In the past few months, there has been a vast amount of biomedical information produced about COVID-19. The Health Sciences Digital Library and Learning Center has created a new COVID-19 Resources Library Guide to quickly refer the UT Southwestern community to high-quality – i.e., primarily clinical and research – information about COVID-19. The guide includes:
Recommendations for searching PubMed
Expanded resources from existing subscriptions
COVID-19 tracking dashboards
Related open access resources
The COVID-19 Resources Library Guide supplements but does not supersede the COVID-19 information provided by the UT Southwestern Emergency Operations Center. The Guide will be updated as the COVID-19 information landscape evolves. Please email the Library if you have identified other key resources that we should consider for inclusion.
The UT Southwestern Library has recently subscribed to Repbase. Maintained by the Genetic Information Research Institute (GIRI), Repbase is a database of prototypic sequences representing repetitive DNA from different eukaryotic species. Repbase is used worldwide as the reference standard for annotating the presence of repetitive DNA in genomic data. GIRI publishes Repbase Reports, a monthly e-journal that reports newly identified repetitive DNA elements, which are subsequently stored and shared in Repbase. GIRI also provides computational tools (Censor and RepbaseSubmitter) and online services for screening and submission of the repeats.
In September 2019 PubMed 2.0 is scheduled to become the default PubMed version, and the existing PubMed is currently planned to be retired completely in January 2020. For now, the PubMed Labs website provides an opportunity to test the new PubMed, get further information, and provide feedback. Further details on the new version are available in a September 2018 article at PubMed Central; however, please note that some PubMed 2.0 features have changed since the article was published.
The major changes to PubMed include:
Search results sorted by “relevance” by default (instead of the current “most recent”) and include text snippets relevant to your query
A new search algorithm that uses machine learning to optimize results
Protocols—also known as methodologies, procedures, techniques, or experiments—are invaluable and popular resources for anyone involved in scientific research, bench work, grant writing, and/or research project planning. Protocols provide practical guidance by describing the design and implementation of a scientific experiment. The foundational information found in protocols is indispensable for fostering standardized research methods and reproducible results.
Protocols offer many benefits, such as:
Save time by accessing highly tested, peer-reviewed techniques and procedures from some of the most established books and journals in your field
Stay up-to-date with the latest cutting-edge methods
Accelerate scientific discovery by accessing the most reliable protocols in the various scientific disciplines
Ensure reproducible results, safeguarding and validating research results
Utilize step-by-step guidelines and troubleshooting tips from authoritative, reliable sources
Avoid reinventing the wheel
The Library provides online access to many popular protocols resources. Most individual protocols articles appearing in these resources are indexed in PubMed/MEDLINE and Embase. Here are a few major protocols options currently offered by the Library:
Cold Spring Harbor Protocols – This resource continues the renowned Cold Spring Laboratory’s long-standing practice of providing trusted, step-by-step laboratory techniques, covering cell and molecular biology, genetics, bioinformatics, protein science, and imaging.
Current Protocols (Wiley) – Creators of the standard protocol format over 30 years ago, this long-standing, “gold standard” offers rigorously reviewed and curated protocols in fields such as molecular biology, microbiology, and stem cell biology.
JoVE Journal of Visualized Experiments – This scientific methods video journal publishes protocols articles along with detailed videos of laboratory procedures for novel methods, innovative techniques of existing techniques, and gold standard protocols for the life and physical sciences.
Methods in Enzymology (Elsevier) – This is one of the most popular and heavily used eBook series offered by the Library, with complete full-text access back to volume 1 (1955). These critically acclaimed, individually themed volumes have served as one of the most highly regarded life sciences standards for more than 50 years, covering research methods in fields such as biochemistry, microbiology, cancer research and genetics.
Methods in Molecular Biology (part of the SpringerProtocols database; click on “Protocols” link) – This respected series offers step-by-step protocols, tips, tricks, shortcuts, and troubleshooting advice in the more than 2,000 MIMB volumes. MIMB is a standard resource in labs throughout the world with each volume providing focused, in-depth coverage on a specific sub-discipline. Online access to MIMB is now part of the SpringerProtocols database, which combines MIMB and other high quality laboratory protocols in biomedicine and the life sciences.
