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Kell DB, Lip GYH, Pretorius E. Fibrinaloid Microclots and Atrial Fibrillation. Biomedicines 2024; 12:891. [PMID: 38672245 PMCID: PMC11048249 DOI: 10.3390/biomedicines12040891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Atrial fibrillation (AF) is a comorbidity of a variety of other chronic, inflammatory diseases for which fibrinaloid microclots are a known accompaniment (and in some cases, a cause, with a mechanistic basis). Clots are, of course, a well-known consequence of atrial fibrillation. We here ask the question whether the fibrinaloid microclots seen in plasma or serum may in fact also be a cause of (or contributor to) the development of AF. We consider known 'risk factors' for AF, and in particular, exogenous stimuli such as infection and air pollution by particulates, both of which are known to cause AF. The external accompaniments of both bacterial (lipopolysaccharide and lipoteichoic acids) and viral (SARS-CoV-2 spike protein) infections are known to stimulate fibrinaloid microclots when added in vitro, and fibrinaloid microclots, as with other amyloid proteins, can be cytotoxic, both by inducing hypoxia/reperfusion and by other means. Strokes and thromboembolisms are also common consequences of AF. Consequently, taking a systems approach, we review the considerable evidence in detail, which leads us to suggest that it is likely that microclots may well have an aetiological role in the development of AF. This has significant mechanistic and therapeutic implications.
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, 2800 Kongens Lyngby, Denmark
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Gregory Y. H. Lip
- Liverpool Centre for Cardiovascular Science at University of Liverpool, Liverpool John Moores University and Liverpool Heart and Chest Hospital, Liverpool L7 8TX, UK;
- Danish Center for Health Services Research, Department of Clinical Medicine, Aalborg University, 9220 Aalborg, Denmark
| | - Etheresia Pretorius
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown St, Liverpool L69 7ZB, UK
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
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The Issues with Journal Issues: Let Journals Be Digital Libraries. PUBLICATIONS 2023. [DOI: 10.3390/publications11010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Science depends on a communication system, and today, that is largely provided by digital technologies such as the internet and web. Despite the fact that digital technologies provide the infrastructure for this communication system, peer-reviewed journals continue to mimic workflows and processes from the print era. This paper focuses on one artifact from the print era, the journal issue, and describes how this artifact has been detrimental to the communication of science, and therefore, to science itself. To replace the journal issue, this paper argues that scholarly publishing and journals could more fully embrace digital technologies by creating digital libraries to present and organize scholarly output.
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Yan W, Liu Q, Chen R, Yi S. Social networks formed by follower–followee relationships on academic social networking sites: an examination of corporation users. Scientometrics 2020. [DOI: 10.1007/s11192-020-03553-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Bugyei KA, Kavi RK, Obeng-Koranteng G. Assessing the Awareness and Usage of Reference Management Software (RMS) Among Researchers of the Council for Scientific and Industrial Research (CSIR) Ghana. JOURNAL OF INFORMATION & KNOWLEDGE MANAGEMENT 2019. [DOI: 10.1142/s021964921950031x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study seeks to ascertain the levels of awareness and usage of reference management software (RMS) among researchers of the Council for Scientific and Industrial Research (CSIR), Ghana. The purpose and benefits as well as challenges associated with the use of these tools were also discussed. Descriptive survey methodology was employed for this study. A web-based questionnaire consisting of both multiple-choice and open-ended questions was used to collect data from 110 scientists in 13 research institutes of the CSIR, Ghana. Results show that overwhelming majority of scientists (80%) are aware and know about RMS. However, the adoption and usage of these tools are low. The percentage of non-usage was higher among the older scientists (22% for over 51 years) as against the younger researchers (9% for 31 to 40 years). Overall, 33.6% do not use RMS at all, and scientists occasionally used RMS. Mendeley was the most popularly used software among respondents. Results also show that most of the respondents got to know about RMS through training workshops and seminars. Most of the respondents had not received any training and for those who had attended a training workshop or seminar, majority of them noted that it was very easy to use. The main purpose of using these tools was for research work and literature review. Major benefits of using RMS packages are automatic generation of references list, electronic creation of bibliographies and changing of referencing style by a click of a button. Challenges associated with the use of these tools were slow internet connection, lack of training, and technical support. The study recommended that CSIR should make the effort to acquire these tools. Scientists should also be given the necessary training and technical support in order to effectively use these softwares.
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Affiliation(s)
| | | | - Grace Obeng-Koranteng
- CSIR — Institute for Scientific and Technological Information, P. O. Box M 32, Accra, Ghana
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Willighagen LG. Citation.js: a format-independent, modular bibliography tool for the browser and command line. PeerJ Comput Sci 2019; 5:e214. [PMID: 33816867 PMCID: PMC7924481 DOI: 10.7717/peerj-cs.214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 07/15/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND Given the vast number of standards and formats for bibliographical data, any program working with bibliographies and citations has to be able to interpret such data. This paper describes the development of Citation.js (https://citation.js.org/), a tool to parse and format according to those standards. The program follows modern guidelines for software in general and JavaScript in specific, such as version control, source code analysis, integration testing and semantic versioning. RESULTS The result is an extensible tool that has already seen adaption in a variety of sources and use cases: as part of a server-side page generator of a publishing platform, as part of a local extensible document generator, and as part of an in-browser converter of extracted references. Use cases range from transforming a list of DOIs or Wikidata identifiers into a BibTeX file on the command line, to displaying RIS references on a webpage with added Altmetric badges to generating "How to cite this" sections on a blog. The accuracy of conversions is currently 27% for properties and 60% for types on average and a typical initialization takes 120 ms in browsers and 1 s with Node.js on the command line. CONCLUSIONS Citation.js is a library supporting various formats of bibliographic information in a broad selection of use cases and environments. Given the support for plugins, more formats can be added with relative ease.
