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At least 1,261 records · Page 70Linked to original sources
PubMed1998

Telematic system for monitoring of asthma severity in patients' homes.

Despite advances in the treatment of asthma the morbidity and mortality of this disease has increased significantly in the past several years. Recent studies have shown that monitoring of asthma severity in the patient home especially combined with patient education can reduce incidence of asthma exacerbation and subsequent hospitalization. The existing methods for home asthma monitoring are limited by four factors; they completely rely on a patient's ability to document and to evaluate test results; there is no easy way for a physician to review data in a timely manner; they use imprecise tools for evaluation of asthma severity and they don't provide clinical decision support tools. The goal of this study is to develop and to evaluate a telematic system for asthma severity monitoring which will minimize patients' efforts in performing self-testing at their homes and allow prompt reciprocal exchange of all relevant information between patients and health care providers. In our setting, patients use portable spirometer and pocket-sized palmtop computer for data exchange. Our system allows daily serial monitoring of asthma severity at patients' homes using Forced Vital Capacity test and symptom diary. The results of the tests become available for physicians review immediately after completion of self-testing procedures via Web browser. The results can be transmitted from patients' homes (or any other remote location) to the medical records database via landline or wireless networks in several minutes. Each time the remote server receives patient's results, it invokes the application which tests the validity of data, analyzes parameters trends and dispatches corresponding messages for the patient and, if necessary, for physicians. Such an approach provides constant feedback loop between asthma patient and physician. The system has been tested in 10 healthy volunteers and asthma patients. Patients participated in the study from two to 21 days. The test results showed that the system provides reliable reciprocal exchange of all relevant information between a physician and asthma patient in home settings. Average transmission time from the patient's palmtop to the remote central data repository was about 1 minute for 14.4 Kbps landline modem, 6 minutes for cellular network and 8 minutes for RAM Mobile network. After transmission, the test results were immediately available for review at our web site.

Asthma↗
PubMed2006

Recent applications of capillary electrophoresis-electrospray ionisation-mass spectrometry in drug analysis.

This review considers applications in 2004-2005 of capillary electrophoresis-electrospray ionisation-mass spectrometry (CE-ESI-MS) to the detection and determination of small molecular mass drug molecules, taken from the Web of Knowledge database. The molecules of small molecular mass less than 1000 Da are chosen according to selected structural classes in which they give ESI signals primarily as [M + H](+) ions. These structural classes are drugs with amine-containing side chains, drugs with N-containing saturated ring structures, 1,4-benzodiazepines, other heterocyclic hypnotics, steroids, bioactive compounds containing phenolic groups, and miscellaneous molecules. Details are given on the fragmentations, where available, that these ionic species exhibit in-source and in ion-trap, triple quadrupole and time-of flight mass spectrometers. The review then gives a critical evaluation of these recent CE-ESI-MS analytical methods for the detection and determination of these small molecular mass drug molecules. Analytical information on, for example, sample concentration techniques, CE separation conditions, recoveries from biological media and limits of detection are provided.

Electrophoresis, Capillary↗
PubMedDate not supplied

Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM.

We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.

Journal Article↗
PubMed2006

MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions.

