Health Sciences Libraries

Posts by Bernadette Swanson

Google Scholar: configure preferences to work with UC-eLinks & EndNote

September 4th, 2012 by Bernadette Swanson or go right to the Scholar Settings:

Configure your preferences in the Firefox web browser, Internet Explorer, etc.

Configure Google Scholar to work with UC-eLinks and EndNote

Customize the Google Scholar Preferences to work with UC-eLinks and the EndNote Bibliographic Management Software.

Use the preferences links down the left side of the page:  Search Results, Language, Library Links.

Search results:

  • select 100 results per page
  • Bibliography Manager: show links to import citations into ENDNOTE (not BibTex).  Save.

Library Links:

  • By default you will see OpenWorldCat – Library Search (that is the backend to our Melvyl Catalog System)
  • Search for California Digital Library –UC-eLinks
  • Select the checkbox.
  • If University of California Davis – UC-eLinks is not already selected, then search for it and select the checkbox.
  • You should have three Library links as shown below (Open WorldCat, University of California Davis and California Digital Library).

Configure Scholar Preferences to work with UC-eLinks and EndNote

Now you should see the UC-eLinks link on the right side of your search results, and the ‘Export to EndNote’ link below each of your search results.

Robotics Meets Neurology, UC Davis Style, with Dr. Sanjay S. Joshi

November 23rd, 2011 by Bernadette Swanson

To introduce the Robotics component for the Virtual Reality, Simulation and Robotics course, the Health Informatics class welcomed Dr. Sanjay S. Joshi, a UC Davis, Associate Professor, in the Department of Mechanical and Aerospace Engineering.  Dr. Joshi heads the Robotics, Autonomous Systems, and Controls Laboratory, an interdisciplinary laboratory consisting of researchers from Mechanical and Aerospace Engineering, Electrical Engineering, Computer Science, and Biomedical Engineering.

To access the full text articles via the links in this blog post, you will need to be either on campus or logged in via the wireless or the virtual private network (VPN) from off campus using your UC Davis login ID and Kerberos pass phrase or password.

Robotics research

"The Rat Pup Robots: the Robots that Act Like Rat 7-10 day old Rat Pups"

The Rat Pup Robots: the Robots that Act like Rats. Dr. Sanjay Joshi’s earlier research covered by UC Davis News and Information.

Chueh, M.; Au Yeung, Y.L.W.; Lei, K.-P.C.; Joshi, S.S. (2008). Following Controller for Autonomous Mobile Robots Using Behavioral Cues. Industrial Electronics, IEEE Transactions on , vol.55, no.8, pp.3124-3132, Aug. 2008. doi: 10.1109/TIE.2008.922605

Or through IEEE Xplore database if you are logged into the VPN from off campus with your UC Davis ID and Kerberos pass phrase or password.

After an introduction to the tiny robots, namely, the Rat Pup Robots, We were introduced to his team’s current research into Brain-Muscle-Computer Interface (BMCI) for severely paralyzed persons.  The team’s research includes a mobile phone Prototype where EMG activity on the surface of a single face muscle site is recorded with a standard electrode.  The researchers then import the analog electrical signal  into an Android based mobile phone and it is digitized via an internal A/D converter.

Dr. Joshi’s research interests include:  Autonomous Systems/Control, Neuro-engineering and  Biorobotics.

He has recently returned from a sabatical appointment at Columbia University, where he held the post of Visiting Associate Professor with the College of Physicians and Surgeons, Department of Neurology.  In the recent publications of Dr. Joshi and his research team, we see the intersection of Neurology, Mechanical and Aerospace, and Electronic Engineering, Computer Science, BioMedical Engineering and great promise for future BMCI research here at UC Davis.<

Current Research Introduced During the Seminar:

Joshi, S. S., Wexler, A. S., Perez-Maldonado, C., & Vernon, S. (2011, April 27 2011-May 1 2011). Brain-muscle-computer interface using a single surface electromyographic signal: Initial results. Paper presented at the Neural Engineering (NER), 2011 5th International IEEE/EMBS Conference on… doi: 10.1109/NER.2011.5910557

