Fecal Microbiota Transplantation for Recurrent Clostridium Difficile
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Administering Unidata on UNIX Platforms
C:\Program Files\Adobe\FrameMaker8\UniData 7.2\7.2rebranded\ADMINUNIX\ADMINUNIXTITLE.fm March 5, 2010 1:34 pm Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta UniData Administering UniData on UNIX Platforms UDT-720-ADMU-1 C:\Program Files\Adobe\FrameMaker8\UniData 7.2\7.2rebranded\ADMINUNIX\ADMINUNIXTITLE.fm March 5, 2010 1:34 pm Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Beta Notices Edition Publication date: July, 2008 Book number: UDT-720-ADMU-1 Product version: UniData 7.2 Copyright © Rocket Software, Inc. 1988-2010. All Rights Reserved. Trademarks The following trademarks appear in this publication: Trademark Trademark Owner Rocket Software™ Rocket Software, Inc. Dynamic Connect® Rocket Software, Inc. RedBack® Rocket Software, Inc. SystemBuilder™ Rocket Software, Inc. UniData® Rocket Software, Inc. UniVerse™ Rocket Software, Inc. U2™ Rocket Software, Inc. U2.NET™ Rocket Software, Inc. U2 Web Development Environment™ Rocket Software, Inc. wIntegrate® Rocket Software, Inc. Microsoft® .NET Microsoft Corporation Microsoft® Office Excel®, Outlook®, Word Microsoft Corporation Windows® Microsoft Corporation Windows® 7 Microsoft Corporation Windows Vista® Microsoft Corporation Java™ and all Java-based trademarks and logos Sun Microsystems, Inc. UNIX® X/Open Company Limited ii SB/XA Getting Started The above trademarks are property of the specified companies in the United States, other countries, or both. All other products or services mentioned in this document may be covered by the trademarks, service marks, or product names as designated by the companies who own or market them. License agreement This software and the associated documentation are proprietary and confidential to Rocket Software, Inc., are furnished under license, and may be used and copied only in accordance with the terms of such license and with the inclusion of the copyright notice. -
The Gut Microbiota and Inflammation
International Journal of Environmental Research and Public Health Review The Gut Microbiota and Inflammation: An Overview 1, 2 1, 1, , Zahraa Al Bander *, Marloes Dekker Nitert , Aya Mousa y and Negar Naderpoor * y 1 Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne 3168, Australia; [email protected] 2 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia; [email protected] * Correspondence: [email protected] (Z.A.B.); [email protected] (N.N.); Tel.: +61-38-572-2896 (N.N.) These authors contributed equally to this work. y Received: 10 September 2020; Accepted: 15 October 2020; Published: 19 October 2020 Abstract: The gut microbiota encompasses a diverse community of bacteria that carry out various functions influencing the overall health of the host. These comprise nutrient metabolism, immune system regulation and natural defence against infection. The presence of certain bacteria is associated with inflammatory molecules that may bring about inflammation in various body tissues. Inflammation underlies many chronic multisystem conditions including obesity, atherosclerosis, type 2 diabetes mellitus and inflammatory bowel disease. Inflammation may be triggered by structural components of the bacteria which can result in a cascade of inflammatory pathways involving interleukins and other cytokines. Similarly, by-products of metabolic processes in bacteria, including some short-chain fatty acids, can play a role in inhibiting inflammatory processes. In this review, we aimed to provide an overview of the relationship between the gut microbiota and inflammatory molecules and to highlight relevant knowledge gaps in this field. -
Text Processing Tools
Tools for processing text David Morgan Tools of interest here sort paste uniq join xxd comm tr fmt sed fold head file tail dd cut strings 1 sort sorts lines by default can delimit fields in lines ( -t ) can sort by field(s) as key(s) (-k ) can sort fields of numerals numerically ( -n ) Sort by fields as keys default sort sort on shell (7 th :-delimited) field UID as secondary (tie-breaker) field 2 Do it numerically versus How sort defines text ’s “fields ” by default ( a space character, ascii 32h = ٠ ) ٠bar an 8-character string ٠foo “By default, fields are separated by the empty string between a non-blank character and a blank character.” ٠bar separator is the empty string between non-blank “o” and the space ٠foo 1 2 ٠bar and the string has these 2 fields, by default ٠foo 3 How sort defines text ’s “fields ” by –t specification (not default) ( a space character, ascii 32h = ٠ ) ٠bar an 8-character string ٠foo “ `-t SEPARATOR' Use character SEPARATOR as the field separator... The field separator is