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Changes to the HSLS Online Collection for 2019

Journals added to the HSLS online collection for 2019 include:

  • Aging Clinical and Experimental Research
  • Cancer Treatment and Research Communications 
  • Evidence-Based Practice
  • JACC: Clinical Electrophysiology1
  • Journal of Alzheimer’s Disease
  • Journal of Animal Science
  • Journal of Complex Networks
  • Journal of Language Evolution
  • Midwifery
  • Nature Biomedical Engineering
  • Nature Human Behaviour
  • Neuro-Oncology Practice
  • Pediatric Dentistry
  • Translational Stroke Research
  • Work, Aging, and Retirement
  1. Availability forthcoming.

HSLS continually adds new open-access journals, so visit our E-journals A-Z list and click on “Show Select Subject” to view titles in your area of interest. Continue reading

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NEJM Resident 360

You probably already know that HSLS subscribes to The New England Journal of Medicine. But did you also know that our subscription gives you free access to NEJM Resident 360?

Resident 360 is a platform for residents, fellows, medical students, and physicians that offers career advice, discussion boards, quizzes, and lots of additional information to help you as you begin your medical career. Resident 360 is broken into seven different sections, each offering information on a different aspect of medicine or residency. The sections include: Continue reading

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Fad or Smart? Artificial Intelligence and Semantics for Literature Searching

There are two approaches to literature searching: improvised discovery, and structured query, each with corresponding online platforms. Discovery is fast and generates ideas, but is generally not reproducible, since it does not use controlled vocabularies. This limits its use for systematic reviews or other published research, for example. Building a query to find citable new evidence is time-consuming, but structured searches using controlled vocabularies are reproducible. Before starting a search in either type, consider your purpose: are you generating ideas? Or documenting reproducible methods? Both methods have value, and HSLS librarians can help you fit both into your research workflow.

New discovery search engines use semantics and artificial intelligence as alternatives to traditional indexing. Additionally, they search the full text of documents, rather than the title and abstract only, resulting in larger but more precise retrieval than traditional title/abstract databases. Their interactive dashboards are optimized for on-the-fly analysis. Try the following three products as examples of current discovery search tools.

 

LENS.org, in six languages, integrates global patent data, regulatory and business data, and scholarly medical literature using both indexing and artificial intelligence. It is completely free to all users. Special filters or “lenses” help searchers identify and analyze various aspects of research, such as the impact of publications on global patents, using its PatCite tool. The structured Scholar Search interface offers filters that retrieve specific funding agencies, or biological sequences in patents (see PatSeq tool). All data sources are open and freely accessible by anyone.

 

Dimensions from Digital Science incorporates natural language processing, machine learning, and artificial intelligence in its search of over 50 million full-text publications, preprints and other documents. Dimensions connects multiple data sources from the complete research lifecycle, enabling robust research analysis. The free version links publications, citations, and altmetrics, with the dashboard supporting analysis of researchers, fields of research, institutions, locations, and research metrics. Because Digital Science owns ReadCube, Figshare and other research services, expect related links. Its weakness may be its restriction to the NIH Relative Citation Ratio (RCR) research indicator, which applies only to NIH and PubMed publications.

 

Semantic Scholar from the Allen Institute of Artificial Intelligence was developed to make highly cited papers easily accessible to academics. Machine learning and artificial intelligence are used to search over 40 million papers, presentations and conferences indexed in PubMed, Springer Nature, Frontiers, Science, MIT Press, Clinical Trials, IEEE, and other sources. Enter search terms or a title, and Semantic Scholar produces a concise list of relevant results. A simple layout, PubMed filters and links to “Highly Influential Citations” and “PDFs” makes it easy to review and save references. A recent review available in JMLA has additional details.

Research discovery may be faster and more effective using one of these tools. Find your favorite and experiment! If you have any questions, please feel free to contact Andrea Ketchum, at ketchum@pitt.edu or 412-648-9757.

~Andrea Ketchum

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Subawards Extend NNLM MAR’s Reach

Kate Flewelling
NNLM MAR
Executive Director

This year, NNLM MAR provided about $450,000 in subawards to Network member organizations in Pennsylvania, New York, New Jersey, and Delaware. Subawards are typically small (this year’s range from just $600 to $20,000) and allow NNLM MAR to expand training of National Library of Medicine resources and increase the access to and use of high quality health information across diverse populations around the region.