Lucas, S. M., Gilley, D. A., Joshi, S. S., Gardner, T. A., & Sundaram, C. P. (2011). Robotics training program: evaluation of the satisfaction and the factors that influence success of skills training in a resident robotics curriculum. J Endourol, 25(10), 1669-1674. doi: 10.1089/end.2010.0713

Perez-Maldonado, C., Wexler, A. S., & Joshi, S. S. (2010). Two-dimensional cursor-to-target control from single muscle site sEMG signals. IEEE Trans Neural Syst Rehabil Eng, 18(2), 203-209. doi: 10.1109/tnsre.2009.2039394

Vernon, S., & Joshi, S. S. (2011). Brain-Muscle-Computer Interface: Mobile-Phone Prototype Development and Testing. Information Technology in Biomedicine, IEEE Transactions on, 15(4), 531-538. doi: 10.1109/TITB.2011.2153208 URL:

For the more Complete Bibliography of Publications, see Dr. Joshi’s website.

View the Poster Presentation [PDF] of their recent work on a new brain-muscle-computer interface at the IEEE Neural Engineering Conference in Cancun, Mexico.

Recent Published Research on the Measuring of Electrical Activity in the Brains of Patients in Vegetative States:

Cruse D, Chennu S, Chatelle C, Bekinschtein TA, Fernández-Espejo D, Pickard, JD, Laureys S, Owen AM. (2011). Bedside detection of awareness in the vegetative state: a cohort study. Lancet. Nov 9. [Epub ahead of print] PubMed PMID: 22078855. DOI: 10.1016/S0140-6736(11)61224-5

Comment on Cruse, Article:

Overgaard M, Overgaard R. (2011). Measurements of consciousness in the vegetative state. Lancet. Nov 9. [Epub ahead of print] PubMed PMID: 22078856. DOI: 10.1016/S0140-6736(11)61591-2

Boly, Melanie, et al. (2011). Preserved Feedforward But Impaired Top-Down Processes in the Vegetative State. Science 332, 858 DOI: 10.1126/science.1202043

Available via the Science Magazine website: [PDF]

Feedback on the Boly article, along with supporting online material on methodology:

To learn more about the Health Informatics Program (Masters Degree and Certificate Program) .

MHI289h is taught by Alberto Odor, MD, as an elective course in the Masters of Health Informatics Program, at UC Davis Medical Center.

Configuring your EndNote Library to work with UC-eLinks & Google Scholar

November 22nd, 2011 by Bernadette Swanson
Configure Google Scholar Preferences to work with UC-eLinks

Google Scholar works with University of California's UC-eLinks!

Options for your EndNote Library

Create a link to the article with DOI number = DOI number here)

This will create a link to the article: e.g.:

The link will work for open access articles, or those to which you or your institution has authorization.

Configure UC-eLinks within Endnote

To use UC-eLinks from within EndNote, make the following modification. Open EndNote:

On the top menu, select Edit | Preferences | Find Full Text (tab)

In the OpenURL Path text box, type in this URL: and click OK.

In the URLs & Links (tab) | OpenURL argument:

Replace WoS with the term EndNote as shown below. Then click Apply.

There can be no spaces in the OpenURL argument:

?sid=ISI:EndNote&aufirst=AUFIRST&aulast=AULAST&issn=ISSN&isbn=ISBN&atitle=ATITLE &title=TITLE&volume=VOLUME&issue=ISSUE&date=DATE&spage=SPAGE&epage=EPAGE

How to use the UC-eLinks feature from within your EndNote Library:

In your EndNote Library, highlight a citation. Then, on the top menu select:

References |  URL | OpenURL Link (shortcut= ctrl-G)

Configure Google Scholar Preferences to work with UC-eLinks & EndNote

To do so: Access Google Scholar at

Or locate the Scholar Preferences by clicking on the wrench icon at the top right side of screen.

Scroll down to Library Links.

WorldCat (a global catalog of library collections) is selected by default.

  1. University of California Davis | select checkbox to activate it
  2. California Digital Library | select checkbox to activate it

Scroll down to Bibliography Manager.

