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At least 1,279 records · Page 71Linked to original sources
PubMed2006

A journal club is an effective tool for assisting librarians in the practice of evidence-based librarianship: a case study.

OBJECTIVE: To establish a journal club for librarians, which aimed to develop appraisal skills and assist in the application of research to practice. METHODS: Fourteen health librarians were invited to attend a journal club. Each month a librarian was responsible for preparing a scenario, choosing a research paper, and selecting a checklist. The paper was appraised by the club, and a critically appraised topic (CAT) prepared. Six months later, a questionnaire was sent to all librarians. RESULTS: Six out of 14 librarians attended the journal club and five out of six returned the questionnaire. All five agreed that attending the journal club helped them develop appraisal skills, write a CAT and be more critical of research. Four agreed they always identified a research paper first, then formulated a question. One librarian agreed that applying results to their own practice was difficult, one disagreed and three were neutral. CONCLUSION: Journal clubs can be effective at developing appraisal skills and writing a CAT, as well as increasing the reading of library research. Librarians still need assistance in identifying and using questions directly from their own practice. The journal club has helped some librarians to apply evidence to practice, but others find the research is not always directly relevant.

Competency-Based Education↗
PubMed1997

Use of the World Wide Web for multisite data collection.

As access to the Internet becomes increasingly available, research applications in medicine will increase. This paper describes the use of the Internet, and, more specifically, the World Wide Web (WWW), as a channel of communication between EDs throughout the world and investigators who are interested in facilitating the collection of data from multiple sites. Data entered into user-friendly electronic surveys can be transmitted over the Internet to a database located at the site of the study, rendering geographic separation less of a barrier to the conduction of multisite studies. The electronic format of the data can enable real-time statistical processing while data are stored using existing database technologies. In theory, automated processing of variables within such a database enables early identification of data trends. Methods of ensuring validity, security, and compliance are discussed.

Computer Communication Networks↗
PubMedDate not supplied

Implementation and evaluation of a medical informatics distance education program.

OBJECTIVE: Given the need for continuing education in medical informatics for mid-career professionals, the authors aimed to implement and evaluate distance learning courses in this area. DESIGN: The authors performed a needs assessment, content and technology planning, implementation, and student evaluation. MEASUREMENTS: The needs assessment and student evaluations were assessed using a combination of Likert scale and free-form questions. RESULTS: The needs assessment indicated much interest in a medical informatics distance learning program, with electronic medical records and outcome research the subject areas of most interest. The courses were implemented by means of streaming audio plus slides for lectures and threaded discussion boards for student interaction. Students were assessed by multiple-choice tests, a term paper, and a take-home final examination. In their course evaluations, student expressed strong satisfaction with the teaching modalities, course content, and system performance. Although not assessed experimentally, the performance of distance learning students was superior to that of on-campus students. CONCLUSION: Medical informatics education can be successfully implemented by means of distance learning technologies, with favorable student satisfaction and demonstrated learning. A graduate certificate program is now being implemented.

Data Collection↗
PubMed2006

Iterated local least squares microarray missing value imputation.

Microarray gene expression data often contains multiple missing values due to various reasons. However, most of gene expression data analysis algorithms require complete expression data. Therefore, accurate estimation of the missing values is critical to further data analysis. In this paper, an Iterated Local Least Squares Imputation (ILLSimpute) method is proposed for estimating missing values. Two unique features of ILLSimpute method are: ILLSimpute method does not fix a common number of coherent genes for target genes for estimation purpose, but defines coherent genes as those within a distance threshold to the target genes. Secondly, in ILLSimpute method, estimated values in one iteration are used for missing value estimation in the next iteration and the method terminates after certain iterations or the imputed values converge. Experimental results on six real microarray datasets showed that ILLSimpute method performed at least as well as, and most of the time much better than, five most recent imputation methods.

Algorithms↗
PubMedDate not supplied

Extending PowerPoint with DICOM image support.

