First major analysis of Human Protein Atlas published, could explain many drug side effects [[Research article summary]


Picture1An image of dyed proteins from the Human Protein Atlas.

From the 23 January 2015 KTH article

A research article published today in Science presents the first major analysis based on the Human Protein Atlas, including a detailed picture of the proteins that are linked to cancer, the number of proteins present in the bloodstream, and the targets for all approved drugs on the market.

The Human Protein Atlas, a major multinational research project supported by the Knut and Alice Wallenberg Foundation, recently launched (November 6, 2014) an open source tissue-based interactive map of the human protein. Based on 13 million annotated images, the database maps the distribution of proteins in all major tissues and organs in the human body, showing both proteins restricted to certain tissues, such as the brain, heart, or liver, and those present in all. As an open access resource, it is expected to help drive the development of new diagnostics and drugs, but also to provide basic insights in normal human biology.

The analysis shows that almost half of the protein-coding genes are expressed in a ubiquitous manner and thus found in all analysed tissues.

The analysis suggests that approximately 3,000 proteins are secreted from the cells and an additional 5,500 proteins are located to the membrane systems of the cells.

“This is important information for the pharmaceutical industry. We show that 70% of the current targets for approved pharmaceutical drugs are either secreted or membrane-bound proteins,” Uhlén says. “Interestingly, 30% of these protein targets are found in all analysed tissues and organs. This could help explain some side effects of drugs and thus might have consequences for future drug development.”

The analysis also contains a study of the metabolic reactions occurring in different parts of the human body. The most specialised organ is the liver with a large number of chemical reactions not found in other parts of the human body.

The study has been carried out by researchers in Sweden at KTH Royal Institute of Technology, Uppsala University, Karolinska Institute, Chalmers University of Technology, Lund University, and Stockholm University.

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Endnote – Free Resource to UT Affliiates to Manage Citations and Incorporate Them into Word [Resource of the Week]

Are you looking for a seamless way to quickly keep citations handy for future reference? Organize the citations into groups of your choosing? Share select groups with others? Incorporate citations into Word through any one of several hundred styles?
Look no further, EndNote is your answer to these questions and more.


The UT Library Endnote Library Guide (LibGuide) provides a great overview for a quick start and links for more detailed information. Included

An EndNote Online account can be used as a collaborative tool to share citation information and attachments. So now libraries can be shared with others.

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UCLA, Yale professors propose new regulations for off-label uses of drugs and devices



Health care providers have to make their own decisions about using drugs off-label, often in the face of uncertain evidence.


From the 13 January 2015 press release


Off-label use of drugs and medical devices — using approved remedies in unapproved ways — has long been a part of medicine. The practice provides public health benefits but also presents some risks.

For the most part, the U.S. Food and Drug Administration allows physicians to prescribe drugs and devices off-label in the same way they are prescribed for their approved uses. The FDA couldn’t require approval for each off-label use because the burden for approval would be so high that few off-label uses would be approved, which would deprive patients of effective treatments for which the drugs weren’t originally intended.

As a result, health care providers have had to make their own decisions about using drugs off-label, often in the face of uncertain evidence.

To address that issue, researchers from the David Geffen School of Medicine at UCLA have proposed a system combining reporting, testing and enforcement regulations, and allowing interim periods of off-label drug prescription. Their recommendations [free full text]  published in the Duke Law Journal, would give patients more treatment options while providing regulators with evidence of the drugs’ safety and efficacy.


Much off-label prescribing of medications and medical devices is beneficial, but without rigorous study it is difficult to know what works and what doesn’t, said Dr. Ryan Abbott, visiting assistant professor of medicine in UCLA’s division of general internal medicine and health services research.

“Even though a drug or device has been approved for one indication, physicians can prescribe them for other uses as well — it’s been part of medical practice for a long time,” said Abbott, a physician and attorney who co-wrote the paper with Yale Law School’s Ian Ayres. “Our proposals are important because there is a tension between providing access to the drugs and devices that could benefit patients in untested ways and the need to prevent harmful uses.”