not considered to be part of either the field preceding or the field following ” separators are the blanks themselves, and fields are ' "٠ " ٠bar with `sort -t ٠foo whatever they separate 12 3 ٠bar and the string has these 3 fields ٠foo data sort fields delimited by vertical bars field versus sort field ("1941:japan") ("1941") 4 sort efficiency bubble sort of n items, processing grows as n 2 shell sort as n 3/2 heapsort/mergesort/quicksort as n log n technique matters sort command highly evolved and optimized – better than you could do it yourself Big -O: " bogdown propensity" how much growth requires how much time 5 sort stability stable if input order of key-equal records preserved in output unstable if not sort is not stable GNU sort has –stable option sort stability 2 outputs, from same input (all keys identical) not stable stable 6 uniq operates on sorted input omits repeated lines counts them uniq 7 xxd make hexdump of file or input your friend testing intermediate pipeline data cf. -
QLOAD Queue Load / Unload Utility for IBM MQ
Queue Load / Unload Utility for IBM MQ User Guide Version 9.1.1 27th August 2020 Paul Clarke MQGem Software Limited [email protected] Queue Load / Unload Utility for IBM MQ Take Note! Before using this User's Guide and the product it supports, be sure to read the general information under "Notices” Twenty-fourth Edition, August 2020 This edition applies to Version 9.1.1 of Queue Load / Unload Utility for IBM MQ and to all subsequent releases and modifications until otherwise indicated in new editions. (c) Copyright MQGem Software Limited 2015, 2020. All rights reserved. ii Queue Load / Unload Utility for IBM MQ Notices The following paragraph does not apply in any country where such provisions are inconsistent with local law. MQGEM SOFTWARE LIMITED PROVIDES THIS PUBLICATION "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Some states do not allow disclaimer of express or implied warranties in certain transactions, therefore this statement may not apply to you. The information contained in this document has not be submitted to any formal test and is distributed AS IS. The use of the information or the implementation of any of these techniques is a customer responsibility and depends on the customer's ability to evaluate and integrate them into the customer's operational environment. While each item has been reviewed by MQGem Software for accuracy in a specific situation, there is no guarantee that the same or similar results will be obtained elsewhere. -
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Philips et al. BMC Genomics (2020) 21:402 https://doi.org/10.1186/s12864-020-06810-9 RESEARCH ARTICLE Open Access Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia Anna Philips1, Ireneusz Stolarek1, Luiza Handschuh1, Katarzyna Nowis1, Anna Juras2, Dawid Trzciński2, Wioletta Nowaczewska3, Anna Wrzesińska4, Jan Potempa5,6 and Marek Figlerowicz1,7* Abstract Background: Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. Results: In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. -
THE HUMAN MICROBIOTA: the ROLE of MICROBIAL COMMUNITIES in HEALTH and DISEASE La Microbiota Humana: Comunidades Microbianas En La Salud Y En La Enfermedad
ACTA BIOLÓGICA COLOMBIANA http://www.revistas.unal.edu.co/index.php/actabiol SEDE BOGOTÁ FACULTAD DE CIENCIAS ARTÍCULODEPARTAMENTO DE DE REVISIÓN BIOLOGÍA INVITADO / INVITED REVIEW THE HUMAN MICROBIOTA: THE ROLE OF MICROBIAL COMMUNITIES IN HEALTH AND DISEASE La microbiota humana: comunidades microbianas en la salud y en la enfermedad Luz Elena BOTERO1,2, Luisa DELGADO-SERRANO3,4, Martha Lucía CEPEDA HERNÁNDEZ3, Patricia DEL PORTILLO OBANDO3, María Mercedes ZAMBRANO EDER3. 1 Facultad de Medicina, Universidad Pontificia Bolivariana. Calle 78B no. 72A-109, Bloque B, Piso 5. Medellín, Colombia. 2 Unidad de Bacteriología y Micobacterias, Corporación para Investigaciones Biológicas, Unidad Pontificia Bolivariana. Carrera 72A no. 78B-141. Medellín, Colombia. 3 Corporación Corpogen. Carrera 5 no. 66A-34. Bogotá D.C., Colombia. 4 Centro de Bioinformática y Biología Computacional- BIOS. Carrera 15B no. 161. Manizales, Colombia. For correspondence. [email protected] Received: 22nd March 2015, Returned for revision: 14th April 2015, Accepted: 10th July 2015. Associate Editor: Nubia Estela Matta Camacho. Citation / Citar este artículo como: Botero LE, Delgado-Serrano L, Cepeda ML, Del Portillo P, Zambrano MM. The human microbiota: the role of microbial communities in health and disease. Acta biol. Colomb. 2016;21(1):5-15. doi: http://dx.doi.org/10.15446/abc.v21n1.49761 ABSTRACT During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. -
From Donor to Patient: Collection, Preparation and Cryopreservation of Fecal Samples for Fecal Microbiota Transplantation
