SEARCH · PubMed Health

Results for “Web application”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 631 records · Page 35Linked to original sources

PubMed2006

Gene and protein nomenclature in public databases.

BACKGROUND: Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. RESULTS: We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. CONCLUSION: In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries considerably increases size and decreases ambiguity. The entries of the curated synonym dictionary are available for manual querying, editing, and PubMed- or Google-search via the ProThesaurus-wiki. For automated querying via custom software, we offer a web service and an exemplary client application.

Abstracting and Indexing↗

PubMedDate not supplied

Spider web survey or whole plant visual sampling? Impact assessment of Bt corn on non-target predatory insects with two concurrent methods.

Impact assessment studies rely on relevant sampling methods. Correct evaluation of methods can be done by their concurrent use in the same sampling site and period. Collecting webs of Theridion impressum L. Koch (Araneae: Theridiidae) may serve as an arthropod sampling method: empty cuticles of prey items remain attached to the back side of the leaves with adhesive silk. Our study aimed to compare the applicability of the two methods concurrently (spider web survey and whole plant visual sampling) in a risk assessment study. The spider web survey recorded more predatory insect families than the whole plant visual sampling. Both methods were able to detect significant differences in the quantity of predatory insects in Bt vs. isogenic plots, but not in the same taxa (Nabidae: spider-web, 2001, Bt > Iso; Coccinellidae: plant sampling, 2001, Iso > Bt; Welsh-test, P < 0.05); thus, they could not confirm each other. The lack of confirmation can be explained by differences in the sensitivity and selectivity of the two methods. A web survey of T. impressum has the practical advantage that although we concentrate only on the one species during field sampling, we gain additional information on a wide range of foliage-dwelling arthropods. Due to several biological uncertainties, interpretation and explanation of the results remain problematic. Thus, additional research--based on in-situ observation and recording of T. impressum-prey interactions--is necessary before we could propose web survey method as a complementary tool in ecological impact assessment.

Animals↗

PubMed2001

National survey of internal medicine residency programs of their 1st-year experience with the electronic residency application service and national resident match program changes.

BACKGROUND: The residency recruitment and selection process is a critical one for residency programs and medical students. In 1999, internal medicine programs conducted the residency match on the Web for the first time using the Electronic Residency Application Service (ERAS). PURPOSE: The authors wished to study the impact of this change on house staff recruitment and quality of match. METHOD: A Web-based survey with e-mail, paper, and fax reminders was sent to all 407 internal medicine residency programs after the 1999 match. RESULTS: Eighty-six percent of reporting programs found the screening of applicants easier. The overall number of applicants varied greatly (48% of programs reported more applicants; 32% reported fewer). The quality of final match was rated the same as previous years by 47%, better by 38%, and worse by 15%. CONCLUSIONS: The transition to ERAS was successful in internal medicine. However, there are several areas that were identified that will improve the ERAS process as it evolves.

Data Collection↗

PubMed2003

From data to knowledge in e-health applications: an integrated system for medical information modelling and retrieval.

The system described in this paper uses the technological advances in information technology in order to influence and improve healthcare practice by enabling the flexible modelling, direct representation and adaptable use of medical knowledge. It aims at resolving a number of difficulties encountered by current information repositories, such as costly customization, reusability, high maintenance and poor information modelling, by employing the architecture of the functional data model (FDM), while maintaining full interoperability with existing systems by means of XML. On the information-modelling front the system supports a variety of modelling techniques that are especially relevant to medical applications, such as complex objects, incomplete or missing information, partially structured data and multimedia content. A prototype implementation of the system has been developed which consists of a multimedia-enhanced version of the functional database language FDL, and a web-based, two-way translator interface between the application's native language and XML. This interface provides full interoperability with other, heterogeneous systems over the web, thus, significantly reducing the complexity of developing distributed healthcare systems and e-health applications.

Computer Communication Networks↗

PubMed2004

Reporting point and interval estimates of effect-size for planned contrasts: fixed within effect analyses of variance.

UNLABELLED: The purpose of this tutorial is threefold: (a) review the state of statistical science regarding effect-sizes, (b) illustrate the importance of effect-sizes for interpreting findings in all forms of research and particularly for results of clinical-outcome research, and (c) demonstrate just how easily a criterion on reporting effect-sizes in research manuscripts can be accomplished. The presentation centers on within-effect analyses of variance including the one-way design for testing pre-post hypotheses and the two-way parallel-groups design for making direct comparisons of competing treatment protocols (e.g., experimental treatment versus control). The presentation is supported with worked examples and a web site containing templates for software applications. EDUCATIONAL OBJECTIVES: The reader will be able to: (1) explain the rationale for the increased use of estimates of effect-size in reporting results in published research manuscripts; (2) describe what an effect-size is (generally considered) and provide a rationale for its importance; (3) distinguish among the many forms of effect-size and apply their features to the most appropriate choices under specific research circumstances; and (4) appropriately report and interpret effect-sizes.

Algorithms↗

PubMed1995

Intra-uterine and juxtanatal repair of syndactyly in foetal mice.

39 foetal mice with genetic syndactyly were identified in utero at 17 days of gestation, and the right hindfoot extruded through the uterus. The syndactylous digits were separated by simple incisions. In one group (n = 25) digit separation was maintained during wound healing by the interdigital application of a silver microclip. Digit separation was also assessed in a second group of newborn mice less than 24 hours old (juxtanatal population, n = 24). Two foetuses (5%) and six newborns (25%) developed digital necrosis following microclip application. In the remaining microclipped animals (23 intrauterine and 10 juxtanatal), microclip application maintained digit separation, allowing wound healing to occur with epithelialization of the separated digits. No inflammation or scar formation occurred. In the third group (n = 22) without microclip application, the digital skin reapproximated and webbing recurred during wound healing. These studies demonstrate the need to maintain digit separation during wound healing following intra-uterine or juxtanatal syndactyly repair.

Animals↗

PubMed2026

Copper-Containing Surface Engineering for Soft-Tissue Biomedical Devices: Structure-Function Relationships and Ion Release-Driven Biological Performance, A Systematic Review.

Copper and copper-based materials have gained increasing attention for the functional modification of implantable medical devices intended for prolonged soft-tissue contact, including vascular stents, catheters, and intrauterine devices. Owing to their broad-spectrum antimicrobial activity, redox reactivity, and involvement in angiogenesis and cellular signaling, copper-based systems offer significant potential for multifunctional surface engineering. However, achieving a balance between antibacterial efficacy, corrosion behavior, controlled ion release, and cytocompatibility remains a critical challenge. This PRISMA-compliant systematic review analyzes copper-containing materials and surface modification strategies for soft-tissue biomedical applications. A structured search of Scopus, Web of Science, and PubMed (2015-2025) identified 65 eligible studies. The review encompasses bulk copper-containing alloys, electrochemical and chemical surface modification techniques, physical vapor deposition approaches, and advanced hybrid systems integrating copper with polymers, hydrogels, or metal-phenolic networks. Across the reviewed literature, antibacterial performance was strongly dependent on copper concentration, microstructural distribution, and spatiotemporal ion release profiles. Moderate, well-controlled copper incorporation frequently improved antibacterial efficacy while maintaining acceptable hemocompatibility and cytocompatibility, particularly in vascular and blood-contacting devices. In contrast, excessive copper loading often accelerated corrosion and induced adverse cellular responses. Emerging multifunctional architectures demonstrated improved regulation of biological interactions, enabling simultaneous antibacterial, antithrombotic, and proendothelial effects. Overall, copper-based surface technologies represent a versatile platform for soft-tissue implant modification. Future translational progress will require precise control of copper release kinetics and comprehensive long-term in vivo validation to ensure safety and sustained therapeutic performance. From the authors' perspective, the most promising future direction involves multifunctional copper-based hybrid coatings capable of dynamically regulating ion release, host tissue integration, and antibacterial performance simultaneously. Strategies integrating hierarchical architectures, stimulus-responsive release systems, and clinically scalable fabrication methods are expected to play a key role in translating copper-containing surfaces from experimental concepts toward commercially viable soft-tissue biomedical devices.

Copper↗

PubMed2003

Visual representation of database search results: the RHIMS Plot.

SUMMARY: An algorithm and software are described that provide a fast method to produce a novel, function-oriented visualization of the results of a sequence database search. Text mining of sequence annotations allows position specific plots of potential functional similarity to be compared in a simple compact representation. AVAILABILITY: The application can be accessed via a web server at http://www.compbio.dundee.ac.uk. The RHIMS software may be obtained by request to the authors.

Algorithms↗

PubMed2001

Practical success of biomanipulation using filter-feeding Fish to control cyanobacteria blooms: a synthesis of decades of research and application in a subtropical hypereutrophic lake.

Lake Donghu is a 32-km2 shallow, subtropical lake near the Yangtze River (P.R. China) that has experienced dramatic changes in the past five decades. These changes include: (1) a trophic state change from mesotrophy to hypertrophy; (2) dense blooms of cyanobacteria during every summer from the 1970s to 1984; (3) a cessation of blooms starting in 1985, with no recurrence; and (4) an increase, coincident with bloom declines, in the production of silver and bighead carp (filter-feeders) by more than tenfold. There are several possible explanations for the disappearance of blooms, including changes in nutrient concentrations, increased zooplankton grazing, and increased grazing on algae by fish. The long-term data suggest that changes in nutrients or in zooplankton were not important, but that the remarkably increased fish densities might have played the key role. To test this hypothesis, in situ enclosure experiments were conducted in three years. The main conclusions are as follows: (1) an increased stocking of the lake with carp played a decisive role in the elimination of cyanobacteria blooms; (2) both silver and bighead carp can eliminate cyanobacteria blooms directly by grazing; (3) zooplankton cannot suppress the blooms; and (4) the lake still is vulnerable to the outbreak of blooms, should fish grazing decline. The critical biomass of carp is approximately 50 g m3. The results suggest the applicability of a new food-web manipulation (increased stocking with filter-feeding fish) for controlling cyanobacteria blooms in hypereutrophic lakes. The approach differs from traditional biomanipulation in Europe and North America, where piscivores are added to control planktivores, and this in turn increases zooplankton and decreases algae. The new biomanipulation method is being used or being tested to counteract cyanobacteria blooms in many Chinese lakes such as Lake Dianchi in Yunnan Province, Lake Chaohu in Anhui Province, and Lake Taihu in Jiangsu Province. The method has great potential as an important component of an integrated approach to counteract cyanobacteria blooms, especially in lakes where nutrient inputs cannot be reduced sufficiently, and where zooplankton cannot effectively control phytoplankton production.

Animals↗

PubMed2004

EnsMart: a generic system for fast and flexible access to biological data.

The EnsMart system (www.ensembl.org/EnsMart) provides a generic data warehousing solution for fast and flexible querying of large biological data sets and integration with third-party data and tools. The system consists of a query-optimized database and interactive, user-friendly interfaces. EnsMart has been applied to Ensembl, where it extends its genomic browser capabilities, facilitating rapid retrieval of customized data sets. A wide variety of complex queries, on various types of annotations, for numerous species are supported. These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation. Users can group and refine biological data according to many criteria, including cross-species analyses, disease links, sequence variations, and expression patterns. Both tabulated list data and biological sequence output can be generated dynamically, in HTML, text, Microsoft Excel, and compressed formats. A wide range of sequence types, such as cDNA, peptides, coding regions, UTRs, and exons, with additional upstream and downstream regions, can be retrieved. The EnsMart database can be accessed via a public Web site, or through a Java application suite. Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets.

Animals↗

PubMed2002

MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison.

Advances in structural genomics and protein structure prediction require the design of automatic, fast, objective, and well benchmarked methods capable of comparing and assessing the similarity of low-resolution three-dimensional structures, via experimental or theoretical approaches. Here, a new method for sequence-independent structural alignment is presented that allows comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary model. The heuristic algorithm is given and then used to show that it can describe random structural alignments of proteins with different folds with good accuracy by an extreme value distribution. From this observation, a structural similarity score between two proteins or two different conformations of the same protein is derived from the likelihood of obtaining a given structural alignment by chance. The performance of the derived score is then compared with well established, consensus manual-based scores and data sets. We found that the new approach correlates better than other tools with the gold standard provided by a human evaluator. Timings indicate that the algorithm is fast enough for routine use with large databases of protein models. Overall, our results indicate that the new program (MAMMOTH) will be a good tool for protein structure comparisons in structural genomics applications. MAMMOTH is available from our web site at http://physbio.mssm.edu/~ortizg/.

Algorithms↗

PubMed2001

CODA: a combined algorithm for predicting the structurally variable regions of protein models.

CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a knowledge based approach, and PETRA, which constructs the region ab initio. FREAD selects from a database of protein structure fragments with environmentally constrained substitution tables and other rule-based filters. FREAD was parameterized and tested on over 3000 loops. The average root mean square deviation ranged from 0.78 A for three residue loops to 3.5 A for eight residue loops on a nonhomologous test set. CODA clusters the predictions from the two independent programs and makes a consensus prediction that must pass a set of rule-based filters. CODA was parameterized and tested on two unrelated separate sets of structures that were nonhomologous to one another and those found in the FREAD database. The average root mean square deviation in the test set ranged from 0.76 A for three residue loops to 3.09 A for eight residue loops. CODA shows a general improvement in loop prediction over PETRA and FREAD individually. The improvement is far more marked for lengths six and upward, probably as the predictive power of PETRA becomes more important. CODA was further tested on several model structures to determine its applicability to the modeling situation. A web server of CODA is available at http://www-cryst.bioc.cam.ac.uk/~charlotte/Coda/search_coda.html.

Algorithms↗

PubMed2003

Nesiritide: a novel approach for acute heart failure.

OBJECTIVE: To review preclinical and clinical information related to nesiritide, a recombinant form of B-type natriuretic peptide approved for treatment of acutely decompensated heart failure. DATA SOURCES: Primary and review articles were identified by MEDLINE search (1966-May 2002) using the key words natriuretic peptide and heart failure, and through secondary sources. Natrecor's document submitted for the Food and Drug Administration (FDA) New Drug Application were obtained from the FDA Web site. STUDY SELECTION/DATA EXTRACTION: Peer-reviewed articles and abstracts of randomized clinical trials in humans were included in this review. DATA SYNTHESIS: Nesiritide has beneficial actions for treatment of heart failure, including arterial and venous dilatation, enhanced sodium and urinary excretion, and suppression of the renin-angiotensin-aldosterone and sympathetic nervous systems. It has been shown to improve hemodynamic parameters, primarily pulmonary capillary wedge pressure, as well as clinical symptoms in patients with acutely decompensated heart failure. Nesiritide produced more rapid hemodynamic improvement and caused significantly fewer adverse effects than intravenous nitroglycerin. The incidence of hypotension, the most common adverse effect, was comparable between nesiritide and nitroglycerin. Additionally, nesiritide is associated with a lower incidence of arrhythmias than dobutamine and has a neutral effect on mortality. CONCLUSIONS: Nesiritide offers an alternative for management of acutely decompensated heart failure. It is considered an option for patients who do not respond to other vasodilators, inotropes, or diuretics and for those at high risk of arrhythmias. Further pharmacoeconomic investigations for nesiritide are warranted.

Half-Life↗

PubMedDate not supplied

Nursing and the Net.

Web technologies, including intranet and internet applications, have become pervasive throughout society. Applications in healthcare settings are evolving rapidly and clearly demonstrating that professional and departmental activities can be enhanced, streamlined, and supported by this new technology. At Mount Sinai Hospital, Toronto, obvious benefits are being derived from evolving internet and intranet applications that support nursing practice and management. The purpose of this paper is to discuss the advantages of internet/intranet functionality for nurses, and to describe an intranet application designed specifically for the adult critical care unit.

Adult↗

PubMed2006

Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics.

The Chemistry Development Kit (CDK) provides methods for common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc. Implemented in Java, it is used both for server-side computational services, possibly equipped with a web interface, as well as for applications and client-side applets. This article introduces the CDK's new QSAR capabilities and the recently introduced interface to statistical software.

Computational Biology↗

PubMed1996

Research takes on a second life. Interview by John McCornack.

The health care industry is embracing the artificial intelligence concepts that Edward H. Shortliffe, M.D., developed in the 1970s. His current work on Web-based information dissemination may yield applications for the next century.

Artificial Intelligence↗

PubMed1998

ATRAS: a decision support application layered on the W3-EMRS architecture.

The creation of portable decision support systems (DSSs) remains an important goal in medical informatics. The Adrenal Test Retrieval and Analysis System (ATRAS) has been developed as an example of a simple yet highly effective decision support application which runs in a system-independent way. It is the first implementation of a decision support application layered on the World Wide Web Electronic Medical Record System (W3-EMRS) architecture, which allows for unified access to remote heterogeneous electronic medical record system (EMRS) databases.

Adrenal Cortex Hormones↗

PubMed1995

Adenosine and PAF dependent mechanisms lead to myocardial reperfusion injury by neutrophils after brief ischaemia.

OBJECTIVE: The aim was to establish whether polymorphonuclear neutrophils can, by themselves, elicit depression of postischaemic heart function immediately after short periods of ischaemia, and to examine the involvement of endogenous adenosine and platelet activating factor (PAF) in the observed phenomena. METHODS: Isolated buffer perfused guinea pig hearts performing pressure-volume work under standardised conditions were subjected to 15 min of global ischaemia. Constant flow reperfusion (5 ml.min-1) was carried out in the presence or absence of homologous neutrophils (approximately 2000 cells.microliters-1 perfusate). After 15 min of reflow, work was resumed and functional recovery assessed another 20 min later. RESULTS: In hearts perfused only with Krebs-Henseleit buffer, postischaemic heart function recovered to 67(SEM 3)% (n = 13) of the preischaemic value. As early as the first minute of reperfusion, the application of neutrophils already led to a significant decrease in recovery to 39(3)% (n = 12; P < 0.05). Without ischaemia, neutrophils did not have any deleterious effect, recovery of external heart work amounting to 91(4)% (n = 6). Adenosine concentrations measured in the coronary effluent after ischaemia were substantially increased during reperfusion from preischaemic values of < 20 nM to about 800 nM. The adenosine A1 receptor antagonist dipropyl-8-cyclopentyl-xanthine prevented the neutrophil dependent loss of heart function, as did application of the PAF receptor antagonist WEB 2086, recoveries being 60(4)% (n = 6) and 58(8)% (n = 6), respectively. In contrast, the A2 antagonist 3,7-dimethyl-1-propargyl-xanthine tended to worsen the neutrophil induced dysfunction of the heart, recovery amounting to 18(2)% (n = 5). CONCLUSIONS: Even after brief ischaemia, neutrophils introduced into the coronary system can exacerbate reperfusion injury. Adenosine, through its A1 receptor, and PAF appear to play a significant role as mediators of this action.

Adenosine↗