Examples of funded projects include:

Library Moon Walk: Over twenty public libraries in 10 counties in New York State are getting staff training on health information resources, hosting health programming, and encouraging their patrons to track their steps in an effort to walk to the moon. The project celebrates the 60th anniversary of the Apollo 11 Moon Landing and serves as a preview for the 2019 Summer Reading Theme, “A Universe of Stories.” Continue reading

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Treasures from the Rare Book Room: Le Rouge, Avis Très Important Aux Personnes Attaquées de Hernies Ou Descentes, Paris 1784

We know very little about the author of an unusual book on hernia found in the Falk Library Rare Book Collection. Jean Pierre Le Rouge was a surgeon at the College of Surgeons in Paris and at the Hôtel-Dieu in the second half of the 18th century and was the author of two books on hernias. He had 17 years of experience working at the biggest hospital in Paris, Hôtel-Dieu, when he published his first popular work Avis très important aux personnes attaquées de hernies ou descentes [Translation: Very important notice to people attacked by hernia] in 1784. A year later, in 1785, his thesis Dissertatio anatomico-chirurgica de perfecta inguinalis herniae simplicis curatione [Translation: Thesis on the treatment of inguinal hernia] appeared. Both books are very scarce.

The popular tract may be considered an early example of consumer health information. It consists of five chapters, in which the author (1) explains the causes and characteristics of different hernia types; (2) gives advice on limiting physical activities when wearing hernia trusses; (3) points out the need to wear supportive bandages or pessaries; (4) discusses palliative treatment focused on reducing hernias by means of bandages illustrated with the cases from his hospital practice; and (5) provides a composition of a plaster for the radical cure of a hernia. Continue reading

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HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

All author names in bold are HSLS-affiliated.

Publications

J. Donovan, T. Chung, M. Klein-Fedyshin, Research & Clinical Instruction Librarian, published “A Meta-Analysis of the Relationship between Parental Drinking and Adolescent Drinking” in PROSPERO International Prospective Register of Systematic Reviews, 2019: CRD42019119545.

B. Fields, R.L. Turner, Coordinator of Liaison Services, M. Naidu, et al., published “Assessments for Caregivers of Hospitalized Older Adults” in Clinical Nursing Research, 2018: 1-21.

J.T. Hanlon, S. Perera, P.J. Drinka, C.J. Crnich, S.J. Schweon, M. Klein-Fedyshin, Research and Clinical Instruction Librarian, C.B. Wessel, Head of Research Initiatives, et al., published “The IOU Consensus Recommendations for Empirical Therapy of Cystitis in Nursing Home Residents” in the Journal of the American Geriatric Society, December 24, 2018. Continue reading

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Classes for February 2019

Painless PubMed, Monday, February 4, noon-1 p.m.

Searching for Dollars: Grant Seeking to Support Research, Wednesday, February 6, 4-5 p.m.

Introduction to Tableau for Data Visualization, Monday, February 11, 9-10 a.m.

Introduction to the Pitt Data Catalog, Tuesday, February 12, 2-3 p.m.

Future Proof your Data: Planning for Reuse, Wednesday, February 13, 11 a.m.-noon

RNA-Seq & CLC Genomics, Wednesday, February 13, 1-4 p.m.

File Naming Best Practices, Thursday, February 14, 10-10:30 a.m.

Data Drop-In Session, Friday, February 15, 8:30-10:30 a.m.

Basic EndNote, Tuesday, February 19, 10-11 a.m.

Save & Customize Your Searches in PubMed, Wednesday, February 20, noon-1 p.m.

Pathway Analysis, Wednesday, February 20, 1-4 p.m.

Painless PubMed, Friday, February 22, 9-10 a.m.

Crafting a Data Management Plan, Monday, February 25, noon-1 p.m.

Advanced EndNote, Tuesday, February 26, 10-11 a.m.

Variant Detection & Analysis: CLC Genomics & IVA, Wednesday, February 27, 1-4 p.m.

Basic Python through Jupyter, Thursday, February 28, 1-4 p.m.

Continue reading

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New Software and 3D Model Records Now in the Pitt Data Catalog

HSLS Pitt Data Catalog, a project by the Health Sciences Library SystemWhen HSLS launched the Pitt Data Catalog last spring, we wanted to provide researchers with flexible options for advertising and sharing their data. Now that the catalog has grown to describe more than 20 Pitt-created datasets, that flexibility has led our collection development in surprising and exciting directions. We have recently added our first records describing software code and 3D models, all created by Charles C. Horn, PhD.

Dr. Horn is an associate professor of medicine who studies gut-brain communication, particularly via the vagus nerve. His research makes use of several open-source software packages, which he demonstrates in his paper (with David M. Rosenberg), “Neurophysiological Analytics for All! Free Open-Source Software Tools for Documenting, Analyzing, Visualizing, and Sharing Using Electronic Notebooks.” Electrophysiological data used to demonstrate the software tools are available in the publication’s data supplements and on Github, where Dr. Horn has also uploaded scripts and a Docker image containing tools to make neurophysiological data analysis easier. Pitt Data Catalog records linking to those software/data packages include:

Dr. Horn has also designed several printable 3D models for experimental apparatuses in electrophysiology. The files shared through the NIH 3D Print Exchange include printable files in a variety of formats, photos, and assembly instructions. The 3D model records in the Pitt Data Catalog are:

We are pleased to host records describing these software packages and models, which are the first of their kind in the wider Data Catalog Collaboration Project.