The authors’ proposal comprises three elements:

  • Improved reporting of off-label use through disclosure of diagnostic codes in reports to the FDA, in detailing data that pharmaceutical companies obtain on physicians’ prescribing habits, and in reports to the FDA and Medicare/Medicaid reimbursement requests. This information, which would omit details that could identify individual patients, could then be shared with academics and pharmaceutical companies for use in research.
  • Expansion of post-market testing requirements for off-label use of drugs and medical devices.
  • A tiered labeling system for drugs consisting of “red box” warnings that prohibit certain off-label uses; informed consent from patients receiving prescriptions for off-label use of some drugs that currently carry “black box” warnings, which identify drugs that pose a significant risk of serious or life-threatening adverse effects; and the creation of a new “grey box” warning that blocks Medicare Part D and Medicaid reimbursements by the Centers for Medicare and Medicaid Services.

“The improved reporting, testing and enforcement regulation would work together to produce a more layered range of regulatory responses,” the authors write. “The FDA, armed with better information about the extent of off-label use and adverse effects, would be in a better position to require post-market testing and to discourage off-label use with new types of warnings if manufacturers fail to provide sufficient, timely evidence of safety and efficacy in that particular extrapolation.”

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PubMed announcement – Retrieving citations with secondary sources


Above Text—

A new PubMed search option “hasdatabanklist” has been created to retrieve citations that carry a value in the Secondary Source ID [SI] field regardless of what the specific value(s) may be. Typically, the SI field contains information about where additional data related to an article are deposited. Please seeMEDLINE Databank Sources to view the list of repository values.

To limit a search to citations that may have deposited data in a repository and acknowledged that deposit in the full text of the article, search using AND hasdatabanklist; for example:

randomized controlled trial [pt] AND hasdatabanklist

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Two upcomging AHRQ sponsored Webinars – January 28 and January 29

From two AHRQ announcements, here and here

Register Now: January 28 AHRQ Webinar on Meeting Stage 3 Meaningful Use Objectives

AHRQ is hosting a webinar January 28 from 12:30 to 2 p.m. ET on meeting stage 3 meaningful use objectives. This presentation will outline findings from research on meaningful use of clinical decision support, care coordination and the use of electronic health records in pediatric primary care settings. Determination of continuing medical education credit with the American Academy of Family Physicians is pending. Registration is open.



Register Now: January 29 Webinar on How Practice Facilitators Can Support Patient Engagement in Primary Care

AHRQ is hosting a webinar January 29 from 3 to 4:30 p.m. ET about how practice facilitators can support patient engagement. Practice facilitators can help practices improve how they engage patients by helping them gather feedback and ideas from their patients and use the information to redesign visits and services to support better patient engagement and improved patient experience. The webinar will feature the experiences of a practice facilitator who worked successfully with practice leaders and patients to transform diabetes care visits in primary care. Patient engagement is a central element of the patient-centered medical home as well as a patient’s own experience of their care. Speakers include:

  • Lyndee Knox, Ph.D., CEO, LA Net Community Health Resource Network, Los Angeles
  • Cindy Brach, M.P.P., senior health policy researcher, AHRQ
  • Adrienne Deswert, R.N., B.S.N., R.N. Care Manager, Annville Family Medicine, Annville, Pennsylvania

This is the fourth in a series of webinars hosted by AHRQ’s Prevention and Chronic Care Program to share the Agency’s tools and resources for training primary care practice facilitators. The first three webinar topics were practice facilitation case studies, use of health information technology and supporting leaders to promote patient safety. Registration is open.


Other continuing education resources may be found in the UT Library Guide BioMedical Resources – Continuing Education



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PubAg – portal to USDA-authored and other highly relevant agricultural research (including nutriton) [Resource of the Week]

From the 13 January 2015 press release

Photo: Two women working at a computer. Link to photo information
The National Agricultural Library’s new literature search tool, PubAg, is user friendly and does not require the public to establish an account or a password. Click the image for more information about it.