  • Select the option: “Show links to import citations into” and select EndNote from the drop down menu.
  • Click on the Save Preferences button at the bottom right.

Health Informatics MHI289: Virtual Reality, Simulation and Robotics and Research across the Disciplines

November 16th, 2011 by Bernadette Swanson

The MHI289h course, Virtual Reality, Simulation and Robotics, an elective in the Masters of Health Informatics Program, gives Alberto Odor, MD, a chance to transmit the use of computer graphics and virtual reality use both physically and virtually for clinical applications.  The virtual reality related courses (MHI289 and MHI214)  are offered on site and around campus through the Health Informatics Master’s Degree, and virtually through the UC Davis Extension  Certificate Program’s Online Learning Campus (with Peter Yellowlees, MD).  The courses draw full-time graduate students and working staff and students from across the medical, IT, informatics, computer science, engineering, library and nursing disciplines.

Although the MHI289 class  meets physically in the Education Building at the UC Davis Medical Center twice per week, the students have  been introduced  to virtual patients, including “METI man” the hospital’s Virtual Patient in the  Center for Virtual Care. They have also toured the virtual medical campus of Imperial College London in Second Life where UK medical student avatars interact with a room full of  scripted  virtual patients through the Second Life Viewer, streamed in realtime via the web.

Back at the UCDMC Center for Virtual Care, an assortment of patient simulators are used, including: adult human patient simulators, pediatric and emergency patient care simulators, and number of focused clinical skills simulators. The physical tours of the Center are led by UC Davis medical faculty and the virtual tours of  both Davis Island and the builds in the NHS funded virtual medical training environment are similarly led by UC Davis medical faculty with the help of avatars and the client viewers used to login to the virtual environments.

Exploring Virtual Environments and Research on the Davis Campus:

More local virtual environments, namely the KeckCAVES were the topic and tour for this week’s classes. The W. M. Keck Center for Active Visualization in the Earth Sciences (KeckCAVES) is a joint project between the UC Davis Department of Geology, IDAV, and the UC Davis Computational Science and Engineering Center (CSE). The MHI289h class will experience the state-of-the-art immersive visualization facility used by earth science researchers from Davis and afar. We had the great  honor of meeting and viewing the research of Dr. Oliver Kreylos, hero to all Kinect  hackers and followers, since his work went viral shortly after the release of Microsoft’s $150.00 Kinect Controller for XBox360 (“where you are the controller”).

Many of us became aware of the tele-immersion research of Dr. Oliver Kreylos, after first seeing his work on YouTube and the international Kinect forums.
This year Oliver Kreylos’ team and collaborators from UC Berkeley, received the “CENIC 2011 Innovations in Networking” award, in the category “High-Performance Research Applications,” for “Tele-Immersion for Physicians,” also known as the combination of 3D Video, Vrui’s collaboration infrastructure, and 3D Visualizer.

Using Kinect for 3D video - tele-immersion

Watch the video: "All Quiet on the Martian Front"

View the video on YouTube |  Uploaded: Dec 20, 2010  | 206,383 views

Here are a few monumental breaking news posts from  Dr. Oliver Kreylos’ home page last November , 2010:

11/16/2010: 11:03pm, “one million views. Insane.”

11/22/2010: Since it’s been prominently featured in my most recent Kinect video, I figured I’d finally publicly release the Nanotech Construction Kit. GPL v2, yadda yadda yadda, you know the drill.

11/22/2010: I was featured in an article about Kinect hacking in the New York Times, 3D glasses and all. Yay!

11/25/2010: Vrui 2.0 has finally been released, after a long delay.

12/02/2010: Kinect package 1.2 with support for multiple Kinect cameras released and avaliable for download on the Kinect Hacking page.

More on Dr. Oliver Kreylos’ Research and Development work, publications and Kinect Hacking.

Related articles:

Kurillo, G, Bajcsy, R, Nahrsted, K, et al. (2008). IEEE Virtual Reality 2008, 269-70.

Vasudevan, R, Kurillo, G, Lobaton, E, et al. (2011). High-Quality Visualization for Geographically Distributed 3-D Teleimmersive Applications. IEEE transactions on multimedia, 13(3), 573-84.

