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Worldview 100

July 27th, 2015 by Mary Wood

The Worldview 100

Scientific American’s Worldview 100 ranks two UC Davis faculty among the top 100 visionaries in biotechnology.
“The visionaries who continue to reshape biotechnology—and the world”

At just 40 years old, biotechnology is a relatively new industry. Its starting point, arguably, was the 1975 Asilomar Conference on Recombinant DNA, at which the potential benefits and hazards of DNA manipulation and the ways it should be regulated were debated and essentially decided upon…Here, we name 100 of the industry’s leading lights in a list we’ve dubbed “The Worldview 100.” The honorees include researchers who provided fundamental insights into biological processes, as well as their colleagues who developed those insights to create the biology-based goods and services that are the essence of biotechnology…

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ROGER BEACHY
Director  |  World Food Center  |  University of California, Davis |  Davis, California, U.S.
This plant biologist visionary and founding president of the Danforth Center knows how to keep things in perspective. “After a series of laboratory successes that followed the discovery of disease-resistant technologies, I self-assuredly referenced ‘being on a roll,’” he told Worldview. “Soon thereafter I took a fall and a long roll down a run at the Purgatory ski resort at a Keystone Conference. To my chagrin and embarrassment, a friend, Jonathan Jones, from the John Innes Center, UK, shouted, ‘Are you still on a roll, Beachy?’—not just one time, but repeatedly in following years.”

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PAM RONALD
Director |  Laboratory for Crop Genetics Innovation & Scientific Literacy  |  University of California, Davis |  Davis, California, U.S.
When Worldview asked Ronald to tell us her greatest contribution to biotechnology, she pointed out her work with rice, in particular, “isolation of the Xa21 resistance gene and the Sub1 submergence tolerance gene in collaboration with my colleagues.” Her pick for the most exciting application of biotech in the past year: the HIV and Ebola vaccines.

 

Colleagues from UCSF and UCB

Atul Butte
Director  |  Institute of Computational Health Sciences  |  University of California, San Francisco  |  San Francisco, California, U.S.
Discussing the new institute, Butte notes, “We hope that we will be successful in making discoveries and developing diagnostics and therapeutics. If we want to change the world of medicine, we have to bring those discoveries into the marketplace and closer to patients.”
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Jennifer Doudna
Li Ka Shing Chancellor’s Professor in Biomedical & Health Sciences  |  University of California  |  Berkeley, California, U.S.
One of the leading researchers who created the CRISPR-Cas9 technology for genome engineering, Doudna believes that we must “increase connections and communications between academic labs and companies” to help biotechnology move ahead even faster.

Comparison of Research Networking Tools and Research Profiling Systems

January 26th, 2012 by

A team of researchers and librarians at Northwestern University have compiled an extensive chart comparing Research Networking tools and Research Profiling Systems. Modeled after a Wikipedia entry comparing reference management software, “Comparison of Research Networking Tools and Research Profiling Systems”  resides at http://en.wikipedia.org/wiki/Comparison_of_Research_Networking_Tools_and_Research_Profiling_Systems.

The team worked hard to ensure inclusion of the most up-to-date and accurate information in the Wikipedia article, but recognize that they may have made inadvertent errors or omissions.  Readers are welcome to edit and update the article at any time on their own.

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.

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

November 22nd, 2011 by
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 = http://dx.doi.org/(input DOI number here)

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

http://dx.doi.org/10.1186/1472-6920-9-53

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: http://ucelinks.cdlib.org:8888/sfx_local 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 http://scholar.google.com/scholar_preferences

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.

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

October 11th, 2011 by

My UC Davis Site

Watch all or part of the video on YouTube

Watch the video onYouTube:

http://www.youtube.com/watch?v=ySv6zjRYnnA

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 Endnote.com 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:
http://www.lib.ucdavis.edu/dept/instruc/research/endnote/
Download your free version of the licensed Endnote X5 using your UC Davis ID and kerberos pass phrase or password.
Check out the EndNote.com 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:
http://www.endnote.com.
Be sure to create your EndNote web account:
http://myendnoteweb.com

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.

http://ucdavis.libguides.com/content.php?pid=265370

Furloughed on Hakone: 2010 NMC Symposium to be held in new academic virtual environment

March 10th, 2010 by

If you are looking for a great way to spend a couple of your March furlough days, how about exploring the new metaverse for the higher education community, while attending this year’s Symposium.  This new environment has the power and potential of Second Life® and has been jointly developed by New Media Consortium (NMC) and Linden Lab (the developers of Second Life®) with none of the constraints that have troubled many of the early educational adopters using Second Life for education purposes.

