Did you know there’s a reproducibility crisis? Well, there is. And it’s shocking.

July 29, 2015

And it’s a concern for everyone involved in research, not to mention the patients who “rely on [researchers] to embrace innovation, make advances and deliver new therapies that will improve their lives.”¹

Reportedly, the reproducibility of a large number of scientific studies has been called into question. Researchers were able to confirm only 11% of the findings in a well-publicized study¹ of 53 published oncology papers. Other papers in fields ranging from cancer to psychology have been mostly unreproducible.

How can this be and what action should we take?

BioMed Central is addressing its concern with the creation and launch on July 23 of a Minimum Standards of Reporting Checklist.  During the trial phase, the use of a reporting checklist will apply to manuscripts submitted to three of its journals: BMC BiologyBMC NeuroscienceGenome Biology, and GigaScience.

The introductory paragraph on the Checklist states:

“BMC Neuroscience advocates full and transparent reporting. Please ensure that your paper provides the information requested below where applicable. On submitting your paper you will be asked to confirm you have included this information, or give reasons for any instances where it is not made available.”

Authors are asked on submission to confirm that they have included the requisite information on the checklist or give reasons for any instances where it is not made available or not applicable. Further, reviewers are asked to confirm the information has been adequately reported and reviewed.

BioMed Central plans to review the data that’s collected during the trial, then relaunch the checklist (with any revisions) across all BioMed Central journals.

What you think?

BioMed Central is interested to hear your ideas (we are, too), not just about the checklist, but about what can be done to tackle the reproducibility problem.

Respond on our blog, the BioMed Central blog, or email reproducibility@biomedcentral.com

You can read the original press release here: www.biomedcentral.com/presscenter/pressreleases/20150723a


¹Drug development: Raise standards for preclinical cancer research. C. Glenn Begley & Lee M. Ellis. Nature 483, 531-533 (29 March 2012)

(Here’s our link to the full text of the paper: http://bit.ly/1KzTYN4)

This article was submitted by Susan Andersen.

Staying Safe and Healthy During Extreme Heat

July 28, 2015

It looks like the next few days are going to be scorchers. Extreme heat can be more than a nuisance; it can also have serious negative health effects. The Centers for Disease Control and Prevention offer the following tips to help avoid heat-related illness:

Stay Cool

  • Stay in air-conditioned buildings as much as possible.
  • Find an air-conditioned shelter.
  • Do not rely on a fan as your primary cooling device.
  • Avoid direct sunlight.
  • Wear lightweight, light-colored clothing.
  • Take cool showers or baths.
  • Check on those most at-risk twice a day.

Stay Hydrated

  • Drink more water than usual.
  • Don’t wait until you’re thirsty to drink more fluids.
  • Drink from two to four cups of water every hour while working or exercising outside.
  • Avoid alcohol or liquids containing high amounts of sugar.
  • Remind others to drink enough water.

Stay Informed

There is also information on heat illness for special populations:

Welcome new librarians!

July 2, 2015

Miner Library is pleased to welcome two new liaison librarians:  Daniel Castillo and Elizabeth (Liz) Grace.

DC and LG

Daniel is a graduate of the Library and Information Science program at Syracuse University and recently worked at URMC as a certified ophthalmic assistant at the Flaum Eye Institute.  Daniel brings a high level of customer service, enthusiasm, professionalism and experience working with our patients and clinicians to this position.  Liz is a graduate of the Library and Information Science program at the University of Pittsburgh and recently worked as a Medical Librarian at The Children’s Institute of Pittsburgh, a pediatric rehabilitation hospital and day school.  Liz provided research, outreach and training services to clinicians, staff, families and the community and is a welcome addition to our team.

The Library Liaison Program at Miner Library partners URMC departments with librarians. Your library liaison can consult with you on database searches, conduct custom literature searches, provide subject-specific resource training and instruction, notify you about new library services and work with you to create appropriate educational materials for your patients and families.

Check Miner’s Staff Directory to find the liaison librarian for your department.

Using your mobile device to scan documents

July 2, 2015

Daniel Trout, a liaison librarian at Miner Library, reviewed three scanning apps in the recent June/July 2015 edition of the MLA News. 

Using your smartphone or mobile device to instantly scan documents can be inexpensive and convenient using the right tools.  TurboScan,  Genius Scan and CamScanner are available for both Android and Apple devices.  Some offer free versions, but the majority of apps cost between $4.99 and $6.99 and allow scanned documents to be emailed from the app and uploaded to a variety of cloud-based storage services.

Evernoteand Google Drive also provide the ability to scan documents via the application and upload to the cloud instantly.

Need more information or have questions?  Contact Daniel Trout directly or check out the attached copy of the review.Scanning DocumentsDT

July 2015 Classes by Miner Library

July 1, 2015

Classes at Miner Library

Here are the classes offered by Miner Library for the upcoming month:

Blackboard Basics for Academic Courses, Clerkships and Residencies
Date: Tuesday, July 7, 2015
Time: 10:00am – 11:30am
Blackboard Advanced Features: Tests and Surveys
Date: Thursday, July 9, 2015
Time: 10:00am – 11:30am
BIO101: You Are What You Eat (and Drink and Breathe…)
Date: Monday, July 20, 2015
Time: 12:00pm – 1:00pm

For a full list of Miner Library’s classes, visit our Classes page.

