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At least 703 records · Page 39Linked to original sources

PubMed2006

Efficacy of pharmacotherapy against core traits of borderline personality disorder: meta-analysis of randomized controlled trials.

We conducted a meta-analysis of published randomized, placebo-controlled clinical trials that evaluated the effect of pharmacotherapy in patients with borderline personality disorder. Comprehensive searches of the MEDLINE, EMBASE, PsychLIT and Cochrane Central Register of Controlled Trials databases were performed using web-based search engines. Twenty articles, reporting 22 placebo-controlled comparisons, were included in the meta-analysis: eight involved antipsychotics, seven antidepressants and seven mood stabilizers. Antidepressants (four studies, standardized mean difference -0.55, 95% confidence interval -0.92, -0.17) and mood stabilizers (six studies, standardized mean difference -1.74, 95% confidence interval -2.76, -0.73) were effective against affective instability and anger, but did not produce significant benefits against impulsivity and aggression, unstable relationships, suicidality and global functioning. Antipsychotics as a class had a positive effect in terms of impulsivity and aggression (three studies, standardized mean difference -0.31, 95% confidence interval -0.63, -0.003), interpersonal relationships (three studies, standardized mean difference -0.52, 95% confidence interval -0.87, -0.17) and global functioning (seven studies, standardized mean difference -0.56, 95% confidence interval -1.00, -0.11). No difference was observed between pharmacotherapy and placebo in terms of participants leaving the study early. Pharmacotherapy can exert a modest beneficial effect on some core traits of borderline personality disorder.

Adolescent↗

PubMed2025

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics.

Data-independent acquisition (DIA)-based mass spectrometry is becoming an increasingly popular mass spectrometry acquisition strategy for carrying out quantitative proteomics experiments. Most of the popular DIA search engines make use of in silico generated spectral libraries. However, the generation of high-quality spectral libraries for DIA data analysis remains a challenge, particularly because most such libraries are generated directly from data-dependent acquisition (DDA) data or are from in silico prediction using models trained on DDA data. In this study, we developed Carafe, a tool that generates high-quality experiment-specific in silico spectral libraries by training deep learning models directly on DIA data. We demonstrate the performance of Carafe on a wide range of DIA datasets, where we observe improved fragment ion intensity prediction and peptide detection relative to existing pretrained DDA models. To make Carafe more accessible to the community, we have integrated Carafe into the widely used Skyline tool.

Journal Article↗

PubMed2000

Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project.

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

Chromosome Mapping↗

PubMed2003

Characterization of topological structure on complex networks.

Characterizing the topological structure of complex networks is a significant problem especially from the viewpoint of data mining on the World Wide Web. "Page rank" used in the commercial search engine Google is such a measure of authority to rank all the nodes matching a given query. We have investigated the page-rank distribution of the real Web and a growing network model, both of which have directed links and exhibit a power law distributions of in-degree (the number of incoming links to the node) and out-degree (the number of outgoing links from the node), respectively. We find a concentration of page rank on a small number of nodes and low page rank on high degree regimes in the real Web, which can be explained by topological properties of the network, e.g., network motifs, and connectivities of nearest neighbors.

Journal Article↗

PubMed2000

Sophisticated quantum search without entanglement

Grover's quantum search algorithm has recently been implemented without entanglement, by replacing multiple particles with a single particle having exponentially many states. We recall that all physical resources must be accounted for to quantify algorithm complexity, and that this scheme typically incurs exponential costs in some other resource(s). In particular, we demonstrate that a recent experimental realization requires exponentially increasing precision. There is, however, a quantum algorithm which searches a "sophisticated" database (not unlike a Web search engine) with a single query, but which we show does not require entanglement even for multiparticle implementations.

Journal Article↗

PubMed2005

Proteomic analysis of somatic embryogenesis in Medicago truncatula. Explant cultures grown under 6-benzylaminopurine and 1-naphthaleneacetic acid treatments.

