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Resource Spotlight: Ingenuity Variant Analysis

August 13, 2018 - 12:19pm by Caitlin Meyer

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at Ingenuity Variant Analysis (IVA). IVA is a web-based tool that combines analytical tools and content from the Ingenuity Knowledge Base to help identify disease variants in human sequencing data.  The product allows you to select multiple samples to analyze together. From there, you can design the forthcoming analysis and add any relevant biological terms to help narrow down the list of variants likely contributing to the disease or phenotype at hand. IVA supports a range of upload formats, including Variant Call Format (VCF), Genome Variation Format (GVF) and Complete Genomics files (Var, MasterVar, High confidence junction, etc.).  After you have set up your data, IVA lets you interact with the data with a series of customizable filters. Some of the filter types include: biological context, genetic analysis, predicted deleterious, cancer driver, pharmacogenetics, and more.  Keep an eye on the library’s class calendar for trainings on IVA and all bioinformatics-related software. In the meantime, Qiagen, the company that produces IVA, has produced webinars, tutorials, and guides to help you get started.  Finally, please note that the library’s license to IVA is for academic and research use only.  Results may not be incorporated into a diagnostic product or service.  Request an IVA account. For questions on how to best use IVA, feel free to contact Rolando Garcia-Milian.

Meet our first Simbonis Intern!

August 6, 2018 - 11:13am by Kelly Perry

We are delighted to share a report on the work of our first Simbonis intern, Emma Brennan-Wydra, who joined the staff in the Medical Historical Library at the end of May 2018.  Emma offered the following glimpses into her life and experiences as our intern: I graduated from Yale College in 2015 with a double major in Chemistry and Women's, Gender, and Sexuality Studies, focusing on the multiple intersections of science, education, gender, bodies, and power. During my time at Yale, I also played flanker for the Yale Women's Rugby Football Club, designed lighting for theater and dance productions, organized a truly astounding number of LGBTQ-related events, and served as the producer of the Fifth Humour, Yale's oldest (and best) sketch comedy troupe. After college, I moved to the Boston area, where I worked as a ballroom dance instructor, played bass in an alternative rock band, and volunteered with the Massachusetts Transgender Political Coalition. I'm now a master's student at the University of Michigan School of Information, where I've mostly been taking classes relating to libraries, archives, and the preservation of information, but I've also dabbled in data science, programming, and survey research methodology. In addition to my coursework, I work as a research assistant at the University of Michigan College of Engineering, where I'm part of a multidisciplinary group studying engineering education, and in the fall, I'll be a teaching assistant for a master's level introductory course in statistics and data analysis. (I also try to find the time to go out salsa or swing dancing, when I can!) After I finish graduate school next spring, I'm hoping to get a position in an academic library. I had visited the Medical Historical Library and the Cushing Center a few times for class as an undergrad at Yale, but to be honest, I didn't know very much about medical libraries before I started my summer internship. One of my personal learning goals for the summer was to learn more about different facets of academic and medical librarianship, both through direct experience and by talking to other librarians, in hopes of developing more specific career plans for myself. In my six weeks at the Medical Historical Library, I've had the opportunity to get to know librarians from every department of the Cushing/Whitney Medical Library and hear more about the work they do, and I've also gotten to work on a number of different projects in and around the Medical Historical Library for myself. Unfortunately, I'm