Have a question? Contact Miner Library’s Answer Desk @ 585-275-3361.

Got bioinformatics support services? No? Well, we do!

June 22, 2015

We’d like to share an article, published in the June 19 edition of Research Connections, about our Bioinformatics Consulting and Education Service. Helene McMurray, head of the BCES and Assistant Professor of Biomedical Genetics, chatted with Bob Marcotte about this innovative and quickly growing service. Bob has done a great job with this overview.

Truly, we couldn’t have said it better ourselves. So we won’t.

And we won’t even make you click again.

The text (reading time: less than 2 minutes) in its entirety, is reproduced below.  Thanks, Bob!


Bioinformatics consultant offers help ‘anywhere in the life cycle of a project’

Jason Mendler, an Assistant Professor at the Wilmot Cancer Institute, is interested in the molecular drivers of chemotherapy refractory acute myeloid leukemia (AML). With help from the University’s Genomics Research Center, he has done RNA sequencing of primitive hematopoietic cells from both healthy donors and AML patients.

When he needed help in refining his analysis of this data, he turned to Helene McMurray, Assistant Professor of Biomedical Genetics and head of the Bioinformatics Consulting and Education Service of the Edward G. Miner Library. He is not the only researcher who has done so.

A year ago, just after she was hired by Miner Library, McMurray averaged one consult a week. Now she’s been meeting with two to three research groups a week — and she’s eager to expand her “practice” even more.

“I’ve been amazed by the demand; it’s really clear that this is needed,” McMurray said.

Informatics involves analyzing large quantities of data to identify patterns and trends. McMurray applies informatics in support of basic and translational science at the Medical Center. She assists researchers investigating topics that range from the health of populations, to in-depth analyses of biological systems in order to better understand, for instance, the development of heart disease or the genetic factors involved in cancer.

We’re willing to help people anywhere in the life cycle of a project, from conception through publication,” McMurray said.

That could include directing researchers new to the field to a computer program or web-based software tool; helping them find, generate or analyze data sets; or engaging them with new collaborators, McMurray said.

Many of the faculty who come in to talk to me are busy with other activities. If they’re clinicians, they’re seeing patients; if they’re researchers they’re writing grants or supervising students. They wear a lot of hats already,” McMurray said. “They don’t necessarily want to learn a new computer language, so they may just want to understand how to better interface with people who know how to do those things.”

She also helps investigators who are already skilled in informatics, have lots of data in hand, but “have hit the wall for one reason or another. They need someone with a fresh set of eyes just to help them get unstuck.”

After receiving her PhD in Microbiology and Immunology from the University in 2003, McMurray did postdoctoral work with Prof. Hartmut “Hucky” Land, studying how genes work together to control cancer. This was her first immersion in genomics and informatics. Since 2009 she has been an assistant professor of Biomedical Genetics here.

The opening for a bioinformatics consultant at the Miner seemed “like a good fit,” given her experience in the field and her interest in teaching, McMurray said. “The data doesn’t scare me. I have knowledge of a lot of different ways to analyze data, but at the same time I know a lot of biology. So when I look at the biological aspects of a project, they also make sense to me.”

Mendler has met with McMurray and with student Sam Moore, who is also assisting Mendler, four times so far. He is well pleased with the advice he has received.

“They’ve been very helpful and available,” Mendler said. “Their help has enabled me to generate a very exciting, novel hypothesis about the basis of chemotherapy refractoriness in AML. I expect this to result in high impact papers and successful grant applications in the years to come.” Click here to learn more.


Have you heard of chikungunya? (Hint: It’s not a new southwestern dish.)

June 3, 2015

mosquitoIf you’re vacationing in the Caribbean, you may want to toss the bikini and wear long sleeves and long pants, instead.

Chikungunya (pronunciation: chik-en-gun-ye) is a virus similar to dengue, causing fever and joint pain. The fever and joint pain are more intense with chikungunya, however, affecting hands, feet, knees, and back, and making daily activities difficult. As of March 6, 2015, over 20 Caribbean countries have reported cases of chikungunya.

Pan American Health Organization/World Health Organization (PAHO/WHO) website tells us that the disease rarely causes death, but joint pain can last months or even years for some people. Complications are more frequent in children under 1 and in people over 65 years of age and/or with chronic diseases (diabetes, hypertension, etc.). There is no specific treatment or vaccine to prevent infection by this virus.

When traveling to countries where chikungunya has been confirmed, take precautions. Use insect repellent, wear long sleeves and pants, and stay in places with air conditioning or window and door screens.

Read the Traveler’s Health Yellow Book for more information on Protection against Mosquitoes, Ticks, Fleas & Other Insects and Arthropods. And check the CDC’s Travel Health website to see if the country you plan to visit has any travel health notices.


Posted by Susan Andersen


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