UNLABELLED: Normal adaptive immune responses operate under major histocompatibility complex (MHC) restriction by binding to specific, short antigenic peptides and presenting them to appropriate T-cell receptors (TcRs). Sequence-structure-function information is critical in understanding the principles governing peptide/MHC (pMHC) and TcR/pMHC recognition and binding. A new database for sequence-structure-function information on TcR/pMHC interactions, MHC-Peptide Interaction Database version T (MPID-T), is now available with the latest available Protein Data Bank (PDB) data and interaction parameters on TcR/pMHC complexes. MPID-T is a manually curated MySQL database containing experimentally determined structures of 187 pMHC complexes and 16 TcR/pMHC complexes available in the PDB. Each structure is manually verified, classified, and analysed for intermolecular interactions (i) between the MHC and its corresponding bound peptide and (ii) between TcR and its bound pMHC complex where TcR structural information is available. The MPID-T database retrieval system has precomputed interaction parameters that include solvent accessibility, hydrogen bonds, gap volume and gap index. Structural visualisation of the TcR/pMHC complex, pMHC complex, MHC or the bound peptide can be performed using freely available graphics applications such as MDL Chime or RasMol, while structural alignment (based on MHC class and peptide length) can be viewed using the Jmol molecular viewer or an MDL Chime-compatible web browser client. MPID-T contains structural descriptors for in-depth characterisation of TcR/pMHC and pMHC interactions. The ultimate purpose of MPID-T is to enhance the understanding of the binding mechanism underlying TcR/pMHC and pMHC interactions by mapping the TcR footprint on the MHC and its bound peptide, as this eventually determines T-cell recognition and binding. AVAILABILITY: The MPID-T database retrieval system is available at http://surya.bic.nus.edu.sg/mpidt CONTACT: Joo Chuan Tong (jctong@i2r.a-star.edu.sg).

Animals↗
PubMed1999

National Academy of Clinical Biochemistry Standards of Laboratory Practice: recommendations for the use of cardiac markers in coronary artery diseases.

The Sixth Conference on the "Standards of Laboratory Practice Series", sponsored by the National Academy of Clinical Biochemistry (NACB), was held on August 4-5, 1998, at the Annual Meeting of the American Association for Clinical Chemistry, in Chicago, IL. An expert committee was assembled to write recommendations on the use of cardiac markers in coronary artery diseases. The NACB Committee prepared a preliminary draft of the guidelines, made them available on the World Wide Web (www.nacb.org), and distributed them before the presentations. The recommendations were divided into four areas: the use of markers in the triage of patients with chest pain, acute coronary syndromes, clinical applications other than acute myocardial infarction and research, and assay platforms and markers of acute myocardial infarction. The recommendations were revised and subsequently re-presented in part at the "Biomarkers in Acute Cardiac Syndromes Conference", sponsored by the Jewish Hospital Heart and Lung Institute, Louisville KY, on October 16-17, 1998. This report lists each recommendation, its scientific justification, and a summary of discussions from conference participants and reviewers. Approximately 100 individuals responded to various versions of these recommendations via direct correspondences, telephone calls to Committee members, electronic mail correspondence to the Committee Chairman, or oral questions and comments raised during one of the two conference presentations. Some of the recommendations were changed to reflect the consensus opinion. In cases in which there was no consensus, the Committee included pertinent discussion without necessarily changing the original recommendations. At times, the Committee members felt that although a particular recommendation might not be the current standard of care today, they anticipate that it likely will be adopted in the near future.

Biomarkers↗
PubMed2000

An XML-Java system for HL7-based healthcare informatics.

Health-Level (HL) 7 message semantics allows effective functional implementation of Electronic Medical Record (EMR)--encompassing both clinical and administrative (i.e. demographic and financial) information--interchange systems, at the expense of complexity with respect the Protocol Data Unit (PDU) structure and the client-side application architecture. In this paper we feature the usage of the Extensible Markup Language (XML) document-object modelling and Java client-server connectivity towards the implementation of a Web-based system for EMR transaction processing. Our solution features an XML-based description of EMR templates, which are subsequently transcribed into a Hypertext Markup Language (HTML)-Javascript form. This allows client-side user interfaceability and server-side functionality--i.e. message validation, authentication and database connectivity--to be handled through standard Web client-server mechanisms, the primary assumption being availability of a browser capable of XML documents and the associated stylesheets. We assume usage of the Internet as the interchange medium, hence the necessity for authentication and data privacy mechanisms, both of which can be constructed using standard Java-based building blocks.

Computer Communication Networks↗
PubMed2006

Lectindb: a plant lectin database.

Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

Algorithms↗
PubMed2002

Data mining of sequences and 3D structures of allergenic proteins.