Springer Nature Experiments – SpringerNature developed this specialized search tool for researchers by researchers. It searches more than 60,000 references from the SpringerProtocols database, Nature Methods, Nature Protocols, and Protocol Exchange (open repository for scientific research protocols). Advanced search options allow filtering by technique, video availability, publication year, article category, etc. to identify relevant content more quickly. While this tool is freely available, UT Southwestern affiliates benefit with direct access to the Library funded full-text articles from the SpringerNature suite of resources.
For assistance with these tools or other reference inquiries, please contact us. We’re here to help.
Open access publishing continues
to grow across all academic disciplines.
Increasingly, the open access publishing model, which provides immediate
access to peer-reviewed research once published, has become susceptible to misuse
by predatory publishers. These predatory
publishers aggressively solicit academics with requests for manuscript
submissions, reviews and editorial board services, creating negative publicity
for legitimate open access journals.1,2 Jeffrey Beall,
formerly at the University of Colorado in Denver, first described predatory
publishers in 2008, and developed the first (now defunct) list of predatory
journals.3
While there is no universally accepted definition of predatory journals, recent publications review key characteristics of potential predatory journals. These journals often use questionable business practices, lack scientific rigor with minimal or no peer review and have little or limited editorial oversight. Predatory journals are usually not indexed in established bibliographic databases, such as MEDLINE, CINAHL, Embase, PsycINFO or Web of Science Master. With more than 10,000 identified potential predatory journals, the dangerous implications to scholarly quality and integrity, academic standards and evidence-based practice cannot be overestimated.1,4-6
“To assist
researchers/authors make an informed decision about where to publish, the
Library is providing access to a pre-defined checklist
that offers guidance on identifying trusted journals,” said Kelly R. Gonzalez,
MSIS, MBA, Assistant Vice President for Library Services. “Additionally, at the UT Southwestern
Library’s Writing
Portal, the Publication
Support for Author Article Processing Charges (APC) handout summarizes a
list of select UT Southwestern Library journal subscriptions which provide
discounted article processing charges.”
For additional information, call
214-648-2001 or click “Live Chat” on the Library’s website to chat Monday –
Friday, 10:00 am – 4:00 pm.
REFERENCES
McCann TV, Polacsek M. False gold: Safely navigating open access publishing to avoid predatory publishers and journals. J Adv Nurs. 2018;74(4):809-817.
Shen C, Bjork BC. ‘Predatory’ open access: a longitudinal study of article volumes and market characteristics. BMC Med. 2015;13:230.
Butler D. Investigating journals: The dark side of publishing. Nature. 2013;495(7442):433-435
Cobey KD, Lalu MM, Skidmore B, Ahmadzai N, Grudniewicz A, Moher D. What is a predatory journal? A scoping review. F1000Research. 2018;7:1001.
Lalu MM, Shamseer L, Cobey KD, Moher D. How stakeholders can respond to the rise of predatory journals. Nature Human Behaviour. 2017;1(12):852-855.
Ross-White A, Godfrey CM, Sears KA, Wilson R. Predatory publications in evidence syntheses. J Med Libr Assoc. 2019;107(1):57-61.
Did you know that the Library offers a resource that can help UT Southwestern labs increase productivity and efficiency?
JoVE’s Science Education collection offers simple, easy-to-understand videos that teach and reinforce laboratory fundamentals. JoVE developed this on-demand learning approach in collaboration with experts at top institutions, ensuring high quality, trusted content. The Library-funded Basic Biology Science Education video database can reduce time spent teaching laboratory basics or providing refreshers to research assistants, students, post docs, and other researchers.
Read about a recent case study at one of UCLA’s labs, which describes how they were able to increase productivity and reduce lab expenses with the animal research training videos that are part of the Basic Biology collection.
Users can view concise lessons repeatedly at any time to help improve learning and retention. An added bonus is the accompanying translation option that allows one to watch the videos and download the accompanying text in other languages such as Chinese, German, and Spanish.
JoVE’s Basic Biology Science Education collection includes the following components:
In addition to the Basic Biology Science Education collection, the Library provides access to allJoVE video journals that focus on biological and medical research. The journals provide experimental techniques, using the same high-quality visual format, with detailed text protocols for increased scientific reproducibility and productivity. JoVE is the leading peer-reviewed, PubMed/Medline indexed methods journal with more than 8,000 published articles. JoVE journal sections include Behavior, Biochemistry, Bioengineering, Biology, Cancer Research, Developmental Biology, Genetics, Immunology and Infection, Medicine, and Neuroscience.