NAL Unveils New Search Engine for Published USDA Research

By Kim Kaplan
January 13, 2015

The National Agricultural Library (NAL) has unveiled PubAg, a user-friendly search engine that gives the public enhanced access to research published by U.S. Department of Agriculture (USDA) scientists. NAL is part of USDA’s Agricultural Research Service (ARS).

PubAg, which can be found at, is a new portal for literature searches and full-text access of more than 40,000 scientific journal articles by USDA researchers, mostly from 1997 to 2014. New articles by USDA researchers will be added almost daily, and older articles may be added if possible. There is no access fee for PubAg.

Phase I of PubAg provides access for searches of 340,000 peer-reviewed agriculturally related scientific literature, mostly from 2002 to 2012, each entry offering a citation, abstract and a link to the article if available from the publisher. This initial group of highly relevant, high-quality literature was taken from the 4 million bibliographic citations in NAL’s database.

Phase II of PubAg, planned for later in 2015, will include the remainder of NAL’s significant bibliographic records.

PubAg has been specifically designed to be easy to use and to serve a number of diverse users including the public, farmers, scientists, academicians and students. There is no requirement for a username, password or any other form of registration to use PubAg.

NAL has one of the world’s largest and most comprehensive compilations of agricultural information available.

The advanced search allows for searching using

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Public Access Compliance Monitor – NIH announcement

The text of the annoucement

                   Public Access Compliance Monitor

Funk K. Public Access Compliance Monitor. NLM Tech Bull. 2015 Jan-Feb;(402):e1.   2015 January 13 [posted]


The Public Access Compliance Monitor (PACM or “compliance monitor”) is a service from the National Library of Medicine that helps users at NIH-funded institutions locate and track the compliance of funded papers with the NIH Public Access Policy at an institutional level. Whether you are looking for a quick snapshot of your institution’s compliance rate or want to take an active role in helping your investigators comply with the policy, PACM can help you get the information you need.

To gain access to the compliance monitor, users must first be assigned a compliance reports (“PACR”) role by an administrator at their institution who is authorized to assign roles in the NIH eRA Commons grants administration system. Users with a PACR role will then have access to the compliance reports for their institution.

PACM provides users with a list of all PubMed citations associated with an institution’s NIH funding and classifies the articles according to compliance status (i.e., Compliant, Non-Compliant, In Process). The compliance monitor also provides detailed information about each article including:


  • a full citation including the PMID (PubMed ID) and link to the PubMed record
  • associated grants and principal investigators
  • NIHMSID (NIH Manuscript Submission Reference Number), where available
  • PMCID (PubMed Central ID), where available
  • key names and dates in the NIHMS, where available
  • article compliance status
  • method A status
  • journal publisher

Compliance reports can be downloaded from these lists and the data filtered based on an institution’s needs.

For more information on the PACR role, the compliance monitor, and the available reports, see the User Guide:

Additonally, an overview video of PACM from The NIH Public Access Policy for Librarians Webinar is available at

Please direct questions concerning the Public Access Compliance Monitor to

By Kathryn Funk
National Center for Biotechnology Information

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When Experts Disagree: The Art of Medical Decision Making – Streamed online lecture

From the NIH Press Release
When Experts Disagree: The Art of Medical Decision Making

January 26, 2015 10:00 a.m. ET
Masur Auditorium, National Institutes of Health,
Bethesda, Maryland

The lectures will be streamed live online [and archived]  at*

NCCIH welcomes acclaimed authors Jerome Groopman, M.D. and Pamela Hartzband, M.D. as featured speakers for the annual Stephen E. Straus Distinguished Lecture in the Science of Complementary Health Therapies. The husband-and-wife team will present “When Experts Disagree: The Art of Medical Decision Making.”

