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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon P, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert R, Knott GJ, Lapinaite A, Pausch P, Cofsky J, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res 2024; 52:D590-D596. [PMID: 37889041 PMCID: PMC10767948 DOI: 10.1093/nar/gkad890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
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Affiliation(s)
- Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elaine Zhang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Hannah M Karp
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Rachel F Weissman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Tomas Hessler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Colognori
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ron Boger
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan V Tran
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Graduate School of Life Sciences, Utrecht University, 3584 CS Utrecht, UT, The Netherlands
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Kevin M Wasko
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Zehan Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Chenglong Xia
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Muntathar J Al-Shimary
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jaymin R Patel
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Vienna C J X Thomas
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Rithu Pattali
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew J Kan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Anna Vardapetyan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Alana Yang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Micaela F Maxwell
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA 23668, USA
| | - Andrew G Murdock
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Glenn C Ramit
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Hope R Henderson
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Roland W Calvert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rebecca S Bamert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Pausch
- LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Joshua C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Genetics Otago, University of Otago, Dunedin 9016, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9016, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, 2629 HZ Delft, The Netherlands
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | | | | | | | - Rodolphe Barrangou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Virginius Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The University of Melbourne, Parkville, VIC 3052, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94158, USA
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Ruprechter T, Horta Ribeiro M, Santos T, Lemmerich F, Strohmaier M, West R, Helic D. Volunteer contributions to Wikipedia increased during COVID-19 mobility restrictions. Sci Rep 2021; 11:21505. [PMID: 34728670 PMCID: PMC8563865 DOI: 10.1038/s41598-021-00789-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Wikipedia, the largest encyclopedia ever created, is a global initiative driven by volunteer contributions. When the COVID-19 pandemic broke out and mobility restrictions ensued across the globe, it was unclear whether contributions to Wikipedia would decrease in the face of the pandemic, or whether volunteers would withstand the added stress and increase their contributions to accommodate the growing readership uncovered in recent studies. We analyze [Formula: see text] million edits contributed from 2018 to 2020 across twelve Wikipedia language editions and find that Wikipedia's global volunteer community responded resiliently to the pandemic, substantially increasing both productivity and the number of newcomers who joined the community. For example, contributions to the English Wikipedia increased by over [Formula: see text] compared to the expectation derived from pre-pandemic data. Our work sheds light on the response of a global volunteer population to the COVID-19 crisis, providing valuable insights into the behavior of critical online communities under stress.
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Affiliation(s)
| | | | - Tiago Santos
- Graz University of Technology, 8010, Graz, Austria
| | | | - Markus Strohmaier
- RWTH Aachen University, 52062, Aachen, Germany
- GESIS - Leibniz Institute for the Social Sciences, 50667, Cologne, Germany
- Complexity Science Hub Vienna, 1080, Vienna, AT, Austria
| | | | - Denis Helic
- Graz University of Technology, 8010, Graz, Austria
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Xie L, Liu M, Zhao L, Cao K, Wang P, Xu W, Sung WK, Li X, Li G. RiceENCODE: A comprehensive epigenomic database as a rice Encyclopedia of DNA Elements. Mol Plant 2021; 14:1604-1606. [PMID: 34455096 DOI: 10.1016/j.molp.2021.08.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Liang Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Minghao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Kai Cao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Peng Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Wenhao Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Department of Computer Science, National University of Singapore, Singapore 117417, Singapore; Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China; Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China.
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Suwannakhan A, Casanova-Martínez D, Yurasakpong L, Montriwat P, Meemon K, Limpanuparb T. The Quality and Readability of English Wikipedia Anatomy Articles. Anat Sci Educ 2020; 13:475-487. [PMID: 31233658 DOI: 10.1002/ase.1910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/14/2019] [Accepted: 06/20/2019] [Indexed: 06/09/2023]
Abstract
Forty anatomy articles were sampled from English Wikipedia and assessed quantitatively and qualitatively. Quantitatively, each article's edit history was analyzed by Wikipedia X-tools, references and media were counted manually, and two readability indices were used to evaluate article readability. This analysis revealed that each article was updated 8.3 ± 6.8 times per month, and referenced with 33.5 ± 24.3 sources, such as journal articles and textbooks. Each article contained on average 14.0 ± 7.6 media items. The readability indices including: (1) Flesch-Kincaid Grade Level Readability Test and (2) Flesch Reading Ease Readability Formula demonstrated that the articles had low readability and were more appropriate for college students and above. Qualitatively, the sampled articles were evaluated by experts using a modified DISCERN survey. According to the modified DISCERN, 13 articles (32.5%), 24 articles (60%), 3 articles (7.5%), were rated as "good," "moderate," and "poor," respectively. There were positive correlations between the DISCERN score and the number of edits (r = 0.537), number of editors (r = 0.560), and article length (r = 0.536). Strengths reported by the panel included completeness and coverage in 11 articles (27.5%), anatomical details in 10 articles (25%), and clinical details in 5 articles (12.5%). The panel also noted areas which could be improved, such as providing missing information in 28 articles (70%), inaccuracies in 10 articles (25%), and lack or poor use of images in 17 articles (42.5%). In conclusion, this study revealed that many Wikipedia anatomy articles were difficult to read. Each article's quality was dependent on edit frequency and article length. Learners and students should be cautious when using Wikipedia articles for anatomy education due to these limitations.
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Affiliation(s)
- Athikhun Suwannakhan
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Daniel Casanova-Martínez
- Morphology Unit, Faculty of Medicine, School of Medicine, University of Valparaíso, San Felipe, Chile
| | | | - Punchalee Montriwat
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Taweetham Limpanuparb
- Science Division, Mahidol University International College, Mahidol University, Nakhon Pathom, Thailand
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Abstract
PROBLEM While ideal curricular structures for effective teaching of evidence-based medicine (EBM) have not been definitively determined, optimal strategies ensure that EBM teaching is interactive and clinically based, aligns with major trends in education and health care, and uses longitudinally integrated, whole-task activities. APPROACH The authors developed a longitudinal, semester-long project, embedded in a first-year medicine course, through which they taught EBM using Wikipedia as a platform. Students worked individually and in small groups to choose a medicine-related Wikipedia article, identify information gaps, search for high-quality resources, appraise the sources, and incorporate the new information into the article (i.e., by editing Wikipedia). Students also applied their new appraisal skills to critique a second article. The authors used an online tool to track and record student editing, and they obtained qualitative data on student perceptions of the project via survey. Duplicate marking of a sample of assignments was performed using the Valid Assessment of Learning in Undergraduate Education critical thinking rubric developed by Finley and Rhodes. OUTCOMES In fall 2017, 101 students made over 1,000 unique edits to 16 online Wikipedia articles, adding over 10,000 words. Through thematic analysis of qualitative data, the authors highlighted several aspects of the project that students appreciated, as well as barriers related to completing their projects. Correlation of the 17 consenting students' final assignments with the critical thinking rubric supports the assignment structure as a tool for assessing critical thinking. NEXT STEPS This authentic task adheres to the principles of high-quality EBM instruction and could be implemented by a variety of health care educational programs. Modifications to the delivery model are underway to address challenges identified.