Projects Using Kinect & Second Life:

research articles using Kinect and Second Life

Hacking Microsoft's Kinect using the FAAST Toolkit - PDF

Leading the hacking of Kinect to use with Avatars in the proprietary virtual environment of  Second Life, is the Institute for Creative Technologies, University of Southern California. USC and OpenNI have released the FAAST  (Flexible Action and Articulated Skeleton Toolkit) and it is available for download.

So where is the peer reviewed literature on Virtual Worlds?

You’ll find peer reviewed articles from Medical/Health Nursing & Engineering, Computer Science, Education, Sociology and Psychology and Multidisciplinary Databases… and more.
Start with the following databases: PubMed (from the Library website), Cinahl, Academic Source Complete and IEEEXplore, Inspec, Web of Science. The UC Davis Harvest Catalog has a selection of electronic and print resources, some published by UC Faculty. A quick search in Harvest: Using the following query and selecting “Subject Words” from the drop-down menu, retrieves over 500 related items:  “shared virtual environments” OR “Second Life” OR “virtual reality”
Click on the link at the top of the Year column to sort your results by year.
Always go through the Library’s website (using the database direct links, database A-Z listing, or Online Journals link) to reach the Library licensed resources. If you are searching from off campus, be sure to login through the Library’s VPN so that you are authenticated as a UC Davis student, staff or faculty member.

“How do I find the actual article?”

When searching the library licensed databases, always use the UC–eLinks to reach the actual article (whether it’s print or online). If it’s not available, use the request from another campus option on the UC-eLinks page.If you already know which of the 795 databases you would like to use, just type in its name on the Databases A-Z page. For Health Informatics research, you really do need use a few of the Subject Guides that focus on the technology across the related disciplines. To locate a specific subject area and the library licensed resources, take a look at the Subject Guides. They have been created by the Library Subject Specialists and you’ll find their contact names and email easily accessible at the top of each subject guide.For UC Davis students , staff and faculty:

Logging in from Off Campus using the VPN

  • Login to the Virtual Private Network (VPN) using your username and Kerberos pass phrase or password.
  • If you are logged in using CITRIX from the UC Davis Medical Center (UCDMC), be sure to open up another browser and login to the VPN
  • On the VPN welcome screen, copy and paste the URLs for the journal articles into the browse field directly below the VPN taskbar (usually at the top right of your screen).
  • If you are new to the VPN, watch the YouTube video walking you through the UC Davis VPN login and UC-eLinks from off campus

You’ll know you are logged in when you reach the VPN Welcome screen [below] and see the VPN task bar (Home, Help & Logout icons) at the top of your browser window. Choose where you want to start… the Library Home page or the Databases A-Z list, etc. If you have a DOI (digital object identifyer for an article) or want to view an unrelated web page,and remain logged into the VPN, use the ‘Browse’ field below the VPN taskbar.

Use the browse field at top right below the VPN task bar
Note: the VPN Taskbar & Browse field indicated by red arrow

MHI289h: Library related session using Second Life for simulation and research with Bernadette Swanson, Nov. 2011:

Workshop on Virtual Environments: Second Life and OpenSimulator
View the PowerPoint on

EndNote X5: downloading the free licensed version for UC Davis students, staff & faculty

October 11th, 2011 by Bernadette Swanson

My UC Davis Site

Watch all or part of the video on YouTube

Watch the video onYouTube:

For Jeff Magnin’s UWP 104 Class, working on an annotated bibliography with the help of EndNote.
Downloading your free licensed version of EndNote X5 from the MyUCDavis website:
The video will also show an example of seeking a citation style that was not available with the download, namely CSE/CBE.
In the case when you don’t find your preferred Output Style, just go to the website and seach for your required Output Style. Download the files and put them into the Styles folders within your EndNote X5 folder. We walk through the process.

