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At least 1,657 records · Page 92Linked to original sources
PubMed2003

Psychoneuroendocrinological links between chronic stress and depression.

OBJECTIVE: The goal of this report is to develop a comprehensive model, which integrates psychosocial and neurobiological aspects, for better understanding the link between chronic stress and mood disorders. METHOD: A selective review of the relevant bibliography was conducted. The significant data were integrated with clinical and preclinical findings, particularly focusing on the effect of the hypothalamo-pituitary-adrenal (HPA) activity on the serotonergic neurotransmission in the CNS. RESULTS: The reviewed data shows that chronic application of stress responses may lead to alterations in the regulation of the HPA system, and the resulting hypercortisolism may be reflected in various psychoneuroendocrinological processes, such as the observed in the serotonergic system, which was implicated in the origin and development of depression. CONCLUSIONS: The analysis of the interactions between the different components of this process, suggests that normalization of the HPA system, either directly through psychopharmacologic strategies, or indirectly through psychotherapeutic approaches oriented to improve the cognitive appraisal of stressful situations, may provide us with more effective diagnostic, preventive, and therapeutic methods in the treatment of widespread anxiety and mood disorders.

Animals↗
PubMed2001

The costs of caring for stroke patients in a GP-led community hospital: an application of programme budgeting and marginal analysis.

There has been little evaluation of the role of community hospitals in the provision of integrated health care services in a primary care-led health system. The aim of this study was to model the probable changes in the use of NHS resources from the introduction of integrated stroke care in a general pracititioner-led community hospital. A programme budgeting and marginal analysis (PBMA) exercise was conducted combining practice data for the 'before' period and data from the literature to model the 'after' period. Data were collected from all patients discharged with a primary diagnosis of stroke 1994-96 in Nairn and Ardersier Total Fundholding pilot site, Highland Health Board, Scotland. Under several assumptions, a policy of early discharge of patients to the community hospital, and/or avoiding admission at the acute trust and admitting patients to the community hospital directly (except emergencies), is likely to result in a reduction of the total annual costs of treating stroke patients, from 183,000 pounds per annum to, at most, 74,000 pounds. The analysis of routine discharge data since integrated stroke care was set up has shown that progress has been made in shifting the treatment of patients from the acute trust to the community hospital. The care of stroke patients in a GP-led community hospital is likely to reduce the use of scarce health service resources. Current evidence suggests that health outcomes are unchanged due to early discharge, but further research is required to ensure that patients' health status and quality of life are maintained before such a policy is widely adopted.

Adult↗
PubMed2007

Characterization of surgically transposed ovaries in integrated PET/CT scan in patients with cervical cancer.

BACKGROUND: The purpose of this study was to determine the ovarian findings on integrated positron emission tomography/computed tomography scans during follow-up in cervical cancer patients with ovarian transposition. METHOD: We retrospectively reviewed the clinical data and integrated 18F-fluorodeoxyglucose positron emission tomography/computed tomography of women with ovarian transposition during radical hysterectomy for cervical cancer between December 2003 and March 2006. RESULTS: Eighty-four premenopausal women had ovarian transposition performed during the study period. Twelve positron emission tomography/computed tomography scans from 11 patients were registered for the current study and three women were diagnosed with metastasis: two in lung and one in pelvis. Two patients complained of menopausal symptoms during follow-up, and the hormonal tests were consistent with it. In the current study, an integrated positron emission tomography/computed tomography scan detected one patient with right lower abdominal mass with increased 18F-fluorodeoxyglucose uptake, which was identified as a transposed right ovary. Clinical information of ovarian transposition was helpful in interpretation of the lesion. In the patient, transposed ovary was associated with increased fluorodeoxyglucose uptake, with standard uptake values ranging from 3.7 to 5.5. Other positron emission tomography/computed tomography scans did not show abnormal uptake of 18F-fluorodeoxyglucose. CONCLUSIONS: Transposed ovary in premenopausal women may appear on integrated positron emission tomography/computed tomography scan as a mass with increased 18F-fluorodeoxyglucose uptake, which may be associated with preserved ovarian function. Clinical information regarding transposition should be noted in order not to interpret these as recurrent or metastatic lesions.