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Speare M. Graduate Student Use and Non-use of Reference and PDF Management Software: An Exploratory Study. JOURNAL OF ACADEMIC LIBRARIANSHIP 2018. [DOI: 10.1016/j.acalib.2018.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Méndez M. Ten simple rules for developing good reading habits during graduate school and beyond. PLoS Comput Biol 2018; 14:e1006467. [PMID: 30307941 PMCID: PMC6181267 DOI: 10.1371/journal.pcbi.1006467] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Marcos Méndez
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
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Chen L, Friedman C, Finkelstein J. Automated Metabolic Phenotyping of Cytochrome Polymorphisms Using PubMed Abstract Mining. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2017:535-544. [PMID: 29854118 PMCID: PMC5977704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pharmacogenetics-related publications, which are increasing rapidly, provide important new pharmacogenetics knowledge. Automated approaches to extract information of new alleles and to identify their impact on metabolic phenotypes from publications are urgently needed to facilitate personalized medicine and improve clinical outcomes. Cytochrome polymorphisms, responsible for a wide variation of drug pharmacodynamics, individual efficacy and adverse effects, have significant potential for optimizing drug therapy. A few studies have addressed specialized efforts to automatically extract cytochrome polymorphisms and their characterizations regarding metabolic phenotypes from the literature. In this paper, we present a novel rule-based text-mining system to extract metabolic phenotypes of polymorphisms from PubMed abstracts with a focus on cytochrome P450. This system is promising as it achieved a precision of 85.71% in a preliminary proof-of-concept evaluation and is expected to automatically provide up-to-date metabolic information for cytochrome polymorphisms, which is critical to advance personalized medicine and improve clinical care.
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Affiliation(s)
- Luoxin Chen
- Department of Biomedical Informatics, Columbia University, New York, NY, US
| | - Carol Friedman
- Department of Biomedical Informatics, Columbia University, New York, NY, US
| | - Joseph Finkelstein
- Department of Biomedical Informatics, Columbia University, New York, NY, US
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Bar-Ilan J. Tale of Three Databases: The Implication of Coverage Demonstrated for a Sample Query. Front Res Metr Anal 2018. [DOI: 10.3389/frma.2018.00006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yan W, Zhang Y. Research universities on the ResearchGate social networking site: An examination of institutional differences, research activity level, and social networks formed. J Informetr 2018. [DOI: 10.1016/j.joi.2017.08.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yan W, Zhang Y, Bromfield W. Analyzing the follower–followee ratio to determine user characteristics and institutional participation differences among research universities on ResearchGate. Scientometrics 2018. [DOI: 10.1007/s11192-018-2637-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zyoud SHH, Fuchs-Hanusch D, Zyoud SH, Al-Rawajfeh AE, Shaheen HQ. A bibliometric-based evaluation on environmental research in the Arab world. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY 2016. [DOI: 10.1007/s13762-016-1180-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Agarwal A, Durairajanayagam D, Tatagari S, Esteves SC, Harlev A, Henkel R, Roychoudhury S, Homa S, Puchalt NG, Ramasamy R, Majzoub A, Ly KD, Tvrda E, Assidi M, Kesari K, Sharma R, Banihani S, Ko E, Abu-Elmagd M, Gosalvez J, Bashiri A. Bibliometrics: tracking research impact by selecting the appropriate metrics. Asian J Androl 2016; 18:296-309. [PMID: 26806079 PMCID: PMC4770502 DOI: 10.4103/1008-682x.171582] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Traditionally, the success of a researcher is assessed by the number of publications he or she publishes in peer-reviewed, indexed, high impact journals. This essential yardstick, often referred to as the impact of a specific researcher, is assessed through the use of various metrics. While researchers may be acquainted with such matrices, many do not know how to use them to enhance their careers. In addition to these metrics, a number of other factors should be taken into consideration to objectively evaluate a scientist's profile as a researcher and academician. Moreover, each metric has its own limitations that need to be considered when selecting an appropriate metric for evaluation. This paper provides a broad overview of the wide array of metrics currently in use in academia and research. Popular metrics are discussed and defined, including traditional metrics and article-level metrics, some of which are applied to researchers for a greater understanding of a particular concept, including varicocele that is the thematic area of this Special Issue of Asian Journal of Andrology. We recommend the combined use of quantitative and qualitative evaluation using judiciously selected metrics for a more objective assessment of scholarly output and research impact.
