing at 59°C for 25 s, and extension at

3´ 72°C for 50 s; and a final extension at 72°C for

Target Sequence Primer Name Sequence 5´ Sequence alignment position 10 min. eae GTTCACTGGACTTC 4598564 - TTATTACCG 4598120

ATCGTCACCAGAG 2.7 Standard curve development and the

Gamma Intimin gene GAATC sensitivity of the qR-PCR assays uspA CCGATACGCTGCCA 299361- Quantitative standard curves were developed

ATCAGT 298515 by using serial dilutions of E. coli strain ACGCAGACCGTAG HB101 and EDL 933 DNA as internal standard

Universal stress protein gene regulator GCCAGAT according standard quantitative procedures with DNA concentrations corresponding to 102 to 108 cells ml-1 similar to a procedure described by Spano et al., (2005) and 2.6. PCR Protocols according to standard quantitative protocols by John M. Walker and Rapley (2008). To A multiplex SYBR Green R-PCR and a quantify PCR product in real-time, the increase singleplex R-PCR developed from our previous of fluorescence signal from the SYBR Green work (Beneduce et al., 2008), were adopted was measured during amplification of the DNA targeting the eae and uspA genes, to allow the from the aforementioned serial dilutions. The quantification and detection of all E. coli quantitative SGR-PCR data were plotted as the strains including the most virulent strain E. coli ΔRn fluorescence signal vs cycle number. The O157 which is an important human pathogen. efficiency of amplification (E) was estimated The SGR-PCRs performed in 20µLPCR from the standard curve data, with the formula: mixtures containing a final concentration of 1X E = (101/slope) – 1,as described by John M. KAPA SYBR® FAST qPCR Master mix Walker and Rapley (2008) and in Applied Universal Buffer(Kapa Biosystems, Boston, Biosystems (2010).Standard curves and other USA), 2.5mM MgCL 1X ROX dye (LOW), 1 2, quantitative raw data analysis performed with U of Hot-Start Taq DNA polymerase and 200 Microsoft Excel Software (Microsoft, nM of each forward and reverse primers(Table Redmond, WA,USA). 1). Of the extracted genomic DNA, 3µL which contained about 10 to 20 ng were added to the reaction test tube and the final volume of 20µL were completed by sterile PCR-grade (RNase 2.8 Dissociation (melt) curve analysis free) water as recommended by Technical Data The real-time PCR instrument has been Sheet(Kapa Biosystems, USA). programmed to include a melting profile immediately following the thermal cycling A modified touchdown-PCR profile(Beneduce protocol. After amplification is complete, the et al., 2008)was conducted to be compatible instrument designed to reheat the R-PCR with the KAPA SYBR FAST kit as follow: products in 3 steps of 95°C for 15sec, then 200 Nabi A./ZJPAS: 2017, 29 (2): 196-207