In this lecture, Drs. Groopman and Hartzband reveal that each of us has a “medical mind,” a highly individual approach to weighing the risks and benefits of treatment.  To ascertain our unique medical minds, they will present probing questions. Are you a minimalist or a maximalist, a believer or a doubter, do you look for natural healing or the latest technology?  Drs. Groopman and Hartzband explain how pitfalls in thinking and the way statistics are presented in pharmaceutical advertisements, the media, and even scientific reports can mislead all of us.  The talk will demonstrate the contrast between the roles of population guidelines and the care of the individual, and explain the complexities of end of life care – all factors that contribute to a person’s “medical mind.” In their talk, Drs. Groopman and Hartzband will weave vivid narratives from real patient experiences with insights from recent cognitive research to demonstrate how to arrive at choices that serve the individual best.

Dr. Groopman’s research interests include studying how viruses cause immune deficiency and cancer, the role of endocannabinoids in hematopoiesis, mechanisms of liver injury due to hepatitis c, and the effects of novel cell cycle inhibitors against mantle cell lymphoma. He has been integral in developing many AIDS-related therapies. Dr. Hartzband’s clinical interests include thyroid disorders, adrenal and pituitary disorders, osteoporosis, and calcium disorders. Together, Drs. Groopman and Hartzband co-authored the book “How Doctors Think” and write a monthly column for the American College of Physicians’ publication “ACP Internist.”


Jerome Groopman, M.D.
Dina and Raphael Recanati Chair of Medicine
Harvard Medical School
Chief of Experimental Medicine
Beth Israel Deaconess Medical Center

Pamela Hartzband, M.D.
Assistant Professor of Medicine
Harvard Medical School
Attending Physician, Division of Endocrinology
Beth Israel Deaconess Medical Center

*CME credit is available to those who attend in person and to those who view the lecture live online.  We will post a self-credit report form on January 26, 2015 which must be returned by 10 pm ET.

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Revised! Mulford Library Home Page

The Mulford Library home page has recently been revised. It is more streamlined with heavily used features front and center.

Here is an overview of the most noticeable changes.

  • Quick Links to popular health science databases (as Access Medicine, Clinical Key, CINAHL) are now in the center of the page under the Articles
  • The Slideshow, again front and center, includes Mulford Library announcements as events and services.
  • The Hours link is on the left side under Quick Links.
  • The Mulford Blog is now on the right side at News and Events. Content still includes updated hours, resources of note, general interest items from the biomedical literature, and relevant news items from the field.
  •  More options (right column) has several drop down menus. These FAQs explain how to find resources, get personalized help, get information about library services, and more.

As always, please do not hesitate to consult with a Mulford reference librarian with your information and resource needs. We are here to save you time and alleviate frustration!


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iBiology aims to convey, through open-access free videos, the knowledge and techniques of modern biology. While accessible to advanced high school students, others interested in these topics could certainly benefit.  Researchers can learn new techniques and instructors have access to supplemental course material. Much of the material is potential review material for post-high school students and others. The About Page succinctly states “[t] his project is made possible by the good will of many biologists who are committed to making their work broadly accessible and to conveying the excitement of biology to a worldwide audience.”  As indicated in the home page, 300 videos are easily accessible in three categories:  iBioSeminars, iBioMagazine, and iBioEducation.

In iBioSeminars prominent biologists ” present lectures that start with a broad introduction to their current work and progress to detailed discussions of their research and experiments”. Topics include  Cancer & Medicine, Genetics & Gene Regulation, Neuroscience, and Techniques.

iBioEducation includes twelve Exploring Biology topics (as Biochemistry and Microbiology) with  lectures, short clips, and seminars.  Registration is required to access the comprehensive discussion questions and assignments that supplement the iBioSeminars as well as iBioSeminars Teaching Tools.


As always, do not hesitate to consult with a Mulford reference librarian with your information and resource needs. We are here to save you time and alleviate frustration!


Related UT Libguides



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