This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts. (+info)
Development and preliminary evaluation of the VPS ReplaySuite: a virtual double-headed microscope for pathology.
(18/75)
BACKGROUND: Advances in computing and telecommunications have resulted in the availability of a range of online tools for use in pathology training and quality assurance. The majority focus on either enabling pathologists to examine and diagnose cases, or providing image archives that serve as reference material. Limited emphasis has been placed on analysing the diagnostic process used by pathologists to reach a diagnosis and using this as a resource for improving diagnostic performance. METHODS: The ReplaySuite is an online pathology software tool that presents archived virtual slide examinations to pathologists in an accessible video-like format, similar to observing examinations with a double-headed microscope. Delivered through a customized web browser, it utilises PHP (Hypertext PreProcessor) to interact with a remote database and retrieve data describing virtual slide examinations, performed using the Virtual Pathology Slide (VPS). To demonstrate the technology and conduct a preliminary evaluation of pathologists opinions on its potential application in pathology training and quality assurance, 70 pathologists were invited to use the application to review their own and other pathologists examinations of 10 needle-core breast biopsies and complete an electronic survey. 9 pathologists participated, and all subsequently completed an exit survey. RESULTS: Of those who replayed an examination by another pathologist, 83.3% (5/6) agreed that replays provided an insight into the examining pathologists diagnosis and 33.3% (2/6) reconsidered their own diagnosis for at least one case. Of those who reconsidered their original diagnosis, all re-classified either concordant with group consensus or original glass slide diagnosis. 77.7% (7/9) of all participants, and all 3 participants who replayed more than 10 examinations stated the ReplaySuite to be of some or great benefit in pathology training and quality assurance. CONCLUSION: Participants conclude the ReplaySuite to be of some or of great potential benefit to pathology training and quality assurance and consider the ReplaySuite to be beneficial in evaluating the diagnostic trace of an examination. The ReplaySuite removes temporal and spatial issues that surround the use of double-headed microscopes by allowing examinations to be reviewed at different times and in different locations to the original examination. While the evaluation set was limited and potentially subject to bias, the response of participants was favourable. Further work is planned to determine whether use of the ReplaySuite can result in improved diagnostic ability. (+info)
Use of history science methods in exposure assessment for occupational health studies.
(19/75)
AIMS: To show the power of history science methods for exposure assessment in occupational health studies, using the dry cleaning industry in Denmark around 1970 as the example. METHODS: Exposure data and other information on exposure status were searched for in unconventional data sources such as the Danish National Archives, the Danish Royal Library, archives of Statistics Denmark, the National Institute of Occupational Health, Denmark, and the Danish Labor Inspection Agency. Individual census forms were retrieved from the Danish National Archives. RESULTS: It was estimated that in total 3267 persons worked in the dry cleaning industry in Denmark in 1970. They typically worked in small shops with an average size of 3.5 persons. Of these, 2645 persons were considered exposed to solvents as they were dry cleaners or worked very close to the dry cleaning process, while 622 persons were office workers, drivers, etc in shops with 10 or more persons. It was estimated that tetrachloroethylene constituted 85% of the dry cleaning solvent used, and that a shop would normally have two machines using 4.6 tons of tetrachloroethylene annually. CONCLUSION: The history science methods, including retrieval of material from the Danish National Archives and a thorough search in the Royal Library for publications on dry cleaning, turned out to be a very fruitful approach for collection of exposure data on dry cleaning work in Denmark. The history science methods proved to be a useful supplement to the exposure assessment methods normally applied in epidemiological studies. (+info)
Communication and re-use of chemical information in bioscience.
(20/75)
The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective. (+info)
Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.
(21/75)
A direct impediment to the optimal use of online databases is the increasing prevalence, severity, and toll of computer and network security incidents. Funding agencies should set up working groups that can provide essential services such as universal backup, archival storage, and mirroring of community resources, consistent with the key goal of security in academia: to preserve data and results for posterity. (+info)
Going, going, still there: using the WebCite service to permanently archive cited web pages.
(22/75)
Scholars are increasingly citing electronic "web references" which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To "webcite" a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its "instructions for authors" accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) "prospectively" before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted "citing articles" (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. (+info)
Physical and mental health costs of traumatic war experiences among Civil War veterans.
(23/75)
BACKGROUND: Hundreds of thousands of soldiers face exposure to combat during wars across the globe. The health effects of traumatic war experiences have not been adequately assessed across the lifetime of these veterans. OBJECTIVE: To identify the role of traumatic war experiences in predicting postwar nervous and physical disease and mortality using archival data from military and medical records of veterans from the Civil War. DESIGN: An archival examination of military and medical records of Civil War veterans was conducted. Degree of trauma experienced (prisoner-of-war experience, percentage of company killed, being wounded, and early age at enlistment), signs of lifetime physician-diagnosed disease, and age at death were recorded. SETTING AND PARTICIPANTS: The US Pension Board surgeons conducted standardized medical examinations of Civil War veterans over their postwar lifetimes. Military records of 17,700 Civil War veterans were matched to postwar medical records. MAIN OUTCOME MEASURES: Signs of physician-diagnosed disease, including cardiac, gastrointestinal, and nervous disease; number of unique ailments within each disease; and mortality. RESULTS: Military trauma was related to signs of disease and mortality. A greater percentage of company killed was associated with signs of postwar cardiac and gastrointestinal disease (incidence risk ratio [IRR], 1.34; P < .02), comorbid nervous and physical disease (IRR, 1.51; P < .005), and more unique ailments within each disease (IRR, 1.14; P < .005). Younger soldiers (<18 years), compared with older enlistees (>30 years), showed a higher mortality risk (hazard ratio, 1.52), signs of comorbid nervous and physical disease (IRR, 1.93), and more unique ailments within each disease (IRR, 1.32) (P < .005 for all), controlling for time lived and other covariates. CONCLUSIONS: Greater exposure to death of military comrades and younger exposure to war trauma were associated with increased signs of physician-diagnosed cardiac, gastrointestinal, and nervous disease and more unique disease ailments across the life of Civil War veterans. Physiological mechanisms by which trauma might result in disease are discussed. (+info)
Detection of EGFR mutations in archived cytologic specimens of non-small cell lung cancer using high-resolution melting analysis.
(24/75)
Mutations of the epidermal growth factor receptor (EGFR), particularly deletional mutations (DEL) in exon 19 and L858R in exon 21, are reportedly correlated with clinical outcome in patients with non-small cell lung cancer (NSCLC) receiving the EGFR tyrosine kinase inhibitors gefitinib and erlotinib, suggesting that detection of EGFR mutations would have an important role in clinical decision making. We established and validated an easy, inexpensive, and rapid method for detecting DEL and L858R from cytologic material by high-resolution melting analysis (HRMA). Dilution for sensitivity studies revealed that DEL and L858R were detectable in the presence of at least 10% and 0.1% EGFR-mutant cells, respectively. We analyzed 37 archived cytological slides of specimens from 29 patients with advanced NSCLC and compared the results with direct sequencing data obtained previously. Of 37 samples, 34 (92%) yielded consistent results with direct sequencing, 2 were false negative, and 1 was indeterminate. The sensitivity of this analysis was 90% (19/21) and specificity, 100% (15/15). These results suggest that HRMA of archived cytologic specimens of advanced NSCLC is useful for detecting EGFR mutations in clinical practice. (+info)