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At least 1,099 records · Page 61Linked to original sources
PubMed2004

Bloader--a batch loader application for MIAMExpress.

UNLABELLED: BLoader is a client server application for annotating and loading large amounts of Microarray data into a local installation of the MIAMExpress database. A set of nested spreadsheets is used to collect the required MIAME annotation. Controlled vocabularies are downloaded from MIAMExpress and ArrayExpress databases to guarantee MIAME compliance. AVAILABILITY: The application is available from the author at http://www.ansorge-group.embl.de/bloader CONTACT: schwager@embl.de SUPPLEMENTARY INFORMATION: For more details on BLoader visit the above web page.

Computer Graphics↗
PubMed2004

SNPbox: web-based high-throughput primer design from gene to genome.

SNPbox is a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects in a standardized manner resulting in high-quality PCR amplicons with a low failure rate. Here, we present the SNPbox web server at http://www.SNPbox.org, which hosts the SNPbox web service as well as the data from SNPbox analysis of all Ensembl exons. The data of this genome-wide SNPbox application can be visualized in Ensembl's ContigView through a DAS (distributed annotation system) annotation server.

DNA Primers↗
PubMed2004

Sources of information on postgraduate medical training programs - 2004 update.

This is the biennial update listing directories, journal articles, Web sites, and general books that aid the librarian, house officer, or medical student in finding information on medical residency and fellowship programs. The World Wide Web provides the most current and complete source of information about postgraduate training programs and specialties. This update goes beyond postgraduate training resources to include selected Web sites and books on resume writing, practice management, personal financial issues, the "Match," exam preparation, job hunting, and the DEA license application process. Print resources are included if they provide information not on the Internet or have features that are particularly useful. The Internet continues to be a major marketing tool for hospitals seeking to recruit the best and brightest for their residency and fellowship programs. Even the smallest community hospital usually has a presence on the 'Net.

Education, Medical, Graduate↗
PubMed2005

"Is Cybermedicine Killing You?"--The story of a Cochrane disaster.

This editorial briefly reviews the series of unfortunate events that led to the publication, dissemination, and eventual retraction of a flawed Cochrane systematic review on interactive health communication applications (IHCAs), which was widely reported in the media with headlines such as "Internet Makes Us Sick," "Knowledge May Be Hazardous to Web Consumers' Health," "Too Much Advice Can Be Bad for Your Health," "Click to Get Sick?," and even "Is Cybermedicine Killing You?". While the media attention helped to speed up the identification of errors, leading to a retraction of the review after only 13 days, a paper published in this issue of JMIR by Rada shows that the retraction, in contrast to the original review, remained largely unnoticed by the public. We discuss the three flaws of the review, which include (1) data extraction and coding errors, (2) the pooling of heterogeneous studies, and (3) a problematic and ambiguous scope and, possibly, some overlooked studies. We then discuss "retraction ethics" for researchers, editors/publishers, and journalists. Researchers and editors should, in the case of retractions, match the aggressiveness of the original dissemination campaign if errors are detected. It is argued that researchers and their organizations may have an ethical obligation to track down journalists who reported stories on the basis of a flawed study and to specifically ask them to publish an article indicating the error. Journalists should respond to errors or retractions with reports that have the same prominence as the original story. Finally, we look at some of the lessons for the Cochrane Collaboration, which include (1) improving the peer-review system by routinely sending out pre-prints to authors of the original studies, (2) avoiding downplay of the magnitude of errors if they occur, (3) addressing the usability issues of RevMan, and (4) making critical articles such as retraction notices open access.

Attitude to Health↗
PubMed1998

WEB-MO--a computer aided learning on WWW.

The paper presents an electronic textbook on World Wide Web (WWW), which present theoretical notions about the eyes' movements. It also contains clinical cases as example for the described notions. The application is being tested at the County Hospital, Department of Neurosurgery, Timisoara, Romania. The reaction of the educators and learners is quite positive. We think there will be a great learning tool for the future.

Computer-Assisted Instruction↗
PubMed2001

Visual Cloning 2000: a DNA sequence analysis program.