not really any closer to identifying a “dream job” because everything has been so interesting! My first project for the summer was processing a recently acquired collection of medical illustrations drawn by Mildred Codding for our library's benefactor and namesake, neurosurgeon Harvey Cushing, along with photographic reprints, notes, correspondence, and other materials that Cushing used in the preparation of his books and articles. Archival processing, I quickly learned, is all about decision-making. As I was planning out how I might want to organize the collection, I found it helpful to imagine what kinds of questions future researchers might be asking. Would the researcher need to find all of the materials from one specific publication, for example, or might they be interested in Cushing's editorial process more broadly? If the materials are organized one way, it might make it easy to answer one type of research question, but other kinds of information or functionality may be lost in exchange. Most of the time with archival processing, there isn't one “right” answer. After I physically organized the materials into new folders and boxes, I began entering information about the collection into ArchivesSpace, an archives-specific information management application that is used across the Yale Library system. This facilitated the creation of a finding aid, which is a document describing an archival collection, designed to help researchers find materials of interest. You can view the finding aid I made here. After I finished the finding aid, I began planning a small exhibition to display some of the beautiful surgical illustrations by Mildred Codding that are part of the new archival collection. The scope of the exhibition quickly broadened to include not only Mildred Codding but also two of the other women who worked with Harvey Cushing: secretary Madeline Stanton and pathologist Louise Eisenhardt. Cushing, like many doctors of the time, employed a large team of female assistants whose work was often uncredited and whose names have been largely forgotten. But these three women—Codding, Stanton, and Eisenhardt—went on to have distinguished careers of their own that extended decades past Cushing's death in 1939. As I began cobbling together a plan for my exhibition, I drew on a variety of sources, including biographies of Harvey Cushing, obituaries and tribute articles, birth and death records, reports from the Peter Bent Brigham Hospital, photographs from the Harvard Medical School Archives, and collections of correspondence and diaries held here at Yale. I also had conversations with others who had some curatorial experience so I could learn more about how to create a strong, cohesive exhibit, and I tried to select items, images, and stories that capture some of what made Codding, Stanton, and Eisenhardt so special. My exhibit, titled Not a "Harem": Codding, Eisenhardt, Stanton, and the Lives and Legacies of Dr. Harvey Cushing's Female Associates, is currently on display in the Cushing Center and also available online. It has been such an honor and a delight to have the opportunity to learn about these exceptional women, and I'm so excited to share what I learned with the public. One of the things that excites me most about my future career as an academic librarian is the day-to-day variety of the work, so having the opportunity to experience a taste of that in my internship has definitely been a plus! In addition to processing an archival collection and curating an exhibition, I've also updated and migrated an online exhibition about the Yale School of Nursing to the new Omeka platform, cataloged glass plate photographic negatives of Harvey Cushing's patients, written and edited labels for an exhibit about tobacco advertising, and more. I've learned so many new skills and technologies through this internship, but I've also gotten to do work that employs my preexisting interests and strengths. Although I previously thought I might want to work as a librarian in a subject specialist role for chemistry or another science field, I've thoroughly enjoyed both the medical and historical aspects of my work here.