Earlier, I sent 21 citations from the Web of Science database to my EndNote Desktop software.
You may also export your citations as text files from databases that do not have the direct EndNote or EndNote Web support. You can easily import these text files in Endnote format into your EndNote database directly from the EndNote file menu. All of these citations can be reformatted into our preferred format, such as CSE/CBE that is being used in the UWP 104 class.
You will be able to organize your citations and place into their own group folders. You’ll be able to sync your EndNote Desktop version with your EndNote Web account and work with either of your EndNote libraries (desktop or Web) when writing your paper using a popular wordprocessing software such as Word or similar. You’ll find the EndNote toolbar available in your Word software. If you do not see it, take a look in the tools menu.
For further help, be sure to check out the UC Davis Endnote website. We offer classes and ongoing support for EndNote and EndNote Web.

Shields Library Instruction website:
Download your free version of the licensed Endnote X5 using your UC Davis ID and kerberos pass phrase or password.
Check out the vendor’s website for ongoing updated tutorials or to request or download specific output styles that do not ship with the EndNote Software. There are over 5000 styles available at their website:
Be sure to create your EndNote web account:

Libguide for Jeff Magnin’s class: Creating an annotated bibliography, Using Google Scholar to download citations into EndNote, Web of Science and citing your sources using CSE/CBE citation style.

Today in PLoS Medicine: position data from cell phone SIM cards used to improve response following disaster

August 31st, 2011 by Bernadette Swanson

Researchers use position data from SIM (subscriber identity module) cards following earthquake disaster to estimate trends and track population movement in Haiti.

PLoS Medicine: a peer-reviewed open-access journal

a peer-reviewed open-access journal

Bengtsson L, Lu X, Thorson A, Garfield R, von Schreeb J, 2011 Improved Response to Disasters and Outbreaks by Tracking Population Movements with Mobile Phone Network Data: A Post-Earthquake Geospatial Study in Haiti. PLoS Med 8(8): e1001083. doi:10.1371/journal.pmed.1001083

Are your Google Scholar Preferences set to work with UC-eLinks & EndNote?

August 11th, 2011 by Bernadette Swanson

We’re looking for a 1996 journal article “Blood pressure and flow rate in the giraffe jugular vein.”
So, if you are using Google Scholar to quickly locate an article, make sure you edit your Scholar Preferences to work with UC-eLinks. Through the UC-eLinks in Google Scholar, you will then be able to to reach full text of any articles in library licensed online journals, or locate the call number (shelf location & library) for the print subscription via links to the library catalogs. If we don’t have a license or subscription for the journal, UC Davis students, staff and faculty can request the article from another library via the the request link in the UC-eLinks window.
Work along with the video to make sure your Scholar Preferences are setup for use with both UC-eLinks, along with bibliographic management software such as EndNote, Refworks, Mendeley, etc. The article could also be found via the UC-eLinks in PubMed. Be sure to use the link to PubMed via the Library’s website and login via the VPN if you are off campus.

setting Google Scholar Preferences to work with UC-eLinks & EndNote

Watch the video on YouTube

Note: To download EndNote or take an introductory class in using EndNote for bibliographic management, writing course papers, articles or your thesis, see the EndNote page on the Library Website.

Update: Google Scholar Preferences for UC-eLinks

May 4th, 2011 by Bernadette Swanson

Activate the University of California ‘UC-eLinks’ within Google Scholar, to reach the UC library licensed subscriptions to journals, books, etc.

Work along with the video to make sure your Scholar Preferences are setup for use with both UC-eLinks and bibliographic management software such as EndNote, Refworks, Mendeley, etc.

At Google Scholar:
Click on Scholar Preferences
Scroll down to Library Links and search for the following two libraries for UC Davis:

  • Type in: Davis OR University of California Davis
  • Type in: California Digital Library

Now, select both checkboxes.
Save Preferences.
The UC-eLinks will show up on the right side of the page.

EndNote Bibliographic Management Software:
If you are using a bibliographic management software such as Endnote, select it from the drop down menu. To download EndNote or take an introductory class in using EndNote for course papers, articles or your thesis, see the EndNote page on the Library Website.

Click on Scholar Preferences linkNow, the UC-eLinks will be visible when searching Google Scholar.
Google Scholar search results with UC-eLinks activated

Open Access Journal: PLoS Pathogens on Cryptococcus gattii

April 23rd, 2010 by Bernadette Swanson

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 Bernadette Swanson

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: