Digital knowledge.
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Information Dissemination↗
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Computer Communication Networks↗
Quantitative microscopy after fluorescence in situ hybridization - a comparison between repeat-depleted and non-depleted DNA probes.
Complex probes used in fluorescence in situ hybridization (FISH) usually contain repetitive DNA sequences. For chromosome painting, in situ suppression of these repetitive DNA sequences has been well established. Standard painting protocols require large amounts of an unlabeled 'blocking agent', for instance Cot-1 DNA. Recently, it has become possible to remove repetitive DNA sequences from library probes by means of magnetic purification and affinity PCR. Such a 'repeat depleted library probe' was hybridized to the q-arm of chromosome 15 of human metaphase spreads and interphase cell nuclei without any preannealing by Cot-1 DNA. Apart from this, 'standard' FISH conditions were used. After in situ hybridization, microscope images were obtained comparable to those achieved with the #15q library probe prior to depletion. The images were recorded by a true color CCD camera. By digital image analysis using 'line scan' and 'area scan' procedures, the painting efficiency expressed in terms of relative fluorescence signal intensity was quantitatively evaluated. The painting efficiency using the repeat depleted probe of chromosome 15q was compared to the painting efficiency after standard FISH. The results indicate that both types of probes are compatible to a high FISH efficiency. Using equivalent probe concentrations, no significant differences were found for FISH with standard painting probes and repeat depleted painting probes.
Cell Nucleus↗
Physical mapping of chromosome 17 cosmids by fluorescence in situ hybridization and digital image analysis.
We used fluorescence in situ hybridization and digital image analysis to localize cosmids along human chromosome 17. Seventy-one cosmids were selected at random from a chromosome 17 library constructed from a partial Sau3AI digest of flow-sorted chromosomes from a mouse-human hybrid cell line. Sixty-three of these (89%) gave a signal only on chromosome 17. The 40 cosmids producing the most distinct hybridization signals in metaphase and interphase cells were precisely mapped using digital image analysis. An additional 20 cosmids, previously mapped by linkage analysis, were also mapped. The order of these probes determined by metaphase mapping was consistent with the order determined by linkage analysis.
Chromosome Mapping↗
E-oncology and health portals: instructions and standards for the evaluation, production organisation and use.
In 2002 the Italian Ministry of Health promoted the institution of a network and a web portal, E-oncology (2), for the seven NHS research institutions specialising in oncology (Istituti di Ricovero e Cura a Carattere Scientifico-IRCCS). One of the aims was to gather and provide information on tumoral pathologies to operators and the public. For an optimum organisation of a health web site it is necessary to comply with the standards internationally used. The World Wide Web Consortium (W3C) has developed guidelines for accessibility and usability of the sites, implemented in Italy through governmental issues. Many international organisations adopt rules and codes of conduct to validate biomedical information and have organised quality portals such as NLM, OMNI, MEDCIRCLE, HON etc. Some terminological standards, such as the MESH thesaurus and UMLS, have been produced by the libraries for a correct management and an effective information retrieval, and are currently used by the most important biomedical web sites. The Dublin Core, metadata standard for the integration of information deriving from heterogeneous archives, has also been developed by the libraries. The easy access to information dims the complex architecture necessary for the construction of a web site. The contribution of different professionals is necessary to guarantee the production of quality medical/health web sites, among them librarians have always been involved with the management of knowledge and their skills are extremely valuable. Furthermore, the libraries' network is essential in order to guarantee universal access to health information, mostly still against payment, and to contribute to overcoming the 'digital divide' and 'second-level digital divide'.
Evaluation Studies as Topic↗
Automated evaluation of tryptic digest from recombinant human growth hormone using ultraviolet spectra and numeric peak information.