VC2000 is a recommendable, easy-to-use and affordable program suited particularly to plot maps of both plasmids and linear DNA fragments for the documentation of cloning procedures. It comes with basic tools for sequence analysis that assist this major utility. A special feature of the program is the integration of web-based tools, providing additional analytical power and flexibility. In this way the user is supplied with the latest versions of these applications.

Cloning, Molecular↗
PubMed2003

Automated biofilm morphology quantification from confocal laser scanning microscopy imaging.

In spite of the immediate visual appeal of confocal laser scanning microscopy images, the extraction of accurate reconstitutions of biofilm morphology requires a lengthy and computational intensive succession of processing steps. However, once performed, it provides ample reward by enabling the quantitative study of biofilm structure. A software suite of image processing tools for full automation of biofilm morphology quantification was developed by integrating preprocessing, segmentation and morphology quantification operations. This software toolbox was implemented in a web server and a user friendly interface was developed to facilitate image submission, storage and sharing, its access being unrestricted for scientific applications. The image bioinformatics tool which results from the integration of the processing operations can be accessed at http://www.itqb.unl.pt:111/clsmip/. Its use is described in this paper and is illustrated with an example of processing of experimental data describing the growth of a mixed species dentrifying biofilm.

Automation↗
PubMed2005

[Measurement of air leak volume after lung surgery using web-camera].

Persistent air leak from the lung is one of the major complications after lung operations, especially in the latest thoracic surgery, where a shorter hospital stay tends to be necessary. However, air leak volume has been rarely measured clinically because accustomed tools of gas flow meter were types which needed contact measure, and those were unstable in long-term use and high cost. We tried to measure air leak volume as follows: (1) Bubble was made in the water seal part of a drain bag. (2) The movement of bubbles was recorded with a web-camera. (3) The data from the movie was analyzed by Linux computer on-line. We believe this method is clinically applicable as a routine work after lung surgery because of non-contact type of measurements, its stableness in long-term, easiness to be handled, and reasonable in cost.

Air↗
PubMed2026

The potential of clustering methods for pre-test triage in sleep medicine: A systematic review.

Sleep disorders exhibit substantial heterogeneity, and traditional classifications may not fully capture clinically relevant subtypes. Clustering techniques can identify patient subgroups that improve phenotypic characterization and may support personalized management. This systematic review evaluated the application of clustering in sleep medicine, with particular focus on its potential use as a pre-test triage tool prior to formal sleep testing. PubMed/MEDLINE, Embase, Web of Science, and Scopus were searched to February 2025. Eligible studies applied clustering to classify sleep disorders in adults. Two reviewers independently conducted screening, data extraction, and risk-of-bias assessment using QUADAS-2. The protocol was registered on PROSPERO. Fifty-one studies (1983-2025) were included, predominantly focused on obstructive sleep apnea (OSA) (n = 38, 74%). Hierarchical clustering (n = 20) and K-means clustering (n = 14) were the most frequently used techniques. Internal validation was reported in only 18% of studies, and external validation was reported in only 1 study. Seven studies relied exclusively on baseline clinical, demographic, or questionnaire data, representing pre-test scenarios, whereas most incorporated polysomnography-derived variables, limiting their applicability to early clinical stratification. Hierarchical clustering was the most commonly applied method; however, the overall lack of validation limits confidence in the robustness and clinical applicability of identified phenotypes. The potential role of clustering as a pre-test triage strategy remains largely unexplored, as most studies focused on post-diagnostic phenotyping and were affected by incorporation bias. Future research should prioritize pre-test clinical variables, rigorously validate internally and externally, and adopt standardized methodological and reporting practices to facilitate clinical translation.

Humans↗
PubMedDate not supplied

Using component technologies for web based wavelet enhanced mammographic image visualization.