MOTIVATION: Many sequences, and in some cases structures, of proteins that induce an allergic response in atopic individuals have been determined in recent years. This data indicates that allergens, regardless of source, fall into discreet protein families. Similarities in the sequence may explain clinically observed cross-reactivities between different biological triggers. However, previously available allergy databases group allergens according to their biological sources, or observed clinical cross-reactivities, without providing data about the proteins. A computer-aided data mining system is needed to compare the sequential and structural details of known allergens. This information will aid in predicting allergenic cross-responses and eventually in determining possible common characteristics of IgE recognition. RESULTS: The new web-based Structural Database of Allergenic Proteins (SDAP) permits the user to quickly compare the sequence and structure of allergenic proteins. Data from literature sources and previously existing lists of allergens are combined in a MySQL interactive database with a wide selection of bioinformatics applications. SDAP can be used to rapidly determine the relationship between allergens and to screen novel proteins for the presence of IgE or T-cell epitopes they may share with known allergens. Further, our novel similarity search method, based on five dimensional descriptors of amino acid properties, can be used to scan the SDAP entries with a peptide sequence. For example, when a known IgE binding epitope from shrimp tropomyosin was used as a query, the method rapidly identified a similar sequence in known shellfish and insect allergens. This prediction of cross-reactivity between allergens is consistent with clinical observations. AVAILABILITY: SDAP is available on the web at http://fermi.utmb.edu/SDAP/index.html

Allergens↗
PubMed2001

Identification of model structure for aquatic ecosystems using regionalized sensitivity analysis.

The Regionalized Sensitivity Analysis (RSA) was developed in 1978, for identifying critical unknown processes in poorly defined systems, thus directing the focus of further scientific investigations. Here, we demonstrate its application to model structure identification, by ranking the constituent hypotheses and identifying the critical elements for progressive revision of the model. Our case study is Lake Oglethorpe--a small monomictic impoundment in South-eastern Georgia, USA. Recent studies indicate that the warm temperate regional climate affords an extended growing season--typically from March to October--which promotes bacterial productivity in the lake. The result is a summer food web dominated by microbial processes, in contrast to the conventional phytoplankton-dominated food chains typically observed in the cold temperate lakes of Europe and North America. Starting with a simple phytoplankton-based food web model and a qualitative definition of system behaviour, we use the RSA procedure to establish the critical role of bacteria-mediated decomposition in Lake Oglethorpe, thus justifying the inclusion of microbial processes. Further analysis reveals the importance of size-dependent selective consumption of phytoplankton and bacteria. Finally, we discuss important practical implications of this novel application of the RSA regarding sampling efficiency and statistical robustness.

Animals↗
PubMed2004

JDotter: a Java interface to multiple dotplots generated by dotter.

UNLABELLED: Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. AVAILABILITY: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location. SUPPLEMENTARY INFORMATION: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.

Computer Graphics↗
PubMed2026

Artificial intelligence (AI) uses in stereotactic radiosurgery (SRS): diagnosis with brain metastasis (BM) - A systematic review.