Renovation prep begins Monday, July 30th

July 26, 2018 - 10:36am by Kelly Perry

Beginning Monday, July 30, you will notice an increase in noise and disruption at the Cushing/Whitney Medical library as work begins to prepare the space for the renovation project. On Monday, the Information Desk and staff will be relocated to the Circulation Desk area at the front of the library. Also on Monday, movers will be on site to relocate and remove furniture in advance of construction.  They will be moving tables and other furniture throughout all floors of the library.  These moves will occur over the course of the day and there will be noise associated with this work, especially between the Information Room and Morse Reading Room.  This work will require the temporary removal and/or relocation of computer workstations. If you require quiet study space, please consider another location during this time.

Not a 'Harem' : Codding, Eisenhardt, Stanton, and the Lives and Legacies of Dr. Harvey Cushing's Female Associates

July 5, 2018 - 2:39pm by Kelly Perry

Want to learn more about the smart and dedicated women who supported the work of our namesake, Harvey Cushing?  Explore our newest exhibition, curated by Emma Brennan-Wydra, Stanley Simbonis Intern for the Medical Library, and now on view in the Cushing Center! Throughout his career, Dr. Harvey Cushing employed a team of women who assisted him as secretaries, typists, medical artists, operative photographers, laboratory technicians, and more.  Cushing's female associates referred to themselves jokingly as his “harem,” but they were far more than that.  These working women were indispensable to Cushing, and their contributions are evident throughout his published works, as well as his diaries and correspondence.  Three of Harvey Cushing's assistants, in particular—secretary Madeline Stanton, neuropathologist Louise Eisenhardt, and medical illustrator Mildred Codding—are remembered not only for their proximity to the famed neurosurgeon, but also as leading lights in their own respective fields, with careers extending decades beyond Cushing's death in 1939. Madeline Stanton, who worked as Cushing's secretary, played a major role in the organization and development of the historical collections at the Yale Medical Library (now the Cushing/Whitney Medical Library).  As Librarian of the Historical Collections from 1949 until 1968, Stanton maintained an “atmosphere of generous and kindly learning” in the Historical Library.  “She always knew,” recalled Gloria Robinson, wife of Yale neurosurgeon Dr. Franklin Robinson.  “She had endless special knowledge.”  (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.) Louise Eisenhardt, whom Cushing originally hired as an editorial assistant, obtained a medical degree for herself in 1925 and worked as Cushing's pathologist.  A leading expert on tumor diagnosis, Eisenhardt was the first woman president of the American Association of Neurological Surgeons and the first managing editor of the Journal of Neurosurgery, a position she held for 22 years.  She was also the curator of the Brain Tumor Registry, Cushing's collection of pathological specimens and patient records, which is now housed in the Cushing Center.  (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.) Mildred Codding was a medical illustrator who worked with Cushing from 1928 until his retirement from the Peter Bent Brigham Hospital in 1932.  Her surgical drawings and anatomical diagrams grace the pages of many of Cushing's published works.  A student and disciple of famed medical illustrator Max Brödel, Codding made masterful use of the carbon dust technique, resulting in wonderfully vivid, detailed, and realistic illustrations of living tissue.  After Cushing's retirement, Codding stayed on as an illustrator at the Brigham.  Her later illustrations appear in a number of major works, including Zollinger's Atlas of Surgical Operations.  (Photograph by Russell B. Harding, courtesy of the Brigham and Women's Hospital Archives.) Learn more about these exceptional women at our new exhibition in the Cushing Center, which features photographs, correspondence, books, slides, and original surgical illustrations by Mildred Codding.  An online companion to the physical exhibition, which includes additional photographs and information, is available here.  

Finding Conference Proceedings

June 28, 2018 - 10:24am by Caitlin Meyer

Despite the promise of tools like Quicksearch and the breadth of massive databases like Scopus, certain types of information simply cannot be found in one place. No need to fret, though! We've got you covered. This series of blog posts will serve as a home of recommended resources and searching tips for hard-to-find types of information. Have a suggestion for a subject? Shoot me an email!  Conference proceedings – the collections of papers and/or abstracts that are presented at conferences – may be published in book format, as special issues of a journal, or as a serial.  Sometimes they are in the format of an abstract, sometimes in the form of a ‘conference paper’. A conference paper may morph into a journal article (usually with substantial additional material) but not always. If a conference abstract is found, then further sleuthing is required to see if the organization supporting the conference published proceedings or stopped at abstracts only. You might do an author search in the following resources to see if the author followed up the conference abstract or paper with a full-length journal article: PubMed, Web of Science, Scopus, Embase, or Google Scholar.  Last resort? Contact the author/researcher directly and ask! Recommended Resources Conference Proceedings Citation Index (Web of Science) Click on ‘More settings’ to restrict your search to specific conference proceedings citation indices or search the entire Web of Science Core Collection. Embase Limit to publication types: conference abstract, conference paper, or conference review.   ProceedingsFirst (OCLC) This is an index of worldwide conference proceedings – every published congress, symposium, conference, exposition, workshop and meeting received by the British Library Document Supply Centre. WorldCat  This ‘world catalog of publications’ is an excellent tool for finding conference proceedings. Search specific conference number and title (16th and “international AIDS conference”), limit by year(s): 1989 or 1990 or 1991 Tips & Tricks Associations usually publish abstracts from their Annual Convention in the association journal in the same issue or special supplement every year. Sometimes both the authors and the title will change when published as a full-length journal article. Make sure to search creatively and read carefully. Society, organization, and association websites frequently have information about their publications, including proceedings and annual meeting abstracts. Requesting conference proceedings through Interlibrary Loan may take longer than traditional requests. It may only ever be available as an abstract (see second bullet point).

