2012 News
The Name Game
The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. In a landmark decision, ICZN has passed an amendment on September 2012, to its rules for the naming of new species described in an electronic-only scientific journal. The name of a new species will be ‘legitimate’ if the journal meets criteria of archiving and the publication is registered on the ICZN’s official online registry, ZooBank.
This decision comes a year after the International Botanical Congress (IBC) XVIII held in Melbourne, Australia accepted new botanical plant names described in online-only papers. For more information about the amendment see:
Knapp S, McNeill J, Turland NJ. 2011. Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? BMC evolutionary biology 11:250. http://www.biomedcentral.com/1471-2148/11/250
Miller JS, Funk VA, Wagner WL, Barrie F, Hoch PC, Herendeen P. 2011. Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress. PhytoKeys 5:1-3. Publisher Full Text
This decision comes a year after the International Botanical Congress (IBC) XVIII held in Melbourne, Australia accepted new botanical plant names described in online-only papers. For more information about the amendment see:
Knapp S, McNeill J, Turland NJ. 2011. Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? BMC evolutionary biology 11:250. http://www.biomedcentral.com/1471-2148/11/250
Miller JS, Funk VA, Wagner WL, Barrie F, Hoch PC, Herendeen P. 2011. Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress. PhytoKeys 5:1-3. Publisher Full Text
Biobank yields results
Biobank stores the genetic and medical information submitted voluntarily by 100,000 Californian adults insured by Kaiser Permanente (KP). In a research study funded in part by a 2-year, $25 million National Institutes of Health (NIH) grant, the researchers from KP announced at the American Society of Human Genetics (ASHG) meeting last month a link between telomeres and aging, as well as specific genetic variants and disease traits.
More information at: http://news.sciencemag.org/scienceinsider/2012/11/largest-us-genetic-biobank-revea.html
More information at: http://news.sciencemag.org/scienceinsider/2012/11/largest-us-genetic-biobank-revea.html
Controlling giant reed
Giant reed (Arundo donax), is a bamboo-like plant that can grow up to 33 feet tall. It was intentionally introduced to California in the early 1800s from the Mediterranean for erosion control along riverbanks and for use in thatching and basket weaving. To support its rapid growth rate, giant reed consumes large amounts of water compared to native vegetation, threatening to worsen the water shortage in places like the Rio Grande Basin, where the densest stands of giant reed are found. It reduces arthropod diversity and abundance and destroys wildlife habitat. Mechanical control methods, such as cutting, chopping, and mowing, have been ineffective and costly to implement, and chemical treatment can impact surrounding vegetation and water. Biological control with insects such as the Arundo wasp (Tetramesa romana) and the Arundo scale (Rhizaspidiotus donacis), may be the best strategy for long-term management of this invasive weed. The aerial photography1 and remote sensing2 estimate infested areas which can be then targeted with insects.
1. Yang, Chenghai, Everitt, James H., and Goolsby, John A. 2011. Mapping Giant Reed (Arundo donax) Infestations along the Texas–Mexico Portion of the Rio Grande with Aerial Photography. Invasive Plant Science and Management. 4(4): 402-410.
2. Yang, Chenghai, Goolsby, John A., Everitt, James H. 2009. Mapping giant reed with QuickBird imagery in the Mexican portion of the Rio Grande Basin. Journal of Applied Remote Sensing 3(1), 033530.
November 14, 2012
Fall 2012 issue of Biofeedback is available
In this issue: Chair's Message, Medical Section Report, MLA Liaison Report, and more! Download the PDF.
e-Science Portal for New England Librarians
The e-Science Portal for New England Librarians (http://esciencelibrary.umassmed.edu) is an openly accessible website targeted specifically for librarians working in research institutions that generate, share, store and/or use data for basic scientific research in the health, biological, and physical sciences.
A collaborative project devoted to educating science and medical librarians on e-Science, the portal was initiated at the University of Massachusetts Medical School through funding from the National Network of Libraries of Medicine. Content for the portal is contributed by a dedicated team of subject specialists from diverse New England research libraries. This team has scoured the web for e-Science news, events, projects, and tutorials.
The e-Science portal is divided into the following key focus areas:
A collaborative project devoted to educating science and medical librarians on e-Science, the portal was initiated at the University of Massachusetts Medical School through funding from the National Network of Libraries of Medicine. Content for the portal is contributed by a dedicated team of subject specialists from diverse New England research libraries. This team has scoured the web for e-Science news, events, projects, and tutorials.
