Article in the Spotlight

By Barnaby Nicolas, MSIS

In our monthly “Article Spotlight” series, we’re showcasing achievements of Mount Sinai faculty and researchers using Altmetrics. This month, we’re looking at an article co-written by Dr. Pamela Sklar, MD, Professor, Psychiatry, Professor, Genetics & Genomics Sciences, Professor, Neuroscience, at Icahn School of Medicine at Mount Sinai. The article examines the use of shared data to provide insights into genetic-variant penetrance.

Citation: Minikel EV, Vallabh SM, Lek M, Estrada K, Samocha KE, Sathirapongsasuti JF, et al. Quantifying prion disease penetrance using large population control cohorts. Science Translational Medicine. 2016;8(322):322ra9.

Article Summary: This study analyzes vast amounts of shared data—from the Exome Aggregation Consortium and the 23andMe database—to provide insights into genetic-variant penetrance and possible treatment approaches for a rare, fatal genetic prion disease. This study was analysis was conducted by a patient-turned-scientist joined with a large bioinformatics team.


BACKGROUND: No longer just buzz words, “patient empowerment” and “data sharing” are enabling breakthrough research on rare genetic diseases. Although more than 100,000 genetic variants are believed to drive disease in humans, little is known about penetrance—the probability that a mutation will actually cause disease in the carrier. This conundrum persists because small sample sizes breed imperfect alliance estimates between mutations and disease risk. More than 100,000 genetic variants are reported to cause Mendelian disease in humans, but the penetrance-the probability that a carrier of the purported disease-causing genotype will indeed develop the disease-is generally unknown. The researchers assessed the impact of variants in the prion protein gene (PRNP) on the risk of prion disease by analyzing 16,025 prion disease cases, 60,706 population control exomes, and 531,575 individuals genotyped by 23andMe Inc. They found that missense variants in PRNP previously reported to be pathogenic are at least 30 times more common in the population than expected on the basis of genetic prion disease prevalence. Although some of this excess can be attributed to benign variants falsely assigned as pathogenic, other variants have genuine effects on disease susceptibility but confer lifetime risks ranging from <0.1 to ~100%. We also show that truncating variants in PRNP have position-dependent effects, with true loss-of-function alleles found in healthy older individuals, a finding that supports the safety of therapeutic suppression of prion protein expression.

URL to this article on Plum X

Dr. Sklar’s profile

Inaugural Medical Education/AIT Annual Retreat – Collaborate to Innovate

By Gali Halevi, PhD, MLS

The Inaugural Medical Education/AIT Annual Retreat was organized to order to develop innovative products and services to Icahn School of Medicine at Mount Sinai (ISMMS) students and faculty. The retreat took place in an offsite location with15 Medical Education, Library, Instructional Design and IT leaders. Overall, the retreat proved to be a successful, fruitful, and exciting day. For 6 hours, participants exchanged ideas potential collaborations, debated feasibility, benefits and risks, and enjoyed sharing their expertise in different areas of medical education.


While enjoying an unofficial and relaxing setting, professional hierarchies disappeared and allowed participants to discuss ideas openly and creatively. Projects ranging from arts and humanities focused activities, to original research, to productivity and assessment systems were brought forth for discussion. At the end of the day, the group came up with 10 projects, each assigned with a leadership team that will be responsible for development and execution. In addition, the team came up with a cross-organizational communications plan to ensure maximum impact.

Now proved to be a successful endeavor, the retreat will become an annual event which will strengthen relationships and allow for innovation going forward.


Participants in the Inaugural MedEd/AIT Annual Retreat: Collaborate to Innovate












Twitter – An Underused Tool for Book Marketing?

By Robin O’Hanlon, MIS and Dr. Gali Halevi, MLS, PhD

With over 320 million active monthly users and magnitude of 350K tweets per minute[i], Twitter is  a powerful marketing tool used by 65.8% of US companies[ii]. Yet, it would appear that  book publishers, at least in the academic arena, are not leveraging Twitter as a marketing tool.