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Affiliation(s)
- Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
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Erren TC, Shaw DM, Morfeld P. Analyzing the Publish-or-Perish Paradigm with Game Theory: The Prisoner's Dilemma and a Possible Escape. SCIENCE AND ENGINEERING ETHICS 2016; 22:1431-1446. [PMID: 26364213 DOI: 10.1007/s11948-015-9701-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 09/03/2015] [Indexed: 05/05/2023]
Abstract
The publish-or-perish paradigm is a prevailing facet of science. We apply game theory to show that, under rather weak assumptions, this publication scenario takes the form of a prisoner's dilemma, which constitutes a substantial obstacle to beneficial delayed publication of more complete results. One way of avoiding this obstacle while allowing researchers to establish priority of discoveries would be an updated "pli cacheté", a sealed envelope concept from the 1700s. We describe institutional rules that could additionally favour high-quality work and publications and provide examples of such policies that are already in place. Our analysis should be extended to other publication scenarios and the role of other stakeholders such as scientific journals or sponsors.
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Affiliation(s)
- T C Erren
- Institute and Policlinic for Occupational Medicine, Environmental Medicine and Prevention Research, University of Cologne, Kerpener Str. 61, 50938, Cologne, Germany.
| | - D M Shaw
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
| | - P Morfeld
- Institute and Policlinic for Occupational Medicine, Environmental Medicine and Prevention Research, University of Cologne, Kerpener Str. 61, 50938, Cologne, Germany
- Institute for Occupational Epidemiology and Risk Assessment (IERA), Evonik Industries AG, Essen, Germany
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An interpretive structural modelling of the features influencing researchers’ selection of reference management software. JOURNAL OF LIBRARIANSHIP AND INFORMATION SCIENCE 2016. [DOI: 10.1177/0961000616668961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Reference management software packages are established as research software packages to help scholars organize their work, improve workflows and ultimately save time. The number of citation management software packages has increased in recent years and therefore choosing an appropriate one has become a challenge for researchers. Scholars always explore the features of an appropriate RMS prior to making an investment to invest in one. Hence, the purpose of this study was to identify and analyze the prominent features in the selection of appropriate reference management software based on an extensive literature review and further to validate this through experts’ opinions. We have utilized the valuable opinions of experts to develop a hierarchical model based on the interpretive structural modelling approach to demonstrate the contextual interrelationship among these factors. Furthermore, the Matrice d’Impacts Croisées-Multiplication Appliquée à un Classement analysis approach has been utilized to classify the identified features based on their dependences and driving power, and to validate the developed interpretive structural modelling-based conceptual model. The developed model in this study can help reference management software developers to understand the correlations among the identified features and their interdependences to further enhance the quality of their products. The academic and practical contributions of the study are discussed.
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Lippi G, Ciaccio M, Giavarina D. Access to scientific information. A national survey of the Italian Society of Clinical Biochemistry and Laboratory Medicine (SIBioC). Diagnosis (Berl) 2016. [PMID: 29536893 DOI: 10.1515/dx-2016-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Digital libraries are typically used for retrieving and accessing articles in academic journals and repositories. Previous studies have been published about the performance of various biomedical research platforms, but no information is available about access preferences. METHODS A six-question survey was designed by the Italian Society of Clinical Biochemistry and Laboratory Medicine (SIBioC) using the platform Google Drive, and made available for 1 month to the members of the society. The information about the survey was published on the website of SIBioC and also disseminated by two sequential newsletters. RESULTS Overall, 165 replies were collected throughout the 1-month survey availability. The largest number of replies were provided by laboratory professionals working in the national healthcare system (44.2%), followed by those working in private facilities (13.9%), university professors (12.7%) and specialization training staff (12.7%). The majority of responders published zero to one articles per year (55.2%), followed by two to five articles per year (37.6%), whereas only 7.3% published more than five articles per year. A total of 34.5% of the responders consulted biomedical research platforms on weekly basis, followed by 33.9% who did so on daily basis. PubMed/Medline was the most accessed scientific database, followed by Scopus, ISI Web of Science and Google Scholar. The impact factor was the leading reason when selecting which journal to publish in. The most consulted journals in the field of laboratory medicine were Clinical Chemistry and Laboratory Medicine and Biochimica Clinica. CONCLUSIONS This survey provides useful indications about the personal inclination towards access to scientific information in our country.
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Affiliation(s)
- Giuseppe Lippi
- 1Section of Clinical Biochemistry, University Hospital of Verona, P.le LA Scuro 10, 37134 Verona, Italy
| | - Marcello Ciaccio
- 3Section of Clinical Biochemistry and Molecular Medicine, University of Palermo, Palermo, Italy; and President of the Italian Society of Clinical Biochemistry and Laboratory Medicine (SIBioC)
| | - Davide Giavarina
- 4Clinical Chemistry and Hematology Laboratory, St. Bortolo Hospital, Vicenza, Italy
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Nilashi M, Ibrahim O, Sohaei S, Ahmadi H, Almaee A. Features Influencing Researchers’ Selection of Reference Management Software. JOURNAL OF INFORMATION & KNOWLEDGE MANAGEMENT 2016. [DOI: 10.1142/s0219649216500325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Reference management software (RMS) is the most important aspect that is essential for all levels of researchers. They are established as research tools to help scholars in organising their work, improving workflows, and ultimately saving time. Choosing an appropriate RMS for managing records and utilising the bibliographic citation has been a challenge among researchers. They always seek for the features of an appropriate RMS prior to making an investment to buy the software. In this paper, a fuzzy logic approach is adopted for assessing the features of RMS from the researchers’ perspectives. Accordingly, a web-based survey was conducted and data collected from the researchers who had experience with different types of RMS. Then, we analyse the effects of RMS features on researcher perception in selecting an appropriate reference management program and find the importance level of those features. This study provides a toolset for RMS developers to identify the importance level of RMS features and accordingly consider these important features in developing the next generation of citation management software.
