jdahm – Page 18 – HSLS Update

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Geneshot: Piercing the Literature to Identify and Predict Relevant Genes

Are you a biomedical researcher searching for information on genes related to a particular disease, pathway, or process? Are you overwhelmed by the vast quantity of associated literature? Have you considered that some genes are more highly investigated than others, which leads to an overabundance of literature to review for some genes as well as a scarcity of information on others?

Geneshot is a new search engine created to bridge this gap and highlight understudied genes by mining publications for mentions of any genes with the search term(s), then prioritizing the genes. Searching for a biomedical term returns two ranked gene lists. The first contains genes reported in the literature and the second contains predicted genes identified via data integration from multiple sources. The underlying data sets are from PubMed, GeneRIF, AutoRIF (more comprehensive than the former), gene-gene co-expression matrix data using ARCHS4, and gene-gene co-occurrence matrix Tagger and Enrichr data. Geneshot can also facilitate hypothesis generation by assessing gene set novelty and proposing additional relevant genes to augment gene sets. A detailed description of the mining and prediction methodology is available in the Geneshot publication. Continue reading →

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OPEN-i®: A Unique Image Search Engine

As the saying goes, “A picture is worth a thousand words.” While it can take hundreds or thousands of words to convey a complicated concept; a single image can easily do the same thing. OPEN-i® is the open access biomedical image search engine from the National Library of Medicine’s Lister Hill Center for Biomedical Communications. OPEN-i® is unique in its ability to index both the article’s text and images from the open source literature and biomedical image collections. OPEN-i® searches and retrieves both abstracts and images (including charts, graphs, clinical images, etc.)

You can conduct a search in OPEN-i® by typing your terms in the search box or by selecting a saved image. From the results display, hover your cursor over an image and a MEDLINE citation will pop-up.

The following limits can be applied to your searches:

Rank By (Newest, Oldest, Diagnosis, Etiology, etc.)
Article Type (Abstract, Book Review, Brief Report, etc.)
Image Type (CT Scan, Graphics, MRI, etc.)
Subsets (Basic Sciences, Clinical Journal, Ethics, etc.)
Collections (PubMed Central, Indiana U. Chest X-rays, USC Orthopedic Surgical Anatomy, etc.)
License Type (Attribution, Attribution noncommercial, Attribution noncommercial no derivatives, etc.)
Specialties (Behavioral Sciences, Biochemistry, Cancer, etc.)
Search In (Titles, Mentions, Abstracts, etc.)

OPEN-i® contains over 3.7 million images from about 1.2 million PubMed Central® articles; over 7,400 chest x-rays with over 3,900 radiology reports; 67,500 images from the NLM History of Medicine collection; and over 2,000 orthopedic illustrations, plus MedPix.

Images are obtained from the following sources:

The Open Access Subset of PubMed Central (PMC)
The Indiana University hospital network
The Orthopedic Surgical Anatomy Teaching Collection at the USC Digital Library
Images from the History of Medicine Division from the U.S. National Library of Medicine
MedPix

For more information about copyright, search help, and technical problems, see the OPEN-i® FAQ page.

*Parts of this article were derived from the OPEN-i® website.

~Jill Foust

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HSLS Staff News

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

Names in bold are HSLS-affiliated

News

Welcome to Anthony Harris, Assistant Learning Management System Developer. Anthony recently graduated from the University of Pittsburgh with a Bachelor of Science in Information Science and will be working with both the NNLM Web Services Office (NWSO) and the NLM All of Us Research Program Training and Education Center (TEC).

Tessa Zindren joined the staff of the National Network of Libraries of Medicine, Middle Atlantic Region, as Program and Outreach Assistant. Tessa will be responsible for maintaining outreach materials, responding to member and staff requests, and reporting to internal and external stakeholders. She has a Bachelor of Science in Business Administration with a major in Marketing from Pitt and was most recently Project Manager at AMG Research.