Adult↗
PubMed2000

Expression databases--resources for pharmacogenomic R&D.

This review aims to outline the primary biological databases that are being generated to understand fundamental biology, identify new drug targets, and to look at compound profiling in a new light. We will give a brief overview of four of the main areas being studied in molecular biology: genomics, pharmacogenomics, pharmacogenetics and proteomics. Looking initially at each data set and some of its potential applications, we will go on to describe some of the potentially enormous advantages gained by fully integrating these data sets.

Animals↗
PubMed2004

Integrating linkage and radiation hybrid mapping data for bovine chromosome 15.

BACKGROUND: Bovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs. RESULTS: The integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments. CONCLUSIONS: Combining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.

Animals↗
PubMed2005

Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

Genome-wide techniques such as microarray analysis, Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS), linkage analysis and association studies are used extensively in the search for genes that cause diseases, and often identify many hundreds of candidate disease genes. Selection of the most probable of these candidate disease genes for further empirical analysis is a significant challenge. Additionally, identifying the genes that cause complex diseases is problematic due to low penetrance of multiple contributing genes. Here, we describe a novel bioinformatic approach that selects candidate disease genes according to their expression profiles. We use the eVOC anatomical ontology to integrate text-mining of biomedical literature and data-mining of available human gene expression data. To demonstrate that our method is successful and widely applicable, we apply it to a database of 417 candidate genes containing 17 known disease genes. We successfully select the known disease gene for 15 out of 17 diseases and reduce the candidate gene set to 63.3% (+/-18.8%) of its original size. This approach facilitates direct association between genomic data describing gene expression and information from biomedical texts describing disease phenotype, and successfully prioritizes candidate genes according to their expression in disease-affected tissues.

Anatomy↗
PubMed2004

In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database.

An extensive analysis of the Arabidopsis thaliana peripheral and integral thylakoid membrane proteome was performed by sequential extractions with salt, detergent, and organic solvents, followed by multidimensional protein separation steps (reverse-phase HPLC and one- and two-dimensional electrophoresis gels), different enzymatic and nonenzymatic protein cleavage techniques, mass spectrometry, and bioinformatics. Altogether, 154 proteins were identified, of which 76 (49%) were alpha-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein. The data were integrated with our analysis of the lumenal-enriched proteome. We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis. The high coverage of the photosynthetic apparatus and the identification of known hydrophobic proteins with low expression levels, such as cpSecE, Ohp1, and Ohp2, indicate an excellent dynamic resolution of the analysis. The sequential extraction process proved very helpful to validate transmembrane prediction. Our data also were cross-correlated to chloroplast subproteome analyses by other laboratories. All data are deposited in a new curated plastid proteome database (PPDB) with multiple search functions (http://cbsusrv01.tc.cornell.edu/users/ppdb/). This PPDB will serve as an expandable resource for the plant community.

Amino Acid Sequence↗
PubMed1975

Integrated steady state rate equations and the determination of individual rate constants.

Integrated steady state rate equations have been used to determine the kinetic constants (Vs, Ks, Vp, and Kp) and rate constants (k1, k2, k3, and k4) of the reversible enzyme mechanism: (see article). The fumarase reaction has been used as a model to illustrate the procedures for determining these constants. In contrast to initial velocity studies, the values of the constants have been obtained by examining the enzyme reaction in only one direction rather than in both forward and reverse directions. To accomplish this, a new procedure is described for fitting data to integrated rate equations which eliminates problems encountered when data are analyzed graphically. The advantages of examining on enzyme reaction in one direction with these new procedures allow this method to be extended to the examination of enzymes with simple mechanisms where initial velocities are difficult to measure because either the substrate or product is not readily available, or because the reaction is not readily reversible.

Animals↗
PubMed1998

Long-latency neurons in auditory cortex involved in temporal integration: theoretical analysis of experimental data.