60°C for 60 sec, and a final 95°C for 15°C for 1.51 to 2.1 and from 1.83 to 1.97 for each individual 96 wells. In the used 7300 A260/A280 and A260/A230 ratios system software, the R-PCR products were consequently, considered to be of a good analyzed to view the melt curve as normalized quality and suitable for the quantitative and reporter (Rn) vs. temperature or as derivative detective SGR-PCR assays. reporter (-Rn) vs. temperature, also called the dissociation curve so that to providing complete melting peak profiles (Applied 3.2. Efficiency of the quantitative R-PCR Biosystems, 2015). assay The Quantitative SGR-PCR was first performed with both primer sets on DNAs 3. RESULTS AND DISCUSSION extracted from the positive controls (E. coli strains HB101 and EDL933) and negative controls. The prepared serial dilutions of DNA 3.1. DNA quality and quantity isolated from pure cultures of E. coli were The combined DNA extraction and the assayed by the quantitative PCR method and BLAUBRAND slide counting methods resulted in successful construction of allowed extracting 20-100 ng/µl of total DNA quantitative standard curves (Figures 1, 2 and from artificially inoculated bloods. In order to 3) for both uspA and eae primers and were in estimate the quality of the extracted DNA, the accordance with the standards described in A260/A280 and the A260/230 ratios, measured Real Time PCR by Dorak (2007) and by spectrophotometric method (Nano-Drop, recommended by John M. Walker and Rapley ND- 1000, USA). The A260/A280 ratio was (2008). The sensitivity of the assay was above1.5 in all extracted DNA samples, and for determined as limit of detection, namely, the the A260/A230 was above1.8. According to lowest concentration at which 95% of the Khare et al. (2014) and Thermo Fisher positive samples are detected (Pasquale Russo technical data sheets (Thermo Fisher Scientific, et al., 2014, Dorak, 2007). Our quantitative R- USA), the absorbance of the nucleic acids at PCR revealed a sensitivity limit of 103cellsmL- 260 nm is 1.6-2.00 times more than the 1 for both uspA and eae gene detection (Figure absorbance at 280 nm and hence the ratio of 2 and 3).When eae primers used, the assay was OD readings at 260 nm to 280 nm should fall able to determine with a good approximation within the range of 1.6-2.0 for any pure and the quantity of E. coli cells spiked in our good quality extracted DNAs. Solutions having samples, ranging from 108 to 102cells mL-1. this ratio below 1.6 are thought to be However, the limit of quantification of the contaminated either by protein or phenol. On methodis about 103 cellsml-1, and that of the other hand, RNA affords a somewhat detection 102 cellsml-1(Figure 3). In addition, higher 260 nm/280 nm ratio, 2.0-2.3. A DNA we were able to detect uspA genes with the preparation with a ratio higher than 2.0 may be same detection limit of 102 cells mL-1 (Figure contaminated with RNA(Khare et al., 2014). 2).Although q-PCR methods are increasingly Therefore, our DNA (isolated from the being used to detect bacterial pathogens in standards and samples) with ODs ranging from different sample sources, detection limits rarely 201 Nabi A./ZJPAS: 2017, 29 (2): 196-207 exceed 102–103 CFU g−1(Pasquale Russo et developing this assay was to overpass the al., 2014), therefore our results revealed enrichment process. One more reason might be efficient detection limits for testing blood and related to the fact that an overnight enrichment other clinical samples also because the of samples in a nonselective medium is infective dose causing severe disease in important for detection of very low levels humans is very low (10 to 100 CFU) for the (between 1 and 10CFU/g of samples) of EHEC pathogenic E. coli including the EHEC O157, contamination(Sharma, 2002), and the and presumably of EHEC O26 and EHEC detection limit and the efficiency of q-PCRs O111 (Willshaw et al., 1994). The most recent depends on the DNA quality which is critical advances in PCR methods are focused on the because the efficiency of PCRs can be reduced reduction of the limits of detection and by inhibitors from the matrix (Elizaquivel and quantification, on the discrimination between Aznar, 2008). In another study, Chaney et al. dead and live cells or the simultaneous (1998)developed a procedure to detect total detection of different foodborne pathogens. bacterial cells in blood products using bacterial The performances of these methods were, in ribosomal RNA-directed probes coupled to some cases, successfully compared with the electrochemiluminescence which is somehow official protocols or with diagnostic similar to the quantification uspA gene of the commercial kits (Pasquale Russo et al., 2014). work, however they obtained a detection range For instance, Sharma (2002) explained that if of 105-108 cells mL-1, while our detection limits the enrichment process removed for samples of were better having a range from 103-108 cells foods and/or feces, these quantitative R-PCR mL-1 for the uspA qR-PCR assay resulting in assays could probably allow the detection of the development of a quantitative standard contamination levels of 103 CFU/g, as the curve with a good regression factor of 0.997 lowest detection limit and he obtained linear for uspA gene (Figure 2). DNA concentrations corresponding to 103 to 108 CFU/ml of an EHEC strain using same target genes and TaqMan based qR-PCR assay.