2010 NMC Symposium on New Media and Learning

The 2010 NMC Symposium on New Media and Learning is the fifteenth in the NMC Series of Virtual Symposia, running March 23-25th. It will explore the impact of new media on teaching, learning, research, and creative inquiry, especially in higher education.  Though the symposium will be conducted in a virtual environment, it will not be about virtual environments. After registering for the conference, attendees will be required to download the Hakone viewer software. Computer requirements are the same as for accessing Second Life®: http://secondlife.com/support/system-requirements/

Orientations will be available for all registered attendees. No previous experience in virtual environments, such as Second Life®, is required.  The environment will be a new one for me, and I will be filming the keynote and sessions for NMC which will be made available, along with all presenters’ materials, through NMC via Creative Commons Licenses following the Symposium.

About the Hakone Project

The NMC has its origins in Hakone,  the location in Japan where a group of hardware manufacturers, software developers, and publishers met in 1993.  It was here where the group realized that the ultimate success of their multimedia-capable products depended upon their acceptance by the higher education community in a way that had never been achieved before. Today, NMC member institutions include hundreds of leading universities, colleges, museums, and research centers, including UC Davis and many of the UCs.

Which Institutions are Members of New Media Consortium (NMC)?

http://www.nmc.org/members

Hakone Lake, Japan (circa 1880s) uploaded to Flickr Creative Commons by NYPL

Hakone Lake, Japan (circa 1880s) uploaded to Flickr Creative Commons by NYPL

User Guide for Hakone environment:

The Hakone wiki serves as the user guide for the environment: http://hakone.wiki.nmc.org/

Suggested Reading before attending the Symposium:  Horizon Report

NMC & Educause publish the highly anticipated annual Horizon Reports charting the landscape of emerging technologies for teaching, learning and creative inquiry. The 2010 Horizon Report is now available. View the earlier reports from the Horizon Project.

Endnote: Looking for an ‘Output Style’ for a Journal that’s not in Endnote X3?

March 3rd, 2010 by

If you are looking for an ‘output style’ for a journal that isn’t loaded in the collection of styles that shipped with EndNote X3, you have a couple of choices – –  your best bet, and to keep X3 quick, lean and mean, is to download  individual output styles as you need them.  The steps for locating the specific output style, downloading and copying it into the appropriate folder within your EndNote application are shown here in the YouTube video.   If you prefer to take a quick glance at the text instructions…  they’ll be included at the bottom of this blog post.

Downloading an Output Style that didn’t ship with Endnote X3

Watch video on YouTube:  http://www.youtube.com/watch?v=zqqG5y7TxSI

Downloading the Output Style for Journal of Medical Entomology

Endnote Website: Locating & downloading the Output Style

  • Open the EndNote website: http://www.endnote.com
  • Click on ‘Support and Services’ tab at top of EndNote page
  • Click on the ‘Output Styles’ on the left navigation bar (green area)
  • Read… then click the Accept button at bottom of page
    You will be taken to the following page: http://www.endnote.com/support/enstyles.asp
  • Look for the search box…  (It’s located just below the two green tabs ‘Style finder’ and ‘Sorting Options’)
  • Type in your journal name,  e.g.: Journal of Medical Entomology
  • Click the Find Styles button to begin the search
  • Once you have located the output style for your specific journal
  • Click the ‘download’ link (or right-click and select a download option if you’re on a mac).

Copy the Output Style (.ens file) to the appropriate folder on your computer:

  • Once the file or zip file(s) are downloaded to your desktop or other location on your computer… copy the file(s) to the appropriate folder in your EndNote program directory.

For PC users:

  • Locate your downloaded file and then copy the file into the appropriate folder within your EndNote application
  • On Windows, it is usually located in Windows—C:\Program Files\EndNote\Styles

For Mac or Mac OS X+ users:

  • Note: files on macs often download to the Downloads folder, but you can change the download location, if you wish, as you’re downloading it.  I always choose the desktop as it’s easier to locate… assuming my desktop is not a mess.
  • On your hard drive (HD): locate the applications folder: Applications: EndNote: Styles
  • Copy the downloaded file  into the Styles folder.

Note: Use the edit menu or right-click to copy and paste the file into the appropriate folder within your Endnote application.

