Department Blog

Health Sciences Libraries

Genetic, health info added to NIH dbGaP

February 27th, 2014 by Mary Wood
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dbGaP – Database of Genotypes and Phenotypes

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Genetic Epidemiology Research on Aging (GERA)

NIH News

UCSF News

Researchers will now have access to genetic data linked to medical information on a diverse group of more than 78,000 people, enabling investigations into many diseases and conditions. The data, from one of the nation’s largest and most diverse genomics projects — Genetic Epidemiology Research on Aging (GERA) — have just been made available to qualified researchers through the database of Genotypes and Phenotypes (dbGaP), an online genetics database of the National Institutes of Health.

The GERA cohort was developed collaboratively by Kaiser Permanente and the University of California, San Francisco (UCSF). The addition of the data to dbGaP was made possible with support from the National Institute on Aging (NIA), National Institute of Mental Health, and NIH.

dbGaP was developed and is managed by the National Center for Biotechnology Information, a division of the National Library of Medicine. Investigators who are interested in applying for access to this database should follow the procedures on the dbGaP website. Specific information on the data can be found here.

Scopus: Access for 2014

February 23rd, 2014 by Amy Studer

During the 2014 calendar year, UC faculty, staff, and students will be able to access the Scopus database.   Scopus is an abstract and citation database of peer-reviewed literature, including some 50 million records, 21,000 titles and 5,000 publishers, and includes tools to track, analyze and visualize research.

Scopus search interface (UC Davis computer network or VPN access required):

http://www.scopus.com/

See the Facts and Figures flyer or Content Overview page for more information about Scopus.

The NIH Public Access Policy: What it Means for You and How to Ensure Compliance

February 4th, 2014 by Amy Studer

The NIH Public Access Policy: What it Means for You and How to Ensure Compliance
Wednesday, February 19, 2014
12:15 pm – 1:45 pm
Education Building Room 2206
To Register: http://lib.ucdavis.edu/dept/instruc/classes/descriptions.php#class134

In 2008, the National Institutes of Health (NIH) announced that investigators funded by the NIH must submit a copy of their final, peer-reviewed manuscripts to PubMed Central (PMC) upon acceptance of publication, to be made publicly available no later than 12 months after the date of publication. Failure to comply with the Public Access Policy will result in funding delays.

If you are involved with NIH-funded research in any capacity, consider attending this workshop to learn more about the Public Access Policy and how to be compliant with it. It will cover:

* what it is and what it means;
* who has to comply;
* how to determine the copyright policy of the journal publishing your manuscript, and;
* the various methods of article submission into PMC, including the NIH Manuscript Submission System (NIHMS).

To register:  http://lib.ucdavis.edu/dept/instruc/classes/descriptions.php#class134

Due to space restrictions, this workshop will be limited to 30 attendees on a first-come, first-served basis.

If you have any questions, please contact:

* Raquel Abad, Health Sciences Librarian, 916.734.3870 | rjabad@ucdavis.edu OR

* Amy Studer, Health & Life Sciences Librarian, 530.752.1678 | astuder@lib.ucdavis.edu

2014 West Virginia Elk River Chemical Release: Information Resources

February 3rd, 2014 by Amy Studer

Adapted from NLM Tech Bull. 2014 Jan-Feb;(396):b5.:

You may be aware from multiple news sources that little information was available about 4-methylcyclohexanemethanol at the time of the spill in West Virginia’s Elk River in early January 2014.

Since the spill, government and private sector scientists have contributed to collecting and verifying information about the chemical.

Here are some new resources about the chemical and the government response:

Please note that in some social media and early news reports, the chemical was MISIDENTIFIED as Methylcyclohexanol (CASRN: 25639-42-3). This is NOT the correct chemical.

In chemical incidents, it is unusual for little online information to be available about a substance. Chemicals can often be readily identified using online resources such as TOXNET and WISER. In the absence of published information, local and state officials request consultation with local, state, federal and industry experts. Typically, following such an incident there is immediate, ongoing, extensive consultation and communication among responders and experts to determine appropriate actions.

When planning for providing health information following chemical incidents, it is critical for institutions and government agencies to know who to contact in uncommon situations as well as knowing the authoritative published sources of chemical information.

Sources

Triclosan and antimicrobial soaps, continued

February 3rd, 2014 by Mary Wood

Environmental Factor
January 2014 Newsletter
National Institute of Environmental Health Sciences

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Research informs policy and regulatory discussion

Researchers central in the national discussion concerning policy and regulatory issues
related to environmental public health

December 2013 New York Times, FDA questions safety of antibacterial soaps, looked at new FDA requirement that manufacturers demonstrate the safety of antimicrobial soaps, citing research by NIEHS Superfund Research Program (SRP) supported scientists…

…including SRP grantees Bruce Hammock and Isaac Pessah of UC Davis, and Robert Tukey of UCSD, who have conducted interdisciplinary studies on the extent of environmental pollution by the antimicrobials triclosan and tricloban, and their potential effects on human health.

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Citations:

Cherednichenko G, Zhang R, Bannister RA, Timofeyev V, Li N, Fritsch EB, Feng W, Barrientos GC, Schebb NH, Hammock BD, Beam KG, Chiamvimonvat N, Pessah IN.  2012. Triclosan impairs excitation-contraction coupling and Ca2+ dynamics in striated muscle. Proc Natl Acad Sci U S A 109(35):14158-14163.

Schebb NH, Ahn KC, Dong H, Gee SJ, Hammock BD.  2012. Whole blood is the sample matrix of choice for monitoring systemic triclocarbon levels. Chemosphere 87(7):825-827.

