From a November 24 Medlib-L(medical librarian)posting
The Bioethics Research Library at Georgetown (BRL) has developed a 1-minute Adobe Captivate tutorial for utilizing PubMed’s bioethics subset limit. This tutorial is available both as a Flash file (http://bioethics.georgetown.edu/databases/howtosearch/) and as a Vimeo video (http://vimeo.com/16661510) BRL also has developed tutorials for its ETHXWeb (covers most topics in bioethics), GenETHX (covers human genetics and ethics topics), International Bioethics Organizations, and Syllabus Exchange databases. The GenETHX tutorial demonstrates accessing the Bioethics Thesaurus Database to identify appropriate search terms for complex concepts. Bioethics Thesaurus terms, many of which are included in MeSH, are useful for refining searches as well as for creating bioethics keyword tags for online documents. Links to the BRL database tutorials can be found at: http://bioethics.georgetown.edu/databases/howtosearch/ An Express Library Technology Improvement Award from the Southeastern/Atlantic Region of the National Network of Libraries of Medicine enabled BRL to develop these tutorials. Kathleen Schroeder, M.D., M.S.I Subject Specialist, Science and Technology Bioethics Research Library, Georgetown University
More than 72,000 clinical photographs illustrate age-related eye disease progression
The National Institutes of Health has expanded a genetic and clinical research database to give researchers access to the first digital study images. The National Eye Institute (NEI), in collaboration with the National Center for Biotechnology Information (NCBI), has made available more than 72,000 lens photographs and fundus photographs of the back of the eye, collected from the participants of the Age-Related Eye Disease Study (AREDS).
These images are now accessible to scientists through NCBI’s online database of Genotypes and Phenotypes, known as dbGaP, which archives data from studies that explore the relationship between genetic variations (genotype) and observable traits (phenotype). Though study descriptions and protocols are publicly accessible, researchers must apply for controlled access to de-identified information about study subjects, including the new images….
…Open-access AREDS data and a link to apply for controlled access to individual-level data, including the new images, can be found on the NEI-AREDS study page athttp://www.ncbi.nlm.nih.gov/gap.
New flow cytometer will help in fight against cancer, asthma, cardiovascular, autoimmune and infectious diseases
A world-first research system to be launched today at the Centenary Institute will give medical researchers in Australia a new weapon in the fight against cancer and other life-threatening diseases. The new BD LSR-9 Flow Cytometer with its nine lasers will be the first user-operated flow cytometer with unprecedented ability to detect and analyse rare cells.
The BD LSR9 Flow Cytometer will be housed at the Centenary Institute as part of the Advanced Cytometry Facility (ACF), which is a joint venture run by the Centenary Institute, the University of Sydney and the Bosch Institute.
Advanced Cytometry Facility Academic Director Professor Nick King said: “Currently, a researcher may have to run a sample of cells two or three times using complex labelling systems to analyse all the unique characteristics of a cell. This makes it very difficult to detect rare cell populations. It’s like a detective at a crime scene gathering two or three sets of partial fingerprints then having to cobble them together to get a complete fingerprint….
About Flow Cytometry
A flow cytometer allows researchers to rapidily analyse large populations of cells. Individual cells are examined and a wide variety of properties of each cell can be recorded. Researchers tag the cell populations with fluorescent dyes and then use the flow cytometer to a pass the cells through a beam of laser light one at a time. This laser light is scattered by the cells and provides a way to measure physical properties of the cell such as size. The laser also excites the different fluorescent dyes attached to cells. These dyes produce light of different colours and allow the researchers to count and analyse the cell types that are present. By examining the cells one by one, researchers can find minute characteristics of the cells to get an accurate profile of rare disease-causing cells.###
About the Centenary Institute: The Centenary Institute is an independent medical research institute, affiliated with Royal Prince Alfred Hospital and the University of Sydney. Our unique blend of highly skilled staff and state-of-the art equipment and facilities has allowed us to become world leaders in three critical areas of medical research – cancer, cardiovascular disease and infectious diseases. For further information about the Centenary Institute, visit www.centenary.org.au
The report reviews the published and grey literature on international variation in the use of medicines in six areas (osteoporosis, atypical anti-psychotics, dementia, rheumatoid arthritis, cardiovascular disease/lipid-regulating drugs (statins), and hepatitis C).
