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Health Sciences Libraries

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

November 23rd, 2011 by

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: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5765686&isnumber=5954041

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, et.al. 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: http://www.sciencemag.org/content/332/6031/858.full.pdf [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.

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

November 16th, 2011 by

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 Slideshare.net

Show statistical information with maps:

February 23rd, 2010 by

GAPMINDER – Unveiling the beauty of statistics for a fact based world view.

This website is worth exploring, in my opinion. There are many options for presenting data from time series short and long. This resource uses a variety of global statistical resources. The address to this resources is: http://www.gapminder.org/ 

At the site look for  video examples such as one linked to below.

See: “200 years that changed the world” which relates health to income.

On the rugged digital shores of Davis Island: in Second Life® with the MH214 Class

October 5th, 2009 by

Over the past couple of months my work as a librarian has extended from the Health Sciences Libraries to the rugged digital shores of Davis Island in the virtual world of Second Life®. Our journey into the popular 3D virtual environment was part of the new online course, MH214, The Internet and the Future of Patient Care which is a collaboration between the UC Davis Extension and the UC Davis Health Informatics Certificate Program. Participants in the course led by Peter Yellowlees MD, were invited to:

“Explore the profound impact of the Internet on the delivery of health care from the patient and provider perspectives, including the Internet’s role as an information source, a communication tool and a conduit for clinical consultations and chronic disease management. Consider the changing nature of the doctor-patient relationship and the potential of the Internet to enhance access to and quality of care. Explore the future of health care in an information age where care will become increasingly personalized and distributed.” Peter Yellowlees MD

Conference Area with Student Blogs on Med. Projects, Davis Island

On the digital shores of Davis Island

UC Davis Online Learning Campus & Second Life®: a Look at the Software

The MH214 course found its home online at the UC Davis Online Learning Campus (which uses the popular Moodle open-source course management system). The students and instructors also used a suite of familiar social networking sites including Facebook, Twitter and Blogspot (e.g.: Peter Yellowlees’ blog), where students followed, commented and shared insights on weekly readings and topics for discussion, then submitting assignments and discussion posts to the MH214 home at the UC Davis Extension’s site.

UC Davis Extension Online Campus Site

UC Davis Extension Online Campus Site

In the Second Life® sessions, students learned some of the basics of building in 3D environments, importing media and touring some of the well known health care, non-profit and government projects such as Cisco’s Virtual Palomar West, Imperial College London’s Medical School and the Second Health Polyclinic, Virtual Ability Island, Virtual Hallucinations (named one of ScienceRoll’s Top 10 Virtual Medical Sites in Second Life®), NOAA and and a variety of other organizations using the environment for learning and health related purposes.

Just How Big is Second Life®?

The total land area of Second Life® is now equivalent to approximately two billion square meters – roughly the size of the state of Rhode Island. There are well over 20,000 CPUs conncected together simulating the virtual environment. This popular virtual world is the brain child of Philip Rosedale, a UC San Diego Engineering Graduate. Prepare to be inspired: TED: Talks with Second Life creator, Philip Rosedale.

Let’s take a look at some of the numbers in the Sept. 22, 2009 Linden Lab press release.

Virtual goods & user created content: residents create more than 250,000 new virtual goods every day. User created content now amounts to more than 270 terabytes and growing 100% every year.

Voice Chat (VoIP): 18 billion minutes of voice chat have been used in Second Life® since voice was introduced in 2007, making Linden Lab a major VoIP provider.

Text Chat: Approximately 1,250 text-based messages are sent every second in Second Life®, and more than 600 million words are typed on an average day.

Where are these people from? Roughly 60% of active Second Life® Residents based outside of the US, representing more than 200 countries, and the Second Life® Viewer available in 10 languages.