Although PowerPoint has become a ubiquitous presentation tool in medical imaging, it does not support the Digital Imaging and Communications in Medicine (DICOM) standard. Users must go through a laborious conversion process that includes guessing the appropriate brightness and contrast to convert 16-bit DICOM images into 8-bit formats. A PowerPoint add-in was developed that incorporates features of a DICOM viewer into a presentation. Users can interactively manipulate large series of 16-bit images in stack mode with scroll, crop, zoom, and window width and level functions, as well as sort through images by location or series. Multiple DICOM image series can be placed on a single slide, and one can interactively scroll through stacks of images during a presentation to demonstrate imaging findings. The problem created by the varying contrast and brightness of different projector systems is overcome by interactively adjusting the image window level during presentations. Bone and lung window views can be shown without having to create separate images. Combining DICOM images into stacks as part of a PowerPoint presentation can result in a more effective and higher-quality presentation of medical images.

Data Display↗
PubMedDate not supplied

Informatics in radiology (infoRAD): portable toolkit for providing straightforward access to medical image data.

Computer-aided analysis of medical images usually involves the development of custom software applications that interpret, process, and ultimately display medical image data. The interpretation stage involves decoding the image data and presenting them to the application developer for further processing. A toolkit has been created specifically for interpreting medical image data; it thus acts as a platform for development of medical imaging applications. The toolkit, which is referred to as NeatMed, is intended to reduce development time by eliminating the need for the application developer to deal directly with medical image data. NeatMed was implemented by using Java, a programming language with a range of attractive features including ease of use, extensive support material, and portability. NeatMed was developed specifically for use in a research environment. Straightforward to use and well documented, it is intended as an alternative to commercially available medical imaging toolkits. NeatMed currently provides support for the Digital Imaging and Communications in Medicine and Analyze medical image file formats. Support material including sample source code is available via the Internet; links to related resources are also provided. Most important, NeatMed is freely available and its continuing development is motivated by requests and suggestions from end users.

Confidentiality↗
PubMed2006

Microarray analysis of gene expression: considerations in data mining and statistical treatment.

DNA microarray represents a powerful tool in biomedical discoveries. Harnessing the potential of this technology depends on the development and appropriate use of data mining and statistical tools. Significant current advances have made microarray data mining more versatile. Researchers are no longer limited to default choices that generate suboptimal results. Conflicting results in repeated experiments can be resolved through attention to the statistical details. In the current dynamic environment, there are many choices and potential pitfalls for researchers who intend to incorporate microarrays as a research tool. This review is intended to provide a simple framework to understand the choices and identify the pitfalls. Specifically, this review article discusses the choice of microarray platform, preprocessing raw data, differential expression and validation, clustering, annotation and functional characterization of genes, and pathway construction in light of emergent concepts and tools.

Cluster Analysis↗
PubMed2000

Knowledge discovery and data mining in toxicology.

Knowledge discovery and data mining tools are gaining increasing importance for the analysis of toxicological databases. This paper gives a survey of algorithms, capable to derive interpretable models from toxicological data, and presents the most important application areas. The majority of techniques in this area were derived from symbolic machine learning, one commercial product was developed especially for toxicological applications. The main application area is presently the detection of structure-activity relationships, very few authors have used these techniques to solve problems in epidemiological and clinical toxicology. Although the discussed algorithms are very flexible and powerful, further research is required to adopt the algorithms to the specific learning problems in this area, to develop improved representations of chemical and biological data and to enhance the interpretability of the derived models for toxicological experts.

Algorithms↗
PubMed2002

Outlier mining in high throughput screening experiments.

A data mining procedure for the rapid scoring of high-throughput screening (HTS) compounds is presented. The method is particularly useful for monitoring the quality of HTS data and tracking outliers in automated pharmaceutical or agrochemical screening, thus providing more complete and thorough structure-activity relationship (SAR) information. The method is based on the utilization of the assumed relationship between the structure of the screened compounds and the biological activity on a given screen expressed on a binary scale. By means of a data mining method, a SAR description of the data is developed that assigns probabilities of being a hit to each compound of the screen. Then, an inconsistency score expressing the degree of deviation between the adequacy of the SAR description and the actual biological activity is computed. The inconsistency score enables the identification of potential outliers that can be primed for validation experiments. The approach is particularly useful for detecting false-negative outliers and for identifying SAR-compliant hit/nonhit borderline compounds, both of which are classes of compounds that can contribute substantially to the development and understanding of robust SARs. In a first implementation of the method, one- and two-dimensional descriptors are used for encoding molecular structure information and logistic regression for calculating hits/nonhits probability scores. The approach was validated on three data sets, the first one from a publicly available screening data set and the second and third from in-house HTS screening campaigns. Because of its simplicity, robustness, and accuracy, the procedure is suitable for automation.