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Affiliation(s)
- Mehrbakhsh Nilashi
- Faculty of Computing, Universiti Technologi Malaysia, Johor, Malaysia
- Department of Computer Engineering, Lahijan Branch, Islamic Azad University, Lahijan, Iran
| | - Othman Ibrahim
- Faculty of Computing, Universiti Technologi Malaysia, Johor, Malaysia
| | - Shamila Sohaei
- Faculty of Computing, Universiti Technologi Malaysia, Johor, Malaysia
| | - Hossein Ahmadi
- Faculty of Management & Social Science, Tehran North Branch, Tehran, Iran
| | - Alireza Almaee
- Organization of Technical and Vocational Training, Lahijan, Guilan, Iran
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Sungur MO, Seyhan TÖ. Writing references and using citation management software. Turk J Urol 2015; 39:25-32. [PMID: 26328132 DOI: 10.5152/tud.2013.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/24/2013] [Indexed: 11/22/2022]
Abstract
The correct citation of references is obligatory to gain scientific credibility, to honor the original ideas of previous authors and to avoid plagiarism. Currently, researchers can easily find, cite and store references using citation management software. In this review, two popular citation management software programs (EndNote and Mendeley) are summarized.
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Affiliation(s)
- Mukadder Orhan Sungur
- Department of Anaesthesiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul, Turkey
| | - Tülay Özkan Seyhan
- Department of Anaesthesiology, İstanbul Faculty of Medicine, İstanbul University, İstanbul, Turkey
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Yusoff NM, Salim SS. A systematic review of shared visualisation to achieve common ground. JOURNAL OF VISUAL LANGUAGES AND COMPUTING 2015. [DOI: 10.1016/j.jvlc.2014.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ananiadou S, Thompson P, Nawaz R, McNaught J, Kell DB. Event-based text mining for biology and functional genomics. Brief Funct Genomics 2015; 14:213-30. [PMID: 24907365 PMCID: PMC4499874 DOI: 10.1093/bfgp/elu015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.
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Erren TC, Shaw DM, Groß JV. How to avoid haste and waste in occupational, environmental and public health research. J Epidemiol Community Health 2015; 69:823-5. [DOI: 10.1136/jech-2015-205543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Bernard J, Daberkow D, Fellner D, Fischer K, Koepler O, Kohlhammer J, Runnwerth M, Ruppert T, Schreck T, Sens I. VisInfo: a digital library system for time series research data based on exploratory search—a user-centered design approach. INTERNATIONAL JOURNAL ON DIGITAL LIBRARIES 2014. [DOI: 10.1007/s00799-014-0134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Gambadauro P, Navaratnarajah R. Reporting of embryo transfer methods in IVF research: a cross-sectional study. Reprod Biomed Online 2014; 30:137-43. [PMID: 25530033 DOI: 10.1016/j.rbmo.2014.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 11/24/2022]
Abstract
The reporting of embryo transfer methods in IVF research was assessed through a cross-sectional analysis of randomized controlled trials (RCTs) published between 2010 and 2011. A systematic search identified 325 abstracts; 122 RCTs were included in the study. Embryo transfer methods were described in 42 out of 122 articles (34%). Catheters (32/42 [76%]) or ultrasound guidance (31/42 [74%]) were most frequently mentioned. Performer 'blinding' (12%) or technique standardization (7%) were seldom reported. The description of embryo transfer methods was significantly more common in trials published by journals with lower impact factor (less than 3, 39.6%; 3 or greater, 21.5%; P = 0.037). Embryo transfer methods were reported more often in trials with pregnancy as the main end-point (33% versus 16%) or with positive outcomes (37.8% versus 25.0%), albeit not significantly. Multivariate logistic regression confirmed that RCTs published in higher impact factor journals are less likely to describe embryo transfer methods (OR 0.371; 95% CI 0.143 to 0.964). Registered trials, trials conducted in an academic setting, multi-centric studies or full-length articles were not positively associated with embryo transfer methods reporting rate. Recent reports of randomized IVF trials rarely describe embryo transfer methods. The under-reporting of research methods might compromise reproducibility and suitability for meta-analysis.
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Affiliation(s)
- Pietro Gambadauro
- Karolinska Institutet, LIME/NASP - C7, 17 177 Stockholm, Sweden; Res Medica Sweden, Gynaecology & Reproductive Medicine, 752 24 Uppsala, Sweden.
| | - Ramesan Navaratnarajah
- Bart's Health NHS Trust, Obstetrics and Gynaecology, The Royal London Hospital, E1 1BB London, UK; Katherine Twining Network, Queen Mary University of London, E1 2AB London, UK
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Šubelj L, Fiala D, Bajec M. Network-based statistical comparison of citation topology of bibliographic databases. Sci Rep 2014; 4:6496. [PMID: 25263231 PMCID: PMC4178292 DOI: 10.1038/srep06496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 09/09/2014] [Indexed: 11/09/2022] Open
Abstract
Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies.