Some of the UC Davis Virtual Locations:

The following video gives a glimpse of two of the UC Davis locations visited during the September 10th session, take a look at the following video capture from the class (available via YouTube) which includes quick visits to the 3D UC Davis Virtual Hallucinations facility (scale replica of the Sacramento County Mental Health Treatment Center on Stockton Blvd.) and the Bioterrorism Defense Training facility based on another Sacramento building to mimic an actual setting that might be used as a Strategic National Stockpile distribution site for Northern California in the event of a bioterrorist attack.

Gathered for the Sept. 10th class discussion & tour of health facilities

Gathered for the Sept. 10th class discussion & tour of health facilities

The instructors for the class were seasoned virtual reality proponents, Peter Yellowlees MD, Martin Leamon MD, Bernadette Daly Swanson MLIS and James (Linden) Cook MD, who is also one of the early developers of the Second Life® and employed by the creator, Linden Lab. The feedback from the students has been positive and will be shared by Peter Yellowlees MD in an upcoming publication.

Broadband, updated Graphics Cards, Headsets with Microphones:

So what does it take to log into virtual worlds? System requirements for Second Life® require broadband Internet access and a compatible graphics card. Options for courses using both Moodle® and the synchronous Second Life®, include the integration of both systems using the open-source SLoodle®, which provides a tested suite of tools whereby content such as course slides can be uploaded into the online course management system and then accessed by the instructors and students in Second Life®.

What are other institutions doing in Second Life®?

New Media Consortium (NMC) provides access to case studies via their online portfolio.

Last month, the University of Texas, entire 16 campus system, announced its participation in a year-long project to explore the use of virtual worlds for learning.

The MH214 Class:

Students logged into the UC Davis Extension’s online learning campus and the virtual world from different parts of the country and across time zones, and brought a rich variety of expertise to the class. The group included professionals already in the fields of health care, IT and education, including a nurse, physician, online records specialists and students from the Certificate Health Informatics Program. At the times when the class logged in, between 6:00 PM PDT and 9:00 PDT, there were between 65,000 – 75,000 people logged in from around the world. We used a combination of text chat, IM and voice (VOIP) and communicated through our microphone/headsets and the more traditional fingertips.

Discussing readings and student blog posts (typing action indicates text chat)

Discussing readings and student blog posts (typing action indicates text chat)

Joining the Virtual World:

Joining the Second Life® community requires creating a user account at the web site, choosing an avatar and name (not your actual name), then downloading the software which is similar to a web browser (shown below). Through the Second Life® viewer the user logs into the 3D world using the avatar name and password.

Check the system requirements for using SL (broadband & updated graphics cards)

Check the system requirements for using SL (broadband & updated graphics cards)

Online Orientation via YouTube Videos, Tutorials at First Login & the Help Islands:

Before registering and downloading the software, the students were encouraged to view one or more of the introductory videos from the MH214 YouTube Playlist.

Introductory videos to Second Life uploaded to YouTube for the class

Explore the website: then join, download software, login

A brief orientation to Second Life®:

As part of the first login, new users can select from a variety of orientation areas. The MH214 class were asked to spend an hour in one of these areas to become familiar with the navigation keys and the Second Life® viewer interface. That week once we were all logged in and feeling a little more oriented, we met at the private class location, UC Davis Island.

Videos showing some of the activities and discussions can be seen on the YouTube video playlist of the MH214 Class

View the YouTube Playlist of videos from the class

View the YouTube Playlist of videos from the class

Looking for Peer-Reviewed Journal Articles on Health care & Second Life®:

Students made use of free peer reviewed journals on the web, as well as journal articles from UC Davis licensed journal subscriptions. Some of the free peer reviewed journals include Journal of Virtual Worlds Research (JVWR) and the Journal of Medical Internet Research. A special issue dedicated to virtual worlds and health care was published by JVWR in August 2009:
Journal of Virtual Worlds Research, Vol 2, No 2: 3D Virtual Worlds for Health and Healthcare and
A Survey of Health-Related Activities on Second Life® in the Journal of Medical Internet Research.

