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At least 991 records · Page 55Linked to original sources

PubMed2001

The Bioinformatics Template Library--generic components for biocomputing.

MOTIVATION: The efficiency of bioinformatics programmers can be greatly increased through the provision of ready-made software components that can be rapidly combined, with additional bespoke components where necessary, to create finished programs. The new standard for C++ includes an efficient and easy to use library of generic algorithms and data-structures, designed to facilitate low-level component programming. The extension of this library to include functionality that is specifically useful in compute-intensive tasks in bioinformatics and molecular modelling could provide an effective standard for the design of reusable software components within the biocomputing community. RESULTS: A novel application of generic programming techniques in the form of a library of C++ components called the Bioinformatics Template Library (BTL) is presented. This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that allows them to be flexibly combined with application specific object-oriented class libraries. AVAILABILITY: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html

Algorithms↗

PubMed2005

SOAP-based services provided by the European Bioinformatics Institute.

SOAP (Simple Object Access Protocol) (http://www.w3.org/TR/soap) based Web Services technology (http://www.w3.org/ws) has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3-9]. These services are available free to all users from http://www.ebi.ac.uk/Tools/webservices.

Biotechnology↗

PubMed2002

EZ-Retrieve: a web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites.

The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool designated EZ-Retrieve that can: (i) retrieve any particular region of human genome sequence from the NCBI database and (ii) analyze retrieved sequences for putative transcription factor-binding sites (TFBSs) as they appear on the TRANSFAC database. The tool is web-based, user-friendly and offers both batch sequence retrieval and batch TFBS prediction. A major application of EZ-Retrieve is the analysis of co-expressed genes that are highlighted as expression clusters in DNA microarray experiments.

Animals↗

PubMed2004

Finding community structure in very large networks.

The discovery and analysis of community structure in networks is a topic of considerable recent interest within the physics community, but most methods proposed so far are unsuitable for very large networks because of their computational cost. Here we present a hierarchical agglomeration algorithm for detecting community structure which is faster than many competing algorithms: its running time on a network with n vertices and m edges is O (md log n) where d is the depth of the dendrogram describing the community structure. Many real-world networks are sparse and hierarchical, with m approximately n and d approximately log n, in which case our algorithm runs in essentially linear time, O (n log(2) n). As an example of the application of this algorithm we use it to analyze a network of items for sale on the web site of a large on-line retailer, items in the network being linked if they are frequently purchased by the same buyer. The network has more than 400 000 vertices and 2 x 10(6) edges. We show that our algorithm can extract meaningful communities from this network, revealing large-scale patterns present in the purchasing habits of customers.

Journal Article↗

PubMedDate not supplied

WORLDMAPPER: the world as you've never seen it before.

This paper describes the Worldmapper Project, which makes use of novel visualization techniques to represent a broad variety of social and economic data about the countries of the world. The goal of the project is to use the map projections known as cartograms to depict comparisons and relations between different territories, and its execution raises many interesting design challenges that were not all apparent at the outset. We discuss the approaches taken towards these challenges, some of which may have considerably broad application. We conclude by commenting on the positive initial response to the worldmapper images published on the web, which we believe is due, at least in part, to the particular effectiveness of the cartogram as a tool for communicating quantitative geographic data.

Algorithms↗

PubMed2006

Mprobe 2.0: computer-aided probe design for oligonucleotide microarray.

UNLABELLED: DNA chips have proven to be effective tools in detecting gene expression levels. Compared with DNA chips using complementary DNA as probes, oligonucleotide microarrays using oligonucleotides as probes have attracted great attention because of their well known advantages. The design of gene-specific probes for each target is essential to the development of oligonucleotide microarrays. We have previously reported the development of a probe design software termed Mprobe 1.0. Here, we present a new version of this software, termed Mprobe 2.0. Several new features are included in Mprobe 2.0. Firstly, a paradox-based sequence database management system has been developed and integrated into the software, which consequently allows interoperability with sequences in GenBank, EMBL, and FASTA formats. Secondly, in contrast to setting a fixed threshold for the secondary structure of probes in Mprobe 1.0 and other related software, Mprobe 2.0 employs a different method. After parameters such as GC type, probe melting temperature and GC contents have been evaluated, candidate probes are sorted by the free energy from high to low value, followed by specificity analysis. Thirdly, Mprobe 2.0 provides users with substantial parameter options in the visual mode. Mprobe 2.0 possesses an easier interface for users to manage sequences annotated in different formats and design the optimal probes for oligonucleotide microarrays and other applications. AVAILABILITY: The program is free for non-commercial users and can be downloaded from the web page http://www.biosun.org.cn/mprobe/ CONTACT: Wuju Li (wujuli@yahoo.com or liwj@nic.bmi.ac.cn).