We identify three broad groups of determinants of international variation in medicines use:
(1) Macro- or system level factors: Differences in reimbursement policies, and the role of health technology assessment, were highlighted as a likely driving force of international variation in almost all areas of medicines use reviewed. A related aspect is patient co-payment, which is likely to play an important role in the United States in particular. The extent to which cost-sharing policies impact on overall use of medicines in international comparison remains unclear.
(2) Service organisation and delivery: Differences in access to specialists are a likely driver of international variation in areas such as atypical anti-psychotics, dementia, and rheumatic arthritis, with for example access to and availability of relevant specialists identified as acting as a crucial bottleneck for accessing treatment for dementia and rheumatoid arthritis.
(3) Clinical practice: Studies highlighted the role of variation in the use and ascertainment methods for mental disorders; differences in the use of clinical or practice guidelines; differences in prescribing patterns; and reluctance among clinicians in some countries to take up newer medicines.
Each of these factors is likely to play a role in explaining international variation in medicines use, but their relative importance will vary depending on the disease area in question and the system context.
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More than 2.5 million images and figures from medical and life sciences journals are now available through Images, a new resource for finding images in biomedical literature. The database was developed and will be maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM) at the National Institutes of Health. Images is available at http://www.ncbi.nlm.nih.gov/images.
Images is expected to have a wide range of uses for a variety of user groups. These include the clinician looking for the visual representation of a disease or condition, the researcher searching for studies with certain types of analyses, the student seeking diagrams that elucidate complex processes such as DNA replication, the professional or educator looking for an image for a presentation, and the patient wanting to better understand his disease.
“Rapid and easy access to images in the biomedical literature should help scientists and others more quickly identify content of interest,” said NCBI Director David Lipman, M.D. “We believe that the new database will be useful for the discovery process, as well as for educational and professional purposes.”
The initial content of Images reflects images and figures contained in NCBI’s PubMed Central full-text digital archive of biomedical and life sciences journal literature, located at http://www.ncbi.nlm.nih.gov/pmc. Images content may be expanded in the future to include other NCBI full-text resources, such as NCBI’s Bookshelf database of biomedical books and reports, at http://www.ncbi.nlm.nih.gov/books.
The Images database enables users to search images based on keywords and a variety of other parameters, such as author and publication date. Images and data can be easily saved to users’ collections and shared with others through the use of My NCBI, a feature that allows users of NCBI resources to customize their search and display preferences, save and share searches, build bibliographies, and perform a variety of other functions.
NCBI creates public databases in molecular biology, conducts research in computational biology, develops software tools for analyzing molecular and genomic data, and disseminates biomedical information, all for the better understanding of processes affecting human health and disease. NCBI (www.ncbi.nlm.nih.gov) is a division of the National Library of Medicine (www.nlm.nih.gov), the world’s largest library of the health sciences.
The National Institutes of Health (NIH) — The Nation’s Medical Research Agency — includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visitwww.nih.gov.
From the October 21 NCBI announcement
The National Center for Biotechnology Information (NCBI) has developed a new tool to help scientists understand how differences in DNA sequences contribute to human health and disease.
The Database of Genomic Structural Variation, or dbVar, will help track large-scale variations in DNA sequences discovered in healthy individuals as well as people with conditions such as autism and cancer. The database also contains comparative data on wide variety of organisms, including plants and livestock, that are important to agriculture.
