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Archive for the ‘NLM Resources’ Category

Zika Virus Content Syndication

The National Library of Medicine Disaster Information Management Research Center has been updating the Zika Virus Health Information Resources incident topic page as new guidance documents and resources are published. Starting today, you can embed the National Library of Medicine Zika Virus page on your Web site by creating a free account on the HHS Content Syndication Storefront. Once you have an account, search for the NLM Zika page to access the code used to embed the webpage on your Web site. Each time we update our Web page, your page will also be updated.

NLM Receives Generous Gift from The DeBakey Medical Foundation

Donald A.B. Lindberg, National Library of Medicine Director from 1984 to 2015, and Michael DeBakey, celebrating DeBakey’s 90th birthday in the rotunda of the NLM Building, October 7, 1998.The National Library of Medicine (NLM) has received a generous gift from The DeBakey Medical Foundation to support development, expansion, and enhanced public access to the NLM’s collection of Michael E. DeBakey archives and associated collections, and to develop related programs in the history of medicine. Initial activities will include digitizing the bulk of the DeBakey archives and making them more readily available for study and analysis, as well as the establishment of Michael E. DeBakey Fellowships in the History of Medicine and a related lecture series.

Michael E. DeBakey, MD (1908–2008), was a legendary American surgeon, educator, and medical statesman. During a career spanning 85 years, his work transformed cardiovascular surgery, helped to develop the Mobile Army Surgical Hospital (MASH), raised medical education standards, and informed national health care policy. He pioneered many operative procedures, including aneurysm repair, coronary bypass, endarterectomy, which routinely save thousands of lives each year. He performed the first successful implantation of a left ventricular assist device and some of the first heart transplants. His inventions included the roller pump (a key component of heart-lung machines), as a medical student, as well as artificial hearts and ventricular assist pumps. Among innumerable other contributions, Dr. DeBakey was a visionary supporter of the NLM, playing a pivotal role in its transformation from the Armed Forces Medical Library in the 1950s, in the establishment of the National Network of Libraries of Medicine in the 1960s, in launching NLM’s outreach initiatives in the 1990s, and in promoting the digitization of its indexes to pre-1960s journal articles. A video profile of Dr. DeBakey is available on the NLM Web site.

The NLM’s collection of Michael E. DeBakey archives dates from the early 1900s to 2009. Containing correspondence, administrative records, diaries, transcripts, publications, speeches, conference and awards material, subject files, photographs, and audiovisual media, the collection reflects the vast expanse of Dr. DeBakey’s life, achievements, and interests as a world-renowned medical statesman, innovator, and champion of humanitarianism and lifelong learning. NLM has already digitized selected items from the DeBakey archives for the Michael E. DeBakey Profiles in Science site. Materials in the DeBakey archives have rich connections to the archives of other individuals and organizations, including NLM’s own archives, as well as to many published works in the NLM collection.

Details of the expanded access to the Michael. E. DeBakey archives held by the Library, as well as the Michael E. DeBakey Fellowships in the History of Medicine and an associated annual Michael. E. DeBakey Lecture in the History of Medicine, will be announced later this year.

NLM Catalog Display Change: Journal Display Removed

At the end of December 2010, NLM launched a redesigned NLM Catalog with a new display format called Journal, available for journals cited in Entrez databases. In December 2015, NLM removed Journal as a display option. Statistics have shown that the Journal display option was seldom used. All of the elements previously in the Journal display are available in the Full display.

Upcoming NCBI Webinars: Sequence Read Archive (SRA) and Resources for Cancer Research

Five ways to submit next-gen sequence data to NCBI’s Sequence Read Archive (SRA)
Wed, February 17, 2016, 10:00-11:00 am PT
In this webinar you will learn how to use five different ways to submit your next gen sequence data to NCBI’s Sequence Read Archive. These include external submission services through Illumina’s BaseSpace, MOTHUR (for microbial ecology data) and the iPlant Collaborative. In addition NCBI provides the new SRA submission portal and soon will offer the ability to upload data to SRA through FTP and the Aspera command line client in the new submission portal.

