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Archive for the ‘News from NLM/NIH’ Category

NCBI Webinar: The Next Generation of Access to Sequencing Data

Friday, February 20th, 2015

Next Wednesday, February 25, NCBI staff will present a webinar on the SRA Toolkit, a system for accessing the approximately 3.4 Petabases of next-generation genomic and expressed sequence data housed in the NCBI Sequence Read Archive (SRA). As data sets become larger, mining information and performing comparisons directly from structured databases becomes increasingly necessary. The SRA Toolkit is not only capable of dumping the data out as a fastq or sam file, but also provides direct analysis and comparison from specific genomics regions across hundreds or thousands of samples.

In the webinar, we will show examples of configuration and use of the Toolkit for both public SRA and controlled access data associated with studies in the Database of Genotypes and Phenotypes (dbGaP).

To register for this webinar: https://attendee.gotowebinar.com/register/2847950984085163009

NIH MedlinePlus Magazine Winter Issue Available

Friday, February 20th, 2015

The Winter 2015 issue of NIH MedlinePlus the Magazine features information on healthy aging with Go4Life, living with Alzheimer’s disease, finding good health information on the Internet, atrial fibrillation, and treating alcohol problems. The cover features Howie Mandel, a host, performer, and producer, who was diagnosed with atrial fibrillation (AFib). He discusses his involvement with the National Stroke Association’s Fibs or Facts campaign that raises awareness about AFib and its increased risk for stroke.

The magazine also recaps the Science Pathfinders at NLM/NIH event on September 26, 2014, where more than 500 middle and high school students at public and private schools in Maryland and the District of Columbia visited the NIH campus in Bethesda to hear presentations from top scientists and medical doctors on the latest advances in medical research. This issue’s HealthLine describes the NIH’s National Institute of Allergy and Infectious Diseases (NIAID) and and the Pharmaceuticals division of GlaxoSmithKline (GSK) small phase 1 clinical trial of the experimental vaccine to prevent Ebola virus disease.

NIH MedlinePlus the Magazine is the free, trusted consumer guide to the vast array of authoritative online health and medical information at MedlinePlus. Published four times a year, the magazine showcases the National Institutes of Health’s (NIH) latest medical research and healthcare information. NIH MedlinePlus the Magazine is freely available as a print subscription, e-mail alerts, and online.

Deadline Extended for Public Comments on Proposals to Enhance Transparency of Clinical Trial Results

Friday, February 20th, 2015

In November, the Department of Health and Human Services (HHS) and the National Institutes of Health (NIH) released for public comment two proposals to increase the transparency of clinical trials via information submitted to ClinicalTrials.gov, a publicly accessible database operated by the National Library of Medicine. One is a Notice of Proposed Rulemaking (NPRM) that describes proposed regulations for registering and submitting summary results of certain clinical trials to ClinicalTrials.gov in compliance with Title VIII of the Food and Drug Administration Amendments Act of 2007 (FDAAA). A major proposed change from current requirements is the expansion of the scope of clinical trials required to submit summary results to include trials of unapproved, unlicensed, and uncleared products. The second proposal is a draft NIH policy that would extend the similar registration and reporting requirements to all clinical trials funded by NIH, regardless of whether they are subject to FDAAA. Both proposals aim to improve public access to information about specified clinical trials, information that is not necessarily available from other public sources.

The public may comment on any aspect of the NPRM or proposed NIH Policy. Written comments on the NPRM should be submitted to docket number NIH-2011-0003. Commenters are asked to indicate the specific section of the NPRM to which each comment refers. Written comments on the proposed NIH Policy should be submitted electronically to the Office of Clinical Research and Bioethics Policy, Office of Science Policy, NIH, via email; mail at 6705 Rockledge Drive, Suite 750, Bethesda, MD 20892; or by fax at 301-496-9839, by March 23, 2015.