The human genome is made up of approximately 3 billion base pairs of DNA arranged into 23 chromosomes. In recent years, scientists have discovered that very large stretches of the genome can be rearranged, duplicated, or deleted. Some of these variations may be associated with disorders such as Down syndrome, while others do not have apparent impact on health. dbVar is one of several tools scientists can use to understand how genomic variations play a role in disease or affect a person’s characteristics.
“An enormous volume of data is now coming from studies that investigate genetic variation,” says NCBI Director, David Lipman, MD. “We are excited to be playing a role in this important area of scientific inquiry by making the data widely available to scientists and integrating it with other National Library of Medicine research tools and the scientific literature.”
dbVar was officially launched in September 2010. The database is part of an international collaboration that includes the recently-launched Database of Genomic Variants archive (DGVa) at the European Bioinformatics Institute (EBI) and theDatabase of Genomic Variants (DGV) in Toronto. The databases are detailed in the October 2010 issue of Nature Genetics.
Members of the dbVar team are Deanna M. Church, John Garner, Timothy Hefferon, John Lopez, and Azat Mardanov.
The Registry of Open Access Repositories (ROAR) exists to promote the development of open access by providing up to date information about repositories of information worldwide.
- Search page (options include country of origin, subjects [medical and non medical] as psychology, internal medicine, dermatology, nursing, environmental sciences, textbooks), keyword entry by user as description and title
- Browse registry with options country, year, repository type (as research, e-theses), and repository software
PubMed Abstracts of biomedical articles will soon include images included in the articles.
The PubMed (**)Abstract display for PubMed Central® (***)articles will be enhanced to include an image strip generated from the soon-to-be-released National Center for Biotechnology Information (NCBI)(****) Images database…
…The image strip will display thumbnails of the article’s first several images. The image strip will also include a See all images link to display all the article’s images in the Images databases, as well as a Free text link to the article. Right and left arrows on each end of the strip will allow you to rotate through the images.
Mousing over an image in the image strip will generate a preview display of the image with its figure caption . Click on the image in the image strip, or the mouseover preview display, and go directly to the figure’s page in PubMed Central….
The Images database will allow you to search millions of scientific images from NCBI full text resources; the database initially includes images from PubMed Central..
….You will be able to search the Images database with terms or detailed search parameters, such as image height, width, and caption. The complete list of search fields is available from the Images Advanced search page. Image results initially display in a summary format (see Figure 4) but may also be viewed in a thumbnail display. Retrieval display order is based on a relevancy algorithm.
**PubMed is the largest indexer of biomedical journal articles in the world. The home page includes links on how to search (tutorials, quick start guide). For further searching assistance, consider consulting with a public, academic, or medical reference librarian. Many articles indexed by PubMed are not freely available on the Internet. Again, check with a local public, academic, or medical library for access to journal articles. The library may charge a fee for some articles.
***PubMedCentral is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature. It is part of the PubMed database (index).
****NCBI (National Center for Biotechnology Information) advances science and health by providing access to biomedical and genomic information. It includes PubMed and PubMedCentral.
[Editor Flahiff’s note: Many postings in this blog, especially Reuters and Health Day press releases, are based on articles indexed in PubMed]
Access to the Occupational Therapy Database(OTD) is free from October 17th to the 23rd.
According to the About page , it is a “a Canadian-based and Canadian-developed occupational therapy journal literature search service”.
The publishers state it “contains over 9000 abstracts from more than 20 global OT journals since 1970″.
A list of the indexed journals may be found here.
Many academic and medical libraries have a paid subscription to OTD. Call ahead and ask for a reference librarian to answer questions about using it (for free) at their library (as the availability of a printer for the public). You may also consider inquiring about other fee-based medical and scientific research databases that might be available (for free) to the public who come to their library.
From the blog Open Medicine dated October 4th, 2010
Bastian H, Glasziou P, Chalmers I (2010) Seventy-Five Trials and Eleven Systematic Reviews a Day: How Will We Ever Keep Up? PLoS Med 7(9): e1000326. doi:10.1371/journal.pmed.1000326
Published: September 21, 2010
- When Archie Cochrane reproached the medical profession for not having critical summaries of all randomised controlled trials, about 14 reports of trials were being published per day. There are now 75 trials, and 11 systematic reviews of trials, per day and a plateau in growth has not yet been reached.