The Medicago truncatula line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than wild-type Jemalong. We have compared proteomes of tissue cultures from leaf explants of these two lines. Both 2HA and Jemalong explants were grown on media containing the auxin 1-naphthaleneacetic acid and the cytokinin 6-benzylaminopurine. Proteins were extracted from the cultures at different time points (2, 5, and 8 weeks), separated by two-dimensional gel electrophoresis, and detected by silver staining. More than 2,000 proteins could be reproducibly resolved and detected on each gel. Statistical analysis showed that 54 protein spots were significantly (P < 0.05) changed in expression (accumulation) during the 8 weeks of culture, and most of these spots were extracted from colloidal Coomassie-stained two-dimensional gel electrophoresis gels and were subjected to matrix-assisted laser desorption ionization time-of-flight mass spectrometry or liquid chromatography-tandem mass spectrometry analysis. Using a publicly available expressed sequence tag database and the Mascot search engine, we were able to identify 16 differentially expressed proteins. More than 60% of the differentially expressed protein spots had very different patterns of gene expression between 2HA and Jemalong during the 8 weeks of culture.

Adenine↗

PubMed2004

LySDB - Lysozyme Structural DataBase.

LySDB (Lysozyme Structural DataBase) is an integrated database containing 740 three-dimensional structures of lysozyme available in the Protein Data Bank. The database can be used to visualize the three-dimensional structure of the entire protein model or the substructures in which the user is interested (for example, insertions and deletions of amino acids) using the three-dimensional atomic coordinates. The database is provided with a search engine with several useful built-in facilities. The public domain graphics program RASMOL has been deployed for visualization. The three-dimensional structures used to create the database are updated at regular intervals and hence the users are provided with the current information available in the literature. The database LySDB is available over the World Wide Web and can be accessed at the URL http://iris.physics.iisc.ernet.in/lysdb/ or http://144.16.71.2/lysdb/.

Computational Biology↗

PubMed2000

A new generation of tools for search, recovery and quality evaluation of World Wide Web medical resources.

Although the Internet is already a valuable information resource in medicine, there are important challenges to be faced before physicians and general users will have extensive access to this information. As a result of a research effort to compile a health-related Internet directory, new tools and strategies have been developed to solve key problems derived from the explosive growth of medical information on the Net and the great concern over the quality of such critical information. The current Internet search engines lack some important capabilities. We suggest using second generation tools (client-side based) able to deal with large quantities of data and to increase the usability of the records recovered. We tested the capabilities of these programs to solve health-related information problems, recognising six groups according to the kind of topics addressed: Z39.50 clients, downloaders, multisearchers, tracing agents, indexers and mappers. The evaluation of the quality of health information available on the Internet could require a large amount of human effort. A possible solution may be to use quantitative indicators based on the hypertext visibility of the Web sites. The cybermetric measures are valid for quality evaluation if they are derived from indirect peer review by experts with Web pages citing the site. The hypertext links acting as citations need to be extracted from a controlled sample of quality super-sites.

Documentation↗

PubMed2000

Computer-assisted discrimination among malignant lymphomas and leukemia using immunophenotyping, intelligent image repositories, and telemicroscopy.

The process of discriminating among pathologies involving peripheral blood, bone marrow, and lymph node has traditionally begun with subjective morphological assessment of cellular materials viewed using light microscopy. The subtle visible differences exhibited by some malignant lymphomas and leukemia, however, give rise to a significant number of false negatives during microscopic evaluation by medical technologists. We have developed a distributed, clinical decision support prototype for distinguishing among hematologic malignancies. The system consists of two major components, a distributed telemicroscopy system and an intelligent image repository. The hybrid system enables individuals located at disparate clinical and research sites to engage in interactive consultation and to obtain computer-assisted decision support. Software, written in JAVA, allows primary users to control the specimen stage, objective lens, light levels, and focus of a robotic microscope remotely while a digital representation of the specimen is continuously broadcast to all session participants. Primary user status can be passed as a token. The system features shared graphical pointers, text messaging capability, and automated database management. Search engines for the database allow one to automatically identify and retrieve images, diagnoses, and correlated clinical data of cases from a "gold standard" database which exhibit spectral and spatial profiles which are most similar to a given query image. The system suggests the most likely diagnosis based on majority logic of the retrieved cases. The system was used to discriminate among three lymphoproliferative disorders and healthy cells. The system provided the correct classification in more than 83% of the cases studied. System performance was evaluated using rigorous statistical assessment and by comparison with human observers.