In a second series of experiments, we utilized the tenfold dilution of positive controls DNAs to test the limit of detection of our method. Our R-PCR assay, revealed positive results for the uspA and eae primers in the whole range of the spiked samples; however eae primers failed to get a quantitative result at concentrations below 103 cells ml-1. This might be related to the presence of inhibitors to the amplification of Figure 1. Sybr Green Real-time PCR amplification eae gene since it targets EPEC/EHEC bacteria curves for the serial dilutions type strains E. coli and its presence is very rare in blood samples, HB101 and tested blood samples targeting the uspA gene calculating the fluorescence changes (ΔRn) also the eae primer product is only 106bps versus Cycle Numbers. Analysed by Applied which may need more time for amplification Biosystems 7300 software version 1.3.0v (Applied Biosystems, USA). (in terms of conventional microbiology means more incubation time), while our goal 202 Nabi A./ZJPAS: 2017, 29 (2): 196-207

Figure 2. Quantitative uspA-SGR-PCR showing the Figure 3. Quantitative eae-SGR-PCR showing the developed standard curve for uspA gene detection in developed standard curve for eae gene detection in the serial dilutions of E. coli positive control HB101 the serial dilutions of E. coli positive control EDL933 strain using Applied BioSystems 7300 software strain using Applied BioSystems 7300 software version 1.3.0v (Applied Biosystems, USA). version 1.3.0v (Applied Biosystems, USA).

3.3. Standard Curve analysis for the and eae genes were 0.997 and 0.995, quantitative uspA-, eae- R-PCR assays respectively.