- Although trials, reviews, and health technology assessments have undoubtedly had major impacts, the staple of medical literature synthesis remains the non-systematic narrative review. Only a small minority of trial reports are being analysed in up-to-date systematic reviews. Given the constraints, Archie Cochrane’s vision will not be achieved without some serious changes in course.
- To meet the needs of patients, clinicians, and policymakers, unnecessary trials need to be reduced, and systematic reviews need to be prioritised. Streamlining and innovation in methods of systematic reviewing are necessary to enable valid answers to be found for most patient questions. Finally, clinicians and patients require open access to these important resources. [editor Flahiff’s emphasis]
If the results of a clinical study are published in a scientific journal, PubMed is the best way to search for information about the article. If you are having challenges searching PubMed, consider the tutorial at the home page of PubMed. You may also ask a reference librarian at a local public, academic, or medical library. Call ahead to see what level of assistance they offer.
Clinicaltrials.gov has the voluntary summaries of some clinical trials. Advanced search has the option Study results (select Studies With Results). Some results may be labelled “proprietary” (information not released to the public, sometimes called “industry secrets” ).
[Related to recent posting here Access to Knowledge for Consumers]
Excerpts from the interview with Melissa Hagemann about the Open Access Movement.
She is program manager in the Open Society Foundations Information Program. She’s also on the advisory board of theWikimedia Foundation, which operates Wikipedia
What is “Open Access”?
Open Access refers to the free online availability of research literature. It was first defined at a meeting organized by the Open Society Foundations in 2001, which led to the Budapest Open Access Initiative. This initiative outlined two strategies for developing OA:
- Open Access Journals, which are journals, freely available worldwide, which do not rely upon the traditional subscription-based business model to generate their revenue; and
- Open Repositories, or archives where all scholarly research articles published by those associated with a university or within a discipline can be deposited.
In 2003, we added a third strategy, which is to advocate for public access to publicly funded research.
What are some of the most notable accomplishments of the open access movement so far?
Probably the single most important victory was a mandate adopted by the U.S. Congress which stipulates that all research funded by the National Institutes of Health (about $29 billion annually) be made freely available online.
While the NIH is the largest funder of research in the world, the OA movement has worked with governments and universities throughout the world to adopt similar mandates, and today there are 230 of them. In addition, there are over 5,500 OA journals and over 1,700 open repositories.
What major obstacles does the movement face at this moment?
As Open Access is so new, one of our main challenges is simply raising awareness of it and explaining the benefits of this new model. At the same time, you can imagine that many within the publishing industry haven’t always been keen supporters of OA.
But I’m curious: How can the publishing industry benefit from Open Access? Wouldn’t they say they need the money to continue publishing? How do you persuade them that OA is a good thing?
While OA journals are freely available online, about half of them charge a processing fee (anywhere from $500 to $3,000 or so) per article. So there are commercial OA journal publishers which are doing quite well. Actually one of the largest OA publishers, BioMed Central, was purchased by Springer (the second largest scientific journal publisher) in 2008, and Springer pledged to keep all of the journals OA.
How can others get involved in advancing the issue?
Participating in an event during OA week is a great way to start! Then I would suggest learning more about OA, and OASIS is one of the best resources for information on the OA movement.
- If you’re a student, I recommend connecting with the Right to Research Coalition.
- If you’re an academic, you can self-archive copies of your research articles in your institutional repository or submit your article to anOA journal. You can also advocate for your institution to adopt an OA mandate at your university; 230 mandates have been adopted worldwide (see www.eprints.org/openaccess/policysignup).
- If you’re in a developing or transition country, the EIFL Open Access Program offers a wealth of support and services for librarians, academics, policymakers, and funders in these countries to tap into.