Image credit:

In order to determine the extent to which academic and scientific books are mentioned in Twitter, we examined Ebrary, a multidisciplinary eBooks database from ProQuest. We uploaded 71,443 eBooks ISBNs numbers from the Levy Library’s Ebrary collection in April 2016 to PLUMx Metrics Dashboard, an altmetics platform . PLUMx Metrics dashboard tracks metrics from over 30 sources, including Twitter and is able to track over 20 different types of outputs, from articles and books to videos by using unique identifiers such as web links, DOI or ISBN.

For this analysis, we chose books that have at least 10 Twitter mentions. Out of the 71,443 books measured, only 39 academic or scientific books have 10 or more Twitter mentions. As can be seen from figure 1, history books received the most Twitter mentions in the past 10 years, followed by semantics and economics.


In most cases Twitter mentions last at least 2 year after publication,  meaning that conversations around their content last for a significant amount of time (see figure 2). Considering that academic and scientific books issue new editions quite often, Twitter can be used to instill interest in current editions until new ones are published.


As books remain an important source of academic and scientific information, their use can be enhanced by using Twitter as a marketing tool. Creating conversation around mentions, their content can be discussed through Twitter by the academic community.  There are several studies that show how scientists use Twitter[iii-v] including mentioning publications, conference presentations, and engaging in scientific discussions. There is no reason books should not be included as a topic for academic discussion on Twitter. Indeed, publishers and authors of scientific books should work to drive Twitter interactions and discussions on books, which can in turn lead to enhanced research impact and visibility.








Lessons in Scientific Publishing Nexus Course registration now – Fall 2016

Levy Library is proud to announce that registration is now open for Lessons in Scientific Publishing, a course in Icahn School of Medicine’s Nexus Learning program for Fall 2016.

From the course description:

“Being published in high quality, reputable journals and ensuring high impact in both traditional and alternative metrics is essential to a successful career today in science and medicine. The aims of this course are to familiarize students with the processes of writing and publishing scientific papers and to learn how to create a professional online presence that will allow their work to be noticed and cited. The course offers ISMMS students the opportunity to become adept in the processes of research organization, article submission and peer-review as well as creating and maintaining online presence to promote their work and their achievements. This course is an ideal option for students interested in research and publishing.”

Lessons in Scientific Publishing was taught as a one credit elective in the Icahn School of Medicine’s  Graduate School of the Biomedical Sciences during the Spring 2016 semester.

For more information, contact course coordinator Rachel Pinotti ( and visit the Lessons in Scientific Publishing course page in the Nexus Learning course catalog

Lessons in Scientific Publishing flyer #2 - Fall 2016_RP Edits

A Full House for our Social Media for Scientists Workshops

By Robin O’Hanlon, MIS

On July 28 and August 4, 2016, Levy Library, in collaboration with the Mount Sinai Marketing and Communications Department, offered 90 minute workshops on Social Media for Scientists. The workshops developed out of conversations between Dr. Marta Filizola, PhD, Dean, (Graduate School of Biomedical Sciences, Professor, Neuroscience, Icahn School of Medicine at Mount Sinai), and Dr. Gali Halevi, PhD, MLS, (Chief Director, Levy Library). The workshop explored topics including traditional scientific metrics (h-Index, Impact Factor), Altmetrics platforms (PlumX), scientist specific public profiles and identifiers (ORCID ID, Research Gate), plus an examination of how scientists can maximize effectiveness of non-scientific social media platforms (Twitter, LinkedIn, Slideshare, YouTube).

Check out the Social Media for Scientists Workshop Work Book, which provides an overview of all topics covered in the workshop, including tactics and strategies for busy scientists who want to leverage social media to increase the impact of their own work and strengthen their professional networks.

Dr. Gali Halevi explaining the PlumX platform.