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Affiliation(s)
- Lovro Šubelj
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Dalibor Fiala
- University of West Bohemia, Faculty of Applied Sciences, Univerzitní 8, CZ-30614 Plzeň, Czech Republic
| | - Marko Bajec
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, SI-1000 Ljubljana, Slovenia
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Tsafnat G, Glasziou P, Choong MK, Dunn A, Galgani F, Coiera E. Systematic review automation technologies. Syst Rev 2014; 3:74. [PMID: 25005128 PMCID: PMC4100748 DOI: 10.1186/2046-4053-3-74] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/26/2014] [Indexed: 02/08/2023] Open
Abstract
Systematic reviews, a cornerstone of evidence-based medicine, are not produced quickly enough to support clinical practice. The cost of production, availability of the requisite expertise and timeliness are often quoted as major contributors for the delay. This detailed survey of the state of the art of information systems designed to support or automate individual tasks in the systematic review, and in particular systematic reviews of randomized controlled clinical trials, reveals trends that see the convergence of several parallel research projects.We surveyed literature describing informatics systems that support or automate the processes of systematic review or each of the tasks of the systematic review. Several projects focus on automating, simplifying and/or streamlining specific tasks of the systematic review. Some tasks are already fully automated while others are still largely manual. In this review, we describe each task and the effect that its automation would have on the entire systematic review process, summarize the existing information system support for each task, and highlight where further research is needed for realizing automation for the task. Integration of the systems that automate systematic review tasks may lead to a revised systematic review workflow. We envisage the optimized workflow will lead to system in which each systematic review is described as a computer program that automatically retrieves relevant trials, appraises them, extracts and synthesizes data, evaluates the risk of bias, performs meta-analysis calculations, and produces a report in real time.
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Affiliation(s)
- Guy Tsafnat
- Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Sydney, Australia
| | - Paul Glasziou
- Centre for Research on Evidence Based Practice, Bond University, Gold Coast, Australia
| | - Miew Keen Choong
- Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Sydney, Australia
| | - Adam Dunn
- Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Sydney, Australia
| | - Filippo Galgani
- Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Sydney, Australia
| | - Enrico Coiera
- Centre for Health Informatics, Australian Institute of Health Innovation, University of New South Wales, Sydney, Australia
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Thelwall M, Kousha K. ResearchGate: Disseminating, communicating, and measuring Scholarship? J Assoc Inf Sci Technol 2014. [DOI: 10.1002/asi.23236] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mike Thelwall
- Statistical Cybermetrics Research Group; School of Mathematics and Computer Science; University of Wolverhampton; Wulfruna Street Wolverhampton WV1 1LY UK
| | - Kayvan Kousha
- Statistical Cybermetrics Research Group; School of Mathematics and Computer Science; University of Wolverhampton; Wulfruna Street Wolverhampton WV1 1LY UK
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H. Wordofa K. Adoption of Web 2.0 in academic libraries of top African universities. ELECTRONIC LIBRARY 2014. [DOI: 10.1108/el-07-2012-0077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
– This study aims to explore the extent of Web 2.0 adoption by libraries of top universities in Africa. It focuses on identifying the extent of utilization, types of Web 2.0 technologies adopted and how these technologies are used.
Design/methodology/approach
– The content analysis method was used. Data was collected by analyzing library websites of 82 top universities in Sub-Saharan Africa. Also, a combination of literature review and document analysis was applied.
Findings
– About half of the libraries in the study adopted one or more Web 2.0 applications. Social networks were the most widely adopted while social bookmarking and tagging were the least used applications. Web 2.0 utilization in African academic libraries was still in early stages.
Research limitations/implications
– This study is mainly based on analysis of library websites. Web 2.0 platforms that were password protected and accessible through intranet were not studied. Therefore, studies that are based on feedback of librarians and patrons are warranted to further investigate Web 2.0 utilization in African libraries.
Practical implications
– Web 2.0 plays a key role in facilitating information sharing, collaboration, and communication between librarians and patrons, and among librarians. It is essential for African libraries to integrate these technologies into library services to enhance the quality of services.
Originality/value
– This is likely the first study about Web 2.0 applications in African academic libraries. It is a useful source for implementing web-based technologies in libraries.
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Mahajan AK, Hogarth DK. Taking control of your digital library: how modern citation managers do more than just referencing. Chest 2014; 144:1930-1933. [PMID: 24297125 DOI: 10.1378/chest.13-0856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Physicians are constantly navigating the overwhelming body of medical literature available on the Internet. Although early citation managers were capable of limited searching of index databases and tedious bibliography production, modern versions of citation managers such as EndNote, Zotero, and Mendeley are powerful web-based tools for searching, organizing, and sharing medical literature. Effortless point-and-click functions provide physicians with the ability to develop robust digital libraries filled with literature relevant to their fields of interest. In addition to easily creating manuscript bibliographies, various citation managers allow physicians to readily access medical literature, share references for teaching purposes, collaborate with colleagues, and even participate in social networking. If physicians are willing to invest the time to familiarize themselves with modern citation managers, they will reap great benefits in the future.