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Affiliation(s)
- Heather Murray
- H. Murray is associate professor, Department of Emergency Medicine and Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada; ORCID: https://orcid.org/0000-0002-8448-2566. M. Walker is research scientist, Department of Emergency Medicine, Queen's University, Kingston, Ontario, Canada; ORCID: https://orcid.org/0000-0002-9312-0874. J. Dawson is research associate at the CHEO Research Institute, Ottawa, Ontario and the Wikipedian in Residence for Cochrane; ORCID: http://orcid.org/0000-0003-1141-9619. N. Simper is researcher, Centre for Teaching and Learning, Queen's University, Kingston, Ontario, Canada; ORCID: http://orcid.org/0000-0002-1309-1074. L.A. Maggio is associate professor, Department of Medicine, and associate director, Scholarly Communication, Graduate Programs in Health Professions Education, Uniformed Services University of the Health Sciences, Bethesda, Maryland; ORCID: http://orcid.org/0000-0002-2997-6133
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Adams CE, Montgomery AA, Aburrow T, Bloomfield S, Briley PM, Carew E, Chatterjee-Woolman S, Feddah G, Friedel J, Gibbard J, Haynes E, Hussein M, Jayaram M, Naylor S, Perry L, Schmidt L, Siddique U, Tabaksert AS, Taylor D, Velani A, White D, Xia J. Adding evidence of the effects of treatments into relevant Wikipedia pages: a randomised trial. BMJ Open 2020; 10:e033655. [PMID: 32086355 PMCID: PMC7045027 DOI: 10.1136/bmjopen-2019-033655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES To investigate the effects of adding high-grade quantitative evidence of outcomes of treatments into relevant Wikipedia pages on further information-seeking behaviour by the use of routinely collected data. SETTING Wikipedia, Cochrane summary pages and the Cochrane Library. DESIGN Randomised trial. PARTICIPANTS Wikipedia pages which were highly relevant to up-to-date Cochrane Schizophrenia systematic reviews that contained a Summary of Findings table. INTERVENTIONS Eligible Wikipedia pages in the intervention group were seeded with tables of best evidence of the effects of care and hyperlinks to the source Cochrane review. Eligible Wikipedia pages in the control group were left unchanged. MAIN OUTCOME MEASURES Routinely collected data on access to the full text and summary web page (after 12 months). RESULTS We randomised 70 Wikipedia pages (100% follow-up). Six of the 35 Wikipedia pages in the intervention group had the tabular format deleted during the study but all pages continued to report the same data within the text. There was no evidence of effect on either of the coprimary outcomes: full-text access adjusted ratio of geometric means 1.30, 95% CI: 0.71 to 2.38; page views 1.14, 95% CI: 0.6 to 2.13. Results were similar for all other outcomes, with exception of Altmetric score for which there was some evidence of clear effect (1.36, 95% CI: 1.05 to 1.78). CONCLUSIONS The pursuit of fair balance within Wikipedia healthcare pages is impressive and its reach unsurpassed. For every person who sought and clicked the reference on the 'intervention' Wikipedia page to seek more information (the primary outcome), many more are likely to have been informed by the page alone. Enriching Wikipedia content is, potentially, a powerful way to improve health literacy and it is possible to test the effects of seeding pages with evidence. This trial should be replicated, expanded and developed. TRIAL REGISTRATION NUMBER IRCT2017070330407N2.
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Affiliation(s)
- Clive E Adams
- Division of Psychiatry and Applied Psychology, University of Nottingham, Nottingham, UK
| | - Alan A Montgomery
- Nottingham Clinical Trials Unit, University of Nottingham, Nottingham, UK
| | - Tony Aburrow
- Health Sciences, Research, John Wiley Ltd, Chichester, UK
| | - Sophie Bloomfield
- Department of Critical Care, East Kent Hospitals University NHS Foundation Trust, Canterbury, Kent, UK
| | - Paul M Briley
- Division of Psychiatry and Applied Psychology, University of Nottingham, Nottingham, UK
| | - Ebun Carew
- General Medicine, Nottingham University Hospitals Healthcare NHS Trust, Nottingham, Nottinghamshire, UK
| | | | - Ghalia Feddah
- Emergency Department, Gold Coast University Hospitals, Gold Coast, Queensland, Australia
| | - Johannes Friedel
- Faculty Management and Business Science, University of Aalen, Aalen, Germany
| | - Josh Gibbard
- The Acute Stroke Unit - Huggett Suite, Royal Lancaster Infirmary, Lancaster, UK
| | - Euan Haynes
- Haematology, Gateshead Health NHS Foundation Trust, Gateshead, Gateshead, UK
| | - Mohsin Hussein
- Department of Radiology, University Hospitals of Leicester NHS Trust, Leicester, Leicester, UK
| | - Mahesh Jayaram
- Psychaitry, University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel Naylor
- Emergency Department, Gold Coast University Hospitals, Gold Coast, Queensland, Australia
| | - Luke Perry
- Department of Anaesthesia, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Lena Schmidt
- Bristol Medical School, University of Bristol Faculty of Health Sciences, Bristol, Bristol, UK
- Fakultät Gesundheit, Sicherheit und Gesellschaft, Hochschule Furtwangen University, Furtwangen, Germany
| | - Umer Siddique
- Community Recovery Psychiatry, North East London NHS Foundation Trust, London, UK
| | - Ayla Serena Tabaksert
- Liaison Psychiatry, Northumbria Healthcare NHS Foundation Trust, North Shields, Tyne and Wear, UK
| | | | - Aarti Velani
- Acute Medicine, Lewisham and Greenwich NHS Trust, London, UK
| | - Douglas White
- Accident and Emergency, Epsom and Saint Helier University Hospitals NHS Trust Epsom Hospital, Epsom, Surrey, UK
| | - Jun Xia
- Nottingham Ningbo GRADE Centre, Nottingham China Health Institute, The University of Nottingham Ningbo, Ningbo, China
- Division of Epidemiology and Public Health, School of Medicine, The University of Nottingham, Nottingham, UK
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Tolj J, Jermen N, Jecić Z. [Medicine in Croatian Lexicography and Encyclopaedistics]. Acta Med Hist Adriat 2019; 17:313-336. [PMID: 32390449 DOI: 10.31952/amha.17.2.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Due to the undeniable importance of medicine in human life, the authors explore the level of attentiveness given to medical topics since the beginnings of Croatian lexicography and encyclopaedistics in the 16th century until today. Specific emphasis is put on the activities of the Miroslav Krleža Institute of Lexicography, as the only Croatian institution which has been systematically involved in the field of lexicography and encyclopaedistics for almost 70 years. The representation and importance of medicine have been established in three ways. Firstly, by chronologically presenting medical terms and topics in the works of Croatian lexicography and encyclopaedistics from the 16th to the 19th century. Subsequently, by systemizing and analysing medical publications published in the 20th century, especially the ones created by the Institute. Lastly, by reviewing the presence of medical terms and topics in other Institute's publications, especially in the Croatian Encyclopaedia. The study shows that medicine has been well represented in Croatian lexicographic and encyclopaedic works, which have played a significant role in establishing Croatian medical terminology and adding to systematization of knowledge in the field of medicine. The authors conclude that lexicography and encyclopaedistics in Croatia have paid adequate attention to medical topics, as well as mirrored the interest of professional and broader community towards medicine.
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Affiliation(s)
- Jasmina Tolj
- Redakcija Hrvatske tehničke enciklopedije, Leksikografski zavod Miroslav Krleža, Frankopanska ulica 26, 10000 Zagreb.
E-pošta:
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8
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Affiliation(s)
- Heather Murray
- Departments of Emergency Medicine and Public Health Sciences, Queen's University, Kingston, Ontario, Canada
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9
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Abstract
This article focuses on what Luis von Ahn called the "twofer," that is, a single solution that elegantly addresses two problems on a large scale. We describe two of von Ahn's creations: reCAPTCHA, which validates a human web presence while also digitizing hard-to-read words, and Duolingo, which teaches new languages while translating the web. We then consider how this approach can be applied to medical education. Embedding Wikipedia-editing into educational settings is one such solution that could both improve the quality of health information available to the public while enhancing the learning of future health professionals.