UV spectra were successfully employed in identifying peptide fragments from a tryptic digest of recombinant-DNA-derived human growth hormone (r-hGH). It was possible to distinguish very similar peptides utilizing a digital comparison of the UV spectra. An automated procedure was developed to generate a calibration library for the tryptic digest of a reference standard. The calibration library was then evaluated for reproducibility and selectivity and found to provide superior performance in correctly identifying ambiguous peaks as compared to the use of a conventional calibration table. Spectral match factors together with numerical information, derived from peak retention time, area and height, were used to arrive at a "peak score" descriptive of the similarity between standard and sample peaks. "Peak scores" could be combined to calculate a "sample score" indicative of overall similarity between an unknown and a standard. The scoring procedure was automated to generate a final report without operator intervention and successfully assigned appropriate scores to similar as well as dissimilar samples, e.g., native and oxidized r-hGH.
Algorithms↗
Net1 and Myeov: computationally identified mediators of gastric cancer.
Gastric adenocarcinoma (GA) is a significant cause of mortality worldwide. The molecular mechanisms of GA remain poorly characterised. Our aim was to characterise the functional activity of the computationally identified genes, NET 1 and MYEOV in GA. Digital Differential Display was used to identify genes altered expression in GA-derived EST libraries. mRNA levels of a subset of genes were quantitated by qPCR in a panel of cell lines and tumour tissue. The effect of pro- and anti-inflammatory stimuli on gene expression was investigated. Cell proliferation and invasion were measured using in an in-vitro GA model following inhibition of expression using siRNA. In all, 23 genes not previously reported in association with GA were identified. Two genes, Net1 and Myeov, were selected for further analysis and increased expression was detected in GA tissue compared to paired normal tissue using quantitative PCR. siRNA-mediated downregulation of Net1 and Myeov resulted in decreased proliferation and invasion of gastric cancer cells in vitro. These functional studies highlight a putative role for NET1 and Myeov in the development and progression of gastric cancer. These genes may provide important targets for intervention in GA, evidenced by their role in promoting invasion and proliferation, key phenotypic hallmarks of cancer cells.
Adenocarcinoma↗
Impact of a rural domestic violence prevention campaign.
Domestic violence is a prevalent health problem that in rural areas is further complicated by limited services, social isolation and the lack of privacy. Little is known about the impact of public health education on awareness, attitudes and behavior of the general public regarding domestic violence. This study sought to measure change in societal attitudes and behavioral intention in response to a seven-month public health education campaign targeting domestic violence in a rural county. From October 1998 to April 1999, the campaign used radio advertisements, posters, mailings to libraries and clergy, printed media articles, printed advertisements and health facility modifications. A random-digit-dialing telephone survey was used to evaluate attitudinal and behavioral changes in the intervention and comparison counties before and after the campaign. The response rates for the pre- (n =378) and postcampaign (n=633) surveys were 73 percent and 65 percent, respectively. Statistically significant increases in slogan and advertising recognition occurred in the intervention county (P=0.03), particularly among men recalling the campaign slogan (P=0.006). In a vignette regarding actions to be taken if the neighbor next door was abusing a partner, significant increases occurred in the intervention county in the percentage of respondents who thought that most people would talk to the victim (P=0.04), consult with friends (P=0.002) or talk to a doctor (P=0.004). Domestic violence agency hotline calls in the intervention county doubled following the campaign. Local public health education campaigns in a rural setting may be a valuable adjunct to national efforts, especially in reaching men.
Adolescent↗
Infrared analysis of urinary stones: a trial of automated identification.
A Search algorithm included in the Opus software of Bruker (Germany) was evaluated for analysis of urinary stones. Three reference libraries containing respectively 85 (single components), 1,059 (binary mixtures) and 4,565 (ternary mixture) digitized spectra were created and used to identify unknown spectra (n=320), applying the automatic procedure. Identification of the major component was correct in 83% of cases but the percentage of identification significantly decreased for the second and the third components. In cases of identification of the two first components, quantitative assessment was correct within tolerance limits +/- 15%. The computer results are judged unsatisfactory with regard to pathology because computer-aided identification is not sufficiently sensitive and specific to differentiate species with similar spectral pattern, even for the identification of main component, and also to detect minor components. It can be of assistance to guide spectral analysis, but it cannot replace human identification.