The best way to find relevant articles in PubMed on research being conducted in the environment or review articles about Second Life®, is to search using the Medical Subject Headings (MeSH) that are the backbone of this massive database.
In order to retrieve relevant articles, this is the query I used:
“User-Computer Interface”[MAJR] AND (virtual environment OR second life)
This query currently retrieves 860 articles… of course, way too many for most purposes, so we encourage adding extra keywords or MeSH terms to the search such as the following query with a focus on consumer health information and education which currently retrieves 212 results:
“User-Computer Interface”[MAJR] AND (virtual environment OR second life) AND (“Education”[MeSH] OR “Consumer Health Information”[Mesh])

Articles related to some of the locations visited included the following two by UC Davis faculty:

Peter Yellowlees, James N. Cook, Shayna L. Marks, Daniel Wolfe, Elanor Mangin. Can virtual reality be used to conduct mass prophylaxis clinic training? A pilot program. Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science. March 2008, 6(1): 36-44.

PM Yellowlees, JN Cook. Education about hallucinations using an internet virtual reality system: a qualitative survey. Academic Psychiatry. 2006 Nov-Dec 2006, 30(6):534-9

View the recent issue of freely available peer reviewed journals

View the recent issue of freely available peer reviewed journals

If You Plan to Visit:

If you’re logging into Second Life®, be sure to contact us. During the registration process you will select a name (not your actual name). Here are our names if you would like to contact us once you log in. Peter is known as Nash Baldwin; Martin is Grommet Wallace; Bernadette is HVX Silverstar and James is James Linden.

Firefox toolbars to the virtual world: MH214 Health Informatics Class toolbar

For anyone using the Firefox browser… or for anyone who wants a quick way to reach the MH214 class locations in Second Life®… read on!
Download and install the toolbar with quick links to the Second Life locations visited during the last sessions, as well as additional links.
Toolbar links include:
Davis Island (private – MH214 students & faculty only.. sorry)
Cisco’s Virtual Palomar West Hospital with RFID tracking for visitors
Imperial College London: Second Health Polyclinic (NHS funding)
Virtual Hallucinations public location (UC Davis)
Library Studios (my island in process)
UC Davis Extension Class Online Campus site

Note: The Second Life® viewer must be installed on your computer to use the toolbar. When you click on the buttons on the toolbar, they will launch the SLurl (SL URL) map site with coordinates for Second Life® and allow you to click through to the location which launches your SL viewer which allows you to login to the chosen location.

Customized Firefox Toolbar for download

Click to view larger image

More about the Mozilla Firefox browser

Take a tour of some of the Medical Builds in Second Life®:

Cisco’s Virtual Palomar West
Second Health London Polyclinic
Virtual Hallucinations (updated version)
on the private Davis Island
Mass Prophylaxis Clinic Training facility on Prophylaxis Island (also private).

YouTube Video:

Tour the locations shown during the 3rd Annual Conference at UCDMC: Innovations in Informatics Conference:
Virtual Tour of the very cool Health & Medical Builds in Second Life® 720p HD version.
Note: an updated Flash video player is required to view HD on YouTube.

Create an account and login to Second Life® to visit the locations

Create an account and login to Second Life® to visit the locations

Sources:

Health Informatics, UC Davis Extension. 2009. Online Certificate Program in Health Informatics. Retrieved October 5, 2009, from http://extension.ucdavis.edu/unit/health_sciences/certificate/health_informatics/

YouTube video playlist for the MH214 Class in Second Life ®
Swanson, B. (2009, Sept. 16). UC Davis Health Informatics Class in Second Life® [Video files]. Retrieved from

http://www.youtube.com/user/HVXSilverstar#g/c/5333F5146C944E14

Bernadette Daly Swanson, MLIS
HVX Silverstar in Second Life®
http://people.lib.ucdavis.edu/~bswanson/