Decision Support Techniques↗

PubMed2001

A novel large-memory neural network as an aid in medical diagnosis applications.

This paper describes the application of a large memory storage and retrieval (LAMSTAR) neural network to medical diagnosis and medical information retrieval problems. The network is based on Minsky's knowledge-lines (k-lines) theory of memory storage and retrieval in the central nervous system. It employs arrays of self-organized map modules, such that the k-lines are implemented via link weights (address correlation) that are being updated by learning. The network also employs features of forgetting and of interpolation and extrapolation, thus being able to handle incomplete data sets. It can deal equally well with exact and fuzzy information, thus being specifically applicable to medical diagnosis where the diagnosis is based on exact data, fuzzy patient interview information, patient history, observed images, and test records. Furthermore, the network can be operated in closed loop with Internet search engines to intelligently use data from the Internet in a higher hierarchy of learning. All of the above features are shown to make the LAMSTAR network suitable for medical diagnosis problems that concern large data sets of many categories that are often incomplete and fuzzy. Applications of the network to three specific medical diagnosis problems are described: two from nephrology and one related to an emergency-room drug identification problem. It is shown that the LAMSTAR network is hundreds and thousands times faster in its training than back-propagation-based networks when used for the same problem and with exactly the same information.

Computational Biology↗

PubMed2004

Multidimensional text classification for drug information.

This paper proposes a multidimensional model for classifying drug information text documents. The concept of multidimensional category model is introduced for representing classes. In contrast with traditional flat and hierarchical category models, the multidimensional category model classifies each document using multiple predefined sets of categories, where each set corresponds to a dimension. Since a multidimensional model can be converted to flat and hierarchical models, three classification approaches are possible, i.e., classifying directly based on the multidimensional model and classifying with the equivalent flat or hierarchical models. The efficiency of these three approaches is investigated using drug information collection with two different dimensions: 1) drug topics and 2) primary therapeutic classes. In the experiments, k-nearest neighbor, naive Bayes, and two centroid-based methods are selected as classifiers. The comparisons among three approaches of classification are done using two-way analysis of variance, followed by the Scheffé's test for post hoc comparison. The experimental results show that multidimensional-based classification performs better than the others, especially in the presence of a relatively small training set. As one application, a category-based search engine using the multidimensional category concept was developed to help users retrieve drug information.

Abstracting and Indexing↗

PubMed2005

Detecting application-level failures in component-based internet services.

Most Internet services (e-commerce, search engines, etc.) suffer faults. Quickly detecting these faults can be the largest bottleneck in improving availability of the system. We present Pinpoint, a methodology for automating fault detection in Internet services by: 1) observing low-level internal structural behaviors of the service; 2) modeling the majority behavior of the system as correct; and 3) detecting anomalies in these behaviors as possible symptoms of failures. Without requiring any a priori application-specific information, Pinpoint correctly detected 89%-96% of major failures in our experiments, as compared with 20%-70% detected by current application-generic techniques.

Algorithms↗

PubMedDate not supplied

Pose-oblivious shape signature.