To quantify PCR product in real-time, the On the other hand, the genome of E. coli increase of fluorescence signal was measured EDL933 which has a length of 5.6 x106 bps of during amplification. The qSGR-PCR data about 5,312 genes harbors only one copy of the were plotted as the ΔRn fluorescence signal vs target eae gene which has been considered in cycle number and the Applied Biosystems this work. This means that any increase of 7300 sequence detection system software DNA copy numbers are corresponding with E. calculates the ΔRn using the equation ΔRn= coli counts (Dorak, 2007), therefore, the + - + (Rn ) - (Rn ) where Rn is the fluorescence detection limit of our qSG R-PCR assays was - 3 -1 signal of the product at any given time and Rn nearly 10 cells mL for the selected eae primer. is the fluorescence signal of the baseline In a study performed by Spano et. al., (2005) emission during cycles 3–15. An arbitrary targeting eae gene, similar results observed threshold was set at the midpoint of the log however they used a probe based qR-PCR + ΔRn vs the cycle number plot and the Ct-value assay, which is more expensive but its which is the cycle number at which the ΔRn sensitivity is higher. An advantage of our PCR crosses this threshold (Figure 1). Standard assay is the development of a quantitative R- curves were developed by using serial dilutions PCR method, using SYBR Green I, which is of E. coli strains HB101 and EDL 933 DNA as inexpensive fluorescent dye binds internal standard (Figure 2 and 3) with DNA nonspecifically to the minor groove of the concentration ranging from 100 to 108cells mL- synthesized double stranded DNA (Westh et 1 similarly to that described by Spano et. al., al., 2009), while using TaqMan probe which (2005) and recommended by Dorak (2007) and anneals inside the amplicon’s sequence has John M. Walker and Rapley (2008). Efficiency improved specificity and quality of PCR signal of amplification (E) was estimated from (Holland et al.,1991) but is more expensive. standard curve data, with the formula: E = Therefore, the specifity of our quantitative (101/slope) – 1 and measured after each qR-PCR assay had to be increased by an adding a melt assay, revealing an amplification efficiency curve analysis to the end of each qSGR-PCR range of 95-97% for all extracted DNAs, while runs. Therefore, our experiments, was able to the squared regression coefficient (R2) for uspA detect E. coli(including putative EPEC O157) in blood samples when at least 103cells mL-1 203 Nabi A./ZJPAS: 2017, 29 (2): 196-207 were present, therefore the limit of detection of to 9.6 × 103 cells mL-1 depending on the type our method was higher than presumptive of sample. Moreover, the maximum number of infective dose for E. coliO157which is 10–100 the pathogen (1.09 x 106 mL-1) was obtained CFU as described by Willshaw et al. (1994) from tested stool samples, while the minimum and by Chaney et al. (1998).In Figures 2 and 3, number (0.9 x 101 mL-1) was obtained from the the standard curves for eae and uspA genes are unspiked positive blood samples (Table 2). The presented showing a lower limit of 8.8x103 resulting sensitivity was lower than a similar cells mL-1 blood samples achieved when uspA works by Westh et al., (2009) using SeptiFast primers used, whereas a limit of 103to tests (Roche Diagnostics GmbH, Germany) 106cellsmL-1 was achieved with eae primers where the presence of individual and the regression factor of the standard curve microorganisms were detectable at lower for the eae primer set was lower; 0.995 (Figure counts, for instance they obtained 3 × 102 CFU 3), this because the fluorescence signal is less mL-1 for E. coli, similar to that obtained by linear with threshold cycles at lower DNA Spano et al. (2005), however, both studies used dilutions (Beneduce et al., 2008) and described probe based R-PCR methods which are by Sharma (2002).The developed standard commercially optimized and are of a higher curves are stating that our method is qualitative sensitivity and efficiency (Dorak, 2007, John and quantitative in the above range of DNA M. Walker and Rapley, 2008). concentrations, and that the qSGR-PCR assay can be a successful molecular tool to identify and quantify E. coli present at concentrations 3.5. Efficiency of uspA-, eae- SGR-PCR 3 -1 greater than10 cell mL . assays in detection of E. coli The advantages of using SYBR Green I assays with R- PCRs is due to three factors: 1) 3.4. Quantitative R-PCR to count E. coli low cost for the dye; 2) ease of assay from samples development, only a pair of primers is required; In the last years, several works compared and 3) the same detection mechanism can be different microbial DNA extraction techniques used for every assay (Dorak, 2007, John M. in order to optimize yield, time, and cost of the Walker and Rapley, 2008). In this study, the sample preparation process depending on the SG R-PCR was applied randomly on different source of the sample (Pasquale Russo et al., samples (urine, diarrheal stool, waste water, 2014, G. Amagliani et al., 2007). As shown in and water), with known bacterial infection. Figure (1), the fluorescence signal was detected Positive PCR assays for uspA genes were only for positive samples in all the experiments repeated twice on the samples collected for this with the different sets of primers. Studies to study to detect the presence of eae gene. No assess the analytical sensitivity & eae were amplified from blood or water quantification of the pathogen DNA tests samples, which means the absence of EPEC described above involved “spiking” blood and/or EHEC including E. coli O157. When samples with known amounts of bacterial cells. the same pathogen inoculated artificially to the This required accurate quantification of unspiked samples, amplification of the eae bacterial cultures (Al_griw, 2011, Chaney et gene was successful confirming that the al., 1998). The result of sensitivity absence of false negative results. Pechorsky et determination of the developed qSGR-PCR al. (2009) reported that conventional culture assay has shown that it is possible to achieve results were significantly similar with PCR the detection threshold of 8.8 × 103 cells mL-1 results for tested samples. In this study, similar 204 Nabi A./ZJPAS: 2017, 29 (2): 196-207 results were obtained when the detective PCR assigned their genera. In our experiment, results were identical for the positive samples, SYBR Green R-PCR was first done as a however the positive samples were very rare singleplex for both eae and uspA primers in and the sample size was limited and no eae separate reaction tubes. The developed SGR- gene could be amplified from the PCR assay for the specific primers of E. coli aforementioned positive samples. However, revealed successful amplification for the uspA detecting the uspA genes provides an evidence and eae genes for the standard positive controls for the presence of any E. coli in the positive (figures 4 and 6), revealing melting blood samples but the developed uspA-SGR- temperature points at 88.1°C and 87.9°C, PCR assay is not specific for the presence of respectively (Table 2) and no significant EPEC E. coli O157, since the eae gene is differences between the sample Tm means and specific for the O157 strains as explained by their population Tm for each of the uspA-, eae- (Spano et al., 2005, Sharma, 2002). Similarly, SGR-PCR assays (Table 2 and Figure 8). Beneduce et. al., (2008) were able to detect E. coli O157 from food samples using the same eae gene as target for their PCR assay, while Chaney et al. (1998) were successful to detect of total bacterial cells in blood products, however they used bacterial ribosomal RNA- directed probes coupled to electrochemiluminescence which is somehow similar to the detection uspA gene in this study. Therefore, this method enables us to detect any E. coli bacteria also from other clinical samples Figure 4. Dissociation curve analysis for the SGR- infected with a putative pathogenic E. coli that PCR assay testing the positive control E. coli strain may be E.coli O157:H7 as reported by (Westh HB101 for the presence of uspA gene revealed a specific Tm curve for the bacterium from artificially et al., 2009, Monday et al., 2007, Sharma, spiked blood samples. Analysed with 7500 real time 2002). cycler (Applied Biosystems, USA).