Dr. Gali Halevi explaining the PlumX platform

Social Media for Scientists

SMS Gabriel

Gabriel J. Bershadscky, Creative Director, Marketing and Communications Department, explaining the evolution of the Mount Sinai brand.

Levy Librarian Robin O'Hanlon, MIS discussing Twitter usage among scientific communities.

Levy Librarian Robin O’Hanlon, MIS discussing Twitter usage among scientific communities.


Measuring Research Impact: h-Index & Beyond – Register Now

Registration is now open for the third Levy Library Research Insider event, “Measuring Research Impact : h- Index and Beyond.”


In this seminar, we invite you to explore critical questions surrounding  the changing landscape of research impact and evaluation. What are “altmetics?” How do they align with or disrupt traditional, citation-based metrics? How can scientists, health care professionals, and technologists leverage social media to increase the impact of their work? Ultimately, how valuable or problematic are measures like h-Index and Impact Factor?

Opening remarks will be given by Dr. Marta Fitzola, PhD, Dean, Graduate School of Biomedical Sciences & Professor, Neuroscience, Icahn School of Medicine at Mount Sinai.

In addition to an outstanding lineup of speakers, this seminar will include a Research ImpactClinic, designed to assist attendees with all their research impact needs. ImpactClinic attendees will have the opportunity to:

  • Sign up for an ORCID ID and Research Gate account
  • Receive demonstrations of Scopus and other tools for calculating research impact metrics
  • Have their h-Index calculated & learn to retrieve Impact Factor scores for scientific articles
  • Request a Mount Sinai PlumX profile 

Speakers include Dr. Gali Halevi, PhD, MLS, Chief Director, Levy Library and Dr. Joshua Drew, PhD, Lecturer & Director MA Conversation Biology Program at Columbia University. Additional speakers include Andrea Michalek, Founder & Co-President of Plum Analytics & Barnaby Nicolas, MSIS, Assistant Director, Mount Sinai Health Systems, ISMMS, who will present on the implementation of Plum Analytics at Mount Sinai.

Visit our registration page to save your seat. 

Contact Robin O’Hanlon ( for additional details.

Article in the Spotlight

By Barnaby Nicolas, MSIS

In our monthly “Article Spotlight” series, we’re showcasing achievements of Mount Sinai faculty and researchers using Altmetrics. This month, we’re looking at an article co-written by Dr. Jonathan Halperin, MD, Professor, Medicine, Cardiology at Icahn School of Medicine at Mount Sinai. The article examines the use of digoxin to treat atrial fibrillation.

Citation: Washam JB, Stevens SR, Lokhnygina Y, Halperin JL, Breithardt G, Singer DE, et al. Digoxin use in patients with atrial fibrillation and adverse cardiovascular outcomes: a retrospective analysis of the Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF). The Lancet.385(9985):2363-70.

Halperin article

Article Summary: This study examines the use and outcomes of digoxin in patients. Digoxin treatment was associated with a significant increase in all-cause mortality, vascular death, and sudden death in patients with AF. This association was independent of other measured prognostic factors, and although residual confounding could account for these results, these data show the possibility of digoxin having these effects. The researchers find that a randomised trial of digoxin in treatment of AF patients with and without heart failure is needed.

BACKGROUND: Atrial fi brillation (AF) is the most common arrhythmia encountered in clinical practice, estimated to currently affect more than 30 million people worldwide. It is associated with increased risk of stroke, heart failure, cognitive impairment, and death, and complicates management of other disorders. Digoxin is a widely used drug for ventricular rate control in patients with atrial fi brillation (AF), despite a scarcity of randomised trial data. The researchers studied the use and outcomes of digoxin in patients in the Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism

Trial in Atrial Fibrillation (ROCKET AF). For this retrospective analysis, the authors included and classifi ed patients from ROCKET AF on the basis of digoxin use at baseline and during the study. Patients in ROCKET AF were recruited from 45 countries and had AF and risk factors putting them at moderate-to-high risk of stroke, with or without heart failure. The researchers used Cox proportional hazards regression models adjusted for baseline characteristics and drugs to investigate the association of digoxin with all-cause mortality, vascular death, and sudden death. ROCKET AF was registered with, number NCT00403767. In 14,171 randomly assigned patients, digoxin was used at baseline in 5239 (37%). Patients given digoxin were more likely to be female (42% vs 38%) and have a history of heart failure (73% vs 56%), diabetes (43% vs 38%), and persistent AF (88% vs 77%; p<0·0001 for each comparison). After adjustment, digoxin was associated with increased all-cause mortality, vascular death, and sudden death.

URL to this article on Plum X

Dr. Halperin’s profile

Levy Library now offers NEJM Resident 360

NEJM Resident 360 is here to make life easier for busy Icahn School of Medicine at Mount Sinai residents. This resource offers clinical content targeted specifically to residents’ needs, guidance in career decisions, and a way to connect with peers. Features such as Rotation Prep help residents solidify their foundational medical knowledge with materials that have been written and curated by a team of physician experts, fellows, and residents, and mapped to 14 common residency rotations in internal medicine.  Each rotation includes brief topic overviews, links to landmark clinical trials and review articles from NEJM and other highly-respected sources, and a selection of test questions from NEJM Knowledge+.


To access NEJM Resident360, visit our databases page. Icahn School of Medicine at Mount Sinai residents must create a personal account to NEJM Resident 360 while on campus. If you’re off campus, you can create an account through our NEJM eJournal subscription.

If you are an Icahn School of Medicine at Mount Sinai resident and you have created a Resident 360 account previously at another institution and want to maintain your current account, you can simply login to their personal 360 account while on campus networks at Mount Sinai Hospital Mount Sinai Beth Israel to get access to the institutional modules that are included in t subscription.

Contact with any questions.

The Complexity of Measuring the Impact of Books: Article in Publishing Research Quarterly · June 2016

By Gali Halevi, MLS, PhD, Barnaby Nicolas, MSIS, Judit Bar-Ilan, PhD


Libraries have been looking for ways to measure the value of their collections for decades. Discovering the amount of downloads, citations and views of journal articles are some of the major methods used by librarians to define how much their collection are used by patrons and whether or not they should keep them. Altmetrics, mainly the ability to track the social impact of scientific artefacts via networks, introduced a new dimension to these evaluations. Nowadays, scientific impact can be measured via traditional metrics such as citations but also via alternate metrics such as downloads, views, clicks and so forth.

That being said, studying the scientific and social impact of books still remains a challenge. The main reason is that books vary in format, content and genre. Books not only adhere to disciplinary or multidisciplinary foci, but also differ in categorical type and targeted audiences. Within the general classification of books into “Fiction” or Non-fiction” classes, books also display a complex categorical structure which includes genres (i.e. science, drama, history) and types (i.e. encyclopedia, dictionary, text book).

In addition, while many platforms can track the number of citations, downloads and views of single chapters of scientific and text books, hardly any can track altmetrics or offer a book-level aggregation of such impact.

Our study endeavored to discover whether there are scholarly evaluation metrics that can be applied to a wide range of books’ types and contents. We analyzed over 70,000 books and collected various metrics per each title including traditional and altmetrics measures. Our results show that books display different impact in each of the measurements and vary by types and content. There isn’t one measure that captures the impact of books across the board.

Therefore, we concluded that books should be evaluated by types and contents while using different measures per each.  We believe that in order to capture the scientific impact of books, it will be important to use a variety of measures. Furthermore, in light of our analysis, we recommend using both traditional metrics such as citations and reviews as well as altmetrics such as social media mentions, downloads, reads and views. Using platforms such as PLUMx can assist in capturing such metrics.

We also recommend creating topic – related books data sets as well as type-related ones. In this manner, the evaluator can track different metrics around topics and types and compare them better. For example, a library looking to evaluate its books collection should create data sets of text books around a specific discipline and benchmark them against.

Full article DOI: 10.1007/s12109-016-9464-5

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