The poor contrast detectability of mammography can be dealt with by domain specific software visualization tools. Remote desktop client access and time performance limitations of a previously reported visualization tool are addressed, aiming at more efficient visualization of mammographic image resources existing in web or PACS image servers. This effort is also motivated by the fact that at present, web browsers do not support domain-specific medical image visualization. To deal with desktop client access the tool was redesigned by exploring component technologies, enabling the integration of stand alone domain specific mammographic image functionality in a web browsing environment (web adaptation). The integration method is based on ActiveX Document Server technology. ActiveX Document is a part of Object Linking and Embedding (OLE) extensible systems object technology, offering new services in existing applications. The standard DICOM 3.0 part 10 compatible image-format specification Papyrus 3.0 is supported, in addition to standard digitization formats such as TIFF. The visualization functionality of the tool has been enhanced by including a fast wavelet transform implementation, which allows for real time wavelet based contrast enhancement and denoising operations. Initial use of the tool with mammograms of various breast structures demonstrated its potential in improving visualization of diagnostic mammographic features. Web adaptation and real time wavelet processing enhance the potential of the previously reported tool in remote diagnosis and education in mammography.

Female↗
PubMed2003

Tools for the automatic identification and classification of RNA base pairs.

Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.

Algorithms↗
PubMed2002

Topical steroid therapy for phimosis.

INTRODUCTION: Circumcision has been the traditional treatment for phimosis. Recent reports of medical management of phimosis with topical steroids quote success rates of 67%-95%. We present our results with topical steroid therapy for treatment of phimosis. MATERIALS AND METHODS: Retrospective review of 69 boys between the age of 3 and 13 years (average 7.4) who were referred to Urology clinic over a one year period (August 1999-2000) with phimosis. Boys without a distal preputial ring were excluded. A course of triamcinolone cream was prescribed and parents/patients were instructed to apply it to the preputial outlet twice daily for one month. Six weeks after treatment initiation patients were reassessed. Results were classified as follows: Full retraction (FR)-entire glans and coronal margin seen, Moderate retraction (MR)-proximal glans seen, residual preputial adhesions, Partial retraction (PR)-distal glans and meatus seen, and Failure (F)-no change. FR, MR, and PR were considered successful outcomes. Statistical analysis was performed with Splus software using the prop.test and ordinal logistic regression procedures. RESULTS: Follow-up ranged from 1-12 months, and 8 patients were lost to follow-up. Of the remaining 61 boys, 82% (12 FR, 26 MR, 12 PR) were successfully managed with topical steroid (95% confidence interval: 69%-90%). Scarring on examination was observed to negatively impact outcome (92% versus 67%) and was statistically significant using ordinal logistic regression (Chi square test=4.48, p-value=0.034). Two boys with severe balanitis xerotica obliterans (BXO) and two boys with buried penis and penoscrotal webbing failed treatment and required surgery. There was an association noted between older age and poorer outcome but this was not statistically significant. There were no local or systemic side effects noted. CONCLUSIONS: Local application of steroid cream to the phimotic foreskin may allow some degree of retraction and avert the need for circumcision. Although the length of follow-up is insufficient to decree ultimate success, topical steroid appears to be a safe and effective treatment for boys over three years of age with evidence of a tight preputial ring. Boys with severe BXO or buried penis and penoscrotal webbing should be considered primarily for surgery.

Administration, Topical↗
PubMed2000

The use of information technology in improving medical performance. Part III. Patient-support tools.

Despite the proliferation of computer-based resources for patients, usefulness has been limited to date. Already, 17,000 biomedical Internet sites exist, and patients are increasingly finding support and knowledge on the Internet, but the accuracy of the information found is highly variable and difficult for patients to assess. Patients have also found value in electronic communication with physicians, although relatively few physicians routinely use email to communicate with patients on a regular basis. Nonetheless, patient-focused information technologies potentially will have profound effects on medical care. With advancing sophistication of technology, patients will increasingly be able to compare and choose doctors using the Internet and to access information that allows them to monitor and regulate the quality of their own care. Further, technologies will likely be developed to allow patients to increasingly manage their own care -- whether they are patients with chronic illnesses such as diabetes or congestive heart failure who use customized software to adjust drug dosages and other treatments or patients with such common illnesses as headache or gastrointestinal infection who access self-management programs that may even write prescriptions for them. Thoughtful analysis and policy development will be critical for ensuring that the benefits are maximized and potential harm minimized. Specific areas include assessing the effects on outcomes and the characteristics of patients and technologies that succeed with self-management, and developing policies regarding liability for Web-based medical transactions and the privacy of information provided to physicians by email and via interactive Web sites.