Resource Spotlight: Scopus

April 19, 2018 - 11:13am by Caitlin Meyer

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at Scopus. Scopus is the single largest abstract and citation database of peer-reviewed literature. Unlike Medline resources like PubMed and Ovid MEDLINE, Scopus is also the home to non-journal literature, like conference abstracts and books. Indexing more than 22,000 journals, Scopus covers science, technology, medicine, social sciences, arts, and humanities - making it a great resource for interdisciplinary projects.  Scopus’ user-friendly interface mimics Google search in its simplicity. No special syntax or subject headings are needed to conduct an initial search. Being an academic resource, though, Scopus offers many functionalities that Google does not:  Author search and author profiles Search by affiliation to gauge the output of a specific school or department The ability to search for certain document types Optional advanced search functionality that lets you search specific fields like chemical or biological entities, editors, funding information, conference information and more Offering data at the article, journal, and author level, Scopus’ broad range of content coverage makes its research impact information robust as well. Users can easily disambiguate authors and navigate to author profile pages that list publications, frequent collaborators, h-index, citation counts, disciplines that the author publishes in, and more. As mentioned above, this level of granular information is also available at the article and journal level.  Scopus is a great place to start your research, a necessary inclusion in most systematic reviews, and a massive time-saver in calculating h-indices.  With something to offer for students, clinicians, researchers, administrative staff and more start exploring Scopus today! For questions on how to best use Scopus, feel free to contact Research & Education Librarian Caitlin Meyer.

Finding Book Chapters

April 3, 2018 - 4:38pm by Caitlin Meyer

Despite the promise of tools like Quicksearch and the breadth of massive databases like Scopus, certain types of information simply cannot be found in one place. No need to fret, though! We've got you covered. This new series of blog posts will serve as a home of recommended resources and searching tips for hard-to-find types of information. Have a suggestion for a subject? Shoot me an email!  Despite being the primary site of scholarly conversation in the sciences, not all disciplines revolve around the journal literature. Often considered "book-based" disciplines include archeology, law, politics/international studies, psychology, philosophy, sociology, history, communications, and media studies. Book chapters are generally cited less than journal articles and there isn't as established of a culture of research impact measurement around book chapters as there is around journal articles. Book chapters are still valuable pieces of academic writing, however, as they provide a home to content that doesn't fit well into the article format. Finding book chapters using electronic resources can be a little bit tricky, as the tools are scattered, but read on for specific tips, tricks, and resources to try out.  Recommended Resources Scopus  After a massive book expansion project completed a few years ago, Scopus is now home to more than 150,000 books. As with the rest of Scopus' massive collection, the books cover a wide range of disciplines. You can limit searches to "Book Chapter" to filter the results as you wish by using the "Document Type" search facet.   ProQuest E-Book Central  ProQuest Ebook Central is a great interdisciplinary resource for finding book chapters, covering Science, Medicine, Social Science, Humanities, and Arts. Enter your search terms and then you can switch to "Chapter Results", which will exclude book titles that met your criteria.   Web of Science  Similar to Scopus, Web of Science is a large interdisciplinary resource that has recently undergone a big book project. Whereas in Scopus you can limit on the front end of your search, Web of Science lets you set a preference for document type after you search.   Google Scholar  If you're looking for a book chapter and you know the title, Google Scholar might be worth a shot. Since it doesn't have any search limiting functionality for chapters, it isn't as good of a resource for pulling chapters on a topic to browse.   Medical Library E-Library  This tool assembled by the medical library allows you to search for e-books and enables browsing books by publisher and subject. It doesn't offer limiting or searching for chapter functionality, but could be useful for browsing.   PsycInfo  Produced by the American Psychological Association, PsycInfo is home to all of the publications from the group. Book chapters are readily available, and the subject matter touches on the psychological aspects of many disciplines. Tips & Tricks    If searching for the title of a book chapter, mark it as a "Keyword" or "All Fields" search instead of "Title". If you mark it as "Title", you might miss out if we have the whole book your chapter is in but it isn't entirely indexed. If you know the name of the book the chapter is in, try using Quicksearch to locate the book and navigate to the chapter that way.  Tools like Scopus have robust author profile systems. Try to search for the author of the chapter, click on their name, then all of their publications (hopefully the chapter you seek) will populate.  If the Yale libraries do not own the chapter, you can request a scan or delivery of the book through interlibrary loan. 