Algorithms↗

PubMed2001

Beginning to manage drug discovery and development knowledge.

Knowledge management approaches and technologies are beginning to be implemented by the pharmaceutical industry in support of new drug discovery and development processes aimed at greater efficiencies and effectiveness. This trend coincides with moves to reduce paper, coordinate larger teams with more diverse skills that are distributed around the globe, and to comply with regulatory requirements for electronic submissions and the associated maintenance of electronic records. Concurrently, the available technologies have implemented web-based architectures with a greater range of collaborative tools and personalization through portal approaches. However, successful application of knowledge management methods depends on effective cultural change management, as well as proper architectural design to match the organizational and work processes within a company.

Artificial Intelligence↗

PubMed1978

Neurovascular free foot flaps in reconstruction of the mutilated hand.

The neurovascular free flap from the first web region of the foot affords unrivalled potential for refurbishing sensibility to the denervated hand. Its greatest application is when no conventional island flap tissue remains for transfer. Its two-point discrimination is only moderate, but when used for thumb reconstruction, its sensibility is adequate because no functional substitute exists. Functionally and cosmetically it is superior to other methods of thumb reconstruction because of its pulp, size, and nail availability. There are no finger identification problems and secondary donor defects are minimal.

Adult↗

PubMed2004

Content-based image retrieval in medical applications.

OBJECTIVES: To develop a general structure for semantic image analysis that is suitable for content-based image retrieval in medical applications and an architecture for its efficient implementation. METHODS: Stepwise content analysis of medical images results in six layers of information modeling incorporating medical expert knowledge (raw data layer, registered data layer, feature layer, scheme layer, object layer, knowledge layer). A reference database with 10,000 images categorized according to the image modality, orientation, body region, and biological system is used. By means of prototypes in each category, identification of objects and their geometrical or temporal relationships are handled in the object and the knowledge layer, respectively. A distributed system designed with only three core elements is implemented: (i) the central database holds program sources, processing scheme descriptions, images, features, and administrative information about the workstation cluster; (ii) the scheduler balances distributed computing; and (iii) the web server provides graphical user interfaces for data entry and retrieval, which can be easily adapted to a variety of applications for content-based image retrieval in medicine. RESULTS: Leaving-one-out experiments were distributed by the scheduler and controlled via corresponding job lists offering transparency regarding the viewpoints of a distributed system and the user. The proposed architecture is suitable for content-based image retrieval in medical applications. It improves current picture archiving and communication systems that still rely on alphanumerical descriptions, which are insufficient for image retrieval of high recall and precision.

Databases as Topic↗

PubMed2026

Predictive Models for Hypoglycemia Risk in Haemodialysis Patients With Diabetic Kidney Disease: Systematic Review and Meta-Analysis.

AIM: To provide evidence for selecting and developing reliable clinical assessment tools for hypoglycemia in diabetic kidney disease patients during haemodialysis. DESIGN: Review. METHODS: Systematic searches were performed in 9 Chinese and English databases to collect literature regarding the development of hypoglycemia risk prediction models in haemodialysis patients with diabetic kidney disease. Two reviewers independently performed literature screening, data extraction, risk-of-bias assessment, and applicability evaluation. The Prediction Model Risk of Bias Assessment Tool was used to assess the risk of bias and applicability of the included studies. Meta-analysis was conducted using R software. DATA SOURCES: CNKI, Wanfang, VIP, CBM, PubMed, Cochrane Library, EMbase, Web of Science, and CINAHL. The search period covered from the establishment date of each database to December 2025. RESULTS: Six studies, comprising six prediction models, were included. Two studies performed internal validation, and three conducted external validation. All models reported the area under the curve, ranging from 0.813 to 0.866, and calibration measures. Four studies were rated as having a high risk of bias, while all six demonstrated good overall applicability. The meta-analysis showed that the pooled AUC value of the six studies was 0.846 (95% CI: 0.823-0.867). CONCLUSION: Research on hypoglycemia risk prediction models in haemodialysis patients with diabetic kidney disease remains in the developmental stage. Although the included prediction models exhibited satisfactory apparent discriminatory ability and clinical applicability, most of the original studies suffered from a high risk of bias and lacked adequate validation. The true predictive performance and clinical application value of these models remain to be further verified. Accordingly, routine and unconditional clinical application is not recommended at this stage. Future studies should include more high-quality, multicenter external validation and develop models with high generalizability, favourable clinical applicability, and robust predictive performance to facilitate early identification of hypoglycemia risk in this population. IMPACT: This study systematically evaluated the hypoglycemia risk prediction models for diabetic kidney disease patients during haemodialysis, and the research on hypoglycemia risk prediction models for maintenance haemodialysis patients during dialysis is still in the development stage. This study provides a reference for clinical medical staff to select or develop hypoglycemia risk prediction and assessment tools for diabetic kidney disease patients during haemodialysis. REPORTING METHOD: This study was conducted in accordance with the relevant guidelines of the EQUATOR Network and followed the TRIPOD-SRMA Checklist. PATIENT OR PUBLIC CONTRIBUTION: No patient or public contribution. TRIAL REGISTRATION: PROSPERO: CRD420251243352.