diseases Review From Donor to Patient: Collection, Preparation and Cryopreservation of Fecal Samples for Fecal Microbiota Transplantation Carole Nicco 1 , Armelle Paule 2, Peter Konturek 3 and Marvin Edeas 1,* 1 Cochin Institute, INSERM U1016, University Paris Descartes, Development, Reproduction and Cancer, Cochin Hospital, 75014 Paris, France; [email protected] 2 International Society of Microbiota, 75002 Paris, France; [email protected] 3 Teaching Hospital of the University of Jena, Thuringia-Clinic Saalfeld, 07318 Saalfeld, Germany; [email protected] * Correspondence: [email protected] Received: 6 March 2020; Accepted: 10 April 2020; Published: 15 April 2020 Abstract: Fecal Microbiota Transplantation (FMT) is suggested as an efficacious therapeutic strategy for restoring intestinal microbial balance, and thus for treating disease associated with alteration of gut microbiota. FMT consists of the administration of fresh or frozen fecal microorganisms from a healthy donor into the intestinal tract of diseased patients. At this time, in according to healthcare authorities, FMT is mainly used to treat recurrent Clostridium difficile. Despite the existence of a few existing stool banks worldwide and many studies of the FMT, there is no standard method for producing material for FMT, and there are a multitude of factors that can vary between the institutions. The main constraints for the therapeutic uses of FMT are safety concerns and acceptability. Technical and logistical issues arise when establishing such a non-standardized treatment into clinical practice with safety and proper governance. In this context, our manuscript describes a process of donor safety screening for FMT compiling clinical and biological examinations, questionnaires and interviews of donors. -
A Type System for Format Strings E
ifact t * r * Comple t te A A n * te W E is s * e C n l l o D C A o * * c T u e m S s E u e S e n I R t v A Type System for Format Strings e o d t y * s E a * a l d u e a t Konstantin Weitz Gene Kim Siwakorn Srisakaokul Michael D. Ernst University of Washington, USA {weitzkon,genelkim,ping128,mernst}@cs.uw.edu ABSTRACT // Untested code (Hadoop) Most programming languages support format strings, but their use Resource r = ... format("Insufficient memory %d", r); is error-prone. Using the wrong format string syntax, or passing the wrong number or type of arguments, leads to unintelligible text // Unchecked input (FindBugs) output, program crashes, or security vulnerabilities. String urlRewriteFormat = read(); This paper presents a type system that guarantees that calls to format(urlRewriteFormat, url); format string APIs will never fail. In Java, this means that the API will not throw exceptions. In C, this means that the API will not // User unaware log is a format routine (Daikon) log("Exception " + e); return negative values, corrupt memory, etc. We instantiated this type system for Java’s Formatter API, and // Invalid syntax for Formatter API (ping-gcal) evaluated it on 6 large and well-maintained open-source projects. format("Unable to reach {0}", server); Format string bugs are common in practice (our type system found Listing 1: Real-world code examples of common programmer 104 bugs), and the annotation burden on the user of our type system mistakes that lead to format routine call failures. -
Human Microbiota Network: Unveiling Potential Crosstalk Between the Different Microbiota Ecosystems and Their Role in Health and Disease
nutrients Review Human Microbiota Network: Unveiling Potential Crosstalk between the Different Microbiota Ecosystems and Their Role in Health and Disease Jose E. Martínez †, Augusto Vargas † , Tania Pérez-Sánchez , Ignacio J. Encío , Miriam Cabello-Olmo * and Miguel Barajas * Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain; [email protected] (J.E.M.); [email protected] (A.V.); [email protected] (T.P.-S.); [email protected] (I.J.E.) * Correspondence: [email protected] (M.C.-O.); [email protected] (M.B.) † These authors contributed equally to this work. Abstract: The human body is host to a large number of microorganisms which conform the human microbiota, that is known to play an important role in health and disease. Although most of the microorganisms that coexist with us are located in the gut, microbial cells present in other locations (like skin, respiratory tract, genitourinary tract, and the vaginal zone in women) also play a significant role regulating host health. The fact that there are different kinds of microbiota in different body areas does not mean they are independent. It is plausible that connection exist, and different studies have shown that the microbiota present in different zones of the human body has the capability of communicating through secondary metabolites. In this sense, dysbiosis in one body compartment Citation: Martínez, J.E.; Vargas, A.; may negatively affect distal areas and contribute to the development of diseases. Accordingly, it Pérez-Sánchez, T.; Encío, I.J.; could be hypothesized that the whole set of microbial cells that inhabit the human body form a Cabello-Olmo, M.; Barajas, M. -