Algorithms↗
COMPUTERIZED BIBLIOGRAPHIC SERVICES FOR BIOMEDICINE.
By its development of improved media for dissemination of information, the National Library of Medicine is fostering a greater awareness and a better understanding of research and development efforts in behalf of public health and clinical medicine, and a more rapid translation of research into clinical application. The library's transformation from a passive repository of information to an active ally of the researcher, teacher, and clinician has led to increased use of medical library facilities and has stimulated thinking through better communication of published information. The library's success in using automation for bibliographic control of medical literature suggests that other disciplines that have not already developed automated techniques of literature-reference retrieval might profitably do so.
Abstracting and Indexing↗
Technical note: a radiological education system--organization of an image library.
A successful radiological library and teaching system should be easy to compile, user-friendly, dynamic and flexible. Nowadays it must be amenable to incorporation into digitally-based communication systems such as personal computers (pc) and picture archiving and communication systems (PACS). This article describes the structural organization and capabilities of such a digital radiological education system, and demonstrates how it fulfils these aims.
Computers↗
Thresholds for human detection of patient setup errors in digitally reconstructed portal images of prostate fields.
PURPOSE: Computer-assisted methods to analyze electronic portal images for the presence of treatment setup errors should be studied in controlled experiments before use in the clinical setting. Validation experiments using images that contain known errors usually report the smallest errors that can be detected by the image analysis algorithm. This paper offers human error-detection thresholds as one benchmark for evaluating the smallest errors detected by algorithms. Unfortunately, reliable data are lacking describing human performance. The most rigorous benchmarks for human performance are obtained under conditions that favor error detection. To establish such benchmarks, controlled observer studies were carried out to determine the thresholds of detectability for in-plane and out-of-plane translation and rotation setup errors introduced into digitally reconstructed portal radiographs (DRPRs) of prostate fields. METHODS AND MATERIALS: Seventeen observers comprising radiation oncologists, radiation oncology residents, physicists, and therapy students participated in a two-alternative forced choice experiment involving 378 DRPRs computed using the National Library of Medicine Visible Human data sets. An observer viewed three images at a time displayed on adjacent computer monitors. Each image triplet included a reference digitally reconstructed radiograph displayed on the central monitor and two DRPRs displayed on the flanking monitors. One DRPR was error free. The other DRPR contained a known in-plane or out-of-plane error in the placement of the treatment field over a target region in the pelvis. The range for each type of error was determined from pilot observer studies based on a Probit model for error detection. The smallest errors approached the limit of human visual capability. The observer was told what kind of error was introduced, and was asked to choose the DRPR that contained the error. Observer decisions were recorded and analyzed using repeated-measures analysis of variance. RESULTS: The thresholds of detectability averaged over all observers were approximately 2.5 mm for in-plane translations, 1.6 degrees for in-plane rotations, 1 degrees for out-of-plane rotations, and 8% change in magnification for out-of-plane translations along the central axis. When one inexperienced observer is excluded, the average threshold for change in magnification is 5%. Experienced observers tended to perform better, but differences between groups were not statistically significant. Thresholds were computed as averages over all observers. Because of the broad range of observer capabilities, some detection tasks were too difficult for some observers, leading to missing threshold values in our data analysis. The missing values were excluded from computation of the average thresholds reported above. The effect of the missing values is to bias the average values toward the best human performance. CONCLUSIONS: Under favorable conditions, humans can detect small errors in setup geometry. The thresholds for error detection reported in this study are believed to represent rigorous but reasonable benchmarks that can be incorporated into studies evaluating algorithms for computer-assisted detection of setup errors in electronic portal images.
Diagnostic Errors↗
The PDA as a reference tool: libraries' role in enhancing nursing education.