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Affiliation(s)
- Sean Tackett
- a Department of Medicine , Johns Hopkins Bayview Medical Center , Baltimore , MD , USA
| | - Shiv Gaglani
- b Johns Hopkins University School of Medicine and Osmosis , Baltimore , MD , USA
| | - James Heilman
- c Department of Emergency Medicine , University of British Columbia , Vancouver , Canada
| | - Amin Azzam
- d Department of Psychiatry , University of California, School of Medicine , San Francisco , CA , USA
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10
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Charlier P, Deo S. Schizophrenia: four examples of historical retrospective diagnosis. Encephale 2018; 44:S55-S57. [PMID: 30935490 DOI: 10.1016/s0013-7006(19)30082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
It is difficult to know precisely the history of a functional disease, unlike the natural history of infectious agents, tumour processes or poly-malformative syndromes. In the case of psychiatry, and especially schizophrenia and psychotic disorders, a retrospective look at artistic productions (writings and drawings) makes it possible to reconstitute a whole section of this pathological context. Through four medieval and modern examples, we will see how it is possible to do a paleo-psychiatry: Opicinus de Canistris (14th c.), the Voynich manuscript (15th c.), Hieronymus Bosch (15th-16th c.), and the Codex Seraphinianus (20th c.).
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Affiliation(s)
- P Charlier
- Section of Medical Anthropology (UVSQ, EA4498, Dante Laboratory), UFR of Health Sciences, 2, avenue de la Source-de-la-Bièvre, 78180 Montigny-Le-Bretonneux, France; CASH & IPES, 403, avenue de la République, 92000 Nanterre, France.
| | - S Deo
- Section of Medical Anthropology (UVSQ, EA4498, Dante Laboratory), UFR of Health Sciences, 2, avenue de la Source-de-la-Bièvre, 78180 Montigny-Le-Bretonneux, France
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Apollonio DE, Broyde K, Azzam A, De Guia M, Heilman J, Brock T. Pharmacy students can improve access to quality medicines information by editing Wikipedia articles. BMC Med Educ 2018; 18:265. [PMID: 30454046 PMCID: PMC6245851 DOI: 10.1186/s12909-018-1375-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Pharmacy training programs commonly ask students to develop or edit drug monographs that summarize key information about new medicines as an academic exercise. We sought to expand on this traditional approach by having students improve actual medicines information pages posted on Wikipedia. METHODS We placed students (n = 119) in a required core pharmacy course into groups of four and assigned each group a specific medicines page on Wikipedia to edit. Assigned pages had high hit rates, suggesting that the topics were of interest to the wider public, but were of low quality, suggesting that the topics would benefit from improvement efforts. We provided course trainings about editing Wikipedia. We evaluated the assignment by surveying student knowledge and attitudes and reviewing the edits on Wikipedia. RESULTS Completing the course trainings increased student knowledge of Wikipedia editing practices. At the end of the assignment, students had a more nuanced understanding of Wikipedia as a resource. Student edits improved substantially the quality of the articles edited, their edits were retained for at least 30 days after course completion, and the average number page views of their edited articles increased. CONCLUSIONS Our results suggest that engaging pharmacy students in a Wikipedia editing assignment is a feasible alternative to writing drug monographs as a classroom assignment. Both tasks provide opportunities for students to demonstrate their skills at researching and explaining drug information but only one serves to improve wider access to quality medicines information. Wikipedia editing assignments are feasible for large groups of pharmacy students and effective in improving publicly available information on one of the most heavily accessed websites globally.
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Affiliation(s)
- Dorie E. Apollonio
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California USA
| | | | - Amin Azzam
- Department of Psychiatry, University of California, San Francisco, San Francisco, California USA
| | | | - James Heilman
- Department of Emergency Medicine, University of British Columbia, Vancouver, BC Canada
| | - Tina Brock
- Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, California USA
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, Australia
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12
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Abstract
In response to the news coverage of scientific events and to science education, people increasingly go online to get more information. This study investigates how patterns of science and technology information-seeking on Google and Wikipedia change over time, in ways that differ between "ad hoc" terms that correspond to news coverage and "cyclic" terms that correspond to the academic period. Findings show that the science and technology activity in Google and Wikipedia was significantly associated with ad hoc and cyclic patterns. While the peak activity in Google and Wikipedia largely overlapped for ad hoc terms, it mismatched for cyclic terms. The findings indicate the importance of external cues such as news media and education, and also of the online engagement process, and particularly the crucial but different role played by Google and Wikipedia in gaining science and technology knowledge. Educators and policy makers could benefit from taking into account those different patterns.
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Abstract
Feminist STS has long established that science's provenance as a male domain continues to define what counts as knowledge and expertise. Wikipedia, arguably one of the most powerful sources of information today, was initially lauded as providing the opportunity to rebuild knowledge institutions by providing greater representation of multiple groups. However, less than ten percent of Wikipedia editors are women. At one level, this imbalance in contributions and therefore content is yet another case of the masculine culture of technoscience. This is an important argument and, in this article, we examine the empirical research that highlights these issues. Our main objective, however, is to extend current accounts by demonstrating that Wikipedia's infrastructure introduces new and less visible sources of gender disparity. In sum, our aim here is to present a consolidated analysis of the gendering of Wikipedia.
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Affiliation(s)
- Heather Ford
- School of Media and Communication, University of Leeds, UK
| | - Judy Wajcman
- Department of Sociology, The London School of Economics and Political Science, UK
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Rudas C, Surányi O, Yasseri T, Török J. Understanding and coping with extremism in an online collaborative environment: A data-driven modeling. PLoS One 2017; 12:e0173561. [PMID: 28323867 PMCID: PMC5360246 DOI: 10.1371/journal.pone.0173561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/24/2016] [Indexed: 12/01/2022] Open
Abstract
The Internet has provided us with great opportunities for large scale collaborative public good projects. Wikipedia is a predominant example of such projects where conflicts emerge and get resolved through bottom-up mechanisms leading to the emergence of the largest encyclopedia in human history. Disaccord arises whenever editors with different opinions try to produce an article reflecting a consensual view. The debates are mainly heated by editors with extreme views. Using a model of common value production, we show that the consensus can only be reached if groups with extreme views can actively take part in the discussion and if their views are also represented in the common outcome, at least temporarily. We show that banning problematic editors mostly hinders the consensus as it delays discussion and thus the whole consensus building process. To validate the model, relevant quantities are measured both in simulations and Wikipedia, which show satisfactory agreement. We also consider the role of direct communication between editors both in the model and in Wikipedia data (by analyzing the Wikipedia talk pages). While the model suggests that in certain conditions there is an optimal rate of “talking” vs “editing”, it correctly predicts that in the current settings of Wikipedia, more activity in talk pages is associated with more controversy.