Some UNIX Commands At
CTEC1863/2007F Operating Systems – UNIX Commands Some UNIX Commands at Syntax: at time [day] [file] Description: Provides ability to perform UNIX commands at some time in the future. At time time on day day, the commands in filefile will be executed. Comment: Often used to do time-consuming work during off-peak hours, or to remind yourself to do something during the day. Other at-related commands: atq - Dump the contents of the at event queue. atrm - Remove at jobs from the queue. Examples: # at 0300 calendar | mail john ^D # # cat > DOTHIS nroff -ms doc1 >> doc.fmt nroff -ms file2 >> doc.fmt spell doc.fmt > SPELLerrs ^D # at 0000 DOTHIS cal Syntax: cal [month] year Description: Prints a calendar for the specified year or month. The year starts from year 0 [the calendar switched to Julian in 1752], so you typically must include the century Comment: Typical syntax: cal 11 1997 cal 1998 /Users/mboldin/2007F/ctec1863/unixnotes/UNIX-07_Commands.odt Page 1 of 5 CTEC1863/2007F Operating Systems – UNIX Commands calendar Syntax: calendar [-] Description: You must set-up a file, typically in your home directory, called calendar. This is a database of events. Comment: Each event must have a date mentioned in it: Sept 10, 12/5, Aug 21 1998, ... Each event scheduled for the day or the next day will be listed on the screen. lpr Syntax: lpr [OPTIONS] [FILE] [FILE] ... Description: The files are queued to be output to the printer. Comment: On some UNIX systems, this command is called lp, with slightly different options. Both lpr and lp first make a copy of the file(s) to be printed in the spool directory. -
Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis
microorganisms Article Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis Anders Esberg 1,* , Linda Johansson 2, Ingegerd Johansson 1 and Solbritt Rantapää Dahlqvist 2,* 1 Department of Odontology, Umeå University, 901 87 Umeå, Sweden; [email protected] 2 Department of Public Health and Medicine, Rheumatology, Umeå University, 901 87 Umeå, Sweden; [email protected] * Correspondence: [email protected] (A.E.); [email protected] (S.R.D.) Abstract: Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality reg- ister for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. Citation: Esberg, A.; Johansson, L.; The results support a deviating oral microbiota composition already in eRA patients compared with Johansson, I.; Dahlqvist, S.R. -
The Role of Tannerella Forsythia and Porphyromonas Gingivalis in Pathogenesis of Esophageal Cancer Bartosz Malinowski1, Anna Węsierska1, Klaudia Zalewska1, Maya M
Malinowski et al. Infectious Agents and Cancer (2019) 14:3 https://doi.org/10.1186/s13027-019-0220-2 REVIEW Open Access The role of Tannerella forsythia and Porphyromonas gingivalis in pathogenesis of esophageal cancer Bartosz Malinowski1, Anna Węsierska1, Klaudia Zalewska1, Maya M. Sokołowska1, Wiktor Bursiewicz1*, Maciej Socha3, Mateusz Ozorowski1, Katarzyna Pawlak-Osińska2 and Michał Wiciński1 Abstract Tannerella forsythia and Porphyromonas gingivalis are anaerobic, Gram-negative bacterial species which have been implicated in periodontal diseases as a part of red complex of periodontal pathogens. Esophageal cancer is the eight most common cause of cancer deaths worldwide. Higher rates of esophageal cancer cases may be attributed to lifestyle factors such as: diet, obesity, alcohol and tobacco use. Moreover, the presence of oral P. gingivalis and T. forsythia has been found to be associated with an increased risk of esophageal cancer. Our review describes theroleofP. gingivalis and T. forsythia in signaling pathways responsible for cancer development. It has been shown that T. forsythia may induce pro-inflammatory cytokines such as IL-1β and IL-6 by CD4 + T helper cells and TNF-α. Moreover, gingipain K produced by P. gingivalis, affects hosts immune system by degradation of immunoglobulins and complement system (C3 and C5 components). Discussed bacteria are responsible for overexpression of MMP-2, MMP-2 and GLUT transporters. Keywords: Esophageal cancer, Tannerella forsythia, Porphyromonas gingivalis Background of cases) and adenocarcinoma (10%). Currently, there is a Cancer is a significant problem in the modern world. It downward trend in the incidence of squamous cell carcin- concerns the entire population. In developed countries, oma and an increase in adenocarcinoma [1].