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Alternative: Downloading the Modified EndNote X3 with the full collection of 3,600 Output Styles:

You can download the entire collection of output styles containing more than 3,600 bibliographic styles for a wide variety of disciplines.  As of mid-February 2010, the modified version of Endnote X3 was made available from the  MyUCDavis website containing all 3,600 output styles.  Use your Kerberos username and password to login to MyUCDavis.  EndNote can be found under UCD Resources | Software | Library.

UC Davis has a campus-wide license allowing all current UC Davis students, faculty and staff to install and use EndNote on computers at work and at home. Another option is to download the zip file of all output styles available from the EndNote website: available for EndNote version 8 and up.

Download a licensed version of Endnote from MyUCDavis

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EndNote at UC Davis:Workshops

http://www.lib.ucdavis.edu/dept/instruc/research/endnote/

Find out more about the EndNote Workshops offered throughout the year at the libraries around campus, and don’t miss the class schedule which includes all instructional sessions offered at the UC Davis Libraries.

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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.

Generation M2 spends 7.38 hours per day using media/digital media

February 1st, 2010 by

This statistics on media/digital media usage by Generation M2 caught my eye, making me put down my coffee cup this morning:

“The use of print media fell from an average of 43 minutes per day in 2004 to 38 minutes in 2009.” 

Pierleoni, Allen.  “Between the Lines.” Sacramento Bee, 1 Feb. 2010: D3. Print.

 

The Henry J. Kaiser Family Foundation released the third in a series of reports on the use of media in the lives of 8-18 year olds, dubbed “Generation M2”.  The study is one of the largest and most comprehensive publicly available sources of media use by 8-18 year olds,  with surveys taken in 1999, 2004 and 2008. Total media use increased  between 2004 and 2009,  from an average of  6.21 hours per day in 2004 to 7.38 hours per day in 2009.  Total media use is the actual number of hours out of the day that are spent using media, taking multitasking into account.  These averages are broken down into three broad categories of video games, print, movies.  The video game category included console players, handheld players and cell phones; print included books, magazines and newspapers; movies included all movies watched on any platform/device.

Read the full report [PDF, 2.7 MB, 85 pages]
Publications from The Henry J. Kaiser Family Foundation are available in PDF format through the Program for the Study of Media and Health:
http://www.kff.org/entmedia/index.cfm

The Henry J. Kaiser Family Foundation’s related statistical resources are available at: StateHealthFacts.org: http://www.statehealthfacts.org/

Peeking at Jakob Nielsen’s ‘Eyetracking Web Usability’

January 14th, 2010 by

The Next Generation Melvyl Catalog  provides a great peek at the long awaited book on eyetracking research by usability gurus, Jakob Nielsen  and Kara Pernice.  By clicking on the ‘Preview this Item’  button & the Google Preview link, the first two chapters are available including images. The  feature is powered by Google preview.  The ‘Preview this Item’ button is available after clicking through to the full description of the book:  http://ucdavis.worldcat.org/oclc/495471898/viewport   
The book is currently in process at UC Santa Cruz and being ordered for UC Davis.

So what is Eyetracking?

In Pernice and Nielsen’s words at the opening of chapter one, “Eyetracking is simply following the trail of where a person is looking. With current technology, it is fairly easy to observe the path where users look on a computer screen.”  The images below are two eyetracking “heatmaps” which use colors to represent the data showing  how much users looked at different parts of the pages.

Eyetrackingheatmap
 

Nielsen, J. (2009), Eyetracking heatmap [screen captures]. Retrieved January 14, 2010, from Useit.com, Eyetracking http://www.useit.com/eyetracking
 

Using eyetracking in your own research:  Free Report on how to run eyetracking studies

Pernice, K., & Nielsen, J. (2009).  How to Conduct and Evaluate Usability Studies Using Eyetracking. Fremont, CA: Nielsen Norman Group. Retrieved January 14, 2010, from http://www.useit.com/eyetracking.

Access the report via the web site: http://www.useit.com/eyetracking/methodology

 or download the free pdf (159 pages, 16MB) http://www.useit.com/eyetracking/methodology/eyetracking-methodology.pdf

 Note on the Library Catalogs: Next Generation Melvyl is one of two catalogs available from the Library’s web site.  It includes the records of all ten UC campuses as well as libraries from around the world.  The Harvest UC Davis Catalog is our local catalog and a great choice for searching our rich and unique collections.

Seeking Permission to use the Copyrighted Images: A quick email to Jakob Nielsen’s office manager, with a cc to Mr. Nielson, resulted in a quick response from Jakob Nielsen stating: “You have permission to use the images.”. Thank you.  It’s always worth asking.