If you have data, code, or models (printable or otherwise) that you would like to include in the Pitt Data Catalog, please contact us at HSLSDATA@pitt.edu or through the “Include your Dataset” button on the Pitt Data Catalog homepage. We are available to talk with you about publicizing your research products through the catalog. The process is quick, free, and tailored to your needs, especially regarding confidentiality and controlling access to your data.

~Helenmary Sheridan

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Introducing Partek® Flow® for Single Cell RNA-Seq Analysis

The HSLS Molecular Biology Information Service (HSLS-MBIS), in collaboration with the Center for Research Computing, is excited to announce the availability of a limited number of licenses for a long-awaited and powerful tool for processing and analyzing single cell RNA-Seq (scRNA-Seq) data—Partek® Flow®.

Partek® Flow® by Partek®

What is scRNA-Seq? It’s a revolutionary next-generation sequencing technology that focuses on the characterization of individual cells, as opposed to bulk populations of cells. This allows biomedical researchers to make previously challenging discoveries such as the elucidation of gene regulatory networks, the reconstruction of cell hierarchies, and the identification of rare cell types. Continue reading

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New Digital Library for UPMC

Mobile view of UPMC-centered website for the libraryHSLS is pleased to launch the new UPMC Health Sciences Digital Library, the easiest and fastest way for UPMC employees to access cutting edge, high quality medical information. The Health Sciences Digital Library, accessible via the UPMC network, provides streamlined access to the “UPMC Collection”—which includes 5,000 health sciences e-journals, 4,500 e-books, 25 databases of topic specific content, and multiple mobile apps.

For information seekers, the portal is intuitive and easy to navigate. Top resources such as PubMed, UpToDate, and Micromedex are one click away. Three A-Z lists provide targeted title searching, while the UPMC library catalog, “HealthCat,” creates advanced library searches. Continue reading

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Finals Week Dog Therapy

During finals week in December, HSLS offered a dog therapy study break for health sciences students. Nearly 100 students gathered in our conference room to de-stress by spending time with three furry friends: Mosie and Hava, both Portuguese water dogs, and Blue, a golden retriever. HSLS would like to thank Rick Oberndorf and Melissa Saul, the pet handlers who volunteered their time to this effort.

students petting a dog Continue reading

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Discover My NCBI: PubMed’s Multifaceted Tool

My NCBI is a free tool developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). It allows you to customize services for PubMed and other NCBI databases. The features of My NCBI will make searching PubMed and managing your search results easy and convenient.

My NCBI features allow you to:

  • save search strategies and results
  • set up an e-mail alert to automatically receive new articles on your topic
  • establish predefined filters for searches and how results display
  • enable the automatic highlighting of search terms in your search results for easier browsing
  • use SciENcv to generate biosketches for the National Institutes of Health, the National Science Foundation, and the Agency for Healthcare Research and Quality
  • access My Bibliography in order to create and maintain a personal bibliography in order to track all of your publications for use in your biosketch

Another nice feature of My NCBI is the ability to easily access everything stored in My NCBI from anywhere in the world without being connected to the Pitt or UPMC networks. Continue reading

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HSLS Staff News

The HSLS Staff News section includes recent HSLS presentations, publications, staff changes, staff promotions, degrees earned, etc.

All author and presenter names in bold are HSLS-affiliated.

Publications

Jonathon Erlen, History of Medicine Librarian, publishedDissertations in the History of Pharmacy” in Pharmacy in History, 60(3): 100, 2018.

Sara P. Myers, Katherine M. Reitz, Charles B. Wessel, Head of Research Initiatives, et al., published “A Systematic Review of Gender-Based Differences in Hirsch Index among Academic Surgeons” in the Journal of Surgical Research,  236: 22-29, 2019. Continue reading

This information is over 2 years old. Information was current at time of publication.

Classes for January 2019

Basic EndNote, Tuesday, January 8, 10-11 a.m.

Painless PubMed*, Thursday, January 10, 9-10 a.m.

Infographics: Sharing Information Visually, Monday, January 14, 1-2 p.m.

Locating and Citing Research Data, Wednesday, January 16, 9-10 a.m.

RNA-Seq & CLC Genomics, Wednesday, January 16, 1-4 p.m.

Presentation Zen: Effective Visuals and Design, Wednesday, January 23, 9-10 a.m.

ChIP-Seq & CLC Genomics, Wednesday, January 23, 1-4 p.m.

Painless PubMed*, Thursday, January 24, 11:30 a.m.-12:30 p.m.

Introduction to the Pitt Data Catalog, Friday, January 25, 11 a.m.-12 p.m.

PowerPoint for Conference Posters, Monday, January 28, 1-3 p.m.

Electronic Research Notebooks: Introduction to LabArchives, Tuesday, January 29, 12-1 p.m.

Gene Regulation, Wednesday, January 30, 1-4 p.m.

Create Biological Diagrams with ePath3D, Thursday, January 31, 10-10:30 a.m.

Continue reading