Biomedical Technology↗
PubMed2003

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

Computer Communication Networks↗
PubMed2006

Use of Web-based materials to enhance anatomy instruction in the health sciences.

Teaching anatomy by dissection is under considerable pressure to evolve and/or even be eliminated, and curricular hours in the dissection laboratory are decreasing. As a possible means of easing this pressure, an online interactive anatomy program has been created to enhance the dissection experience, observational learning, and three-dimensional comprehension of human anatomy. An assessment was made of the utility of the program in preparing students for dissection laboratories and for examinations. The efficacy of the application was evaluated by first-year students and faculty with pre- and post-use surveys in anatomy courses at three medical schools. It was found that students felt better prepared if they utilized the Web site prior to their dissection laboratory, and faculty reported spending less time explaining basic concepts or techniques. It is concluded that a comprehensive online program significantly enhances the quality and efficiency of instruction in human anatomy in the dissection laboratory and could prove to be a useful tool at other institutions.

Anatomy↗
PubMed2005

Ultrasonographic contrast media: has the time come in obstetrics and gynecology?

OBJECTIVE: The aim of this work was to review the technical aspects and clinical applications of contrast media (microbubbles and nanomolecular agents) in obstetric and gynecologic ultrasonographic imaging. METHODS: With the use of a computerized database (MEDLINE) and several Web-based search engines (Google Scholar and Copernic), relevant articles on ultrasonographic contrast media were reviewed. References cited in these articles and not obtained via the search engines were also reviewed. RESULTS: Ultrasonographic contrast media constitute a new and expanding technology. They are frequently used, for example, in adult cardiology. Extensive research in laboratory setups, animals, and human subjects has shown their safety and huge potential as an adjunctive tool in clinical practice. They increase signals returning from insonated tissues and are particularly effective as intravascular agents, enhancing color and Doppler signals, for instance. Preliminary results in tumor imaging are encouraging. The ultrasonographic contrast media permit pharmacokinetic perfusion studies, which may be of enormous clinical importance in the study of early cancer development. Targeted imaging and therapies are becoming a reality. Microbubbles have already brought a new dimension to diagnostic ultrasonographic imaging. Many authors have described the clinical value of these agents in liver, prostate, and breast imaging, among others. Newer types of media, the nanomolecules, are now emerging as the latest in imaging enhancers as well as therapeutic agent carriers. CONCLUSIONS: Although showing potential in imaging of the uterus and fallopian tubes as well as some obstetric applications, the contrast media, in particular the nanomolecules, seem to be most promising in ovarian cancer.

Contrast Media↗
PubMed2026

Profiler: an open web platform for multi-omics analysis.

MOTIVATION: High-throughput multi-omics technologies produce increasingly large and heterogeneous datasets that are difficult to analyze without advanced computational expertise. Existing bioinformatics tools are often fragmented or limited to specific omics types, hindering reproducibility and accessibility. There is a critical need for an integrated, user-friendly, and scalable platform capable of supporting multi-omics analyses across different data modalities. RESULTS: We present Profiler, an open-source, modular platform that unifies data import, quality control, preprocessing, statistical testing, machine and deep learning, biomarker discovery, pathway and drug-target enrichment, and survival modeling within a single reproducible environment. Built in Python with Streamlit, Profiler is available as both a web-based platform deployed on high-performance computing and a desktop version for local execution, enabling flexible usage across computational infrastructures. Profiler supports diverse omics modalities, including proteomics, transcriptomics, lipidomics, and electroencephalogram data. Through applications to glioblastoma proteomic, pancancer, and multi-omics datasets, Profiler reproduced known molecular subtypes, revealed potential therapeutic targets, and generated fully traceable analysis reports within minutes. By integrating advanced analytics behind an intuitive interface, Profiler democratizes multi-omics analysis and provides a robust, scalable foundation for systems biology and precision medicine research. AVAILABILITY AND IMPLEMENTATION: Profiler is open-source and freely available via its web platform (https://prism-profiler.univ-lille.fr) and GitHub (web version: https://github.com/yanisZirem/Profiler_v1_requests_datatests, desktop version: https://github.com/yanisZirem/prism-profiler), and archived on Zenodo (DOI: https://doi.org/10.5281/zenodo.17478158).

Software↗