Characteristics of Open Access Journals in Six Subject Areas
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Bioinformatics
Bioinformatics Bioinformatics is the combination of biology and information technology. The discipline encompasses any computational tools and methods used to manage, analyze and manipulate large sets of biological data. Essentially, bioinformatics has three components: The creation of databases allowing the storage and management of large biological data sets. The development of algorithms and statistics to determine relationships among members of large data sets. The use of these tools for the analysis and interpretation of various types of biological data, including DNA, RNA and protein sequences, protein structures, gene expression profiles, and biochemical pathways. The term bioinformatics first came into use in the 1990s and was originally synonymous with the management and analysis of DNA, RNA and protein sequence data. Computational tools for sequence analysis had been available since the 1960s, but this was a minority interest until advances in sequencing technology led to a rapid expansion in the number of stored sequences in databases such as GenBank. Now, the term has expanded to incorporate many other types of biological data, for example protein structures, gene expression profiles and protein interactions. Each of these areas requires its own set of databases, algorithms and statistical methods. Bioinformatics is largely, although not exclusively, a computer-based discipline. Computers are important in bioinformatics for two reasons: First, many bioinformatics problems require the same task to be repeated millions of times. For example, comparing a new sequence to every other sequence stored in a database or comparing a group of sequences systematically to determine evolutionary relationships. In such cases, the ability of computers to process information and test alternative solutions rapidly is indispensable. -
Bibliometric Study of Pain After Spinal Cord Injury
Hindawi Neural Plasticity Volume 2021, Article ID 6634644, 15 pages https://doi.org/10.1155/2021/6634644 Review Article Bibliometric Study of Pain after Spinal Cord Injury Yi-Zu Wang ,1 Cheng-Cheng Wu ,1 and Xue-Qiang Wang 1,2 1Department of Sport Rehabilitation, Shanghai University of Sport, 399 Changhai RD, Shanghai 200438, China 2Department of Rehabilitation Medicine, Shanghai Shangti Orthopaedic Hospital, 188 Hengren RD, Shanghai 200438, China Correspondence should be addressed to Xue-Qiang Wang; [email protected] Received 30 November 2020; Revised 31 January 2021; Accepted 9 February 2021; Published 20 February 2021 Academic Editor: Yazhuo Kong Copyright © 2021 Yi-Zu Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. The prevalence of comorbid pain after spinal cord injury (SCI) is relatively high in clinical observations and has continued to increase over time. Neuropathic pain (70.14%) is the most popular subject in academic journals after SCI. However, studies that used the bibliometric method to analyze comorbid pain after SCI are still lacking. This study is aimed at combining and integrating acquired information to analyze the global trends of research on the comorbidity of pain after SCI in the last three decades (1990–2019). Methods. Systematic works of literature published from 1990 to 2019 were obtained from the Web of Science Core Collection. CiteSpace software was used to analyze the relationship of publication year with the country, institution, journals, authors, references, and keywords. -
Cancer Informatics (A)
Cancer Open Access: Full open access to this and thousands of other papers at Informatics http://www.la-press.com. Computational Advances in Cancer Informatics (A) §§Xiaoqian Jiang §§Bairong Shen Assistant Professor of Biomedical Informatics, University Professor of Systems Biology, Soochow University, of California San Diego, La Jolla, CA, USA. Suzhou, Jiangsu, China. §§Rui Chen §§Rong Xu Research Assistant Professor of Computer Science, Hong Assistant Professor, Division of Medical Informatics, Case Kong Baptist University, Kowloon Tong, China. Western Reserve University, Cleveland, OH, USA. §§Samuel Cheng §§Song Yi Associate Professor of Electrical and Computing Research Fellow of Genetics, Harvard Medical School, Engineering, University of Oklahoma, Norman, OK, USA. Boston, MA, USA. §§Xia Jiang Assistant Professor of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA. Supplement Aims and Scope C a n c e r I n f o r m a t i c s r e p r e s e nt s a h y b r i d d i s c i p l i n e e n c o m p a s s i n g §§ Gene Set Enrichment Analysis the fields of oncology, computer science, bioinformatics, sta- §§ Hybrid Computing tistics, computational biology, genomics, proteomics, metabo- §§ Efficient Cloud Storage and Retrieval lomics, pharmacology, and quantitative epidemiology. The §§ Matching of Expression Patterns common bond or challenge that unifies the various disciplines §§ Multi-Modal Analysis is the need to bring order to the massive amounts of data gen- §§ Splice Variations and Chip Seq System Algorithms erated by researchers and clinicians attempting to find the §§ Rapid High-Throughput Analysis underlying causes and effective means of treating cancer. -