Humans↗

PubMed2001

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

OBJECTIVE: We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. MATERIALS/METHODS: This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. CONCLUSION: This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

Computer-Assisted Instruction↗

PubMed2002

A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators.

Accurate identification of species that are consumed by vertebrate predators is necessary for understanding marine food webs. Morphological methods for identifying prey components after consumption often fail to make accurate identifications of invertebrates because prey morphology becomes damaged during capture, ingestion and digestion. Another disadvantage of morphological methods for prey identification is that they often involve sampling procedures that are disruptive for the predator, such as stomach flushing or lethal collection. We have developed a DNA-based method for identifying species of krill (Crustacea: Malacostraca), an enormously abundant group of invertebrates that are directly consumed by many groups of marine vertebrates. The DNA-based approach allows identification of krill species present in samples of vertebrate stomach contents, vomit, and, more importantly, faeces. Utilizing samples of faeces from vertebrate predators minimizes the impact of dietary studies on the subject animals. We demonstrate our method first on samples of Adelie penguin (Pygoscelis adeliae) stomach contents, where DNA-based species identification can be confirmed by prey morphology. We then apply the method to faeces of Adelie penguins and to faeces of the endangered pygmy blue whale (Balaenoptera musculus brevicauda). In each of these cases, krill species consumed by the predators could be identified from their DNA present in faeces or stomach contents.

Animals↗

PubMedDate not supplied

Virtual reality, telemedicine, web and data processing innovations in medical and psychiatric education and clinical care.

OBJECTIVE: This article highlights technology innovations in psychiatric and medical education, including applications from other fields. METHOD: The authors review the literature and poll educators and informatics faculty for novel programs relevant to psychiatric education. RESULTS: The introduction of new technologies requires skill at implementation and evaluation to assess the pros and cons. There is a significant body of literature regarding virtual reality and simulation, including assessment of outcomes, but other innovations are not well studied. CONCLUSIONS: Innovations, like other uses of technology, require collaboration between parties and integration within the educational framework of an institution.

Delivery of Health Care↗

PubMed2005

Propulsive force calculations in swimming frogs. II. Application of a vortex ring model to DPIV data.

Frogs propel themselves by kicking water backwards using a synchronised extension of their hind limbs and webbed feet. To understand this propulsion process, we quantified the water movements and displacements resulting from swimming in the green frog Rana esculenta, applying digital particle image velocimetry (DPIV) to the frog's wake. The wake showed two vortex rings left behind by the two feet. The rings appeared to be elliptic in planform, urging for correction of the observed ring radii. The rings' long and short axes (average ratio 1.75:1) were about the same size as the length and width of the propelling frog foot and the ellipsoid mass of water accelerated with it. Average thrust forces were derived from the vortex rings, assuming all propulsive energy to be compiled in the rings. The calculated average forces (F(av)=0.10+/-0.04 N) were in close agreement with our parallel study applying a momentum-impulse approach to water displacements during the leg extension phase. We did not find any support for previously assumed propulsion enhancement mechanisms. The feet do not clap together at the end of the power stroke and no "wedge-action" jetting is observed. Each foot accelerates its own water mantle, ending up in a separate vortex ring without interference by the other leg.

Animals↗

PubMed2002

New application tracks nursing care, results.

More accurate information available both for self-evaluation and benchmarking. Outcome performance improvement can be tracked over time. Web-based version is under development.