An 1835 illustration featured in the National Library of Medicine’s #ColorOurCollections Coloring Book.
Art Therapy, Adult Coloring Books and Your Mental Health
According to the American Art Therapy Association, art therapy is a mental health profession in which the process of making and creating artwork is used to “explore feelings, reconcile emotional conflicts, foster self-awareness, manage behavior and addictions, develop social skills, improve reality orientation, reduce anxiety and increase self-esteem.”
The Health Benefits of Adult Coloring Books
Despite the fact that coloring and art therapy aren’t quite the same thing, coloring does offer a slew of mental benefits. Coloring definitely has therapeutic potential to reduce anxiety, create focus, or bring [about] more mindfulness. Groundbreaking research in 2005 proved anxiety levels dropped when subjects colored mandalas, which are round frames with geometric patterns inside. Simply doodling, though, had no effect in reducing the other subjects’ stress levels.
Just like meditation, coloring also allows us to switch off our brains from other thoughts and focus only on the moment, helping to alleviate free-floating anxiety. It can be particularly effective for people who aren’t comfortable with more creatively expressive forms of art. Now get coloring!
The South and North Campus Branch Libraries will have coloring stations with crayons and pages of science and medical related material for you to enjoy this month.
Download these free science and medical-related coloring books featured at the Library coloring tables this month:
SciFinder, a chemical and other sciences research database, now features a new version of the CAS Structure Editor that does not require the use of a Java plugin. The Java version of the editor is still available for your users, who can now easily select their preferred editor.
The new editor queries the same content
researchers have always accessed. There is some missing functionality in the new editor. SciFinder chose to release the limited version due to the pressing need of some users who were experiencing Java-related issues. For more information on the plugin-free, Non-Java CAS Structure Editor, visit http://www.cas.org/products/scifinder/system-requirements-web.
Additionally, the latest SciFinder release features the following updates:
Analyze reaction answer sets by reagent to more quickly identify your synthesis of interest.
View substance and supplier information simultaneously now that our popular Quick View feature is available from Commercial Sources answer sets. In addition, many top catalog entries now feature direct links to supplier emails from right within SciFinder.
Update account information more easily with a new account management link to myCAS® available in Preferences.
SciPlannerTM how-to guides are now more easily accessible to help you make use of the full power of the features and functionality available within SciPlanner.
For SciFinder questions, including how to conduct specific searches, please contact the CAS Customer Center at help@cas.org or 800-753-4227.
Journal of Visualized Experiments (JoVE) is a peer reviewed, PubMed-indexed video journal devoted to the publication of biological, medical, chemical and physical research. UTSW institutional online access is now available for three sections: General; Neuroscience; Clinical & Translational Medicine.
In addition to the three sections named above,
there are six more sections with limited open access. These sections are Immunology & Infection; Bioengineering; Applied Physics; Chemistry; Behavior; Environment. Limited open access is also available to some videos in the other sections:
after a 2 year embargo all videos available thru PubMed
if author(s) pay a publishing fees in advance of publication to allow open access to his/her/their video
if publisher provides complimentary access to selected videos for limited time periods
Students in the Graduate School of Biomedical Sciences are now able to submit electronic theses or dissertations (ETDs) online using Vireo. Everything students need for this is available at the Library’s Electronic Theses & Dissertations portal:
Dissertation preparation instructions
Thesis/dissertation template
Student guide to online ETD submission
Online submission system login
Vireo is an online ETD submission system developed by the Texas Digital Library (TDL). It is used by many institutions in Texas, including Texas A&M University, Texas Tech University, and the University of Texas at Austin.
As the largest ETD contributor, the Graduate School was selected by the Library as the first of the three degree-granting schools at UT Southwestern to test and implement Vireo. The Medical School and the School of Health Professions will work with the Library to implement Vireo after the system receives an upgrade later this year.
Using Vireo, students can submit an ETD online, track the status of an ETD, and submit comments or corrections as needed through the system. For Graduate School and Library staff, information about each ETD is available within the system, making processing much quicker and more efficient.
The UT Southwestern Library has recently subscribed to 