The e-Science portal is divided into the following key focus areas:
- About e-Science: Overview of e-Science, definitions, data sharing practices of researchers, cyberinfrastructure, policy, open science advocacy
- e-Science and Libraries: ARL reports, library roles, competencies needed by e-Science librarians, librarian education programs, blogs that post about e-Science/open science issues
- Data Support Services: Data management planning guides and resources, funder requirements, data curation, data repositories, science data literacy instruction, and research information networks
- e-Science Community: e-Science Community Blog with news/events/opportunities and commentaries, projects in New England, national projects, links to regional and global organizations
- Science Primers: overviews and tutorials on life sciences, physical sciences, and engineering; Science Boot Camp presentations, research tools
- About the Portal: mission and scope of portal, organization of content, portal staff, advisory, and editorial boards, content contributors, and selection criteria for content
Scientific Fraud
Scientific misconduct contributes to more retractions than previously realized, according to a new analysis (1) published online ahead of print on October 1, 2012 in Proceedings of the National Academy of Sciences. Here is the abstract of the article:
“A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3%of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ~10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes.”
(1) F. Fang et al. “Misconduct accounts for the majority of retracted scientific publications.” Proceedings of the National Academy of Sciences. Published online before print October 1, 2012, doi: 10.1073/pnas.1212247109
“A detailed review of all 2,047 biomedical and life-science research articles indexed by PubMed as retracted on May 3, 2012 revealed that only 21.3%of retractions were attributable to error. In contrast, 67.4% of retractions were attributable to misconduct, including fraud or suspected fraud (43.4%), duplicate publication (14.2%), and plagiarism (9.8%). Incomplete, uninformative or misleading retraction announcements have led to a previous underestimation of the role of fraud in the ongoing retraction epidemic. The percentage of scientific articles retracted because of fraud has increased ~10-fold since 1975. Retractions exhibit distinctive temporal and geographic patterns that may reveal underlying causes.”
(1) F. Fang et al. “Misconduct accounts for the majority of retracted scientific publications.” Proceedings of the National Academy of Sciences. Published online before print October 1, 2012, doi: 10.1073/pnas.1212247109
Privacy Resources on the Internet
“Privacy Resources and Sites on the Internet” by Marcus P. Zillman, is a comprehensive listing of privacy resources currently available on the Internet. These include associations, indexes, search engines as well as individual websites and sources that supply the latest technology and information about privacy and how it relates to you and the Internet. Here are some of the resources listed: Health Privacy Project, EPIC Online Guide to Privacy Resources, Privacy Rights Clearinghouse.
Source: ResourceShelf Blog
Source: ResourceShelf Blog
August 28, 2012
Summer 2012 issue of Biofeedback is available
In this issue: Chair's Message, Chicago Conference Reports, Book Reviews, Division Awards, and more! Download the PDF.
Science in three dimensions: The print revolution
Three-dimensional printers are opening up new worlds to research. Biologists have been experimenting with printing human cells — either individually or in multi-cell blobs — that fuse together naturally. These techniques have successfully produced blood vessels and beating heart tissue. The ultimate dream of printing out working organs is still a long way off — if it proves possible at all. But in the short term, researchers see potential for printing out 3D cell structures far more life-like than the typical flat ones that grow in a Petri dish.
For example, Organovo, a company based in San Diego, California, has developed a printer to build 3D tissue structures that could be used to test pharmaceuticals. The most advanced model it has created so far is for fibrosis: an excess of hard fibrous tissue and scarring that arises from interactions between an organ's internal cells and its outer layer. The company's next step will be to test drugs on this system. "It might be the case that 3D printing isn't the only way to do this, but it's a good way," says Keith Murphy, a chemical engineer and chief executive of Organovo.
Read the entire story at: http://www.nature.com/news/science-in-three-dimensions-the-print-revolution-1.10939?WT.ec_id=NATURE-20120705
For example, Organovo, a company based in San Diego, California, has developed a printer to build 3D tissue structures that could be used to test pharmaceuticals. The most advanced model it has created so far is for fibrosis: an excess of hard fibrous tissue and scarring that arises from interactions between an organ's internal cells and its outer layer. The company's next step will be to test drugs on this system. "It might be the case that 3D printing isn't the only way to do this, but it's a good way," says Keith Murphy, a chemical engineer and chief executive of Organovo.
Read the entire story at: http://www.nature.com/news/science-in-three-dimensions-the-print-revolution-1.10939?WT.ec_id=NATURE-20120705
Social Media: A Guide for Researchers
This guide http://www.rin.ac.uk/our-work/communicating-and-disseminating-research/social-media-guide-researchers has been produced by by Alan Cann of the Department of Biology at the University of Leicester, and Konstantia Dimitriou and Tristram Hooley of the International Centre for Guidance Studies, and published by the Research Information Network. The guide provides researchers with an understanding of social media, and its possible uses within the research process.