Census Panel Discussion: Recap and Additional Resources

March 20, 2018 - 1:14pm by Lindsay Barnett

Update: On Monday, March 26th, the Commerce Department announced that the 2020 Census will reinstate the citizenship question for the first time in 70 years.  Our panelists discussed some of the dire and far-reaching consequences a Census undercount can have on public and economic health, as well as political representation.  A number of states are planning legal action in response to this decision.  See "What Can We Do?" below for a list of organizations advocating for a fair and trustworthy Census.   Thanks to all who joined us on Tuesday, February 27th for a fascinating discussion: What happens to community health when data is compromised? A discussion panel on the 2020 Census and other survey data. A special thanks to our phenomenal panelists who made this session possible: Rachel Leventhal-Weiner – Data Engagement Specialist at Connecticut Data Collaborative Contact Rachel at rlw@ctdata.org. Kenya Flash – Pol. Sci., Global Affairs & Gov. Info. Librarian at the Center for Science and Social Science Information, Yale University Miriam Olivares – GIS Librarian at the Center for Science and Social Science Information, Yale University Jim Hadler – Senior Consultant, Infectious Disease and Medical Epidemiology, Connecticut and Yale Emerging Infections Program, New York City Department of Health and Mental Hygiene, Council of State and Territorial Epidemiologists  And our Moderator, Kyle Peyton, PhD candidate in Political Science, Yale University, ISPS Policy Fellow.   For those of you who could not attend, or want to stay involved in the discussion, here are some highlights and additional resources.   What does Census data do?: Informs other population surveys Acts as an integral part of geospatial work Helps determine public health funding based on incidence Allows for analysis of social determinants of health through the American Community Survey, which fills in important details of population data that the decennial Census outlines.    Read more about the links between Census data and public health in these articles: Using the Census to understand the link between flu and poverty in New Haven, CT Exploring the relationship between poverty and premature mortality in New York City   Why is the Census endangered? A question about citizenship status has been proposed for the 2020 Census.  This question has the potential to significantly reduce response rates among already undercounted immigrant and minority communities, jeopardizing the accuracy of the data collected and driving up costs as more resources are used to follow-up with non-responders.  As Census data drives redistricting and federal funding, an inaccurate count puts vulnerable communities at risk of not receiving necessary funding and resources.  Inaccurate Census data also hinders efforts of public health officers to initiate effective disease prevention programs in high risk communities. In addition, underfunding of the Census has the potential to result in an inaccurate count, as fewer resources are available for field testing and follow-up of non-responders, among other issues.  The impacts of an undercount would be felt long after 2020, at both the local and national level.  Lack of funding doesn’t just affect the decennial Census, many Census programs and other federal surveys are at risk.  As Census data provides the infrastructure for numerous policy, commerce, and research efforts, stripping resources from the Census is like tearing up our roads and highways!    What can we do? Reach out to your congressional representative and demand a fair and thorough count!  A full count is in their self-interest as well as the communities they represent.  Follow The Census Project, a network of organizations that “support a fair and accurate 2020 Census and a comprehensive American Community Survey”. https://thecensusproject.org/ The National Democratic Redistricting Committee (NDRC) is building a strategy to end gerrymandering and create fairer maps in the 2021 redistricting process. https://democraticredistricting.com/ The Count on Stats initiative of the American Statistical Association aims to educate and advocate for the importance of trustworthy federal statistics.  https://www.amstat.org/policy-and-advocacy/count-on-stats The Council of Professional Associations on Federal Statistics devoted to increasing the public’s knowledge of Federal statistics and creating dialog around the value of Federal statistics for the public good. https://www.copafs.org/ At the local level, The Connecticut Data Collaborative aims to “empower an ecosystem of data users by democratizing access to public data and building data literacy”.  In addition to offering processed and machine-readable datasets through their data portal, the CT Data Collaborative offers a monthly open data conference call and provides updates in federal and state data in the news, in addition to various events. https://ctdata.org/ Register for the next Open Data Call and learn more about The CT Data Collaborative’s events here: https://ctdata.org/academy/ Contact a librarian at CWML for questions and additional resources about the Census and its impact on public health!  