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Affiliation(s)
- Amit K Mahajan
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL
| | - D Kyle Hogarth
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, IL.
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Affiliation(s)
- Mike Thelwall
- Statistical Cybermetrics Research Group, School of Technology; University of Wolverhampton; Wulfruna Street Wolverhampton WV1 1LY UK
| | - Kayvan Kousha
- Statistical Cybermetrics Research Group, School of Technology; University of Wolverhampton; Wulfruna Street Wolverhampton WV1 1LY UK
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Alvarez MDCA, França I, Cuenca AMB, Bastos FI, Ueno HM, Barros CR, Guimarães MCS. Information literacy: perceptions of Brazilian HIV/AIDS researchers. Health Info Libr J 2013; 31:64-74. [PMID: 24237629 DOI: 10.1111/hir.12047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/16/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Information literacy has evolved with changes in lifelong learning. Can Brazilian health researchers search for and use updated scientific information? OBJECTIVES To describe researchers' information literacy based on their perceptions of their abilities to search for and use scientific information and on their interactions with libraries. METHODS Semi-structured interviews and focus group conducted with six Brazilian HIV/AIDS researchers. Analyses comprised the assessment of researchers as disseminators, their interactions with librarians, their use of information and communication technology and language. RESULTS Interviewees believed they were partially qualified to use databases. They used words and phrases that indicated their knowledge of technology and terminology. They acted as disseminators for students during information searches. Researchers' abilities to interact with librarians are key skills, especially in a renewed context where libraries have, to a large extent, changed from physical spaces to digital environments. DISCUSSION Great amounts of information have been made available, and researchers' participation in courses does not automatically translate into adequate information literacy. Librarians must help research groups, and as such, librarians' information literacy-related responsibilities in Brazil should be redefined and expanded. CONCLUSIONS Students must develop the ability to learn quickly, and librarians should help them in their efforts. Librarians and researchers can act as gatekeepers for research groups and as information coaches to improve others' search abilities.
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Differential nutrient limitation of soil microbial biomass and metabolic quotients (qCO2): is there a biological stoichiometry of soil microbes? PLoS One 2013; 8:e57127. [PMID: 23526933 PMCID: PMC3602520 DOI: 10.1371/journal.pone.0057127] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 01/17/2013] [Indexed: 11/24/2022] Open
Abstract
Background Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils. Methodology/Principal Findings To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability. Conclusions/Significance Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats.
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Romero-Torres M, Acosta-Moreno LA, Tejada-Gómez MA. Ranking de revistas científicas en Latinoamérica mediante el índice h: estudio de caso Colombia. REVISTA ESPANOLA DE DOCUMENTACION CIENTIFICA 2013. [DOI: 10.3989/redc.2013.1.876] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Nawaz R, Thompson P, Ananiadou S. Negated bio-events: analysis and identification. BMC Bioinformatics 2013; 14:14. [PMID: 23323936 PMCID: PMC3561152 DOI: 10.1186/1471-2105-14-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 01/10/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified as a key challenge in biomedical relation extraction. In this article, we focus on the problem of identifying negated bio-events, given gold standard event annotations. RESULTS We have conducted a detailed analysis of three open access bio-event corpora containing negation information (i.e., GENIA Event, BioInfer and BioNLP'09 ST), and have identified the main types of negated bio-events. We have analysed the key aspects of a machine learning solution to the problem of detecting negated events, including selection of negation cues, feature engineering and the choice of learning algorithm. Combining the best solutions for each aspect of the problem, we propose a novel framework for the identification of negated bio-events. We have evaluated our system on each of the three open access corpora mentioned above. The performance of the system significantly surpasses the best results previously reported on the BioNLP'09 ST corpus, and achieves even better results on the GENIA Event and BioInfer corpora, both of which contain more varied and complex events. CONCLUSIONS Recently, in the field of biomedical text mining, the development and enhancement of event-based systems has received significant interest. The ability to identify negated events is a key performance element for these systems. We have conducted the first detailed study on the analysis and identification of negated bio-events. Our proposed framework can be integrated with state-of-the-art event extraction systems. The resulting systems will be able to extract bio-events with attached polarities from textual documents, which can serve as the foundation for more elaborate systems that are able to detect mutually contradicting bio-events.
