Department Blog

Health Sciences Libraries

Open Access Journal: PLoS Pathogens on Cryptococcus gattii

April 23rd, 2010 by

If you were listening to NPR this morning, you may have caught the story of a new strain of Cryptococcus gattii (C. gattii) found in Oregon, and heard about the recently published article by Duke researchers in the open access journal, PLoS Pathogens

Laptop with open access journals PLOS and BIOone article

..In their study, EJ Byrnes, examine the expansion of an outbreak of the fungus, Cryptococcus gattii, in the Pacific Northwest. Cryptococcus gattii had been considered a tropical fungus. Since the 1999 outbreak of the fungus on the temperate Vancouver Island, the researchers document the expansion that is causing disease in humans and animals in the United States.
Their work was published in the open source peer-reviewed journal, PLOS Pathogens this week:

Byrnes EJ III, Li W, Lewit Y, Ma H, Voelz K, et al. 2010 Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States. PLoS Pathog 6(4): e1000850. doi:10.1371/journal.ppat.1000850

You may also be interested in the recently published article by Rotstein, which is the first reported infection of C. gattii in a dolphin from Hawaii. The article is also available via open access through BioOne.

Rotstein, D, West, K, Levine, G, et al. (2010). CRYPTOCOCCUS GATTII VGI IN A SPINNER DOLPHIN (STENELLA LONGIROSTRIS) FROM HAWAII. Journal of zoo and wildlife medicine, 41(1), 181-183.

NIH Compliance: Getting your PMID & PMCID numbers

April 22nd, 2010 by

How can I find the PMCID number in PubMed?

To check if there has been a PMCID (PubMed Central ID number) assigned to your article, you will need to locate the article in Pubmed. Then, change your ‘Display Settings’ (the link at the top left of your search results will open up the drop-down menu). Select ‘Abstract’ view from the drop-down menu.

Pubmed Display Settings set to Abstract View

Once you can see your article in abstract view, take a look below the abstract for the PMID number and an associated PMCID number. If you do not see the PMCID, it may be still in process.

If you have a batch of PubMed results and would like to check to see if there are associated PMCIDs, you can selectively send the PMIDs to a text file or to the clipboard, and then use the PMID to PMCID Converter at the Pubmed Central website to check for any associated PMCIDs.

Select Citations to be Sent to Text File or Clipboard

With your search results for your articles in Pubmed displayed in your browser window, click on the ‘Send to’ drop down menu  and select  File and also  PMID as format.  Your results will be sent to a text file on your computer.

Pubmed Author Results and Send to Menu in PMID format

Try out the PMID to PMCID Tool at Pubmed Central

Now you are ready to take your text file of PMIDs over to the Pubmed Central site: PMID to PMCID Converter .
(Note: Alternatively, you can save your PMIDs to the clipboard when in PubMed and then use the option to input the PMIDs from the clipboard into the PMID to PMCID Converter).

PMID to PMCID Converter Tool showing results saved to a text file

Read more about the NIH Public Access Policy and How To Comply:

Animal Welfare in Veterinary Medical Education and Research

April 19th, 2010 by Mary Wood

The 2009 Animal Welfare Symposium titled “Swimming with the Tide: Animal Welfare in Veterinary Medical Education and Research”  held last November, was jointly sponsored by the American Veterinary Medical Association (AVMA) and the Association of American Veterinary Medical Colleges (AAVMC).  The speakers, who presented information on the role of the veterinary profession in animal welfare education, research, and advocacy, were invited to submit their presentations for publication in the Journal of  Veterinary Medical Education (JVME).  The goal was to make this information more widely available, as a guide to interested veterinary faculty in their planning and implementation of curricula that include animal-welfare topics.


JVME volume 31, issue 1, 2010:  the Table of Contents is available as a pdf and with links in PubMed.


Titles of papers include:coverfig

Animal Welfare: A Complex Domestic and International Public-Policy Issue
Animal Ethics and Public Expectations: The North American Outlook
Evolution of Animal-Welfare Education for Veterinary Students
Expertise and Advocacy in Animal-Welfare Decision Making: Considerations for a Veterinary Curriculum in Animal Welfare


Policies included:

AAVMC Policy: Use of Animals in Education
AVMA Policy: Use of Animals in Research, Testing, and Education
AVMA Animal Welfare Principles




Psychiatric Service Dogs and PTSD

April 14th, 2010 by Mary Wood

A recent New York Times article by Janie Lorber describes how psychiatric service dogs are being used to help veterans suffering from post-traumatic stress disorder (PTSD).  Due to the success stories, there is legislation proposing a pilot program that would provide service dogs to veterans with PTSD, and research is being federally funded to determine if scientific studies support the anecdotal reports.

While not all related to the military, there have been scientific studies published on animal-assisted therapy for the treatment of PTSD.  The following databases and resources may be useful in a search:megtrees1.png



..DTIC Department of Defense funded and related research  (search  PTSD and dogs)

..PsycINFO (search KW=(ptsd) and KW=(animal-assisted or pets)psychiatric AND dogs)

..US Dept Veteran Affairs (search dogs)

..Googlescholar   (search “animal assisted” OR “service dogs” “ptsd”veterans psychiatric service dogs)


An interesting aside is that the puppies described in this article are raised and trained by prisoners through Puppies Behind Bars, a program based in New York state.  At least in this scenario, a single dog is providing therapy for two people with very different needs.

Bioethics Collection

April 6th, 2010 by Mary Wood

The C. John Tupper Bioethics Library Collection

is a special collection in the Blaisdell Medical Library, located in Sacramento at the UC Davis Medical Center.  The collection consists of books and journals covering every interpretation of the word BIOETHICS.  A sampling of title words creates the following word cloud, illustrating the range and diversity of the growing collection.


While the browse-able physical collection is in the medical library in the middle of the UC Davis Medical Center, the holdings are indexed (by author, title, and subject headings) in the Harvest online catalog and available for borrowing, like most everything in BML.

Titles in the Bioethics Collection


title words: encyclopedias IRB ethics research human subjects stem cells law healthcare bioethics law medical ethics biomedical ethics clinical bioethics ethical issues critical care biomedical research ethics moral medicine palliative care ethics evidence based medical ethics bioethical issues clinical ethics health ethics forensic ethics public health ethics Islamic bioethics ethics bioethics ethics psychiatric research psychiatric ethics ethical patient care ethical dilemmas pediatrics nursing ethics ethics epidemiology Journals Bioethics Cambridge Quarterly Review Healthcare Ethics Hastings Center Report Journal Clinical Ethics Journal Law Medical Ethics American Journal Bioethics