PubMed Subject Filter Strategies Updated for 2015

Friday, February 20th, 2015

PubMed subject filter strategies are reviewed each year to determine if modifications are necessary. Modifications may include revisions due to changes in Medical Subject Heading (MeSH) vocabulary or MEDLINE journals, adding or deleting terms, and changing parts of a strategy to optimize retrieval. The following subset strategies were recently revised:

Opportunity to Affect the Future of the National Library of Medicine

Friday, February 13th, 2015

You have a unique opportunity to affect the future of the National Library of Medicine. As Dr. Donald A.B. Lindberg retires after 30 years as director of NLM, Dr. Francis Collins, Director of the National Institutes of Health, has convened a “Working Group to Chart the Course for the NIH National Library of Medicine.” The group’s charge and members: http://www.nih.gov/about/director/02032015_working-group_nlm.htm.

Consider responding to this time-sensitive NIH Request for Information (RFI), soliciting input into the deliberations of the working group of the advisory committee to the NIH Director. This is a very important opportunity to contribute feedback of the value of the National Library of Medicine, and to directly influence the future of this organization.

Your response must be submitted electronically at http://grants.nih.gov/grants/rfi/rfi.cfm?ID=41, and will ONLY be accepted through March 13, 2015.

Please share this information with colleagues and friends who might wish to respond with thoughts about how the NLM, and especially the collections, programs, and resources, have contributed to their research, teaching, education, and professional development.

List of Serials Indexed for Online Users

Friday, February 13th, 2015

The List of Serials Indexed for Online Users (LSIOU), 2015 edition, is now available in XML format. The 2015 edition contains 14,856 serial titles, including titles currently indexed for MEDLINE as well as titles indexed over time which have ceased or changed titles. The titles are listed alphabetically by the journal title abbreviation. Tailored lists of indexed journals may be generated from the NLM Catalog. While the XML version of the LSIOU is a snapshot in time, the results of a search in the NLM Catalog will provide a “real time” list for the LSIOU.

For a “real time” list for the LSIOU, enter reportedmedline in the search box and click “Search.” For a list of only the currently indexed MEDLINE journals, enter currentlyindexed in the search box and click “Search.” Display and sort formats are selected from the results page; click on the Display Settings pull-down menu to choose a display format (for example, the Journal display) and an appropriate sort (for example, Title or Title Abbreviation). To save the entire list as one document, click on the “Send to” pull-down menu, with “File” as the destination, choose a format and sort order, and then click “Create File.” Click “Save” in the File Download pop-up box. Provide your directory location and desired file name.

Additional information about journals indexed for MEDLINE can be found via the links from the MEDLINE/PubMed Resources web page. This page includes Journals Recently Accepted by NLM for Inclusion in MEDLINE, a list of titles selected by the Literature Selection Technical Review Committee (LSTRC) that meets three times per year in February, June, and October. Results from those meetings appear online about six weeks after each meeting, both on the web page and in the NLM Catalog. For additional details about searching the NLM Catalog, visit NLM Catalog Quick Tours and Searching for Journals in the NLM Catalog.

Funding Opportunity from the National Institute on Drug Abuse

Friday, February 13th, 2015

Seek, Test, Treat and Retain For Youth and Young Adults Living with or at High Risk for Acquiring HIV (R01)

The purpose of this Funding Opportunity Announcement (FOA) is to examine delivery models of HIV-focused services (testing, linkage, engagement and retention in care) for high risk or already HIV+ infected youth and young adults. Applications should incorporate substance use into study aims and service delivery objectives should address access to substance use prevention, screening, and treatment.  The developmental, structural, and systemic factors related to serving youth need to be clearly incorporated into study aims, rather than simple incremental refocusing of existing interventions to younger people.