NCBI resources for cancer research
Wed, March 2, 2016, 10:00-11:00 am PT
This workshop provides an overview of NCBI molecular resources for cancer researchers. In the first part of the webinar you will learn to more effectively use the Entrez text-based search system and the BLAST sequence similarity search tool to find data relevant to cancer research including sequence, variation, gene and expression information. The second part of the presentation will focus on accessing large-scale genomics datasets. You will learn how to search for, access and download DNA-seq, RNA-seq, Epigenomics and Metagenomics datasets and how to access the tools and APIs at NCBI that can be used to extract relevant subsets of that data for cancer research.

National Library of Medicine Announces MedPix®, Free Online Medical Image Database

MedPix Home Page – NLM’s Medical Image DatabaseThe National Library of Medicine has announced the launch of MedPix®, a free online medical image database originally developed by the Departments of Radiology and Biomedical Informatics at the Uniformed Services University in Bethesda, MD. The MedPix collection categorizes and classifies the image and patient data for each of several subsets of image database applications (e.g. radiology, pathology, ophthalmology, etc.). The content material is both high-quality and high-yield and includes both common and rare conditions. Most cases have a proven diagnosis (pathology, clinical follow-up). The teaching file cases are peer-reviewed by an Editorial Panel. The primary target audience includes resident and practicing physicians, medical students, nurses and graduate nursing students and other post-graduate trainees. The material is organized by disease category, disease location (organ system), and by patient profiles.

The foundation for MedPix was a radiology study tool that was originally developed by Dr. J.G. Smirniotopoulos in 1984. In the early 1990s, as radiology was moving from film to digital imaging, there was simultaneously a merger of the diagnostic imaging residency programs of the two premier military hospitals: Walter Reed Army Medical Center and the National Naval Medical Center. In the summer of 1999, a Web-based digital teaching file based on the radiology study tool was built at USUHS to allow the two military training programs to share teaching file cases, a training requirement. Soon, other military hospitals and several civilian institutions joined MedPix. Over the past 16 years, MedPix has amassed an impressive collection of over 53,000 images from over 13,000 cases. Continuing Medical Education (CME) and Nurse Education (CNE) were added to the MedPix system in 2001.

As a public education service, the NLM and MedPix provide the storage service, indexing, and Web server hosting. Individuals as well as institutions may participate. Contributed content may be copyrighted by the original author/contributor. No additional software is required; an Internet browser is all you need!

New 2016 MeSH Headings: Zika Virus Infection and Zika Virus

On January 27, 2016, two new MeSH headings were added to the 2016 MeSH Browser in response to increased reports in the literature about the Zika virus outbreak and its tentative association with microcephaly in newborns as well as possible paralysis and Guillain-Barre Syndrome in adults:

The terms also appeared in the MeSH export file available to licensees on January 27, 2016. Indexing for the new headings began January 28, 2016. In addition, NLM Indexing staff will review citations previously indexed on this topic to determine if the new headings should be applied to the citations. Here is a suggested interim PubMed search strategy to retrieve citations on Zika until the review of previously indexed citations is completed:

Zika [tiab]

Using the [tiab] search tag finds citations that have already been indexed with MeSH or are still in process. The tag restricts retrieval to the article title, abstract, or author keyword fields and prevents false drops from other fields such as author name.

A Zika Virus Health Information Resources page, from the Disaster Information Management Research Center at NLM, gathers resources on the emerging health issues arising from the Zika Virus. For additional information see the article, NLM Disaster Information Management Research Center Resource List Updates.

Selected Zika Virus Health Information Resources Compiled by NLM

For decades, the mosquito-transmitted Zika virus was mainly seen in equatorial regions of Africa and Asia, where it caused a mild, flu-like illness and rash in some people. About ten years ago, Zika outbreaks spread to the Pacific islands. Then, last spring, Zika appeared in South America, where it has so far infected more than 1 million Brazilians. A recent study published in The Lancet suggests that Zika virus could eventually reach regions of the United States in which 60% of the population resides. Humid, subtropical parts of the country might support the spread of Zika virus all year round, including southern Texas and Florida. With no vaccine or treatment currently available to prevent or treat Zika infection, the best way for individuals, and pregnant women in particular, to protect themselves is to avoid traveling to places where Zika is known to be present. If an individual has to live or work in such a region, the CDC recommends strict precautions to avoid mosquito bites, including wearing protective clothing, using insect repellants, and sleeping in rooms with window screens or air conditioning.