BACKGROUND: Brain metastases (BM) are the most common intracranial tumors in adults, and stereotactic radiosurgery (SRS) has become a mainstay of management. However, several diagnostic challenges persist in the SRS pathway, particularly the differentiation of radiation necrosis (RN) from true tumor progression, which conventional MRI and even advanced imaging techniques often cannot reliably resolve. Recent advances in artificial intelligence (AI) offer the potential to address these diagnostic limitations. This systematic review synthesizes current literature on AI applications for MRI-based diagnostic decision support in BM patients undergoing SRS, with a focus on radiomics and deep learning tools for distinguishing RN from progression, classifying molecular and histologic subtypes, and predicting treatment response. METHODS: A systematic review was performed in accordance with PRISMA guidelines. PubMed, Web of Science, and Scopus were searched using a targeted query combining terms related to AI, brain metastasis, diagnosis or imaging, and SRS. After screening 483 records and applying strict inclusion and exclusion criteria, 18 studies published between 2015 and 2025 were included. Data were extracted on study design, cohort characteristics, imaging modality, AI methodology, validation strategy, and reported diagnostic performance. RESULTS: Among the 18 included studies, AI models demonstrated strong performance across diagnostic tasks in the BM-SRS pathway. The differentiation of RN from true tumor progression was the most extensively studied application, addressed by 14 of 18 studies, with reported AUCs ranging from 0.71 to 0.94. Support vector machines, random-forest ensembles, convolutional neural networks, and transformer-based multimodal architectures were widely used. The literature evolved from single-sequence radiomic classifiers in 2018 to multimodal deep learning frameworks fusing imaging with clinical and genomic data in 2025. Contrast-enhanced T1-weighted MRI was the dominant imaging input, and texture-based radiomic features (GLCM, GLSZM, GLDM, and wavelet-derived features) were the most consistently predictive. The highest-performing models reached AUCs of 0.85-0.91 through multimodal integration of imaging with clinical and genomic features, and consistently outperformed expert neuroradiologist read on matched cases. Remaining studies addressed longitudinal segmentation-based detection of local failure and adverse radiation effects, BRAF mutation status in melanoma BM, early Gamma Knife treatment response, and primary tumor histology classification, with more variable performance. CONCLUSION: AI models, particularly those integrating MRI-derived radiomic features with clinical and genomic data, show high accuracy in supporting diagnostic decisions for BM patients treated with SRS. The post-SRS differentiation of radiation necrosis from true tumor progression has reached the greatest level of maturity and is closest to clinical translation, with potential to reduce unnecessary biopsies, personalize surveillance intervals, and rationalize treatment-pathway decisions. Other diagnostic applications, including molecular subtyping and primary tumor histology classification, remain exploratory and require further multicenter validation. Integration of AI tools into multidisciplinary tumor-board workflows, combined with prospective validation and standardized reporting, will be essential to realize the full clinical benefits of AI in SRS for brain metastases.

Humans↗
PubMed2006

Applications of the Colorado Visible Human Project in gastroenterology.

Several applications of the University of Colorado Visible Human project have recently been developed in clinical gastroenterology, including a textbook of endoscopic ultrasound anatomy, an internet-based journal, articles on internet web-sites, and simulators. Details surrounding some of these projects are described.

Colorado↗
PubMed1990

The distally-based dorsal hand flap.

The planning and clinical applications of a series of reverse dorsal hand flaps are described. This new flap is based on a direct cutaneous branch of the dorsal metacarpal artery. It is particularly useful in resurfacing web spaces as well as dorsal metacarpal and phalangeal skin defects. The behaviour of 21 such flaps, all raised in the form of an island, was that of a conventional axial pattern flap.

Adolescent↗
PubMed2026

Molecular DNA enrichment methods for parasite genomic sequencing in clinical samples: a systematic review.

Parasitic diseases such as malaria, Chagas disease, leishmaniases, and helminthiases are major causes of sickness and death in low- and middle-income countries. The high genetic diversity of these pathogens affects virulence, immune evasion, and diagnostic accuracy. Although Whole Genome Sequencing (WGS) is a powerful tool for tracking genetic variants and drug resistance, low parasitemia and the predominance of host DNA limit its application to clinical samples. This study systematically reviewed molecular strategies to improve the recovery of parasite DNA from clinical samples, following PRISMA 2020 guidelines and registered in PROSPERO. Searches of PubMed, Scopus, Web of Science, and LILACS up to December 2025 identified 20 eligible studies, most of which focused on protozoa, particularly Plasmodium spp. The main approaches included hybridization capture, selective whole-genome amplification, host DNA depletion, and in silico enrichment via adaptive sampling. Overall, no single method is suitable for all parasites analyzed; the optimal approach depends on the pathogen, sample type, and research objective. The review emphasizes that parasite DNA enrichment is essential for enabling WGS in clinical settings, underscoring the need for protocol standardization and cost-effectiveness analyses to support public health genomic surveillance.