"The PDA as a Reference Tool: The Libraries' Role in Enhancing Nursing Education" is a pilot project funded by the University of Massachusetts President's Office Information Technology Council through their Professional Development Grant program in 2004. The project's goal is to offer faculty and students in nursing programs at two University of Massachusetts campuses access to an array of medical reference information, such as handbooks, dictionaries, calculators, and diagnostic tools, on small handheld computers called personal digital assistants. Through exposure to the variety of information resources in this digital format, participants can discover and explore these resources at no personal financial cost. Participants borrow handhelds from the University Library's circulation desks. The libraries provide support in routine resynchronizing of handhelds to update information. This report will discuss how the projects were administered, what we learned about what did and did not work, the problems and solutions, and where we hope to go from here.
Advertising↗
EST databases as multi-conditional gene expression datasets.
Large-scale expression data, such as that generated by hybridization to microarrays, is potentially a rich source of information on gene function and regulation. By clustering genes according to their expression profiles, groups of genes involved in the same pathways or sharing common regulatory mechanisms may be identified. Publicly-available EST collections are a largely unexplored source of expression data. We previously used a sample of rice ESTs to generate 'digital expression profiles' by counting the frequency of tags for different genes sequenced from different cDNA libraries. A simple statistical test was used to associate genes or cDNA libraries having similar expression profiles. Here we further validate this approach using larger samples of ESTs from the UniGene projects (clustered human, mouse and rat ESTs). Our results show that genes clustered on the basis of expression profile may represent genes implicated in similar pathways or coding for different subunits of multi-component enzyme complexes. In addition we suggest that comparison of clusters from different species, may be useful for confirmation or prediction of orthologs.
Animals↗
Interactive brain atlas with the Visible Human Project data: development methods and techniques.
A prototype of an interactive digital brain atlas was developed by using the Visible Human Project data set of the National Library of Medicine. This data set provides corresponding axial magnetic resonance images, computed tomographic images, and cryosections of the brain. The prototype was developed to demonstrate the techniques and methods that will be used throughout the development process of the atlas. The atlas has a graphical user interface, supports user interaction with various representations of the brain (i.e., two-dimensional and three-dimensional [3D]), and displays multiple images simultaneously. Motion sequences of the 3D brain were incorporated in the atlas to provide an important link between two-dimensional brain slices and volume-rendered 3D anatomic structures. Volume visualization tools were used to interactively render, rotate, and reslice the volumetric brain data. The brain was segmented with manual tracing, thresholding, and morphologic algorithms and then rendered with volume-rendering tools.
Anatomy, Cross-Sectional↗
MECHANIZATION OF CATALOGING PROCEDURES.
The Columbia-Harvard-Yale Medical Libraries Computerization Project has put into operation its mechanized procedure for the production of catalog cards. Cards produced are in final form ready to be filed into a card catalog. Catalogers prepare copy on a worksheet from which punched cards are punched. An IBM 1401 computer processes the decklets of punched cards on magnetic tape to produce the expanded decklets of punched cards needed to print the various packs of catalog cards required to go into different catalogs. Next, the computer punches the expanded decklets of cards to operate an 870 Document Writer, which types out the catalog cards in final form. Cost of cards ready to file is 12.5 cents per card.
Cataloging↗
A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells.
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.
Alternative Splicing↗
The end of print: digitization and its consequence--revolutionary changes in scholarly and social communication and in scientific research.
The transformation from print to digital media for scientific communication, driven in part by the growth of the Internet and the tremendous explosion in the amount of information now available to everybody, is creating fundamental changes in institutions such as publishers, libraries, and universities that primarily exist for the creation, management, and distribution of information and knowledge. Scientific, technological, and medical journals are the first publications to be completely transformed from print to digital format but monographs are beginning to appear in digital format as well and soon all communication and publishing of scientific information will be entirely electronic. In fact, this change is affecting all components of the scientific enterprise, from personal correspondence and laboratory methods to peer reviewing and the quality assessment of scientific research. Along with these radical and rapid changes in information presentation and distribution are coincident changes in the expectations of both the public and other scientists, with both groups demanding ever more rapid, open, and global access to scientific information than has been available in the past. The consequence of this revolution in the mechanics of communications technology is threatening the very existence of a number of highly regarded institutions such as intellectual property, commercial publishers, scientific societies, and academic libraries and might soon begin to threaten even the traditional university.
Communication↗