On the other hand, the NTC which contained 3.6. Melt peak analysis and Tm efficiency for no DNA template resulted in no amplifications, the detective uspA-, eae- SGR-PCR assays conferring a successful gene-specific SGR- Post-amplification melting-curve analysis, PCR assay, and the absence of non-specific also called dissociation curve analysis is a products as described by (Dorak, 2007, John simple, straightforward way to ensure R-PCR M. Walker and Rapley, 2008) (Figure 5). When specificity for the target primers. Peaks in the applying the same PCR conditions on the melt curve can indicate the melting peaks of unspiked samples, 5 out of 45 revealed positive the target or can identify nonspecific PCR amplification for uspA primer and were amplification (Dorak, 2007, John M. Walker positive for the presence of E. coli resulting in and Rapley, 2008). In the 7300 system a specific Tm peaks (Tm = 88) (Figure 4 and software, that used to analyze our results, we 6), whereas when the assay conducted on observed the melt curve as normalized reporter DNAs extracted from suspected patients’ blood (Rn) vs. temperature or as derivative reporter samples, it resulted in negative amplification (−Rn′) vs. temperature and the amplified DNAs with the eae primers, suggesting the absence of were identified based on their melt peaks and EPEC E. coli in the unspiked samples, however 205 Nabi A./ZJPAS: 2017, 29 (2): 196-207 more 2 positive reactions resulted from Table 2. Statistical analysis comparing the average diarrheal samples (Table 2 and Figure 5) melt peaks Tm and theoretical Tm for both uspA-SGR- PCR and SGR-PCR assays suggesting the infection with Enteropathogenic eae- E. coli which could be E. coli O157 due to the Statistical Analysis Tm values (°C) presence of the eae gene. eae uspA gene gene Minimum 87.40 88.00 25% Percentile 87.55 88.00 Median 87.75 88.40 75% Percentile 87.98 88.40 Maximum 88.20 88.40

Mean 87.77 88.27 Std. Deviation 0.2733 0.2309 Figure 5. SYBR Green qR-PCR assay targeting eae Std. Error of Mean 0.1116 0.1333 gene for the none template controls (NTC) and Negative control strains revealed no amplification and no detection using Applied Biosystems 7300 software version 1.3.0v (Applied Biosystems, USA).

Figure 6. Dissociation curve analysis of the SGR- PCR assay targeting the uspA gene, showing same Figure 8. Average Tm values for amplifications of eae Tm specific melt peaks with variable fluorescence and uspA genes revealed from all positive E. coli and intensities (sample copy number variations) for the Enteropathogenic E. coli using the SG R-PCR assays, tested samples (positives) using the 7500 real time including the E. coli O157:H7 strain EDL 933 and cycler (Applied Biosystems, USA). HB101. In a study by S. Ram et al. (2007) the uidA gene have been amplified to quantify E. coli from water samples using a similar qSG-PCR technique, whereas K. C. Jinneman et al. (2003) used the qSG-PCR technique to amplify the stx2 gene which is an indicator to detect EPEC and/or EHEC from environmental