A 3D shape signature is a compact representation for some essence of a shape. Shape signatures are commonly utilized as a fast indexing mechanism for shape retrieval. Effective shape signatures capture some global geometric properties which are scale, translation, and rotation invariant. In this paper, we introduce an effective shape signature which is also pose-oblivious. This means that the signature is also insensitive to transformations which change the pose of a 3D shape such as skeletal articulations. Although some topology-based matching methods can be considered pose-oblivious as well, our new signature retains the simplicity and speed of signature indexing. Moreover, contrary to topology-based methods, the new signature is also insensitive to the topology change of the shape, allowing us to match similar shapes with different genus. Our shape signature is a 2D histogram which is a combination of the distribution of two scalar functions defined on the boundary surface of the 3D shape. The first is a definition of a novel function called the local-diameter function. This function measures the diameter of the 3D shape in the neighborhood of each vertex. The histogram of this function is an informative measure of the shape which is insensitive to pose changes. The second is the centricity function that measures the average geodesic distance from one vertex to all other vertices on the mesh. We evaluate and compare a number of methods for measuring the similarity between two signatures, and demonstrate the effectiveness of our pose-oblivious shape signature within a 3D search engine application for different databases containing hundreds of models.

Algorithms↗

PubMed2001

MPtopo: A database of membrane protein topology.

The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.

Algorithms↗

PubMed2004

Comparison of acute lethal toxicity of commonly abused psychoactive substances.

AIMS: To determine the acute lethal toxicity of a range of psychoactive substances in terms of the dose customarily used as a single substance for non-medical purposes. DESIGN AND METHOD: A structured English-language literature search was conducted to identify experimental studies and clinical reports that documented human and non-human lethal doses of 20 abused substances that are distributed widely in Europe and North America. Four inclusion criteria were specified for the reports, and approximately 3000 relevant records were retrieved from search engines at Biosis, Science Citation Index, Google and the National Library of Medicine's Gateway. In order to account for different drug potencies, a 'safety ratio' was computed for each substance by comparing its reported acute lethal dose with the dose most commonly used for non-medical purposes. FINDINGS: The majority of published reports of acute lethal toxicity indicate that the decedent used a co-intoxicant (most often alcohol). The calculated safety ratios varied between substances by more than a factor of 100. Intravenous heroin appeared to have the greatest direct physiological toxicity; several hallucinogens appeared to have the least direct physiological toxicity. CONCLUSIONS: Despite residual uncertainties, the substantial difference in safety ratios suggests that abused substances can be rank-ordered on the basis of their potential acute lethality.

Humans↗

PubMed2004

Systematic review: has disease outcome in Crohn's disease changed during the last four decades?

BACKGROUND: Disease outcome in Crohn's disease might have changed during the last four decades. Disease outcome measurement in Crohn's disease has methodological difficulties because of patient selection and lack of proper definition of diagnostic and outcome measurement criteria. AIM: To assess possible changes in disease outcome in Crohn's disease during the last four decades. METHODS: A systematic literature search was performed using the MEDLINE search engine and major international conference libraries. Articles and abstracts were selected according to stringent inclusion criteria. RESULTS: Forty articles and nine abstracts complied with the inclusion criteria. Seven studies with a median follow-up time between 11.1 and 17 years showed standard mortality ratios in Crohn's disease ranging between 2.16 and 0.72 with a tendency of decline during the last four decades. One study with 11.4 years mean follow-up time showed a statistically significant increased relative risk for colorectal cancer that was not confirmed by three others. Sixteen publications applied in the disease recurrence category. Probability of first resective surgery ranged between 38 and 96% during the first 15 years after diagnosis. The overall recurrence and surgical recurrence rates after first resective surgery ranged between 50 and 60, and 28 and 45% respectively during the following 15 years without an apparent time trend. CONCLUSION: This structured literature review provides no hard evidence for change in disease outcome in Crohn's disease during the last four decades.

Crohn Disease↗

PubMed2006

Home ultraviolet B phototherapy for psoriasis: discrepancy between literature, guidelines, general opinions and actual use. Results of a literature review, a web search, and a questionnaire among dermatologists.