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Affiliation(s)
- Csilla Rudas
- Institute of Physics, Budapest University of Technology and Economics, Budapest, Hungary
| | - Olivér Surányi
- Institute of Physics, Eötvös Loránd University, Budapest, Hungary
| | - Taha Yasseri
- Oxford Internet Institute, University of Oxford, Oxford, United Kingdom
- Alan Turing Institute, London, United Kingdom
| | - János Török
- Institute of Physics, Budapest University of Technology and Economics, Budapest, Hungary
- Institute of Physics, Eötvös Loránd University, Budapest, Hungary
- * E-mail:
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Azzam A, Bresler D, Leon A, Maggio L, Whitaker E, Heilman J, Orlowitz J, Swisher V, Rasberry L, Otoide K, Trotter F, Ross W, McCue JD. Why Medical Schools Should Embrace Wikipedia: Final-Year Medical Student Contributions to Wikipedia Articles for Academic Credit at One School. Acad Med 2017; 92:194-200. [PMID: 27627633 PMCID: PMC5265689 DOI: 10.1097/acm.0000000000001381] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
PROBLEM Most medical students use Wikipedia as an information source, yet medical schools do not train students to improve Wikipedia or use it critically. APPROACH Between November 2013 and November 2015, the authors offered fourth-year medical students a credit-bearing course to edit Wikipedia. The course was designed, delivered, and evaluated by faculty, medical librarians, and personnel from WikiProject Medicine, Wikipedia Education Foundation, and Translators Without Borders. The authors assessed the effect of the students' edits on Wikipedia's content, the effect of the course on student participants, and readership of students' chosen articles. OUTCOMES Forty-three enrolled students made 1,528 edits (average 36/student), contributing 493,994 content bytes (average 11,488/student). They added higher-quality and removed lower-quality sources for a net addition of 274 references (average 6/student). As of July 2016, none of the contributions of the first 28 students (2013, 2014) have been reversed or vandalized. Students discovered a tension between comprehensiveness and readability/translatability, yet readability of most articles increased. Students felt they improved their articles, enjoyed giving back "specifically to Wikipedia," and broadened their sense of physician responsibilities in the socially networked information era. During only the "active editing months," Wikipedia traffic statistics indicate that the 43 articles were collectively viewed 1,116,065 times. Subsequent to students' efforts, these articles have been viewed nearly 22 million times. NEXT STEPS If other schools replicate and improve on this initiative, future multi-institution studies could more accurately measure the effect of medical students on Wikipedia, and vice versa.
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Affiliation(s)
- Amin Azzam
- A. Azzam is associate clinical professor, Department of Psychiatry, University of California, San Francisco, San Francisco, California
| | - David Bresler
- D. Bresler is resident physician, Department of Psychiatry, University of California, Los Angeles, Los Angeles, California
| | - Armando Leon
- A. Leon is resident physician, San Mateo County Psychiatry Residency Training Program, San Mateo, California
| | - Lauren Maggio
- L. Maggio is associate professor, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Evans Whitaker
- E. Whitaker is education and information consultant for medicine, Library and Center for Knowledge Management, University of California, San Francisco, San Francisco, California
| | - James Heilman
- J. Heilman is clinical assistant professor, Department of Emergency Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jake Orlowitz
- J. Orlowitz is head, Wikipedia Library, Wikimedia Foundation, San Francisco, California
| | - Valerie Swisher
- V. Swisher is board member, Translators Without Borders, and chief executive officer, Content Rules, Inc., Los Gatos, California
| | - Lane Rasberry
- L. Rasberry is Wikipedian in residence, Consumer Reports, Yonkers, New York
| | | | - Fred Trotter
- F. Trotter is data journalist, DocGraph, Houston, Texas
| | - Will Ross
- W. Ross is project manager, Mendocino Informatics, Inc., Mendocino, California
| | - Jack D. McCue
- J.D. McCue is emeritus professor of medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
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17
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HANDONG MA, WENG CHUNHUA. IDENTIFICATION OF QUESTIONABLE EXCLUSION CRITERIA IN MENTAL DISORDER CLINICAL TRIALS USING A MEDICAL ENCYCLOPEDIA. Pac Symp Biocomput 2016; 21:219-230. [PMID: 26776188 PMCID: PMC4717913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Precision medicine requires precise evidence-based practice and precise definition of the patients included in clinical studies for evidence generalization. Clinical research exclusion criteria define confounder patient characteristics for exclusion from a study. However, unnecessary exclusion criteria can weaken patient representativeness of study designs and generalizability of study results. This paper presents a method for identifying questionable exclusion criteria for 38 mental disorders. We extracted common eligibility features (CEFs) from all trials on these disorders from ClinicalTrials.gov. Network Analysis showed scale-free property of the CEF network, indicating uneven usage frequencies among CEFs. By comparing these CEFs' term frequencies in clinical trials' exclusion criteria and in the PubMed Medical Encyclopedia for matching conditions, we identified unjustified potential overuse of exclusion CEFs in mental disorder trials. Then we discussed the limitations in current exclusion criteria designs and made recommendations for achieving more patient-centered exclusion criteria definitions.
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Affiliation(s)
- MA HANDONG
- Department of Biomedical Informatics, Columbia University, 622 West 168 Street, PH-20 New York, NY, 10032, USA
| | - CHUNHUA WENG
- Department of Biomedical Informatics, Columbia University, 622 West 168 Street, PH-20 New York, NY, 10032, USA
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18
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Torous J, Franzan J, O'Connor R, Mathew I, Keshavan M, Kitts R, Boland R. Psychiatry Residents' Use of Educational Websites: A Pilot Survey Study. Acad Psychiatry 2015; 39:630-633. [PMID: 26077007 DOI: 10.1007/s40596-015-0335-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 03/12/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE Psychiatry residents have numerous online educational resources readily available to them although currently there are no data regarding residents' use and perception of such websites. METHODS A survey was offered to 62 residents from all four years of training as well as recent graduates of a single psychiatry residency training program. RESULTS Residents reported utilizing online resources on average 68 % of the time, in comparison to 32 % on average for printed materials. Residents reported UpToDate, PubMed, and Wikipedia as the most visited websites and ranked each highly but for different purposes. Thirty-five percent of residents felt that insufficient faculty guidance was a barrier to use of these educational websites. CONCLUSIONS Pilot data indicate psychiatry residents use online resources daily for their education in various settings. Resident perceptions of individual website's trustworthiness, ease of use, and sources of clinical decision-making and personal learning suggest potential opportunities for educators to better understand the current use of these resources in residency training. Reported barriers including lack of faculty guidance suggest opportunities for academic psychiatry. Further study is necessary at multiple sites before such results may be generalized.
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19
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Abstract
Wikipedia has quickly become one of the most frequently accessed encyclopedic references, despite the ease with which content can be changed and the potential for ‘edit wars’ surrounding controversial topics. Little is known about how this potential for controversy affects the accuracy and stability of information on scientific topics, especially those with associated political controversy. Here we present an analysis of the Wikipedia edit histories for seven scientific articles and show that topics we consider politically but not scientifically “controversial” (such as evolution and global warming) experience more frequent edits with more words changed per day than pages we consider “noncontroversial” (such as the standard model in physics or heliocentrism). For example, over the period we analyzed, the global warming page was edited on average (geometric mean ±SD) 1.9±2.7 times resulting in 110.9±10.3 words changed per day, while the standard model in physics was only edited 0.2±1.4 times resulting in 9.4±5.0 words changed per day. The high rate of change observed in these pages makes it difficult for experts to monitor accuracy and contribute time-consuming corrections, to the possible detriment of scientific accuracy. As our society turns to Wikipedia as a primary source of scientific information, it is vital we read it critically and with the understanding that the content is dynamic and vulnerable to vandalism and other shenanigans.