Figure 7. Dissociation curve analysis of the amplified samples (Pasquale Russo et al., 2014). On the eae gene using SGR-PCR assay for the positive other hand and to test the efficiency of our eae- control and 2 positive diarrhoeal stool samples SGR-PCR detection from blood, the showing same Tm specific melt peaks with variable fluorescence intensities (sample copy number aforementioned negative samples were spiked variations). Analysed with 7500 real time cycler with our positive type strain EDL933 (E. coli (Applied Biosystems, USA). O157:H7) cells and resulted in positive reactions with specific Tm profiles (Figure 5 206 Nabi A./ZJPAS: 2017, 29 (2): 196-207 and 7). Similarly, in a study to quantify Microbiology Laboratory of Erbil Teaching Helicobacter pylori in waste water samples by Hospital) and PAR Private Policlinics, for their Spano et al. (2005), the authors spiked the helps in collection of the samples. negative samples with the positive control to avoid any false negative results. Whereas, Conflict of Interest Deepa Anbazhagan et al. (2011), used the The author declares no conflict of interests. SGR-PCR technique only as a detection assay REFERENCES for some pathogens including E. coli, basing on BENEDUCE, L., SPANO, G., NABI, A. Q., dissociation curve analysis and the PCR LAMACCHIA, F., MASSA, S., AOUNI, R. & product melt peaks. They obtained a detection HAMAMA, A. 2008. Occurrence and efficiency of 93.47 % from control and sample characterization of Escherichia coli O157 and other testing’s, and they concluded that the serotypes in raw meat products in Morocco. J Food Prot, 71, 2082-6. conventional culture results were comparable BENEDUCE, L., SPANO, G., NABI, A. Q., TERZI, V., with their PCR assay. Therefore, the FIOCCO, D. & MASSA, S. 2007. Assessment of a aforementioned observations confers that the quantitative PCR method for the detection of developed SGR-PCR assay enables us to detect Helicobacter pylori in environmental samples. any E. coli from clinical and other samples, and Fresenius Environmental Bulletin, 16, 749-755. CHANEY, R., RIDER, J. & PAMPHILON, D. 1998. the failure of the assay on unspiked samples Direct detection of bacteria in cellular blood products was not due to inhibition of the enzyme by using bacterial ribosomal RNA-directed probes humic substances from environmental DNA coupled to electrochemiluminescence. Transfusion extraction procedure. Medicine, 9, 177-188. CHEN, J. & GRIFFITHS, M. 1998. PCR differentiation 4. CONCLUSIONS of Escherichia coli from other Gram‐negative bacteria using primers derived from the nucleotide Despite of relatively low positive data of sequences flanking the gene encoding the universal quantitative detection when using eae and uspA stress protein. Letters in applied microbiology, 27, primers to test the blood samples and unspiked 369-371. healthy bloods, both sets of primers showed to CURSONS, R. T., JEYERAJAH, E. & SLEIGH, J. W. be useful for identification of E. coli strains 1999. The use of polymerase chain reaction to detect septicemia in critically ill patients. Crit Care Med, that harbour pathogenicity genes. The 27, 937-40. developed standard curves confirms that our DARK, P. M., DEAN, P. & WARHURST, G. 2009. method is qualitative and quantitative in the Bench-to-bedside review: the promise of rapid above range of DNA concentrations, and that infection diagnosis during sepsis using polymerase the qSG R-PCR assay can be a successful chain reaction-based pathogen detection. Crit Care, 13, 217. molecular tool to identify and quantify all and DEEPA ANBAZHAGAN, WANG SEOK MUI, pathogenic E. coli directly from blood samples MARZIDA MANSOR, GRACIE ONG SIOK YAN, without pre-enrichment steps, when presenting MOHD YASIM YUSOF & SEKARAN, S. D. 2011. at concentrations greater than 102 cell.mL-1. DEVELOPMENT OF CONVENTIONAL AND REAL-TIME MULTIPLEX PCR ASSAYS FOR Acknowledgements THE DETECTION OF NOSOCOMIAL The author would like to thank Maj. Aras M. PATHOGENS Brazilian Journal of Microbiology, 448-458. Mawlood (Head of Forensic Laboratories) and Gen. Jabbar A. Shareef (GM of General DORAK, M. T. 2007. Real-time PCR. Taylor & Francis Directorate for Criminal Evidences), where Group, Second Edition. part of the project conducted. Moreover, the ELIZAQUIVEL, P. & AZNAR, R. 2008. A multiplex author thanks Mr. Mahmood Nuri (Head of RTi-PCR reaction for simultaneous detection of 207 Nabi A./ZJPAS: 2017, 29 (2): 196-207

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