Algorithms↗
PubMed2005

Visualization methods for statistical analysis of microarray clusters.

BACKGROUND: The most common method of identifying groups of functionally related genes in microarray data is to apply a clustering algorithm. However, it is impossible to determine which clustering algorithm is most appropriate to apply, and it is difficult to verify the results of any algorithm due to the lack of a gold-standard. Appropriate data visualization tools can aid this analysis process, but existing visualization methods do not specifically address this issue. RESULTS: We present several visualization techniques that incorporate meaningful statistics that are noise-robust for the purpose of analyzing the results of clustering algorithms on microarray data. This includes a rank-based visualization method that is more robust to noise, a difference display method to aid assessments of cluster quality and detection of outliers, and a projection of high dimensional data into a three dimensional space in order to examine relationships between clusters. Our methods are interactive and are dynamically linked together for comprehensive analysis. Further, our approach applies to both protein and gene expression microarrays, and our architecture is scalable for use on both desktop/laptop screens and large-scale display devices. This methodology is implemented in GeneVAnD (Genomic Visual ANalysis of Datasets) and is available at http://function.princeton.edu/GeneVAnD. CONCLUSION: Incorporating relevant statistical information into data visualizations is key for analysis of large biological datasets, particularly because of high levels of noise and the lack of a gold-standard for comparisons. We developed several new visualization techniques and demonstrated their effectiveness for evaluating cluster quality and relationships between clusters.

Algorithms↗
PubMed2005

Dynamic covariation between gene expression and proteome characteristics.

BACKGROUND: Cells react to changing intra- and extracellular signals by dynamically modulating complex biochemical networks. Cellular responses to extracellular signals lead to changes in gene and protein expression. Since the majority of genes encode proteins, we investigated possible correlations between protein parameters and gene expression patterns to identify proteome-wide characteristics indicative of trends common to expressed proteins. RESULTS: Numerous bioinformatics methods were used to filter and merge information regarding gene and protein annotations. A new statistical time point-oriented analysis was developed for the study of dynamic correlations in large time series data. The method was applied to investigate microarray datasets for different cell types, organisms and processes, including human B and T cell stimulation, Drosophila melanogaster life span, and Saccharomyces cerevisiae cell cycle. CONCLUSION: We show that the properties of proteins synthesized correlate dynamically with the gene expression profile, indicating that not only is the actual identity and function of expressed proteins important for cellular responses but that several physicochemical and other protein properties correlate with gene expression as well. Gene expression correlates strongly with amino acid composition, composition- and sequence-derived variables, functional, structural, localization and gene ontology parameters. Thus, our results suggest that a dynamic relationship exists between proteome properties and gene expression in many biological systems, and therefore this relationship is fundamental to understanding cellular mechanisms in health and disease.

Animals↗
PubMed2006

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

BACKGROUND: In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, such evidence is often incomplete and usually uncertain. The extrinsic evidence is usually not sufficient to recover the complete gene structure of all genes completely and the available evidence is often unreliable. Therefore extrinsic evidence is most valuable when it is balanced with sequence-intrinsic evidence. RESULTS: We present a fairly general method for integration of external information. Our method is based on the evaluation of hints to potentially protein-coding regions by means of a Generalized Hidden Markov Model (GHMM) that takes both intrinsic and extrinsic information into account. We used this method to extend the ab initio gene prediction program AUGUSTUS to a versatile tool that we call AUGUSTUS+. In this study, we focus on hints derived from matches to an EST or protein database, but our approach can be used to include arbitrary user-defined hints. Our method is only moderately effected by the length of a database match. Further, it exploits the information that can be derived from the absence of such matches. As a special case, AUGUSTUS+ can predict genes under user-defined constraints, e.g. if the positions of certain exons are known. With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly. CONCLUSION: Sensitive probabilistic modeling of extrinsic evidence such as sequence database matches can increase gene prediction accuracy. When a match of a sequence interval to an EST or protein sequence is used it should be treated as compound information rather than as information about individual positions.

Algorithms↗
PubMed2003

Educating patients about anesthesia: a systematic review of randomized controlled trials of media-based interventions.