Rtms Modulated Anterior Cingulate Cortex for Pain
Tzabazis et al. Molecular Pain 2013, 9:33 http://www.molecularpain.com/content/9/1/33 MOLECULAR PAIN RESEARCH Open Access Shaped magnetic field pulses by multi-coil repetitive transcranial magnetic stimulation (rTMS) differentially modulate anterior cingulate cortex responses and pain in volunteers and fibromyalgia patients Alexander Tzabazis1*, Carina Mari Aparici2, Michael C Rowbotham7, M Bret Schneider4,5,6, Amit Etkin3,5 and David C Yeomans1 Abstract Background: Repetitive transcranial magnetic stimulation (rTMS) has shown promise in the alleviation of acute and chronic pain by altering the activity of cortical areas involved in pain sensation. However, current single-coil rTMS technology only allows for effects in surface cortical structures. The ability to affect activity in certain deep brain structures may however, allow for a better efficacy, safety, and tolerability. This study used PET imaging to determine whether a novel multi-coil rTMS would allow for preferential targeting of the dorsal anterior cingulate cortex (dACC), an area always activated with pain, and to provide preliminary evidence as to whether this targeted approach would allow for efficacious, safe, and tolerable analgesia both in a volunteer/acute pain model as well as in fibromyalgia chronic pain patients. Methods: Part 1: Different coil configurations were tested in a placebo-controlled crossover design in volunteers (N = 16). Tonic pain was induced using a capsaicin/thermal pain model and functional brain imaging was performed 15 by means of H2 O positron emission tomography – computed tomography (PET/CT) scans. Differences in NRS pain ratings between TMS and sham treatment (NRSTMS-NRSplacebo) which were recorded each minute during the 10 minute PET scans. -
Bioinformatics and Biology Insights Structural and Functional Insights
Bioinformatics and Biology Insights OPEN ACCESS Full open access to this and thousands of other papers at REVIEW http://www.la-press.com. Structural and Functional Insights on the Myosin Superfamily Divya P. Syamaladevi1,2, James A. Spudich1,3,* and R. Sowdhamini1,* 1National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bellary Road, Bangalore, India. 2Sugarcane Breeding Institute (SBI-ICAR), Coimbatore, Tamilnadu, India. 3Department of Biochemistry, Stanford University, Stanford, California. *Corresponding authors email: [email protected]; [email protected] Abstract: The myosin superfamily is a versatile group of molecular motors involved in the transport of specific biomolecules, vesicles and organelles in eukaryotic cells. The processivity of myosins along an actin filament and transport of intracellular ‘cargo’ are achieved by generating physical force from chemical energy of ATP followed by appropriate conformational changes. The typical myosin has a head domain, which harbors an ATP binding site, an actin binding site, and a light-chain bound ‘lever arm’, followed often by a coiled coil domain and a cargo binding domain. Evolution of myosins started at the point of evolution of eukaryotes, S. cerevisiae being the simplest one known to contain these molecular motors. The coiled coil domain of the myosin classes II, V and VI in whole genomes of several model organisms display differences in the length and the strength of interactions at the coiled coil interface. Myosin II sequences have long-length coiled coil regions that are predicted to have a highly stable dimeric interface. These are interrupted, how- ever, by regions that are predicted to be unstable, indicating possibilities of alternate conformations, associations to make thick fila- ments, and interactions with other molecules. -
Potential Predatory and Legitimate Biomedical Journals
Shamseer et al. BMC Medicine (2017) 15:28 DOI 10.1186/s12916-017-0785-9 RESEARCHARTICLE Open Access Potential predatory and legitimate biomedical journals: can you tell the difference? A cross-sectional comparison Larissa Shamseer1,2* , David Moher1,2, Onyi Maduekwe3, Lucy Turner4, Virginia Barbour5, Rebecca Burch6, Jocalyn Clark7, James Galipeau1, Jason Roberts8 and Beverley J. Shea9 Abstract Background: The Internet has transformed scholarly publishing, most notably, by the introduction of open access publishing. Recently, there has been a rise of online journals characterized as ‘predatory’, which actively solicit manuscripts and charge publications fees without providing robust peer review and editorial services. We carried out a cross-sectional comparison of characteristics of potential predatory, legitimate open access, and legitimate subscription-based biomedical journals. Methods: On July 10, 2014, scholarly journals from each of the following groups were identified – potential predatory journals (source: Beall’s List), presumed legitimate, fully open access journals (source: PubMed Central), and presumed legitimate subscription-based (including hybrid) journals (source: Abridged Index Medicus). MEDLINE journal inclusion criteria were used to screen and identify biomedical journals from within the potential predatory journals group. One hundred journals from each group were randomly selected. Journal characteristics (e.g., website integrity, look and feel, editors and staff, editorial/peer review process, instructions to authors, -