- If you’re based in the United States, you can support the Alliance for Taxpayer Access, which advocates for public access to publicly funded research in the U.S.
Many health news items posted here are derived from copyrighted material, including articles from biomedical journals.
Of course, many biomedical journals provide (as the New England Journal of Medicine) provide portions of their journals free of charge online. Quite a few biomedical journals allow free access to articles older than a specified time (as 6 month, 1 year, 2 years).
Recently Released by Consumers International: “Access to Knowledge for Consumers”
October 15, 2010 00:07
Information Program grantee [from the Open Society Initiatives]Consumers International has released the results of a global survey designed to expose the obstacles consumers face in gaining access to education and cultural materials. The survey was conducted in 13 languages, covering 15,000 consumers across 24 countries.
The survey found that “The biggest barriers that consumers face in accessing copyright works are those created by copyright law. Even so, consumers around the world will choose original copyright works over pirated copies, provided that they are available at an affordable price.”
[Editor Flahiff’s emphasis]
While borrowing from libraries and other cultural institutions provided a viable alternative for some consumers priced out of original copyrighted works, the survey found that, particularly in developing countries, “access to libraries is limited and the works they carry are few.” [Editor Flahiff’s note…She saw this first hand during a short Peace Corps service project trip to Liberia, West Africa in May 2009 ]Although the authors of the survey saw “copyleft” initiatives like Open Educational Resources and Free and Open Source Software as great ways to help consumers vault access barriers, they concluded that governments needed to act “to address consumers’ needs for lower cost original materials to buy, borrow and access online.”
The purpose of this book is to provide an accessible introduction to the A2K movement and the institutions, concepts and issues involved in it, for those who would like to become involved but don’t know where to start. In a truly collaborative exercise, information from various freely-licensed sources has been combined with text especially written for this book, and the whole has been made available for you to freely copy, share and modify.
The Faculty of 1,000 has a prototype site for their new open access F1000 Posters. This site will be a repository of posters from across the life sciences and medicine. Submissions are voluntary, but will only be included after a review process. In the future the site will have improved viewing of the posters, interactive tools, and full search capabilities.
From the Web site
ABOUT F1000 POSTERS
Our aim in building F1000 Posters is to give poster presenters and supporting societies the opportunity to make their work known to a wider audience. It will also enable much greater discussion on new research, hopefully opening up opportunities for new collaborations which will help advance scientific research as a whole. Posters deposited here will be reviewed by our world-renowned Faculty who will select posters that they consider to be particularly interesting and important and write evaluations for inclusion in our award-winning F1000 evaluation service.
A LOST RESOURCE
The early scientific information presented in conference posters is universally agreed to be an important resource but, unfortunately, it is almost always completely lost once a conference is over. As a result, posters are only viewed by a handful of people before they disappear, either forever or until the research is later published as a paper. Some important work may never get published, particularly if it focuses on negative results or case studies. The system of removing posters from view after a conference is over represents a vast loss to the scientific community of unique and potentially valuable information.
Posters advertising Faculty of 1000
- A4 size –http://f1000posters.com/doc/F1000_Posters_A4.pdf;
- A3 size –http://f1000posters.com/doc/F1000_Posters_A3.pdf
- US letter size – http://f1000posters.com/doc/F1000_Posters_USLetter.pdf
For more information, contact Faculty of 1000, firstname.lastname@example.org
They have other options, including
* We would be happy to send you professionally printed copies of the
posters – just tell us which size you prefer – small (A4) or large (A3)
– and the best mailing address to use
* We could send you banner-type versions of these posters to put on your
institutional pages as appropriate (or simply some text and a logo) –
just tell us what you require
* Additionally, do you know of any students who might be keen to earn a
little extra money by putting up a whole series of posters around all
the relevant departments on your campus? We would then mail them a
whole batch of printed posters.
- First articles now live on F1000 Research (eurekalert.org)