BACKGROUND: Home ultraviolet B (UVB) phototherapy is a debated treatment. It is currently being prescribed for patients with psoriasis, although literature on the subject is scarce. Despite the apparent contradiction between clinical practice and literature, no systematic study of either has been conducted. OBJECTIVES: To assess and compare the available publications and guidelines about home UVB phototherapy for psoriasis with the actual opinions and use of this therapy. METHODS: The literature and guidelines were searched using databases, search engines and e-mail. A postal survey of 343 Dutch dermatologists and 142 dermatologists from 32 other countries was carried out; 255 and 102 dermatologists respectively responded. Outcome measures were the reported advantages, drawbacks and prescription rates of home UVB phototherapy. RESULTS: Fourteen publications (nonrandomized) and six guidelines concerning home UVB phototherapy for psoriasis were identified. Most were reticent about the use of this treatment. Publications describing nonclinical research (7/14) reported most of the drawbacks mentioned (24/31). Home UVB phototherapy was prescribed to 5% (median) of all patients with psoriasis in The Netherlands who required UVB. However, 28% (68/244) of the Dutch dermatologists prescribed home UVB in 20 to 100% of their cases. Dermatologists from other countries reported that 0-10% of UVB treatments were offered at home. For both Dutch and other dermatologists, the most important reasons for prescribing home UVB concerned time and travel distance (80%, i.e. 163 of 205 and 75%, i.e. 33 of 44). Therapy-related drawbacks (such as poor service and equipment) were the objections mentioned most often (55%, i.e. 103 of 186 and 63%, i.e. 57 of 91). Concerns about the medicolegal liability of home UVB were rarely expressed by individual respondents, but frequently mentioned in the various reports. CONCLUSIONS: A discrepancy exists between the actual use of home UVB phototherapy and the general opinions found in publications. The treatment is prescribed for a considerable number of patients despite the fact that literature and guidelines advise caution. Personal and nonevidence-based opinions on this therapy are widespread while randomized clinical studies have thus far not been conducted.

Attitude of Health Personnel↗

PubMed2006

Effectiveness of non-pharmacological interventions for fatigue in adults with multiple sclerosis, rheumatoid arthritis, or systemic lupus erythematosus: a systematic review.

AIM: This paper reports a systematic review of non-pharmacological interventions for fatigue in adults with three common autoimmune conditions. BACKGROUND: A considerable proportion of people with multiple sclerosis, rheumatoid arthritis, and systemic lupus erythematosus experience compromised quality of life due to fatigue. Recent reviews of pharmacotherapies for fatigue in these conditions remain inconclusive, and systematic evidence for effectiveness of non-pharmacological interventions was unavailable. Our paper addresses this gap. METHODS: The literature search used the key words fatigue, energy, multiple sclerosis, rheumatoid arthritis and systemic lupus. It included 19 electronic databases and libraries, three evidence-based journals, two internet search engines, was dated 1987-2006, and limited to English. Non-pharmacological experimental studies about fatigue comprising more than five adults were included. Meta-analysis was not possible due to diverse interventions and outcome measures, therefore studies were analysed by types of interventions used to reduce fatigue. RESULTS: Of 653 hits, 162 papers were reviewed, and 36 met the inclusion criteria. Thirty-three primary studies reported 14 randomized controlled trials and 19 quasi-experimental designs. Most interventions were tested with people with multiple sclerosis. Exercise, behavioural, nutritional and physiological interventions were associated with statistically significant reductions in fatigue. Aerobic exercise was effective, appropriate and feasible for reducing fatigue among adults with chronic autoimmune conditions. Electromagnetic field devices showed promise. The diversity of interventions, designs, and using 24 different instruments to measure fatigue, limited comparisons. CONCLUSION: Low impact aerobic exercise gradually increasing in intensity, duration and frequency may be an effective strategy in reducing fatigue in some adults with chronic auto-immune conditions. However, fatigue is a variable and personal experience and a range of behavioural interventions may be required. Well-designed studies testing these promising strategies and consensus on outcome fatigue measures are needed.

Adult↗