Application Due Date: April 14, 2015 (Letter of Intent due February 15, 2015)

Learn more here: RFA-DA-15-019

Eligibility Information:

Higher Education Institutions

  • Public/State Controlled Institutions of Higher Education
  • Private Institutions of Higher Education

The following types of Higher Education Institutions are always encouraged to apply for NIH support as Public or Private Institutions of Higher Education:

  • Hispanic-serving Institutions
  • Historically Black Colleges and Universities (HBCUs)
  • Tribally Controlled Colleges and Universities (TCCUs)
  • Alaska Native and Native Hawaiian Serving Institutions
  • Asian American Native American Pacific Islander Serving Institutions (AANAPISIs)

Nonprofits Other Than Institutions of Higher Education

For-Profit Organizations

Governments

Other

  • Independent School Districts
  • Public Housing Authorities/Indian Housing Authorities
  • Native American Tribal Organizations (other than Federally recognized tribal governments)
  • Faith-based or Community-based Organizations
  • Regional Organizations

About NIDA:

NIDA’s mission is to lead the Nation in bringing the power of science to bear on drug abuse and addiction.  This charge has two critical components. The first is the strategic support and conduct of research across a broad range of disciplines. The second is ensuring the rapid and effective dissemination and use of the results of that research to significantly improve prevention and treatment and to inform policy as it relates to drug abuse and addiction.

NLM to Host A Tribute to Marshall Nirenberg

Monday, February 9th, 2015

Fifty years ago, as a scientist at the National Institutes of Health, Dr. Marshall W. Nirenberg (1927–2010) completed his first summary of the genetic code—one of the most significant documents in the history of twentieth-century science. This summary, now in the collections of the National Library of Medicine, is a painstakingly handwritten chart of the discovery of how sequences of DNA, known as “triplets,” direct the assembly of amino acids into the structural and functional proteins essential to life. Dr. Nirenberg would go on to win the Nobel Prize in Physiology or Medicine in 1968 for this work, sharing the award with Robert W. Holley of Cornell University and Har Gobind Khorana of the University of Wisconsin at Madison “for their interpretation of the genetic code and its function in protein synthesis.”

This spring, the National Library of Medicine (NLM) will host a public program—A Tribute to Marshall Nirenberg—to celebrate the fiftieth anniversary of this scientific accomplishment. The event will be webcast on Tuesday, March 17, from 10:00am to 12:30pm (Pacific). The event will also be free and open to the public, in the NLM’s Lister Hill Auditorium, Building 38a, on the Bethesda campus of the National Institutes of Health. More information about the event and a list of speakers are available on the NLM website.

Learn more about Dr. Nirenberg, his work, and his accomplishments at NLM’s Profiles in Science website and in a recent post on the NLM History of Medicine Division’s blog, Circulating Now. Throughout 2015 NLM will continue to celebrate the fiftieth anniversary of Nirenberg’s discovery through additional posts on Circulating Now.

NIH Manuscript Submission System Refresh

Monday, February 9th, 2015

The NIH Manuscript Submission System (NIHMS) got a refresh this week. The NIHMS system supports the deposit of manuscripts into PubMed Central (PMC), as required by the NIH Public Access Policy and other participating funder (Howard Hughes Medical Institute). Are you a librarian who serves an NIH funded investigator or project? If so consider skimming through the NIHMS FAQStep-by-Step Tutorials, and Glossary.

From its Overview page:

The National Institutes of Health (NIH) developed the NIH Manuscript Submission (NIHMS) system to facilitate the submission of peer-reviewed manuscripts for inclusion in PubMed Central (PMC) in support of the NIH Public Access Policy. Since its inception in 2005, NIHMS has expanded to support the public access policies of other organizations and government agencies (for more details, see the Funders List). The NIHMS system allows users, such as authors, principal investigators, and publishers to supply material for conversion to XML documents in a format that can be ingested by PMC. Depositing a manuscript in NIHMS for inclusion in PMC is a multi-step process, requiring an author to approve the deposited files and associated funding before conversion and the PMC-ready version after conversion.

NLM Launches New Twitter Stream for K-12 Science Educators

Monday, February 9th, 2015

A new NLM Twitter stream with resources for K-12 science educators can be found at: @NLM_K12

Also available for K-12 science educators is this directory of web resources from NLM’s Specialized Information Services division