Research: increasing value, reducing waste

January 29th, 2014 by Mary Wood

logo_site

Clinical Series
January 8, 2014

Executive summary

The Lancet presents a Series of five papers about research… These papers set out some of the most pressing issues, recommend how to increase value and reduce waste in biomedical research, and propose metrics for stakeholders to monitor the implementation of these recommendations.
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Papers

Clinical Series
The Lancet commissions Series and themed issues to highlight clinically important topics and areas of health and medicine that are pertinent to physicians’ practice. They are groups of two or three articles which provide an in depth view of individual clinical areas, and are an ideal source of up-to-date knowledge.

NIH plans to enhance reproducibility

January 27th, 2014 by Mary Wood
27 January 2014

“Francis S. Collins and Lawrence A. Tabak discuss initiatives that the US National Institutes of Health is exploring to restore the self-correcting nature of preclinical research.”
Nature 505, 612–613 (30 January 2014) doi:10.1038/505612a

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Reproducibility-logo.

Nature | Special

Challenges in irreproducible research

“…Nature has published a series of articles about the worrying extent to which research results have been found wanting…  Journals, research laboratories and institutions and funders all have an interest in tackling issues of irreproducibility. We hope that the articles contained in this collection will help.”

Reporting animal studies: ARRIVE news

January 24th, 2014 by Mary Wood
NC3Rs-ARRIVE-guidelines-Z-card-300x263
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Editorial
Open Science and Report Animal Studies: Who’s Accountable?
Jonathan A. Eisen, Emma Ganley, Catriona J. MacCallum
(2014) PLoS Biol 12(1): e1001757. doi:10.1371/journal.pbio.1001757
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Perspective
Two Years Later: Journals Are Not Yet Enforcing the ARRIVE Guidelines on Reporting Standards for Pre-Clinical Animal Studies
Baker D, Lidster K, Sottomayor A, Amor S
(2014) PLoS Biol 12(1): e1001756. doi:10.1371/journal.pbio.1001756
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from NC3Rs Blog
…The ARRIVE (Animal Research: Reporting of In Vivo Research) guidelines, published in 2010 in PLOS Biology, were developed … to improve the reporting of animal research to ensure maximum benefit and to minimise unnecessary animal studies…

Research published this week in PLOS Biology shows experimental flaws and inadequacies in the reporting of animal research in the field of neuroimmunology …

PLOS Biology published an editorial to coincide with the original article
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PLOS journals are requesting authors to use the ARRIVE guidelines checklist when submitting relevant manuscripts to ensure reporting of animal research meets minimum standards. In April 2013, Nature journals adopted a similar approach and introduced editorial measures to improve transparency of research which includes a checklist incorporating elements of the ARRIVE guidelines…
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Perspective
Improving Bioscience Research Reporting: The ARRIVE Guidelines for Reporting Animal Research
Kilkenny C, Browne WJ, Cuthill IC, Emerson M, Altman DG
(2010) PLoS Biol 8(6): e1000412. doi:10.1371/journal.pbio.1000412

Progress in Genetics and Genomics of Nonhuman Primates

December 11th, 2013 by Mary Wood

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.ILAR Journal Volume 54(2)
Progress in Genetics and Genomics of Nonhuman Primates

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The articles in this issue discuss the current understanding of the genetics and genomics of apes and old world monkeys.

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Articles include

Palermo et al. / Old World Monkeys and New Age Science: The Evolution of Nonhuman Primate Systems Virology

Shen et al. / The Essential Detail: The Genetics and Genomics of the Primate Immune Response

Tardif et al. /  IACUC Review of Nonhuman Primate Research

PLoS Medicine article: Good reasons to search in ClinicalTrials.gov

December 9th, 2013 by Amy Studer

A new article out of PLoS Medicine (December 6, 2013) provides some good reasons for adding ClinicalTrials.gov to the list of resources consulted routinely for evidence-based treatment decisions:

Riveros, C., et al., Timing and Completeness of Trial Results Posted at ClinicalTrials.gov and Published in Journals. PLoS Med, 2013. 10(12): p. e1001566.

Access at:  http://www.plosmedicine.org/article/info%3Adoi/10.1371/journal.pmed.1001566

The authors compared the reporting on clinical trials of drugs in ClinicalTrials.gov with corresponding journal publications for timeliness of publication and completeness (flow of participants, efficacy results, adverse events, and serious adverse events) of posted results.  Reporting in ClinicalTrials.gov was significantly more complete than in the published journal articles.

Accessing drug information from ClinicalTrials.gov may help address potential publication, reporting, and time-lag biases that have been identified in journal literature, thereby supplementing information gathering for evidence-based practice.  ClinicalTrials.gov is “designed to complement, not replace, the journal publication” because results are presented as tabular data, without interpretation, and are not peer-reviewed (Zarin, Tse, Williams, Califf, & Ide, 2011, page 3).

Reference:

Zarin, D. A., Tse, T., Williams, R. J., Califf, R. M., & Ide, N. C. (2011). The ClinicalTrials.gov results database–update and key issues. N Engl J Med, 364(9), 852-860. doi: 10.1056/NEJMsa1012065.

Links to Resources:

ClinicalTrials.gov website:  http://clinicaltrials.gov/

For help with finding information in ClinicalTrials.gov, contact hslref@lib.ucdavis.edu

Try searching for a drug by name in DailyMed, and then link to related ClinicalTrials.gov information from the menu on the left side of the page.