UNLABELLED: In this systematic review, we compared the effectiveness of media-based patient education about anesthesia. Fifteen randomized controlled trials (n = 1506) were identified after a systematic search of electronic databases (MEDLINE, EMBASE, CINAHL, PSYCINFO, The Cochrane Controlled Trials Registry), published articles, and contact with authors. Outcomes assessed were anxiety, knowledge, and patient satisfaction. Anxiety levels before anesthesia were less intense in subjects receiving the video and printed information compared with those receiving no intervention (weighted mean difference of 3; 95% confidence interval [95%CI], 1-5 Spielberger's State and Trait Anxiety Inventory). Patients in the video group were more likely to answer all knowledge questions correctly compared with patients with no intervention (relative risk of 6.64; 95%CI, 2.05-21.52). The level of knowledge about pain management was higher in the video group compared with patients with no intervention (weighted mean difference of 17%; 95%CI, 9-25). However, the level of patient satisfaction with the intervention (expectation versus actual anesthetic experience) was similar between the groups (relative risk of 1.06; 95%CI, 0.93-1.22). This systematic review supports the use of video and printed information about general process and risks of anesthesia for patient education before surgery. IMPLICATIONS: The effectiveness of media-based interventions for educating patients about general process and risks of anesthesia were compared in this systematic review. The use of video and/or printed information can decrease patient anxiety and increase patient knowledge. However, patient satisfaction was similar between media-based intervention and nonintervention groups.

Adult↗
PubMed2001

Introduction to resources in molecular genetics.

Perhaps no other discipline has experienced as dramatic an information explosion in recent years as has the field of molecular genetics. While the flood of scholarly publications stemming from this research has been extensively indexed in MEDLINE, a number of new databases have been developed that provide direct access to the primary sequence data as well as to curated, reference information. A select group of these databases, including NCBI's GenBank, LocusLink, RefSeq, OMIM, and Genes and Disease, is examined. Following a brief description of each database, a proposed instructional program for their integration into an undergraduate genetics course at the University of Vermont is described.

Data Display↗
PubMed2001

LabVelocity: online tools for life science products, protocols, technical information, MEDLINE searches, and laboratory calculations.

As the pace of life science discovery increases, so do the demands on researchers. To remain competitive in the life science industry, researchers must use every tool at their disposal to keep up with new products, protocols, news, and literature in their field. While there are now myriad Web sites that assist researchers with this problem, many suffer from confusing user interfaces, poorly designed search engines, and a narrow information focus. Here, we present LabVelocity, a user-friendly Web site that provides a free multidisciplinary information-gathering service for the life science research community. Using LabVelocity, a researcher can quickly find the products, protocols, technical references, news, MEDLINE abstracts, and interactive software tools necessary for an experiment. This aggregation of information can streamline experimental planning and is especially useful when researchers want to set up a new laboratory or to venture outside their field of expertise.

Algorithms↗
PubMedDate not supplied

DICOM: key concepts--part I.

In this issue and next, we're investigating different sections of the DICOM Standard to get a grip on what it's all about. The bottom line is to facilitate communication and DICOM addresses all the technical aspects to allow complying OEMs to talk to one another. In part 2, IT World completes its overview on DICOM by exploring UID, networking with DICOM, conformance, and conformance statements.

Computer Communication Networks↗
PubMedDate not supplied

A multi-channel simultaneous data acquisition and waveform generator system designed for medical applications.

To meet the needs of our research programmes on auditory prostheses for the totally deaf, a 15-channel data acquisition and waveform generator system with flexible triggering, pacing and linking was developed. It allows both synchronous and asynchronous operation at high speed. Each channel of the system, which is controlled by a simple personal computer, has an on-board microcontroller, a 512 kWord signal memory, a voltage input and both voltage and current outputs. The system includes a master pacer and trigger unit with elaborate hardware and software triggering options. This paper describes the system hardware and the software used to control it. Finally, some of its application are demonstrated. The flexibility of the system makes it widely applicable in the field of biomedical engineering.

Animals↗
PubMedDate not supplied

A generic approach to the management of time-related signals and images in medicine.

A framework concept for design and implementation of medical workstations is described by (a) its underlying principles, (b) the handlers provided by the concept, (c) the available data structures and (d) the graphical user interface (GUI). The design principle takes care of a modular approach both for the framework and for the applications. The GUI provides a coherent look and feel for applications based on toolkits for displaying data objects and application control. The data handler allows management of n-dimensional data matrices in a multi-vendor environment, whereas the parameter handler takes care of the data object description. An implementation of a medical workstation exploiting the framework concept is presented.

Computer Graphics↗