Evolutionary Bioinformatics Phylotempo
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central Evolutionary Bioinformatics OPEN ACCESS Full open access to this and thousands of other papers at SHORT REPORT http://www.la-press.com. PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences Melissa M. Norström1,*, Mattia C.F. Prosperi2,*, Rebecca R. Gray3, Annika C. Karlsson1 and Marco Salemi2 1Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden. 2University of Florida, College of Medicine, Department of Pathology, Immunology and Laboratory Medicine and Emerging Pathogens Institute, Gainesville, Florida, USA. 3Department of Zoology, University of Oxford, Oxford, UK. *These authors contributed equally. Corresponding author email: [email protected] Abstract: Serially-sampled nucleotide sequences can be used to infer demographic history of evolving viral populations. The shape of a phylogenetic tree often reflects the interplay between evolutionary and ecological processes. Several approaches exist to analyze the topology and traits of a phylogenetic tree, by means of tree balance, branching patterns and comparative properties. The temporal clustering (TC) statistic is a new topological measure, based on ancestral character reconstruction, which characterizes the temporal structure of a phylogeny. Here, PhyloTempo is the first implementation of the TC in the R language, integrating several other topological measures in a user-friendly graphical framework. The comparison of the TC statistic with other measures provides multifaceted insights on the dynamic processes shaping the evolution of pathogenic viruses. The features and applicability of PhyloTempo were tested on serially-sampled intra-host human and simian immunodeficiency virus population data sets. -
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ОТКРЫТЫЙ ДОСТУП. ОТКРЫТЫЕ АРХИВЫ ИНФОРМАЦИИ УДК 022.42 Я. Л. Шрайберг, М. В. Гончаров, А. И. Земсков, К. А. Колосов Открытый доступ: зарубежный и отечественный опыт – состояние и перспективы Представлены определение открытого доступа, его развитие и состояние в зарубежных странах и в России, обозначены перспективы ОД. Ключевые слова: открытый доступ, определения, критерии, модели, журналы открытого доступа, репозитарии открытого доступа, тематические репозитарии, институциональные репозитарии, преимущества, недостатки, перспективы, зарубежный опыт, отечественный опыт. Определения Открытого доступа (ОД) разработаны на конференциях в Будапеште (февраль 2002 г.), Бетесде (июнь 2003 г.) и Берлине (октябрь 2003 г.). Согласно исходному определению, выработанному в рамках Будапештского проекта Открытого доступа (Budapest Open Access Initiative), ОД определяется, как «не имеющий финансовых или иных барьеров, кроме доступа к самому Интернету». Для того чтобы работа считалась находящейся в ОД, правообладатель должен заранее дать разрешение пользователям «копировать, использовать, распространять, передавать и показывать произведение публично, изготовлять и распространять производные работы в любом цифровом формате для любой ответственной цели, при условии соответствующего признания авторства…». Это положение является ключевым, и в принципе его можно считать единым определением. ОД не связан с отменой, реформированием или нарушением авторского права. Юридической основой ОД служит либо ясно выраженное согласие правообладателя, либо переход документа -
S1 Is Associated with Chronic Low Back Pain
Kong et al. Molecular Pain 2013, 9:43 http://www.molecularpain.com/content/9/1/43 MOLECULAR PAIN RESEARCH Open Access S1 is associated with chronic low back pain: a functional and structural MRI study Jian Kong1,2*, Rosa B Spaeth1,Hsiao-YingWey1,2, Alexandra Cheetham1, Amanda H Cook1, Karin Jensen1, Ying Tan1, Hesheng Liu1, Danhong Wang1,MarcoLLoggia1,2, Vitaly Napadow2, Jordan W Smoller1, Ajay D Wasan3 and Randy L Gollub1,2 Abstract A fundamental characteristic of neural circuits is the capacity for plasticity in response to experience. Neural plasticity is associated with the development of chronic pain disorders. In this study, we investigated 1) brain resting state functional connectivity (FC) differences between patients with chronic low back pain (cLBP) and matched healthy controls (HC); 2) FC differences within the cLBP patients as they experienced different levels of endogenous low back pain evoked by exercise maneuvers, and 3) morphometric differences between cLBP patients and matched HC. We found the dynamic character of FC in the primary somatosensory cortex (S1) in cLBP patients, i.e., S1 FC decreased when the patients experienced low intensity LBP as compared with matched healthy controls, and FC at S1 increased when cLBP patients experienced high intensity LBP as compared with the low intensity condition. In addition, we also found increased cortical thickness in the bilateral S1 somatotopically associated with the lower back in cLBP patients as compared to healthy controls. Our results provide evidence of structural plasticity co-localized with areas exhibiting FC changes in S1 in cLBP patients. Keywords: Chronic low back pain, fMRI, Functional connectivity, Cortical thickness, Primary somatosensory cortex Introduction administration of comparable experimental pain, differ- Chronic low back pain (cLBP) is one of the most com- ences in activation during emotional decision-making mon reasons for all physician visits in the USA and is a tasks [13], reduced deactivation in several key default leading cause of disability [1,2]. -
