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bioRxiv: a free open access archive for unpublished preprints in the life sciences

bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.
bioRxiv accepts preprints of articles covering all aspects of research in the life sciences. Categories include:
  • Bioengineering
  • Cancer biology
  • Cell biology
  • Ecology
  • Epidemiology
  • bioRxiv logoGenomics
  • Molecular biology
  • Neuroscience
  • Pharmacology and toxicology
  • Scientific Communication and Education
and more.
Readers may add public comments to articles on bioRxiv. Comments are moderated to ensure they conform to the standards of normal professional discourse.
Once an article is published in a journal, bioRxiv will automatically update the preprint with a link to the published version.

Free online does not equal open access

Lots of articles are freely available online. Does that mean they are open access? Nope.

Here’s a nice post on the difference between public access  and open access:

http://info.hsls.pitt.edu/updatereport/?p=6481.

Basically, the difference is in copyright ownership:

“In public access, funding agencies make research results freely available, while still retaining traditional copyright restrictions. As with a published journal article, anyone can read the findings, but no one may redistribute the content without permission. In OA, the content is freely available and may be reused or even republished by others without having to gain permission. Many OA authors choose to protect their content by applying a Creative Commons or similar license to their work.”

For more information, read the original post.

If you only use PubMed to find public health articles, you may be missing lots!

PubMed is a great source of journal article citations on most public health topics. It’s where I usually start. But there are many other article databases you should use, depending on your topic. Here are a few examples:

Embase is an international index including over 2,000 journals not in Medline/PubMed, as well as conference abstracts. Broad biomedical scope with strong coverage in drug, pharmaceutical, and toxicological research, including economic evaluations and healthcare policy & management. Includes a PICO search tool, as well as drug, device, and disease searches.

Global Health is a public health database particularly strong for finding articles from or about countries in the “Global South.” Topics such as environmental health, nutrition, infectious diseases, and more are covered.

Sociological Abstracts offers access to the international literature in sociology, demography, social psychology, and related disciplines in the social and behavioral sciences. If your research is on families, social relationships, peer groups, etc., you should try this database.

This is but a small sample of the databases offered by the UC Berkeley Library. For more public health databases, please visit our Databases in Public Health guide.

 

Call for Comment: Marian Koshland Bioscience, Natural Resources & Public Health Library

Bioscience Library
The creation of a more inclusive Marian Koshland Bioscience, Natural Resources, & Public Health Library builds on research and teaching trends with access to emerging technologies in these disciplines, and aligns with the vision identified in the University Library Strategic Plan. (Photo by Cade Johnson for the University Library)

A Call for Comment, issued by the School of Public Health Dean Stefano Bertozzi, College of Natural Resources Dean J. Keith Gilless, College of Letters & Science’s Division of Biological Sciences Dean Michael Botchan, and University Librarian Jeffrey MacKie-Mason, encourages all interested parties to carefully read the proposed plan for the Sheldon Margen Public Health Library and the Marian Koshland Bioscience & Natural Resources Library at UC Berkeley and to share comments and recommendations.

The comment period is open through Friday October 6, 2017. We invite you to submit comments via email to libraryforum@lists.berkeley.edu.

We are sharing the proposed reconfiguration of these two important libraries in the Life & Health Sciences Division of the University Library to better address current campus and research needs. Part of the classical core of the campus, the Valley Life Sciences Building is home to the Marian Koshland Bioscience & Natural Resources Library, and the future home of the “Marian Koshland Bioscience, Natural Resources & Public Health Library”.

Read the proposed plan.

DO NOT PUBLISH, or Sometimes, open data/open access not ideal

A recent essay in Science makes the case that, at least when writing up research on endangered species, complete transparency could be harmful. The prolific increase in online publishing, whether it be articles, reports, or data, creates significant problems in this field, namely:

  1. Unrestricted access to species location information is facilitating a surge in wildlife poaching, with many species at risk. Poaching has been documented in species within months of their taxonomic description in journals.
  2. Unrestricted access to location data and habitat descriptions can disrupt the often delicate relationships between scientists and landowners. Trespassing has occurred when location data is published.
  3. Unrestricted access to species information has the potential to accelerate habitat destruction and create other negative disturbances. The digital age has brought a desire among many nature enthusiasts to observe, photograph, and sometimes remove animals and plants.

Some fields such as paleontology and archaeology have long maintained restrictions on the publication of site locations and promoted government policies and regulations to limit collection and trade in fossils, artefacts, and culturally sensitive and/or scientifically important material. Organizations such as the U.S. Forest Service do not disclose geospatial data in order to protect research sites. Other solutions include modification of research permits so that endangered species locations are not automatically uploaded into wildlife databases and masking such records on private land, as presently occurs in some states in the United States.

Is this relevant to any public health research? Other than personally identifiable information, what types of health data should not be made widely available?

JAMAevidence: New evidence resource from the library

The UCB Library recently purchased access to JAMAevidence.

JAMAevidence is a resource of evidence-based tools and more, including Users’ Guides to the Medical Literature. This online guide includes Education Guide slide sets, audio summaries, calculators, and critical appraisal and information cycle worksheets – these are not included in the print version.

The Users’ Guides 29 chapters are under these headings:

  • The Foundations
  • Therapy
  • Harm (Observational Studies)
  • Diagnosis
  • Prognosis
  • Summarizing the Evidence
  • Moving From Evidence to Action

Enjoy!