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Affiliation(s)
- Adam M. Wilson
- Geography Department, University at Buffalo, Buffalo, NY, United States of America
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
| | - Gene E. Likens
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
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Plewig G. [Manual of Skin and Venereal Diseases (Jadassohn) and supplementary series (Marchionini): monumental encyclopedias]. J Dtsch Dermatol Ges 2015; 12 Suppl 4:22-4. [PMID: 25366436 DOI: 10.1111/ddg.12475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Stoeva M, Tabakov S, Lewis C, Tabakova V, Thurston J, Smith P. Radiation protection aspects of EMITEL Encyclopaedia of Medical Physics. Radiat Prot Dosimetry 2015; 165:513-517. [PMID: 25848099 DOI: 10.1093/rpd/ncv080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Encyclopaedia of Medical Physics EMITEL was developed under the EU pilot project European Medical Imaging Technology e-Encyclopaedia for Lifelong Learning. This large reference material includes 3400 articles on 2100 pages supported by thousands of illustrations. All materials are available free at the website, www.emitel2.eu. The articles are grouped in seven categories--physics of: X-ray diagnostic radiology, nuclear medicine, radiotherapy, magnetic resonance imaging, ultrasound imaging, radiation protection and general terms. The radiation protection part of EMITEL includes 450 articles. These were organised in several sub-groups including: nuclear and atomic physics; ionizing radiation interactions and biological effects; radiation detection and measurement; dosimetric quantities and units; and general radiation protection and international bodies. EMITEL project was developed over 3 y and attracted as contributors 250+ senior specialists from 35 countries. After its successful launching, EMITEL is actively used by thousands of professionals around the world.
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Affiliation(s)
- M Stoeva
- Department of Medical Imaging, Medical University, Plovdiv, Bulgaria
| | - S Tabakov
- Department of Medical Engineering and Physics, King's College, London, UK
| | - C Lewis
- Department of Medical Engineering and Physics, King's College, London, UK
| | - V Tabakova
- Department of Medical Engineering and Physics, King's College, London, UK
| | | | - P Smith
- International Organisation for Medical Physics (IOMP), York, UK
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Herbert VG, Frings A, Rehatschek H, Richard G, Leithner A. Wikipedia--challenges and new horizons in enhancing medical education. BMC Med Educ 2015; 15:32. [PMID: 25879421 PMCID: PMC4384304 DOI: 10.1186/s12909-015-0309-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 02/17/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Wikipedia gains growing attention as a provider of health information. This study aimed to investigate the use, relevance and challenges of Wikipedia among medical students. METHODS An online questionnaire was made accessible to students at five medical universities in Germany, Austria, and Norway. Besides demographical data, the questions covered the role of Wikipedia in the academic life of medical students. The questionnaire investigated if the students had ever found erroneous medical entries and whether they corrected these. RESULTS A frequent use of Wikipedia in general is statistically significant correlated with a frequent use in medical studies (p < 0.001). Information retrieved from Wikipedia is predominantly critically appraised either by comparing it to profound knowledge (79%) and/or to specific literature (75%). Despite most (97%) respondents disclosed that they already had found false information in Wikipedia, recognized errors were seldomly corrected (~20%). CONCLUSIONS The information retrieved from Wikipedia is critically appraised. However, we found shortcomings in handling erroneous entries. We argue for professional responsibility among medical students in dealing with this dynamic resource. Moreover, we encourage medical schools to supplement information to Wikipedia to further benefit from the vast possibilities of this platform.
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Affiliation(s)
- Verena G Herbert
- Dermatologikum Hamburg, Stephansplatz 5, 20354, Hamburg, Germany.
| | - Andreas Frings
- Department of Ophthalmology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | | | - Gisbert Richard
- Department of Ophthalmology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Andreas Leithner
- Department of Orthopaedics, Medical University of Graz, Graz, Austria.
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Schlegel DR, Crowner C, Elkin PL. Automatically Expanding the Synonym Set of SNOMED CT using Wikipedia. Stud Health Technol Inform 2015; 216:619-623. [PMID: 26262125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Clinical terminologies and ontologies are often used in natural language processing/understanding tasks as a method for semantically tagging text. One ontology commonly used for this task is SNOMED CT. Natural language is rich and varied: many different combinations of words may be used to express the same idea. It is therefore essential that ontologies and terminologies have a rich set of synonyms. One source of synonyms is Wikipedia. We examine methods for aligning concepts in SNOMED CT with articles in Wikipedia so that newly-found synonyms may be added to SNOMED CT. Our experiments show promising results and provide guidance to researchers who wish to use Wikipedia for similar tasks.
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Affiliation(s)
- Daniel R Schlegel
- Department of Biomedical Informatics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Chris Crowner
- Department of Biomedical Informatics, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Peter L Elkin
- Department of Biomedical Informatics, University at Buffalo, SUNY, Buffalo, NY, USA
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Antipova A. [Vladimir Zederbaum" (1883-1942): Physician, journalist, contributor to the Russian "Jewish, Encyclopedia". A research report]. Luzif Amor 2015; 28:119-131. [PMID: 26939252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Vol. 15 o f the "Jewish Encyclopedia" (St. Petersburg 1908-1913) contains an article on Freud, signed by Vladimir Zederbaum. The data for the article were provided by Max Eitingon. This paper addresses the question of whether Zederbaum himself was Eitingon's contact. Several archives produced a lot of information about Zederbaum's medical and journalistic activities in St. Petersburg. However, to date no connection between the two men could be established.
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Al Ateeq A, Al Moamary E, Daghestani T, Al Muallem Y, Al Dogether M, Alsughayr A, Altuwaijri M, Househ M. Using a digital marketing platform for the promotion of an internet based health encyclopedia in saudi arabia. Stud Health Technol Inform 2015; 208:12-16. [PMID: 25676939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The objective of this paper is to investigate the experiences of using a digital marketing platform to promote the use of an internet based health encyclopedia in Saudi Arabia. Key informant interviews, meeting documentation, and Google Analytics were the data collection sources used in the study. Findings show that using a digital marketing platform led to a significant increase in the number of visitors to the health encyclopedia. The results demonstrate that digital marketing platforms are effective tools to be used for promoting internet based health education interventions. Future work will examine long-term educational impacts and costs in using digital marketing platforms to promote online healthcare sites in Saudi Arabia.
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Affiliation(s)
- Asma Al Ateeq
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Eman Al Moamary
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Tahani Daghestani
- King Abdullah International Medical Research Center, Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Yahya Al Muallem
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Majed Al Dogether
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Abdulrahman Alsughayr
- Department of Family Medicine, College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Majid Altuwaijri
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Mowafa Househ
- College of Public Health and Health Informatics, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard - Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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Vydiswaran VGV, Mei Q, Hanauer DA, Zheng K. Mining consumer health vocabulary from community-generated text. AMIA Annu Symp Proc 2014; 2014:1150-1159. [PMID: 25954426 PMCID: PMC4419967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Community-generated text corpora can be a valuable resource to extract consumer health vocabulary (CHV) and link them to professional terminologies and alternative variants. In this research, we propose a pattern-based text-mining approach to identify pairs of CHV and professional terms from Wikipedia, a large text corpus created and maintained by the community. A novel measure, leveraging the ratio of frequency of occurrence, was used to differentiate consumer terms from professional terms. We empirically evaluated the applicability of this approach using a large data sample consisting of MedLine abstracts and all posts from an online health forum, MedHelp. The results show that the proposed approach is able to identify synonymous pairs and label the terms as either consumer or professional term with high accuracy. We conclude that the proposed approach provides great potential to produce a high quality CHV to improve the performance of computational applications in processing consumer-generated health text.