Publications

M.A. Bowman, D.J. Buysse, J.E. Foust, Research and Instruction Librarian, et al., published “Disturbed Sleep as a Mechanism of Race Differences in Nocturnal Blood Pressure Non-Dipping,” in Current Hypertension Reports, 21(7), May 22, 2019. Continue reading →

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Classes for July 2019

Painless PubMed, Tuesday, July 2, 9–10 a.m.

Single Cell Transcriptomics, Wednesday, July 10, 10 a.m.–12 p.m. (morning session) and 1–4 p.m. (afternoon session)

Reporting Guidelines: A Pathway to Transparent Writing Equals Better Results, Thursday, July 11, 10–10:30 a.m.

Basic EndNote, Monday, July 15, 9:30–10:30 a.m.

Painless PubMed, Tuesday, July 16, 9:30–10:30 a.m.

Bioinformatics Data Analysis: Options 4 Rigor, Tuesday, July 16, 12–1 p.m.

Gene Expression Visualization, Wednesday, July 17, 1–4 p.m.

Basic Python through Jupyter, Thursday, July 18, 1–4 p.m.

Advanced EndNote, Friday, July 19, 10–11 a.m.

Visualized Searches: VOSViewer for Literature Analysis, Friday, July 19, 12–1 p.m.

ChIP-Seq & Partek Flow, Tuesday, July 23, 1–4 p.m.

Introduction to Data Management, Wednesday, July 24, 10–11 a.m.

Research Metrics and Publication Reports: Showcasing Impact, Tuesday, July 30, 4–5 p.m. Continue reading →

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‘Of Mice and Men’ and Bad Reporting of Science

It’s easy to get caught up in splashy health news reporting that sounds like a miraculous medical breakthrough. Enticing headlines such as “Compounds Found in Carrots Reverse Alzheimer’s-Like Symptoms” or “Exercise during Pregnancy Protects Children from Obesity” can raise false hope in patients when science reporters and press releases fail to delineate animal from human studies in the headline. Even worse, it might be necessary to read half the article before discovering it is not reporting a human study. Although animal studies often do show great promise, a drug or therapy that works effectively in mice, for example, can often fail to work in humans.

Recently, James Heathers, a postdoctoral researcher at Boston’s Northeastern University, took issue with this health news reporting tactic and chose to confront the hype with humor by creating a Twitter account @justsaysinmice. Simply by adding the phrase ‘in mice’ to the sensationalized health headline, these tweets are an attempt to counter bad reporting one news story at a time. Since it began in April, @justsaysinmice has gained 59,000 followers.

For those of us without a trendy Twitter idea who want to learn and use best practices for communicating biomedical research for public consumption, turn to HSLS resources. To locate books, begin with a PittCat ‘subject heading browse’ using the phrase communication in medicine. You can also browse journals that publish on this topic, such as Journal of Health Communication and Health Communication, or contact a librarian by phone, chat, or e-mail through Ask a Librarian. Additional helpful resources are available online from the NIH including a Checklist for Communicating Science and Health Research to the Public, and the use of plain language for clear communication.

~Rebecca Abromitis

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Falk Library Construction Updates

HSLS Construction Scaife Hall Corner Exterior Drawing A new Falk Library is on the way! As part of the Scaife Hall West Wing construction project, Falk Library is embarking on an exciting renovation project. Highlights of the new space will include updated and expanded learning and study spaces, integrated technology areas, modular seating, and a new entrance on Lothrop Street, convenient for all health sciences students.

While the expansion and renovation of the library will provide exciting opportunities, there will be disruptions and adjustments as the project evolves.

In early May, over 90,000 volumes of bound journals and print books were moved to the University’s Thomas Boulevard storage facility. Although housed off site, the materials are readily accessible to library users via an HSLS Document Delivery Request. The Current Collection, a companion to HSLS’s extensive e-book collection, will remain in Falk Library as well as the small Leisure Reading Collection and the Rare and Special Collections.

For more information about the Falk Library construction project including updates, frequently asked questions, and other information, please visit the HSLS Construction web page.

~Fran Yarger

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Accidentally Hiding Behind Your ORCID iD? Change Your Privacy Setting to Power Up

Why do you need an ORCID iD? First, to enable others to find you and your work, and second, to automate funding, publishing, and other reporting requirements. Help ORCID work for you!