Sage Research Methods: An Essential Resource for Researchers

SRM logo

Sage Research Methods, recently purchased by UC Berkeley, is an essential online resource for anyone doing research or learning how to do research. With more than 800 books, reference works, and journal articles from SAGE’s research methods list, SAGE Research Methods provides information on writing a research question, conducting a literature review, choosing a research method, collecting and analyzing data, and writing up the findings.

Sage Research Methods will help you:

and more.

Highly recommended, try it!

141 Things You Can Learn About Your Community in Just 3 Clicks

Use Community Commons to quickly build a report about any state, county, or group of counties in the USA! Within a minute or so, you will see information on 141 indicators (as of today) including health outcomes, physical environment, clinical care, social and economic factors, and demographics. Use this information for assessment, case-making, advocacy, grant applications, presentations and much more.

Information can be displayed as a table, pie chart, map, or downloaded to Excel.

To get started click here.

Enjoy!

Webcast: BD2K Open Data Science Symposium

Big Data to Knowledge

Open Data Science Symposium: How Open Data and Open Science are Transforming Biomedical Research; Details at http://event.capconcorp.com/wp/bd2k-odss/

The Open Data Science Symposium is open to the public and will be available through a webcast.

Big Data is an underutilized resource for innovation and discovery in biomedical research and the NIH is committed to unleashing its full potential by making it an open and easily accessible resource. The Open Data Science Symposium will feature discussions with the leaders in big data, open science, and biomedical research while also showcasing the finalists of the Open Data Science Prize, a worldwide competition to harness the innovative power of open data.

Please Register for the Open Data Science Symposium by November 18, 2016.

Registration is free.

Who Should Attend:

Join us for this meeting if you are interested in:

  • Learning how NIH and other agencies are utilizing new models and funding approaches to support open innovation and open science
  • Exploring the challenges, opportunities, and implications of a changing biomedical research landscape in which openness is the default across the globe
  • Seeking to use open data in your own research and looking for inspiration from international teams who have developed award-winning prototypes
  • Watching live demos of all six Open Science Prize semifinalists, and participating in the awards process through casting your vote for your favorite innovation

Event Highlights:

  • Dialogue between current NIH Director, Dr. Francis Collins, and former NIH and former NCI Director, Dr. Harold Varmus, on open science at the National Institutes of Health
  • Live demonstrations of six award-winning prototypes developed by international teams competing for the Open Science Prize.
  • Panel discussion on new models for advancing data sharing capability through innovative infrastructure and initiatives with perspectives from leading international organizations such as ELIXIR, Wellcome Trust, and Global Alliance for Genomics and Health.
  • Keynote by John Wilbanks, Chief Commons Officer at Sage Bionetworks, who has been named by Seed Magazine as one of the “revolutionary minds” and featured in Scientific American for his visionary thinking.

Acknowledgements

This symposium is funded through the NIH Big Data to Knowledge Initiative, which was launched in December 2013 as a trans-NIH program with funding from all 27 Institutes and Centers as well as the NIH Common Fund.

The Open Science Prize is made possible through a collaboration between NIH and the Wellcome Trust. The Howard Hughes Medical institute is also contributing funds for this effort.

2016 Ig Nobel Winners Announced !!

The 2016 Ig Nobel Prize winners were recently announced. Each year, scientists (and others) vie (or are chosen without their knowledge or consent) for this sought-after prize.

This year’s winners include:

REPRODUCTION PRIZE [EGYPT] — The lateAhmed Shafik, for studying the effects of wearing polyester, cotton, or wool trousers on the sex life of rats, and for conducting similar tests with human males. REFERENCE: “Effect of Different Types of Textiles on Sexual Activity. Experimental study,” Ahmed Shafik, European Urology, vol. 24, no. 3, 1993, pp. 375-80. REFERENCE: “Contraceptive Efficacy of Polyester-Induced Azoospermia in Normal Men,” Ahmed Shafik, Contraception, vol. 45, 1992, pp. 439-451.

MEDICINE PRIZE [GERMANY] — Christoph Helmchen, Carina Palzer, Thomas Münte, Silke Anders, and Andreas Sprenger, for discovering that if you have an itch on the left side of your body, you can relieve it by looking into a mirror and scratching the right side of your body (and vice versa). REFERENCE: “Itch Relief by Mirror Scratching. A Psychophysical Study,” Christoph Helmchen, Carina Palzer, Thomas F. Münte, Silke Anders, Andreas Sprenger, PLoS ONE, vol. 8, no 12, December 26, 2013, e82756.

PSYCHOLOGY PRIZE [BELGIUM, THE NETHERLANDS, GERMANY, CANADA, USA] — Evelyne Debey, Maarten De Schryver, Gordon Logan, Kristina Suchotzki, and Bruno Verschuere, for asking a thousand liars how often they lie, and for deciding whether to believe those answers. REFERENCE: “From Junior to Senior Pinocchio: A Cross-Sectional Lifespan Investigation of Deception,” Evelyne Debey, Maarten De Schryver, Gordon D. Logan, Kristina Suchotzki, and Bruno Verschuere, Acta Psychologica, vol. 160, 2015, pp. 58-68.

PERCEPTION PRIZE [JAPAN] — Atsuki Higashiyama and Kohei Adachi, for investigating whether things look different when you bend over and view them between your legs. REFERENCE: “Perceived size and Perceived Distance of Targets Viewed From Between the Legs: Evidence for Proprioceptive Theory,” Atsuki Higashiyama and Kohei Adachi, Vision Research, vol. 46, no. 23, November 2006, pp. 3961–76.

… and several more.

Enjoy science!

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