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Affiliation(s)
- Raheel Nawaz
- National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Paul Thompson
- National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Sophia Ananiadou
- National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Rakhshan V. Reliance of scientific publication on citation management software: the new generation. J Dent Res Dent Clin Dent Prospects 2013; 6:158-9. [PMID: 23277864 PMCID: PMC3529931 DOI: 10.5681/joddd.2012.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/26/2012] [Indexed: 11/17/2022] Open
Affiliation(s)
- Vahid Rakhshan
- Department of Dental Anatomy and Morphology, Dental Branch, Islamic Azad University, Tehran, Iran
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Accelerating Scientists’ Knowledge Turns. COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE 2013. [DOI: 10.1007/978-3-642-37186-8_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Davis PM. The persistence of error: a study of retracted articles on the Internet and in personal libraries. J Med Libr Assoc 2012; 100:184-9. [PMID: 22879807 DOI: 10.3163/1536-5050.100.3.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE To determine the accessibility of retracted articles residing on non-publisher websites and in personal libraries. METHODS Searches were performed to locate Internet copies of 1,779 retracted articles identified in MEDLINE, published between 1973 and 2010, excluding the publishers' website. Found copies were classified by article version and location. Mendeley (a bibliographic software) was searched for copies residing in personal libraries. RESULTS Non-publisher websites provided 321 publicly accessible copies for 289 retracted articles: 304 (95%) copies were the publisher' versions, and 13 (4%) were final manuscripts. PubMed Central had 138 (43%) copies; educational websites 94 (29%); commercial websites 24 (7%); advocacy websites 16 (5%); and institutional repositories 10 (3%). Just 16 [corrected] (5%) full-article views included a retraction statement. Personal Mendeley libraries contained records for 1,340 (75%) retracted articles, shared by 3.4 users, on average. CONCLUSIONS The benefits of decentralized access to scientific articles may come with the cost of promoting incorrect, invalid, or untrustworthy science. Automated methods to deliver status updates to readers may reduce the persistence of error in the scientific literature.
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The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so. Drug Discov Today 2012. [PMID: 23207804 DOI: 10.1016/j.drudis.2012.11.008] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A recent paper in this journal sought to counter evidence for the role of transport proteins in effecting drug uptake into cells, and questions that transporters can recognize drug molecules in addition to their endogenous substrates. However, there is abundant evidence that both drugs and proteins are highly promiscuous. Most proteins bind to many drugs and most drugs bind to multiple proteins (on average more than six), including transporters (mutations in these can determine resistance); most drugs are known to recognise at least one transporter. In this response, we alert readers to the relevant evidence that exists or is required. This needs to be acquired in cells that contain the relevant proteins, and we highlight an experimental system for simultaneous genome-wide assessment of carrier-mediated uptake in a eukaryotic cell (yeast).
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Archambault PM, van de Belt TH, Grajales Iii FJ, Eysenbach G, Aubin K, Gold I, Gagnon MP, Kuziemsky CE, Turgeon AF, Poitras J, Faber MJ, Kremer JAM, Heldoorn M, Bilodeau A, Légaré F. Wikis and collaborative writing applications in health care: a scoping review protocol. JMIR Res Protoc 2012; 1:e1. [PMID: 23612481 PMCID: PMC3626140 DOI: 10.2196/resprot.1993] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/19/2012] [Accepted: 02/22/2012] [Indexed: 11/24/2022] Open
Abstract
The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. While researchers have conducted systematic reviews on a range of software-based information and communication technologies as well as other social media (eg, virtual communities of practice, virtual peer-to-peer communities, and electronic support groups), none have reviewed collaborative writing applications in the medical sector. The overarching goal of this project is to explore the depth and breadth of evidence for the use of collaborative writing applications in health care. Thus, the purposes of this scoping review will be to (1) map the literature on collaborative writing applications; (2) compare the applications’ features; (3) describe the evidence of each application’s positive and negative effects as a KT intervention in health care; (4) inventory and describe the barriers and facilitators that affect the applications’ use; and (5) produce an action plan and a research agenda. A six-stage framework for scoping reviews will be used: (1) identifying the research question; (2) identifying relevant studies within the selected databases (using the EPPI-Reviewer software to classify the studies); (3) selecting studies (an iterative process in which two reviewers search the literature, refine the search strategy, and review articles for inclusion); (4) charting the data (using EPPI-Reviewer’s data-charting form); (5) collating, summarizing, and reporting the results (performing a descriptive, numerical, and interpretive synthesis); and (6) consulting knowledge users during three planned meetings. Since this scoping review concerns the use of collaborative writing applications as KT interventions in health care, we will use the Knowledge to Action (KTA) framework to describe and compare the various studies and collaborative writing projects we find.
In addition to guiding the use of collaborative writing applications in health care, this scoping review will advance the science of KT by testing tools that could be used to evaluate other social media. We also expect to identify areas that require further systematic reviews and primary research and to produce a highly relevant research agenda that explores and leverages the potential of collaborative writing software. To date, this is the first study to use the KTA framework to study the role collaborative writing applications in KT, and the first to involve three national and international institutional knowledge users as part of the research process.
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Affiliation(s)
- Patrick Michel Archambault
- Centre de santé et de services sociaux Alphonse-Desjardins (Centre hospitalier affilié universitaire de Lévis), Lévis, QC, Canada.
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Kell DB. Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? Bioessays 2012; 34:236-44. [PMID: 22252984 PMCID: PMC3321226 DOI: 10.1002/bies.201100144] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a ‘landscape’ representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems ‘hard’, but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the ‘best’ experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, Lancs, UK.
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Affiliation(s)
- K K Mueen Ahmed
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
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Kim T. Building student proficiency with scientific literature using the Zotero reference manager platform. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 39:412-415. [PMID: 22081544 DOI: 10.1002/bmb.20551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
While mastery of the scientific literature is a strongly desirable trait for undergraduate students, the sheer volume of the current literature has complicated the challenge of teaching scientific literacy. Part of the response to this ever-increasing volume of resources includes formal instruction in the use of reference manager software while engaging students with the primary literature. This article describes the incorporation of the reference manager program Zotero into a chemical literature course to facilitate the use of digital resources and to better enable them to use proper citation skills in their technical writing.