Privacy has justifiably become a major concern over the past several years, as access to Social Security numbers, bank accounts, credit cards, and social media accounts have been compromised. However, ORCID does not store any such non-public personal data. It is easy, however, to inadvertently constrain ORCID’s benefits by choosing an excessively restrictive privacy setting. Continue reading →

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HSLS Participation at the Medical Library Association’s Annual Conference

HSLS librarians were active participants in the Medical Library Association’s Annual Meeting held in Chicago, Il, from May 3-8, 2019.

Paper Presentations

Kate Flewelling, NNLM MAR Executive Director, presented “Distracted in the Library: Supporting Staff and Patrons with ADHD.”

Lightning Talks

Carrie Iwema, Coordinator of Basic Science Services, presented “Collaborating for Classes: Training Initiatives for the Mutual Benefit of Libraries and Their Institutional Partners.” Co-authors were Melissa Ratajeski, Coordinator of Data Services, and Ansuman Chattopadhyay, Assistant Director for Molecular Biology Information Services.

Melissa Ratajeski, Coordinator of Data Services, presented “Practicing What We Preach: Making Our Own Research Data Open Access.” Co-author was Carrie Iwema, Coordinator of Basic Science Services. Continue reading →

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HSLS Librarians Honored at MLA

Michele Klein-Fedyshin, MSLS, AHIP, BA, BSN, RN, was named a Fellow of the Medical Library Association (FMLA). Fellows are elected by the Board of Directors in recognition of sustained and outstanding contributions to health sciences librarianship and to the advancement of the purposes of MLA.

Recognitions continued with Barbara Epstein, MSLS, AHIP, FMLA, and Melissa Ratajeski, MLIS, AHIP, RLAT, for completing their term as Immediate Past President and Chapter Council Chair, respectively. Elaina Vitale, MLIS, was selected for the 2019-20 cohort of the MLA Rising Star program, which gives members the opportunity to develop skills and knowledge needed to become a leader in MLA. In addition, Carrie Iwema, PhD, MLS, AHIP was recognized for serving on the MLA Educational Steering Committee, which received the 2019 President’s Award. Continue reading →

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Treasures from the Rare Book Room: A Unique Portuguese Thesis on Hernia

Among the many rare books donated by the family of Dr. Mark Ravitch, is a handwritten thesis on inguinal hernia. Its author, Joaquim Antonio dos Prazeres-Batalhoz, was a Portuguese naval surgeon and one of the first graduates of the Royal Surgical School in Lisbon. When the Régia Escola de Cirurgia de Lisboa opened in 1825 to educate surgeons, the school was associated with the Hospital de São José. It offered courses in seven subjects over a five-year period, but could not award medical degrees due to an insufficient curriculum. However, its graduates could practice medicine in places where there were no physicians that were educated at the University of Coimbra (the oldest university in Portugal with full privileges).

Students at the Régia Escola de Cirurgia de Lisboa had to pass exams in all subjects in order to graduate and they were required to take a three-day test: first, students defended a thesis on a surgical subject of their choice; next, they were examined in a surgical clinical setting; and finally, they had to pass a medical clinic examination. All submitted theses were manuscripts. In 1836, some of the manuscripts were published, although it was not required until 1869. Consequently, early theses are very rare. Batalhoz’s thesis is a unique manuscript written in 1827, the second year of the School’s existence. It consists of four chapters discussing, in sequence: (1) the anatomy of the body areas where inguinal hernias form; (2) the definition of inguinal hernia, its division, nomenclature, and formation; (3) the diagnosis of inguinal hernia; and (4) the treatment of inguinal hernia. The author refers to his predecessors and contemporaries, showing familiarity with foreign writings. The manuscript has sporadic crossed-out words and corrections to the main text, as well as marginal notes, but otherwise it is a very neat and clean copy written on Gior Magnani paper. A modern binder misspelled the author’s name as Ratalhoz and took the liberty to interleave the shorter pages with additions (originally glued to the page it followed) between the numbered pages.

Thése sobre a hernia inguinal can be viewed in the Rare Book Room by appointment.