Source: ResourceBlog of the The ResourceShelf Newsletter
Source: ResourceBlog of the The ResourceShelf Newsletter
New Enviro-Health Link pages released
The National Library of Medicine (NLM) Division of Specialized Information Services (SIS) has released two new web guides.
"Epigenomics" http://sis.nlm.nih.gov/enviro/epigenomics.html provides links to resources related to epigenetics and epigenomics, scientific areas focused on changes in the regulation of gene activity and expression which are not dependent on gene sequence.
"Water Pollution" http://sis.nlm.nih.gov/enviro/waterpollution.html directs users to resources on drinking water, water pollution, bottled water, water regulations and standards, disinfection byproducts, and Pharmaceuticals and Personal Care Products as Pollutants (PPCPs).
These resources provide pre-formulated PubMed and TOXNET searches as well as links to related databases and data repositories.
"Epigenomics" http://sis.nlm.nih.gov/enviro/epigenomics.html provides links to resources related to epigenetics and epigenomics, scientific areas focused on changes in the regulation of gene activity and expression which are not dependent on gene sequence.
"Water Pollution" http://sis.nlm.nih.gov/enviro/waterpollution.html directs users to resources on drinking water, water pollution, bottled water, water regulations and standards, disinfection byproducts, and Pharmaceuticals and Personal Care Products as Pollutants (PPCPs).
These resources provide pre-formulated PubMed and TOXNET searches as well as links to related databases and data repositories.
INFO-EXPO in Chicago
The SLA INFO-EXPO is a showcase of the latest industry products and a place to network with top service providers, colleagues and friends. Find out who is exhibiting at SLA 2012!
Chicago Sightseeing Tips
To honor the return of the SLA Annual Conference after 37 years, the SLA Illinois Chapter Members are offering 37 sightseeing ideas for your visit to Chicago.
Chicago Restaurant Guide
To honor the return of the SLA Annual Conference after 37 years, the SLA Illinois Chapter Members are presenting 37 of their favorites restaurants, some haute, some not, with proximity to the conference hotels and convention center (sadly, none in walking distance of McCormick Place for a quick lunch) and good value for the dollar. In these choices we tried to offer a variety of cuisine, ambiance, and local color, but the wealth of Chicago’s eateries lie in the city’s 77 neighborhoods. The attached Google Spreadsheet (SLA 2012 Restaurant Guide) will guide you to our favorites which are further afield.
More information at: http://sla2012.wordpress.com/restaurant-guide
More information at: http://sla2012.wordpress.com/restaurant-guide
May 7, 2012
Spring 2012 issue of Biofeedback is available
In this issue: Chair's Message, Conference Program & Sponsors, Medical Section Report, Book Reviews, and more! Download the PDF.
March 29, 2012
DBIO Program at the Annual Conference
March 29, 2012
SLA Annual Conference
Read more at http://dbiosla.org/events/sla_conference/index.html
HTA in Integrated Care for a Patient Centered System
Workshop: Transforming information services in a changing HTA environment
Join us for a full day pre-conference workshop at the 9th Annual Meeting of HTA in Integrated Care for a Patient Centered System Conference, http://www.htai2012.org/
Content: This workshop will focus on advanced information retrieval and management methods to inform health technology assessment and will be composed of four sessions:
Rapid review methodologies and processes - a comparison between IHE and CADTH
Social and demographic search strategy techniques
A review of international resource sharing agreements, copyright and cost containment strategies
Information services for patient-centred care - the evolution of Spanish health libraries
Speakers:
• Liz Dennett, Institute of Health Economics
• Dagmara Chojecki, Institute of Health Economics
• David Kaunelis, Canadian Agency for Drugs and Technologies in Health (CADTH)
• Catherine Voutier, Melbourne Health
• Sigrid Droste, Institute for Quality and Efficiency in Healthcare (IQWiG)
• Rocío Rodríguez López, Andalusian Agency for Health Technology Assessment (AETSA)
Venue: Euskalduna Conference Centre and Concert Hall, Bilbao, Spain
Date: Sunday June 24th, 2012
Organiser: The Information Resources Group of HTAi
Pre-conference workshops are open both to members and non-members of HTA
COST: 100 Euro before April 30; 110 Euro after April 30
HTAI Member Registration: https://ercisa.eventszone.net/myCongress5/form.php?thisFormCongress=htai2012&thisFormLanguage=en
Non HTAi Members – please email registration@htai2012.com
For more information, please contact Catherine Voutier, HTAi Information Resources Group Chair: catherine.voutier@mh.org.au