Adaptive sampling↗
PubMed2004

Development of the Draft 2005 recommendations of the ICRP: a collection of papers. A report of ICRP supporting guidance 4.

In 1997, the International Commission on Radiological Protection (ICRP) initiated a project intended to lead up to the replacement of its 1990 Recommendations (Publication 60)with a view to producing new, consolidated Recommendations 10-15 years after those of 1990. In order to stimulate comprehensive discussion, an open and iterative consultation process was used. An initial set of conceptual proposals to be considered by the Commission,and two later progress reports describing how and why ideas evolved in interaction with the radiological protection community, were published in the Journal of Radiological Protection (JRP). These three papers are reproduced here with kind permission by the Institute of Physics Publishing. As a result of consultation on the initial conceptual proposals and subsequent debate, the Commission has now drafted a proposed text for its 2005 Recommendations. This is intended not as a radical revision, but as a more coherent statement of current policy and as implification in its application. The summary of that draft is also reproduced here, while the full text, which is subject to public consultation until 31 December 2004, can be down loaded from the Commission's web site, www.icrp.org.

Humans↗
PubMed2005

The role of web-based environmental information in urban planning--the environmental information system for planners.

The Environmental Information System for Planners (EISP) is a proof of concept web-based system designed to support decision making within the UK planning framework by making information on environmental issues more widely accessible. It incorporates relevant outputs from the Natural Environment Research Council (NERC) Urban Regeneration and the Environment (URGENT) research programme and from research directly commissioned by the Office of the Deputy Prime Minister (ODPM). It supports three principal planning functions carried out by local authorities: pre-planning enquiries, development control decisions and strategic planning. Eleven environmental science themes are incorporated: Air quality, Shallow undermining, Landslide susceptibility, Groundwater protection, Flood risk, Drainage, Land contamination, Proximity to landfill, Biodiversity, Natural and Man-made heritage. Decision flow diagrams represent detailed analysis of workflow in each theme, taking account of best practice, regulatory responsibilities and planning guidance. Industry-standard web technologies integrate the flows and provide access to the system via secure web pages. Underpinning the system is an environmental geographical information system (GIS) containing up-to-date data, information and models relevant to each theme. The modular system design allows new legislation and local priorities and datasets to be easily incorporated. Web technology delivers information and research data that have hitherto been difficult for the non-specialist to access and have therefore been under-exploited. The study has demonstrated a successful application of the principles of e-Governance in an area where informed decisions commonly require specialist information. The system, if rolled out nationally, offers potential economic benefits and efficiency savings for both planners and developers.

City Planning↗
PubMed2002

BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.

MOTIVATION: Understanding the biochemistry of a newly sequenced organism is an essential task for post-genomic analysis. Since, however, genome and array data grow much faster than biochemical information, it is necessary to infer reactions by comparative analysis. No integrated and easy to use software tool for this purpose exists as yet. RESULTS: We present a new software system--BioMiner--for analyzing and visualizing biochemical pathways and networks. BioMiner is based on a new comprehensive, extensible and reusable data model--BioCore--which can be used to model biochemical pathways and networks. As a first application we present PathFinder, a new tool predicting biochemical pathways by comparing groups of related organisms based on sequence similarity. We successfully tested PathFinder with a number of experiments, e.g. the well studied glycolysis in bacteria. Additionally, an application called PathViewer for the visualization of metabolic networks is presented. PathViewer is the first application we are aware of which supports the graphical comparison of metabolic networks of different organisms. AVAILABILITY: http://www.zbi.uni-saarland.de/chair/projects/BioMiner SUPPLEMENTARY INFORMATION: Additional information on experimental results can be found on our web site.

Biochemistry↗