Following are selections from a list of resources gathered by the National Library of Medicine to assist public health departments, health care providers, librarians, and others seeking authoritative information on the virus and disease. In addition, Zika Virus and Zika Virus Infection are new terms included in NLM’s Medical Subject Headings (MeSH) vocabulary.

Centers for Disease Control and Prevention (CDC), U.S. Department of Health and Human Services

World Health Organization (WHO)

Pan American Health Organization (PAHO), World Health Organization

NLM Announces Pill Image Recognition Challenge

The National Library of Medicine (NLM) announced its Pill Image Recognition Challenge January 19, 2016 in the Federal Register. The Pill Image Recognition Challenge will also be posted on Challenge.gov. The submission period for the Challenge is April 4, 2016 to May 31, 2016, with winners announced August 1, 2016.

The Pill Image Recognition Challenge is a National Institutes of Health (NIH) Challenge under the America COMPETES (Creating Opportunities to Meaningfully Promote Excellence in Technology, Education, and Science) Reauthorization Act of 2010 (Public Law 111-358). Through this Challenge the National Library of Medicine (NLM) seeks algorithms and software to match images of prescription oral solid-dose pharmaceutical medications (pills, including capsules and tablets). The objective of the Challenge is the development and discovery of high-quality algorithms and software that rank how well consumer images of prescription pills match reference images of pills in the authoritative NLM RxIMAGE database. NLM will use the Challenge entries (i.e., algorithm and software) to create a future API (Application Programming Interface) and a future software system for pill image recognition; the API will be freely accessible and the system will be freely usable.

For further details, visit the NLM News & Events page.

New AIDSinfo HIV/AIDS Treatment Guidelines App Released!

The National Library of Medicine (NLM) has announced the release of a new AIDSinfo Treatment Guidelines app for both iOS and Android devices. The AIDSinfo Treatment Guidelines app provides mobile access to the HIV/AIDS medical practice guidelines developed by working groups of the NIH Office of AIDS Research Advisory Council. The guidelines include recommendations by expert panels on the treatment of HIV infection and related opportunistic infections in adults, adolescents, and children and on the management of perinatal HIV infection.

Health care providers surveyed on the AIDSinfo website expect mobile access to up-to-date HIV information at the point of care even when an Internet connection is unavailable. Designed to meet that expectation, the app automatically refreshes guidelines content when the user is connected to a wireless or cellular data network. When wireless Internet access is not available, app users can view and search the guidelines offline, and the app will check for and download any updates when the user is back online and connected again.

Available for both iOS and Android devices, the free AIDSinfo Guidelines app includes several features to personalize the app to meet individual needs. Using these features, app users can:

  • View only guideline recommendations or tables
  • Receive alert notifications when a new guideline is released or guideline content is updated
  • Bookmark sections of a guideline
  • Add notes to sections of a guideline
  • Share guidelines and notes via social media, email, or text
  • Search for information within guidelines
  • Use the guideline spell suggest feature for searching when connected to wireless or using cellular data

The free Guidelines app may also be downloaded from the AIDSinfo website. NLM encourages feedback on this app and other features of AIDSinfo. Please email your comments and suggestions to ContactUs@aidsinfo.nih.gov.

Resources for Aliso Canyon Natural Gas (Methane) Leak

Several local and state California agencies, as well as federal agencies, are responding to the natural gas leak at the Southern California Gas Company Aliso Canyon Facility that is affecting the Porter Ranch neighborhood in Los Angeles. The National Library of Medicine Disaster Information Management Research Center (NLM Disaster Health) provides information on public health aspects of chemical incidents for the benefit of health professionals and volunteers who may be responding to an incident and for people living in or concerned about an affected region. The primary releases from the well are natural gas (methane) and odorants (tertiary butyl mercaptan and tetrahydrothiophene). The area is also being affected by “oily mist” containing assorted chemicals: benzene, toluene, ethylene, xylene, and other organics consistent with oil residues from the former oil drilling facility site. Air sampling has also noted radon and hydrogen sulfide.

A resource guide with a compilation of links on the gas leak and specific chemicals detected was prepared by NLM staff members Cindy Love, Siobhan Champ-Blackwell, and Stacey Arnesen. Contributions from NN/LM PSR staff were made by Kelli Ham, Lori Tagawa, and Alan Carr. A PDF version of the guide is also available.