~Gosia Fort

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HSLS Staff News

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

Names in bold are HSLS-affiliated

Publications

Mary Lou Klem, Research and Instruction Librarian, Ahlam A. Saleh, Patricia J. Devine, et al., authored the forthcoming article, “Librarians and Health Literacy: A Scoping Review,” in Library and Information Science Research.

Presentations

Kate Flewelling, NNLM MAR Executive Director, presented on current NLM and NNLM initiatives to the Pennsylvania Governor’s Advisory Council on Library Development in Carlisle, PA, on May 30, 2019. Continue reading →

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HSLS Classes for June 2019

Painless PubMed, Monday, June 3, 10–11 a.m.

Advanced PowerPoint for Presentations, Monday, June 3, 2–3:30 p.m.

NGS Secondary Analysis with CLC Genomics, Tuesday, June 4, 10 a.m.–12 p.m.

NGS Secondary Analysis with Microbial Prosuite, Tuesday, June 4, 1–3 p.m.

Causal Variant Identification with Ingenuity Variant Analysis, Tuesday, June 4, 3–4 p.m.

Pathway Analysis with Ingenuity Pathway Analysis (Seminar), Wednesday, June 5, 10 a.m.–12 p.m.

Pathway Analysis with Ingenuity Pathway Analysis (Hands-On), Wednesday, June 5, 1–3 p.m.

Introduction to Tableau for Data Visualization, Friday, June 7, 10–11 a.m.

PowerPoint for Conference Posters, Friday, June 7, 1–3 p.m.

Finding Retracted Articles, Thursday, June 13, 10–10:30 a.m.

Basic EndNote, Friday, June 14, 10–11 a.m.

Advanced EndNote, Friday, June 14, 11 a.m.–12 p.m.

Painless PubMed, Tuesday, June 18, 12–1 p.m.

Getting Systematic About Systematic Reviews, Wednesday, June 19, 10–11 a.m.

From Protocol to Publication: Selecting the Right Reporting Guideline for Your Paper, Study, or Article, Wednesday, June 19, 3–4 p.m.

PechaKucha Basics for Presentations, Friday, June 21, 3–4 p.m.

Bulk RNA-Seq, Wednesday, June 26, 1–4 p.m.

Managing Data for Comprehensive Lit Reviews: DistillerSR, Thursday, June 27, 10–10:30 a.m.

Introduction to Data Management, Thursday, June 27, 2–3 p.m.

Continue reading →

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New to Borrow: Powerful Laptops Loaded with Bioinformatics Software

Do you need to analyze NGS data but don’t have the computational power on your laptop or desktop to run it locally? The HSLS Molecular Biology Information Service (MBIS) and HSLS Technology have loaded two laptops with all current MBIS software (see figures below). They can be borrowed from the HSLS Technology Help Desk with a valid Pitt ID for use both within and outside of the library. The laptops can be checked out for four hours and are renewable online, but must be returned before the library closes.

Laptop specifications:

Model: Dell Precision 7710
Monitor: 17.3” (3840 x 2160 @ 60Hz)
OS: Windows 10 Pro 64-bit
Processor: Intel Core i7 6920HQ @ 2.90GHz
Memory: 32GB
Video card: 4095MB Nvidia Quadro M5000M
SDD: 953GB PM961 NVMe SAMSUNG 1024GB
Battery life: ~3 hours

Contact the HSLS Molecular Biology Information Service with any questions.

~Carrie Iwema

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Enter the Art on the Brain Coloring Contest

Top view and close up of desktop with creative brain sketch. Brainstorm and art concept Want to de-stress and win a neuro-themed prize? You’re invited to compete in a ‘brainy’ coloring contest—one of the related activities surrounding the ongoing Art on the Brain exhibit at Falk Library.

Why a coloring contest? Coloring allows anyone to be creative, and there’s no right or wrong technique. And despite what you learned as a child, you can even feel free to color outside the lines! Plus, briefly moving the focus of your busy brain away from your screens to engage in the simple act of coloring can be relaxing, fun, or even meditative. Continue reading →