Join us for a full day pre-conference workshop at the 9th Annual Meeting of HTA in Integrated Care for a Patient Centered System Conference, http://www.htai2012.org/
Content: This workshop will focus on advanced information retrieval and management methods to inform health technology assessment and will be composed of four sessions:
Speakers:
• Liz Dennett, Institute of Health Economics
• Dagmara Chojecki, Institute of Health Economics
• David Kaunelis, Canadian Agency for Drugs and Technologies in Health (CADTH)
• Catherine Voutier, Melbourne Health
• Sigrid Droste, Institute for Quality and Efficiency in Healthcare (IQWiG)
• Rocío Rodríguez López, Andalusian Agency for Health Technology Assessment (AETSA)
Venue: Euskalduna Conference Centre and Concert Hall, Bilbao, Spain
Date: Sunday June 24th, 2012
Organiser: The Information Resources Group of HTAi
Pre-conference workshops are open both to members and non-members of HTA
COST: 100 Euro before April 30; 110 Euro after April 30
HTAI Member Registration: https://ercisa.eventszone.net/myCongress5/form.php?thisFormCongress=htai2012&thisFormLanguage=en
Non HTAi Members – please email registration@htai2012.com
For more information, please contact Catherine Voutier, HTAi Information Resources Group Chair: catherine.voutier@mh.org.au
February 9, 2012
Winter 2012 issue of Biofeedback is available
In this issue: Chair's Message, Election Results, Webinar Series, Medical Section Report, Book Reviews, and more! Download the PDF.
JSTOR-opens-limited-free-access-option
Unsubscribed visitors will be allowed to check out three “items” from the JSTOR archive every two weeks, which they will be able to read for free. In order to prevent piracy, the texts will be displayed as image files (so that text cannot be copied). Users will not be able to download the files.
Read more at: http://www.insidehighered.com/news/2012/01/13/jstor-opens-limited-free-access-option-non-subscribing-scholars#ixzz1jRdqEyfGInside Higher Ed
Read more at: http://www.insidehighered.com/news/2012/01/13/jstor-opens-limited-free-access-option-non-subscribing-scholars#ixzz1jRdqEyfGInside Higher Ed
Bubblegram imaging: Novel approach to view the inner structure of a virus
Researchers at the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), part of NIH, working in collaboration with the group of Dr. Lindsay Black at the University of Maryland Medical School, Baltimore, have solved the problem of seeing inside viruses. They have developed a new way to see structures within viruses that were not clearly seen before. Their findings are reported in the Jan. 13 issue of Science (1).
"We first used low doses of radiation and recorded images in which the inner structure of the virus was invisible," said Dr. Steven (NIAMS). "Next, we used high doses of radiation, and found that the inner structure could be seen as a cylinder of bubbles." While the inner structure was damaged, the team was able to superimpose the images, using three-dimensional computer reconstruction. As a result, they were able to clearly visualize the viral structure. The investigators call this technique bubblegram imaging.
For more information on the NIAMS Laboratory of Structural Biology Research, visit
http://www.niams.nih.gov/Research/Ongoing_Research/Branch_Lab/Structural_Biology/default.asp.
The html version of this release contains images of a virus and blow-up of inner virus structure at
http://www.niams.nih.gov/News_and_Events/Press_Releases/2012/inner_workings_virus.jpg .
(1) Wu, Weimin, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, and Alasdair C. Steven. 2012. Bubblegrams Reveal the Inner Body of Bacteriophage. Science 335(6065): 182.
"We first used low doses of radiation and recorded images in which the inner structure of the virus was invisible," said Dr. Steven (NIAMS). "Next, we used high doses of radiation, and found that the inner structure could be seen as a cylinder of bubbles." While the inner structure was damaged, the team was able to superimpose the images, using three-dimensional computer reconstruction. As a result, they were able to clearly visualize the viral structure. The investigators call this technique bubblegram imaging.
For more information on the NIAMS Laboratory of Structural Biology Research, visit
http://www.niams.nih.gov/Research/Ongoing_Research/Branch_Lab/Structural_Biology/default.asp.
The html version of this release contains images of a virus and blow-up of inner virus structure at
http://www.niams.nih.gov/News_and_Events/Press_Releases/2012/inner_workings_virus.jpg .
(1) Wu, Weimin, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, and Alasdair C. Steven. 2012. Bubblegrams Reveal the Inner Body of Bacteriophage. Science 335(6065): 182.