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Affiliation(s)
| | - Qiaozhu Mei
- School of Information, University of Michigan, Ann Arbor, MI ; Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI
| | - David A Hanauer
- Department of Pediatrics, University of Michigan, Ann Arbor, MI ; School of Information, University of Michigan, Ann Arbor, MI
| | - Kai Zheng
- School of Public Health Department of Health Management and Policy, University of Michigan, Ann Arbor, MI ; School of Information, University of Michigan, Ann Arbor, MI
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Harshaw C, Marcinowski E, Campbell J. Communicating developmental psychobiology to the masses: why psychobiologists should contribute to Wikipedia. Dev Psychobiol 2014; 56:1439-41. [PMID: 25132415 DOI: 10.1002/dev.21239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/26/2014] [Indexed: 11/06/2022]
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Affiliation(s)
- Thomas J Hwang
- From the Blackstone Group, London (T.J.H.); and the Children's Hospital Informatics Program and the Division of Emergency Medicine, Boston Children's Hospital (F.T.B.), the Department of Pediatrics (F.T.B.) and the Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine (J.D.S.), Harvard Medical School, and Brigham and Women's Hospital (J.D.S.) - all in Boston
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Liao P, Hussain M, Mohan A, Nischal PM, Pai SA. News from here and there. Natl Med J India 2014; 27:186-187. [PMID: 25668099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Bould MD, Hladkowicz ES, Pigford AAE, Ufholz LA, Postonogova T, Shin E, Boet S. References that anyone can edit: review of Wikipedia citations in peer reviewed health science literature. BMJ 2014; 348:g1585. [PMID: 24603564 PMCID: PMC3944683 DOI: 10.1136/bmj.g1585] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/10/2014] [Indexed: 12/03/2022]
Abstract
OBJECTIVES To examine indexed health science journals to evaluate the prevalence of Wikipedia citations, identify the journals that publish articles with Wikipedia citations, and determine how Wikipedia is being cited. DESIGN Bibliometric analysis. STUDY SELECTION Publications in the English language that included citations to Wikipedia were retrieved using the online databases Scopus and Web of Science. DATA SOURCES To identify health science journals, results were refined using Ulrich's database, selecting for citations from journals indexed in Medline, PubMed, or Embase. Using Thomson Reuters Journal Citation Reports, 2011 impact factors were collected for all journals included in the search. DATA EXTRACTION Resulting citations were thematically coded, and descriptive statistics were calculated. RESULTS 1433 full text articles from 1008 journals indexed in Medline, PubMed, or Embase with 2049 Wikipedia citations were accessed. The frequency of Wikipedia citations has increased over time; most citations occurred after December 2010. More than half of the citations were coded as definitions (n = 648; 31.6%) or descriptions (n=482; 23.5%). Citations were not limited to journals with a low or no impact factor; the search found Wikipedia citations in many journals with high impact factors. CONCLUSIONS Many publications are citing information from a tertiary source that can be edited by anyone, although permanent, evidence based sources are available. We encourage journal editors and reviewers to use caution when publishing articles that cite Wikipedia.
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Affiliation(s)
- M Dylan Bould
- Department of Anesthesiology, Children's Hospital of Eastern Ontario, University of Ottawa, 401 Smyth Road, Ottawa, ON, Canada, K1H 8L1
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Affiliation(s)
- Lane Rasberry
- Consumer Reports, 101 Truman Avenue, Yonkers, NY 10703, USA
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Abstract
OBJECTIVE The objective of the paper is to understand leadership in an online community, specifically, Wikipedia. BACKGROUND Wikipedia successfully aggregates millions of volunteers' efforts to create the largest encyclopedia in human history. Without formal employment contracts and monetary incentives, one significant question for Wikipedia is how it organizes individual members with differing goals, experience, and commitment to achieve a collective outcome. Rather than focusing on the role of the small set of people occupying a core leadership position, we propose a shared leadership model to explain the leadership in Wikipedia. Members mutually influence one another by exercising leadership behaviors, including rewarding, regulating, directing, and socializing one another. METHOD We conducted a two-phase study to investigate how distinct types of leadership behaviors (transactional, aversive, directive, and person-focused), the legitimacy of the people who deliver the leadership, and the experience of the people who receive the leadership influence the effectiveness of shared leadership in Wikipedia. RESULTS Our results highlight the importance of shared leadership in Wikipedia and identify trade-offs in the effectiveness of different types of leadership behaviors. Aversive and directive leadership increased contribution to the focal task, whereas transactional and person-focused leadership increased general motivation. We also found important differences in how newcomers and experienced members responded to leadership behaviors from peers. APPLICATION These findings extend shared leadership theories, contribute new insight into the important underlying mechanisms in Wikipedia, and have implications for practitioners who wish to design more effective and successful online communities.
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Conti NA. [Diderot and the French encyclopedia]. Vertex 2013; 24:472-473. [PMID: 24511566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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Abstract
How different cultures evaluate a person? Is an important person in one culture is also important in the other culture? We address these questions via ranking of multilingual Wikipedia articles. With three ranking algorithms based on network structure of Wikipedia, we assign ranking to all articles in 9 multilingual editions of Wikipedia and investigate general ranking structure of PageRank, CheiRank and 2DRank. In particular, we focus on articles related to persons, identify top 30 persons for each rank among different editions and analyze distinctions of their distributions over activity fields such as politics, art, science, religion, sport for each edition. We find that local heroes are dominant but also global heroes exist and create an effective network representing entanglement of cultures. The Google matrix analysis of network of cultures shows signs of the Zipf law distribution. This approach allows to examine diversity and shared characteristics of knowledge organization between cultures. The developed computational, data driven approach highlights cultural interconnections in a new perspective. Dated: June 26, 2013
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Affiliation(s)
- Young-Ho Eom
- Laboratoire de Physique Théorique du CNRS, IRSAMC, Université de Toulouse, UPS, Toulouse, France
| | - Dima L. Shepelyansky
- Laboratoire de Physique Théorique du CNRS, IRSAMC, Université de Toulouse, UPS, Toulouse, France
- * E-mail:
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36
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John HV. Translating leprosy: the expert and the public in Stanley Stein's anti-stigmatization campaigns, 1931-60. J Hist Med Allied Sci 2013; 68:659-687. [PMID: 24106217 DOI: 10.1093/jhmas/jrs018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This article examines three campaigns through which patient activist Stanley Stein sought to combat the stigmatized connotations of the word "leprosy." In 1931, soon after starting the first patient newspaper at the U.S. national leprosy hospital at Carville, Stein became convinced of the necessity of finding an alternative to "leprosy." His ensuing campaign to promote the use of the words "Hansen's Disease" to describe the condition from which he and fellow Carville patients suffered became his most passionate and life-long project. In the 1950s, Stein became involved in efforts to change the translation of "leprosy" in the Bible. Finally, in 1960, he waged a campaign to de-stigmatize encyclopedia entries on leprosy. These campaigns illustrate how even elevation of the medical expert and a seeming disdain for the public can function as a protest of medical authority and reveal a presumption that a significant degree of authority actually resides with the public.