Benchmarking↗

PubMed2001

Beyond requirements: residency management through the Internet.

HYPOTHESIS: An Internet application could collect information to satisfy documentation required by the Residency Review Committee. Beyond replacing a difficult and inefficient paper system, it would collect, process, and distribute information to administration, faculty, and residents. DESIGN: Descriptive study. SETTING: An integrated residency of 18 services at a university teaching hospital with 4 affiliated institutions. PARTICIPANTS: Residency administrators, faculty, and residents. INTERVENTIONS: The application included a procedure recorder, resident evaluation of faculty and rotations, goals and objectives (stratified by service and resident level), and matching faculty evaluation of residents with these goals as competencies. Policies, schedules, research opportunities, clinical site information, and curriculum support were created. MAIN OUTCOME MEASURES: Degree of compliance with Residency Review Committee standards, number of deficiencies corrected, and quantity and quality of information available to administration, faculty, and residents. RESULTS: The Internet system increased resident compliance for faculty and rotation evaluations from 20% and 34%, respectively, to 100%, which was maintained for 22 months. These evaluations can be displayed individually, in summary grids, and as postgraduate year-specific averages. Faculty evaluations of residents can be reviewed throughout the system. The defined category report for procedures, which had deficiencies in the preceding 6 years, had none for the last 2 years. The Internet application provides Accreditation Council for Graduate Medical Education-validated operative logs to regulatory agencies. CONCLUSIONS: A Web-based system can satisfy requirements and provide processed data that are of better quality and more complete than our paper system. We are now able to use scarce time and personnel to nurture developing surgical residents instead of shuffling paper.

Connecticut↗

PubMed2003

Increased microvascular permeability in the hamster cheek pouch induced by oxidized low density lipoprotein (oxLDL) and some fragmented apolipoprotein B proteins.

OBJECTIVE AND DESIGN: Oxidized low-density lipoproteins (oxLDL) and protein fractions obtained by size exclusion chromatography of oxLDL were tested for vascular permeability effects on topical application to the hamster cheek pouch. MATERIALS: The hamster cheek pouch was prepared for intravital microscopy observations of macromolecular leakage at post capillary venules (=leaks) with FITC-dextran as tracer. TREATMENT: OxLDL (0.1 mg/ml), PAF (platelet activation factor, 50-100 nM) and protein fractions of oxLDL (10 microg/ml) were applied topically to hamster cheek pouches. RESULTS: Application of oxLDL and PAF resulted in reversible increases in the number of leaks. The PAF-antagonist WEB 2170, L-NAME and a beta(2)-adrenoceptor agonist inhibited (P<0.01) almost completely the macromolecular leakage induced with oxLDL or PAF. Protein fractions were found to be more effective than unfractionated oxLDL in inducing plasma leakage as calculated on mg/ml-basis. CONCLUSION: Hamster oxLDL is a potent inducer of macromolecular leakage increase in the hamster cheek pouch microcirculation. The principal effect is mediated by PAF-like structures produced by the oxidation of the LDL-particle but oxLDL also contains low molecular weight proteins that could contribute to the overall vascular permeability increasing effect of ox LDL.

Adrenergic beta-2 Receptor Agonists↗

PubMed2005

CoCoDat: a database system for organizing and selecting quantitative data on single neurons and neuronal microcircuitry.

We present a novel database system for organizing and selecting quantitative experimental data on single neurons and neuronal microcircuitry that has proven useful for reference-keeping, experimental planning and computational modelling. Building on our previous experience with large neuroscientific databases, the system takes into account the diversity and method-dependence of single cell and microcircuitry data and provides tools for entering and retrieving published data without a priori interpretation or summarizing. Data representation is based on the framework suggested by biophysical theory and enables flexible combinations of data on membrane conductances, ionic and synaptic currents, morphology, connectivity and firing patterns. Innovative tools have been implemented for data retrieval with optional relaxation of search criteria along the conceptual dimensions of brain region, cortical layer, cell type and subcellular compartment. The relaxation procedures help to overcome the traditional trade-off between exact, non-interpreted data representation in the original nomenclature and convenient data retrieval. We demonstrate the use of these tools for the construction, tuning and validation of a multicompartmental model of a layer V pyramidal cell from the rat barrel cortex. CoCoDat is freely available at . Its application is scalable from offline use by individual researchers via local laboratory networks to a federation of distributed web sites in platform-independent XML format using Axiope tools.

Action Potentials↗