SDSU Primo Central Database Selections, February 15, 2017
SDSU Primo Central Database Selections, February 15, 2017 Provider Resource name ARTstor, Inc. The ARTstor Digital Library Alexander Street Press Classical Music Library Alexander Street Press Classical Scores Library: Volume I Alexander Street Press Classical Scores Library: Volume II Alexander Street Press Contemporary World Music Alexander Street Press Dance in Video Alexander Street Press Jazz Music Library (U.S.) Alexander Street Press Music Online: Listening (North America) Alexander Street Press Opera In Video Alexander Street Press Smithsonian Global Sound for Libraries American Geosciences Institute GeoRef (ProQuest) American Institute of Physics AIP Journals American Institute of Physics AIP Open Access American Medical Association The JAMA Network American Psychological Association (APA) PsycARTICLES American Psychological Association (APA) PsycCRITIQUES American Society for Microbiology Journals.ASM.org American Society of Civil Engineers American Society of Civil Engineers - ASCE Proceedings American Society of Civil Engineers American Society of Civil Engineers - ASCE Standards American Society of Civil Engineers American Society of Civil Engineers - ASCE ebooks Annual Reviews Annual Reviews Association for Computing Machinery ACM Digital Library BMJ Publishing Group BMJ Journals BMJ Publishing Group BMJ Open Access and Free Journals Bentham Science Publishers Bentham Science - Journals Bibliothèque Nationale de France Gallica Bibliothèque Nationale de France Gallica Ebooks Bibliothèque Nationale de France Gallica Periodicals -
Story Abstract
SAGE Publisher 2017 Data analysis by Katherine Laprade Story SAGE, which defines itself as the “world’s largest independent academic publisher” on its website, bought Libertas Academica in 2016, which is one step in moving to the open access space. SAGE publishes more than 1000 journals and offer the possibility of hybrid gold open access publishing for almost all of them. It’s the first time this research team looks at the current state of the Open Access options available with SAGE. Data from 2016 and 2017 will be analyzed. This article will also examine the journals from Libertas Academica and look at the APC variations with previous years to determine if the APCs changed when SAGE acquired their journals. Finally, this analysis includes a comparison of the APC metadata available in DOAJ for this publisher. Abstract SAGE, which defines itself as the “world’s largest independent academic publisher” on its website, bought Libertas Academica in 2016, which is one step in moving to the open access space. SAGE publishes more than 1000 journals and offer the possibility of hybrid gold open access publishing for almost all of them. 165 journal published by SAGE are in fully open access. In 2016, around 86% of fully open access journals have an APC. The APC average is 1084 USD. In 2017, around 84% of fully open access journals have an APC, but only 16% of those have an APC in DOAJ. Of the APCs available in DOAJ, around 33% varies from the APCs found in SAGE. Less than 2% of fully open access journals have an APPC. -
Clinical Medicine Insights: Cardiology Ecallantide for the Treatment Of
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central Clinical Medicine Insights: Cardiology OPEN ACCESS Full open access to this and thousands of other papers at REVIEW http://www.la-press.com. Ecallantide for the Treatment of Hereditary Angiodema in Adults Michael Lunn and Erin Banta Penn State Hershey Section of Allergy and Immunology, Hershey, PA 17033, USA. Corresponding author email: [email protected] Abstract: Hereditary angioedema (HAE) is a clinical disorder characterized by a deficiency of C1 esterase inhibitor (C1-INH). HAE has traditionally been divided into two subtypes. Unique among the inherited deficiencies of the complement system, HAE Types I and II are inherited as an autosomal dominant disorder. The generation of an HAE attack is caused by the depletion and/or consumption of C1-inhibitor manifested as subcutaneous or submucosal edema of the upper airway, face, extremities, or gastrointestinal tract mediated by bradykinin. Attacks can be severe and potentially life-threatening, particularly with laryngeal involvement and treatment of acute attacks in the United States has been severely limited. In December 2009 the FDA approved ecallantide for the treatment of acute HAE attacks. Ecallantide is a small recombinant protein acting as a potent, specific and reversible inhibitor of plasma kallikrein which binds to plasma kallikrein blocking its binding site, directly inhibiting the conversion of high molecular weight kininogen to bradykinin. Administered subcutaneously, ecallantide was demonstrated in two clinical trials, EDEMA3 and EDEMA4, to decrease the length and severity of acute HAE attacks. Although there is a small risk for anaphylaxis, which limits home administration, ecallantide is a novel, safe, effective and alternative treatment for acute HAE attacks.