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Affiliation(s)
- Thomas Kim
- Department of Chemistry, Rochester Institute of Technology, Rochester, New York 14623, USA.
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Rzepa HS. The past, present and future of Scientific discourse. J Cheminform 2011; 3:46. [PMID: 21999632 PMCID: PMC3208583 DOI: 10.1186/1758-2946-3-46] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 10/14/2011] [Indexed: 11/22/2022] Open
Abstract
The science journal is 346 years old in 2011, having evolved continuously but largely incrementally over that period. Its reinvention for an online presence has largely preserved its previously printed nature, in the sense that much of the increased functionality which is potentially offered by this new medium has yet to be exploited. In the present article an attempt is made to discuss two previously published papers, one in 1953 and the other in 2010, and to illustrate how additional functionality can be implemented in the form of accessible data sourced from quantum mechanical calculation and how subsequent discourse in the form of blogs may add to the process. In this sense, the reader of this article is invited to try for themselves whether these enhancements improve their scientific understanding, and whether such enhanced journals are good models for the future evolution of the genre.
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Affiliation(s)
- Henry S Rzepa
- Department of Chemistry, Imperial College London, Exhibition Road Campus, London SW7 2AZ, UK.
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47
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Garten Y, Coulet A, Altman RB. Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics 2011; 11:1467-89. [PMID: 21047206 DOI: 10.2217/pgs.10.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The biomedical literature holds our understanding of pharmacogenomics, but it is dispersed across many journals. In order to integrate our knowledge, connect important facts across publications and generate new hypotheses we must organize and encode the contents of the literature. By creating databases of structured pharmocogenomic knowledge, we can make the value of the literature much greater than the sum of the individual reports. We can, for example, generate candidate gene lists or interpret surprising hits in genome-wide association studies. Text mining automatically adds structure to the unstructured knowledge embedded in millions of publications, and recent years have seen a surge in work on biomedical text mining, some specific to pharmacogenomics literature. These methods enable extraction of specific types of information and can also provide answers to general, systemic queries. In this article, we describe the main tasks of text mining in the context of pharmacogenomics, summarize recent applications and anticipate the next phase of text mining applications.
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Affiliation(s)
- Yael Garten
- Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
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Kell DB. Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration. ANNALS OF BOTANY 2011; 108:407-18. [PMID: 21813565 PMCID: PMC3158691 DOI: 10.1093/aob/mcr175] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/03/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The soil represents a reservoir that contains at least twice as much carbon as does the atmosphere, yet (apart from 'root crops') mainly just the above-ground plant biomass is harvested in agriculture, and plant photosynthesis represents the effective origin of the overwhelming bulk of soil carbon. However, present estimates of the carbon sequestration potential of soils are based more on what is happening now than what might be changed by active agricultural intervention, and tend to concentrate only on the first metre of soil depth. SCOPE Breeding crop plants with deeper and bushy root ecosystems could simultaneously improve both the soil structure and its steady-state carbon, water and nutrient retention, as well as sustainable plant yields. The carbon that can be sequestered in the steady state by increasing the rooting depths of crop plants and grasses from, say, 1 m to 2 m depends significantly on its lifetime(s) in different molecular forms in the soil, but calculations (http://dbkgroup.org/carbonsequestration/rootsystem.html) suggest that this breeding strategy could have a hugely beneficial effect in stabilizing atmospheric CO(2). This sets an important research agenda, and the breeding of plants with improved and deep rooting habits and architectures is a goal well worth pursuing.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK.
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49
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Kell DB. Breeding crop plants with deep roots: their role in sustainable carbon, nutrient and water sequestration. ANNALS OF BOTANY 2011; 108:407-418. [PMID: 21813565 DOI: 10.1093/aob/mbr175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND The soil represents a reservoir that contains at least twice as much carbon as does the atmosphere, yet (apart from 'root crops') mainly just the above-ground plant biomass is harvested in agriculture, and plant photosynthesis represents the effective origin of the overwhelming bulk of soil carbon. However, present estimates of the carbon sequestration potential of soils are based more on what is happening now than what might be changed by active agricultural intervention, and tend to concentrate only on the first metre of soil depth. SCOPE Breeding crop plants with deeper and bushy root ecosystems could simultaneously improve both the soil structure and its steady-state carbon, water and nutrient retention, as well as sustainable plant yields. The carbon that can be sequestered in the steady state by increasing the rooting depths of crop plants and grasses from, say, 1 m to 2 m depends significantly on its lifetime(s) in different molecular forms in the soil, but calculations (http://dbkgroup.org/carbonsequestration/rootsystem.html) suggest that this breeding strategy could have a hugely beneficial effect in stabilizing atmospheric CO(2). This sets an important research agenda, and the breeding of plants with improved and deep rooting habits and architectures is a goal well worth pursuing.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK.
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Jacinto T, Morais A, Fonseca JA. How to write a scientific paper - searching and managing biomedical information. REVISTA PORTUGUESA DE PNEUMOLOGIA 2011; 17:190-4. [PMID: 21680136 DOI: 10.1016/j.rppneu.2011.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 05/02/2011] [Indexed: 11/25/2022] Open
Affiliation(s)
- T Jacinto
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
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