IBM Releases Tool for finding Patents with Molecular and Chemical Data
A new analytical tool, called SIIP, from IBM is helping scientists scan patents for information about molecular data and chemical information. SIIP housed in the IBM SmartCloud, processes documents in the U.S. Patent and Trademark Office, the European Patent Office and the World Intellectual Property Organization, as well as the public domain Relevant Products/Services documents in the U.S. National Library of Medicine's MEDLINE database. SIIP uses image analysis and enhanced optical recognition of chemical images and symbols to quickly obtain the information, a process that otherwise could take months to do manually. SIIP was originally developed for IBM'S own use, and it has been used by hundreds of experts in the company for management and licensing. The company said that many top life-sciences companies also use SIIP because of its special focus on sifting patents for biological and chemical information. SIIP is only available by subscription. IBM Global Business Services also provides consulting services for clients using SIIP. More information about IBM SIIP is available at http://www-935.ibm.com/services/us/gbs/bao/siip/
Because of the value of the retrieved information to the scientific community, IBM has donated to the National Institutes of Health an SIIP-created database of more than 2.5 million unique chemical compounds, along with the references in the literature. The database, extracted from millions of patents and scientific documents, is expected to allow medical researchers to more readily understand relationships between chemical compounds.
Credit: ResourceBlog
Read more at:
http://www.cio-today.com/news/IBM-Tool-Scans-Patents-for-Key-Data/story.xhtml?story_id=13000C0BFI9U&full_skip=1
and
http://www-03.ibm.com/press/us/en/pressrelease/36181.wss
New Journal for Biology Researchers Edited by Researchers
Scientists unhappy with the power of editors at top tier journals start a new peer-reviewed publication with active researchers at the helm. eLife, the new top-tier, open-access research journal will be launched in 2012 with the support of the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust.
Editor-in-chief Randy Schekman, former editor in-chief of Proceedings of the National Academy of Sciences, and managing executive editor Mark Patterson, previously the Director of Publishing at PLoS, will be joined by deputy editors, Fiona Watt, currently at the University of Cambridge, UK, and Detlef Weigel from the Max Planck Institute for Developmental Biology, Tubingen, Germany. They will be supported by around 15-20 senior editors – researchers who represent a broad range of biomedical and life science research fields.
The first issue of eLife is expected late next year. The journal will utilize the Creative Commons Attribution 3.0 license (CC BY 3.0) so that the content can be shared and used without restriction.
Randy Schekman, a cell biology researcher at the University of California is launching this new open access journal, which is run strictly by active researchers in an attempt to address some of the complaints about scientific publishing. Although there are many specialist journals headed by scientists, the top tier publications are often run by professional editors who do not work in a lab, and who do not moderate the peer-review process. Many researchers have complained that their manuscripts are rejected on the opinion of one reviewer, even when the remaining two reviews are glowing. To stem this problem Schekman plans to have referees discuss their opinions in a private online forum and come to a consensus—a process mediated by the senior editor—ideally within a month of the paper’s submission.
Read more at: http://www.hhmi.org/news/elife20111107.html
and
http://wellcometrust.wordpress.com/2011/11/07/elife-a-journal-by-scientists-for-scientists/
Editor-in-chief Randy Schekman, former editor in-chief of Proceedings of the National Academy of Sciences, and managing executive editor Mark Patterson, previously the Director of Publishing at PLoS, will be joined by deputy editors, Fiona Watt, currently at the University of Cambridge, UK, and Detlef Weigel from the Max Planck Institute for Developmental Biology, Tubingen, Germany. They will be supported by around 15-20 senior editors – researchers who represent a broad range of biomedical and life science research fields.
The first issue of eLife is expected late next year. The journal will utilize the Creative Commons Attribution 3.0 license (CC BY 3.0) so that the content can be shared and used without restriction.
Randy Schekman, a cell biology researcher at the University of California is launching this new open access journal, which is run strictly by active researchers in an attempt to address some of the complaints about scientific publishing. Although there are many specialist journals headed by scientists, the top tier publications are often run by professional editors who do not work in a lab, and who do not moderate the peer-review process. Many researchers have complained that their manuscripts are rejected on the opinion of one reviewer, even when the remaining two reviews are glowing. To stem this problem Schekman plans to have referees discuss their opinions in a private online forum and come to a consensus—a process mediated by the senior editor—ideally within a month of the paper’s submission.
Read more at: http://www.hhmi.org/news/elife20111107.html
and
http://wellcometrust.wordpress.com/2011/11/07/elife-a-journal-by-scientists-for-scientists/
Rev. December 2012