It's March Madness at Cushing/Whitney Medical Library!

March 16, 2018 - 12:53pm by Caitlin Meyer

Join us March 21st and 22nd for March Madness at Cushing/Whitney Medical Library.  We'll be offering special classes comparing popular library resources. What tool or database has what it takes to win it all?  All classes are free and will be held in SHM L 103, also known as the TCC or computer classroom. Schedule:  Research Impact Scopus vs Web of Science Wednesday, March 21st at 1:00PM Both Scopus and Web of Science offer access to huge amounts of literature, track citations, offer insights into research impact, and cover multiple disciplines. Which tool reigns supreme? Which one does what better? Literature Searching Ovid Medline vs PubMed Wednesday, March 21st at 4:00 PM Ovid MEDLINE and PubMed both search the MEDLINE journals - but which interface is better? Which database best suits your needs? Ovid’s search building feature and clean interface make it a strong candidate, but strong enough to beat out PubMed’s legacy and features like automatic term mapping? Join Alexandria Brackett for this showdown and decide for yourself! Point of Care Bedlam UpToDate vs DynaMed Plus  Thursday, March 22nd at 11:30 AM During this game (class), we will compare the differences between these two point of care tools. We will assess the validity of the information, the currency of their resources, and the different perks of the two products, including calculators, guidelines, patient education information, and more. Come to this class to help you decide which tool is best for you and your patient care. Refereed by Alexandria Brackett.  Citation Management  EndNote vs Zotero  Both EndNote and Zotero help you manage your references and PDFs, make the creation of bibliographies a breeze, and integrate into paper-writing software such as Microsoft Word for easy citing while you're writing. Both are free. Which is right for you? Which does what better? Come decide for yourself with a showdown refereed by Caitlin Meyer. 

Resource Spotlight: Incidence & Prevalence Database

March 14, 2018 - 3:44pm by Caitlin Meyer

Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection. In this edition of Resource Spotlight, we’ll be looking at the Incidence & Prevalence Database (IPD). Made available by Clarivate Analytics, IPD is a compendium of global epidemiological data from hundreds of sources. The collection of data is intended to provide a comprehensive overview of your research topic - whether that be incidence, prevalence, morbidity, mortality, trends, cost, risk-factors, or disease classifications.  The sources integrated into IPD include government reports, medical journals, market investment reports, medical and scientific associations, national and international healthcare surveys, trade journals, database audits, and industry contacts. The website is updated monthly with new information and government statistics are typically updated annually.  In addition to the data sets procured from sources mentioned above, IPD also features:  Hundreds of “Article Reviews”, where expert analysts condense information into digestible pieces “IPD Summaries”, tables of worldwide and regional incidence and prevalence data  A self-produced “Global Incidence and Prevalence Report with Map” Information on U.S. patient discharges IPD offers some advanced searching functionality that allows users to search by countries or regions, by certain publication criteria (author, title, date), by ICD Code, or by their controlled vocabulary of keywords.  The Incidence & Prevalence Database may be useful to those involved in clinical research, public health, market research, product development, business development, and more.  Start exploring the Incidence & Prevalence Database today! For questions on how to best use IDP, feel free to contact Public Health Librarian Kate Nyhan.
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