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Affiliation(s)
- Heather Varughese John
- Program in the History of Science and Medicine, Yale University, 333 Cedar Street, Sterling Hall of Medicine, L132, New Haven, Connecticut 06520
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Xu Y, Wang Y, Sun JT, Zhang J, Tsujii J, Chang E. Building large collections of Chinese and English medical terms from semi-structured and encyclopedia websites. PLoS One 2013; 8:e67526. [PMID: 23874426 PMCID: PMC3706590 DOI: 10.1371/journal.pone.0067526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/18/2013] [Indexed: 11/19/2022] Open
Abstract
To build large collections of medical terms from semi-structured information sources (e.g. tables, lists, etc.) and encyclopedia sites on the web. The terms are classified into the three semantic categories, Medical Problems, Medications, and Medical Tests, which were used in i2b2 challenge tasks. We developed two systems, one for Chinese and another for English terms. The two systems share the same methodology and use the same software with minimum language dependent parts. We produced large collections of terms by exploiting billions of semi-structured information sources and encyclopedia sites on the Web. The standard performance metric of recall (R) is extended to three different types of Recall to take the surface variability of terms into consideration. They are Surface Recall (R(S)), Object Recall (R(O)), and Surface Head recall (R(H)). We use two test sets for Chinese. For English, we use a collection of terms in the 2010 i2b2 text. Two collections of terms, one for English and the other for Chinese, have been created. The terms in these collections are classified as either of Medical Problems, Medications, or Medical Tests in the i2b2 challenge tasks. The English collection contains 49,249 (Problems), 89,591 (Medications) and 25,107 (Tests) terms, while the Chinese one contains 66,780 (Problems), 101,025 (Medications), and 15,032 (Tests) terms. The proposed method of constructing a large collection of medical terms is both efficient and effective, and, most of all, independent of language. The collections will be made publicly available.
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Affiliation(s)
- Yan Xu
- State Key Laboratory of Software Development Environment, Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education, Beihang University, Beijing, China
- Microsoft Research Asia, Beijing, China
| | - Yining Wang
- Microsoft Research Asia, Beijing, China
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | | | | | | | - Eric Chang
- Microsoft Research Asia, Beijing, China
- * E-mail:
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Köckerling F, Köckerling D, Lomas C. Cornelius Celsus--ancient encyclopedist, surgeon-scientist, or master of surgery? Langenbecks Arch Surg 2013; 398:609-16. [PMID: 23344725 PMCID: PMC3627856 DOI: 10.1007/s00423-013-1050-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/13/2013] [Indexed: 01/31/2023]
Abstract
PURPOSE The Roman nobleman Cornelius Celsus (25 BC-AD 50) wrote a general encyclopedia (De Artibus) dealing with several subjects, among which some had medical content (De Medicina), an eight-volume compendium, including two books about surgery (VII + VIII). It is the most significant medical document following the Hippocratic writings. In 1443, Pope Nicolas V rediscovered the work of Cornelius Celsus, despite it having been forgotten for several centuries, and it was the first medical and surgical book to be printed (AD 1478). Up until the nineteenth century, 60 editions were published in Latin as well as numerous translations in European languages, the last of which was a French translation in 1876. While Celsus' work is the best account of Roman medicine as practiced in the first century of the Christian era and its influence persisted until the nineteenth century, there is controversy as to whether Cornelius Celsus himself actually practiced as a surgeon or was only an encyclopedist who collected in the Latin language the medical knowledge available at that time. METHODS The detailed analysis of the surgical techniques described by Celsus, the modifications tailored to the findings, possible complications, detailed description of pre- and postsurgical activities, give the general impression that he himself practiced surgery at least within his family and among his dependents. In addition, his descriptions give a clear insight into the astonishingly high standard of surgical knowledge available at the time of Celsus. RESULTS His work thus reflects the state of knowledge of his time, which is why he also assumed the role of teacher and scientist. As such, his meets the modern criteria addressed to a surgeon-scientist, who apart from the practical surgical activity, also had a role as teacher of surgery and scientist. Whether Cornelius Celsus had inaugurated a new surgical technique and was the first to describe that, and as such can be described as a master of surgery, cannot be corroborated. CONCLUSION Cornelius Celsus deserves a firm place in the history of surgery because with his publication De Medicina, Book VII + VIII, he has preserved Roman surgical knowledge in the first century of the Christian era and, thanks to the use of Latin in medicine and surgery, this continues to be retained up till the present day.
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Affiliation(s)
- F Köckerling
- Department of Surgery, Vivantes Hospital Spandau, Neue Bergstraße 6, 13585 Berlin, Germany.
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Liu F, Moosavinasab S, Agarwal S, Bennett AS, Yu H. Automatically identifying health- and clinical-related content in wikipedia. Stud Health Technol Inform 2013; 192:637-641. [PMID: 23920634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Physicians are increasingly using the Internet for finding medical information related to patient care. Wikipedia is a valuable online medical resource to be integrated into existing clinical question answering (QA) systems. On the other hand, Wikipedia contains a full spectrum of world's knowledge and therefore comprises a large partition of non-health-related content, which makes disambiguation more challenging and consequently leads to large overhead for existing systems to effectively filter irrelevant information. To overcome this, we have developed both unsupervised and supervised approaches to identify health-related articles as well as clinically relevant articles. Furthermore, we explored novel features by extracting health related hierarchy from the Wikipedia category network, from which a variety of features were derived and evaluated. Our experiments show promising results and also demonstrate that employing the category hierarchy can effectively improve the system performance.
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Affiliation(s)
- Feifan Liu
- NLP R&D, Nuance Communication Inc., Burlington, MA, USA
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41
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Piazzi A, Piazzi G, Testa L, Coccanari dè Fornari MA. [The representation of Italian psychiatry in Italian Treccani Encyclopedia in 1930's]. Med Secoli 2013; 25:541-564. [PMID: 25807782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The article reconstruct the situation of Italian psychiatry around 1930, using as unusual sources the pages of the Enciclopedia Italiana di Scienze, Lettere e Arti. This important work, conceived in 1925 and finished in 1937, is due - as well known - to the strong interest of Giovanni Gentile and to his capacity to involve in the project a great part of Italian intellectual world, without any ideological preclusion. The section devoted to Medical Sciences, including Psychiatry, was directed by Nicola Pende (1880-1970) and Giacinto Viola (1870-1943). A prevalent positivistic approach to science is well testified by their specific attention to preventive and social medicine, researches in Genetics and in biotypological constitutions. Psycopathological and psycological lemmas are very limited, underlying the medical disinterest towards contemporary philosophy and psycology.
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Affiliation(s)
- Andrea Piazzi
- Azienda ASL RM G, SPDC, Ospedale S. Giovanni Evangelista, Tivoli
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Abstract
In this paper we present statistical analysis of English texts from Wikipedia. We try to address the issue of language complexity empirically by comparing the simple English Wikipedia (Simple) to comparable samples of the main English Wikipedia (Main). Simple is supposed to use a more simplified language with a limited vocabulary, and editors are explicitly requested to follow this guideline, yet in practice the vocabulary richness of both samples are at the same level. Detailed analysis of longer units (n-grams of words and part of speech tags) shows that the language of Simple is less complex than that of Main primarily due to the use of shorter sentences, as opposed to drastically simplified syntax or vocabulary. Comparing the two language varieties by the Gunning readability index supports this conclusion. We also report on the topical dependence of language complexity, that is, that the language is more advanced in conceptual articles compared to person-based (biographical) and object-based articles. Finally, we investigate the relation between conflict and language complexity by analyzing the content of the talk pages associated to controversial and peacefully developing articles, concluding that controversy has the effect of reducing language complexity.
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Affiliation(s)
- Taha Yasseri
- Department of Theoretical Physics, Budapest University of Technology and Economics, Budapest, Hungary.
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44
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Affiliation(s)
- Steve D. M. Brown
- Professor Steve Brown is Chair of the International Steering Committee for the IMPC and Director of the MRC Mammalian Genetics Unit at MRC Harwell, Oxford, UK
- Author for correspondence ()
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Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, Sandstrom R, Bates D, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Harding L, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature 2012; 489:75-82. [PMID: 22955617 PMCID: PMC3721348 DOI: 10.1038/nature11232] [Citation(s) in RCA: 1898] [Impact Index Per Article: 158.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.
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Affiliation(s)
- Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | | | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Kavita Garg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Abigail K. Ebersol
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tristan Frum
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Lisa Harding
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Ericka M. Johnson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Bryan Lajoie
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Bum-Kyu Lee
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Darin London
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Dimitra Lotakis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Fidencio Neri
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Eric D. Nguyen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexias Safi
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Minerva E. Sanchez
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Amartya Sanyal
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | - Anthony Shafer
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Jeremy M. Simon
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Lingyun Song
- Institute for Genome Sciences and Policy, Duke University, Durham, NC
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Zhancheng Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Zhuzhu Zhang
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Boris Lenhard
- Bergen Center for Computational Science, University of Bergen, Bergen, Norway
| | - Muneesh Tewari
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael O. Dorschner
- Dept. of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - R. Scott Hansen
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Patrick A. Navas
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | | | - Vishwanath R. Iyer
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
| | - Jason D. Lieb
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Shamil R. Sunyaev
- Dept. of Medicine, Division of Genetics, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Peter J. Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Rajinder Kaul
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA
| | - Terrence S. Furey
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Job Dekker
- Program in Gene Function, University of Massachusetts Medical School, Worcester, MA
| | | | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA
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Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature 2012; 489:101-8. [PMID: 22955620 PMCID: PMC3684276 DOI: 10.1038/nature11233] [Citation(s) in RCA: 3699] [Impact Index Per Article: 308.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
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Affiliation(s)
- Sarah Djebali
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Carrie A. Davis
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Angelika Merkel
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Timo Lassmann
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Ali M. Mortazavi
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Andrea Tanzer
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Wei Lin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Felix Schlesinger
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Chenghai Xue
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Georgi K. Marinov
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Jainab Khatun
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Brian A. Williams
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Chris Zaleski
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Maik Röder
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Rehab F. Abdelhamid
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Tyler Alioto
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Igor Antoshechkin
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Michael T. Baer
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Nadav S. Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Philippe Batut
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kimberly Bell
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Ian Bell
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Sudipto Chakrabortty
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Xian Chen
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Jacqueline Chrast
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Joao Curado
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas Derrien
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Jorg Drenkow
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Erica Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Jacqueline Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Radha Duttagupta
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Emilie Falconnet
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Meagan Fastuca
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kata Fejes-Toth
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Pedro Ferreira
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Sylvain Foissac
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Melissa J. Fullwood
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Hui Gao
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - David Gonzalez
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Assaf Gordon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Harsha Gunawardena
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Cedric Howald
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Sonali Jha
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Philipp Kapranov
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
- St. Laurent Institute, One Kendall Square, Cambridge, MA
| | - Brandon King
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Colin Kingswood
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Oscar J. Luo
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Eddie Park
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Kimberly Persaud
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Jonathan B. Preall
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Paolo Ribeca
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Brian Risk
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Daniel Robyr
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Michael Sammeth
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Lorian Schaffer
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Lei-Hoon See
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Atif Shahab
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Jorgen Skancke
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ana Maria Suzuki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hazuki Takahashi
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hagen Tilgner
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Diane Trout
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Nathalie Walters
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Huaien Wang
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - John Wrobel
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Yanbao Yu
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Xiaoan Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Tim Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Alexandre Reymond
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Gregory Hannon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Morgan C. Giddings
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Yijun Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Barbara Wold
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Piero Carninci
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas R. Gingeras
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
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47
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Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender M, Groudine M, Kaul R, Stamatoyannopoulos JA. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012; 489:83-90. [PMID: 22955618 PMCID: PMC3736582 DOI: 10.1038/nature11212] [Citation(s) in RCA: 566] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 05/10/2012] [Indexed: 01/04/2023]
Abstract
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.
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Affiliation(s)
- Shane Neph
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | | | - Alex P. Reynolds
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Haugen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Benjamin Vernot
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Robert E. Thurman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Audra K. Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Matthew T. Maurano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Richard Humbert
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Eric Rynes
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Hao Wang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Shinny Vong
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kristen Lee
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Daniel Bates
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Morgan Diegel
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Vaughn Roach
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Douglas Dunn
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jun Neri
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Anthony Schafer
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - R. Scott Hansen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - Tanya Kutyavin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Erika Giste
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Molly Weaver
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Peter Sabo
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Miaohua Zhang
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | | | - Rachel Byron
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Michael Bender
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Mark Groudine
- Basic Sciences Division, Fred Hutchison Cancer Research Center, Seattle, WA 98109
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195
| | - John A. Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Division of Oncology, Deparment of Medicine, University of Washington, Seattle, WA 98195
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48
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Abstract
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.
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49
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Abstract
The vast non-coding portion of the human genome is full of functional elements and disease-causing regulatory variants. The principles defining the relationships between these elements and distal target genes remain unknown. Promoters and distal elements can engage in looping interactions that have been implicated in gene regulation. Here we have applied chromosome conformation capture carbon copy (5C) to interrogate comprehensively interactions between transcription start sites (TSSs) and distal elements in 1% of the human genome representing the ENCODE pilot project regions. 5C maps were generated for GM12878, K562 and HeLa-S3 cells and results were integrated with data from the ENCODE consortium. In each cell line we discovered >1,000 long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites. We observed significant correlations between gene expression, promoter-enhancer interactions and the presence of enhancer RNAs. Long-range interactions show marked asymmetry with a bias for interactions with elements located ∼120 kilobases upstream of the TSS. Long-range interactions are often not blocked by sites bound by CTCF and cohesin, indicating that many of these sites do not demarcate physically insulated gene domains. Furthermore, only ∼7% of looping interactions are with the nearest gene, indicating that genomic proximity is not a simple predictor for long-range interactions. Finally, promoters and distal elements are engaged in multiple long-range interactions to form complex networks. Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships.
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Affiliation(s)
| | | | - Gaurav Jain
- Program in Systems Biology, Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605-0103, USA
| | - Job Dekker
- Program in Systems Biology, Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605-0103, USA
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50
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Reavley NJ, Mackinnon AJ, Morgan AJ, Alvarez-Jimenez M, Hetrick SE, Killackey E, Nelson B, Purcell R, Yap MBH, Jorm AF. Quality of information sources about mental disorders: a comparison of Wikipedia with centrally controlled web and printed sources. Psychol Med 2012; 42:1753-1762. [PMID: 22166182 DOI: 10.1017/s003329171100287x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Although mental health information on the internet is often of poor quality, relatively little is known about the quality of websites, such as Wikipedia, that involve participatory information sharing. The aim of this paper was to explore the quality of user-contributed mental health-related information on Wikipedia and compare this with centrally controlled information sources. METHOD Content on 10 mental health-related topics was extracted from 14 frequently accessed websites (including Wikipedia) providing information about depression and schizophrenia, Encyclopaedia Britannica, and a psychiatry textbook. The content was rated by experts according to the following criteria: accuracy, up-to-dateness, breadth of coverage, referencing and readability. RESULTS Ratings varied significantly between resources according to topic. Across all topics, Wikipedia was the most highly rated in all domains except readability. CONCLUSIONS The quality of information on depression and schizophrenia on Wikipedia is generally as good as, or better than, that provided by centrally controlled websites, Encyclopaedia Britannica and a psychiatry textbook.
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Affiliation(s)
- N J Reavley
- Orygen Youth Health Research Centre, Centre for Youth Mental Health, University of Melbourne, Parkville, VIC, Australia.
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