A previous experimental study (He et al., 1997) found 132 duration-selective neurons with long latencies of greater than 30 ms in the dorsal zone of cat auditory cortex. The mechanism by which such long-latency neurons integrate information during their latent period is investigated by analysis of the temporal relationship between the stimulus and neuronal response. In the present study, we developed a one-layer perceptron to examine the above temporal relationship of the experimental results. The acoustic stimulus was represented as a contiguous series of sequential short time epochs. The perceptron was trained by using the spike data as the desired outputs and the acoustic stimuli (in digital format) as the inputs. The adaptive weights between the outputs and the inputs after training indicated the temporal relationship between neuronal responses and the stimuli. The contribution of each time epoch of the stimulus could be either positive or negative: the positive contribution corresponds to excitatory input and the negative contribution to inhibitory input. Long-duration-selective neurons were found to receive mainly excitatory input along the entire effective stimulus duration. However, duration-tuned neurons received excitatory input for only the time period from the stimulus onset to their best durations, and inhibitory thereafter. The temporal integration pattern of short-duration-selective neurons was similar to duration-tuned neurons. However, short-duration-selective neurons received excitatory input only at the beginning of the stimulus. Each of the duration-threshold neurons integrated auditory information only for a restricted time period of the stimulus, suggesting that they have a time window over the stimulus time domain. Non-duration-threshold neurons have time windows extending from the stimulus onset onward. The assembly of duration-threshold neurons and non-duration-threshold neurons may collectively represent the time axis of the stimulus.

Acoustic Stimulation↗
PubMed2003

The "two-headed" latent inhibition model of schizophrenia: modeling positive and negative symptoms and their treatment.

RATIONALE: Latent inhibition (LI), namely, poorer performance on a learning task involving a previously pre-exposed non-reinforced stimulus, is disrupted in the rat by the dopamine (DA) releaser amphetamine which produces and exacerbates psychotic (positive) symptoms, and this is reversed by treatment with typical and atypical antipsychotic drugs (APDs) which on their own potentiate LI. These phenomena are paralleled by disrupted LI in normal amphetamine-treated humans, in high schizotypal humans, and in schizophrenia patients in the acute stages of the disorder, as well as by potentiated LI in normal humans treated with APDs. Consequently, disrupted LI is considered to provide an animal model of positive symptoms of schizophrenia with face, construct and predictive validity. OBJECTIVES: To review most of the rodent data on the neural substrates of LI as well as on the effects of APDs on this phenomenon with an attempt to interpret and integrate these data within the framework of the switching model of LI; to show that there are two distinct LI models, disrupted and abnormally persistent LI; to relate these findings to the clinical condition. RESULTS: The nucleus accumbens (NAC) and its DA innervation form a crucial component of the neural circuitry of LI, and are involved at the conditioning stage. There is a clear functional differentiation between the NAC shell and core subregions whereby damage to the shell disrupts LI and damage to the core renders LI abnormally persistent under conditions that disrupt LI in normal rats. The effects of shell and core lesions parallel those produced by lesions to the major sources of input to the NAC: entorhinal cortex lesion, like shell lesion, disrupts LI, whereas hippocampal lesion, like core lesion, produces persistent LI with changes in context, and basolateral amygdala (BLA) lesion, like core lesion, produces persistent LI with extended conditioning. Systemically induced blockade of glutamatergic as well as DA transmission produce persistent LI via effects exerted at the conditioning stage, whereas enhancement of DA transmission disrupts LI via effects at the conditioning stage. Serotonergic manipulations can disrupt or potentiate LI via effects at the pre-exposure stage. Both typical and atypical APDs potentiate LI via effects at conditioning whereas atypical APDs in addition disrupt LI via effects at pre-exposure. Schizophrenia patients can exhibit disrupted or normal LI as a function of the state of the disorder (acute versus chronic), as well as persistent LI. CONCLUSIONS: Different drug and lesion manipulations produce two poles of abnormality in LI, namely, disrupted LI under conditions which lead to LI in normal rats, and abnormally persistent LI under conditions which disrupt it in normal rats. Disrupted and persistent LI are differentially responsive to APDs, with the former reversed by both typical and atypical APDs and the latter selectively reversed by atypical APDs. It is suggested that this "two-headed LI model" mimics two extremes of deficient cognitive switching seen in schizophrenia, excessive and retarded switching between associations, mediated by dysfunction of different brain circuitries, and can serve to model positive symptoms of schizophrenia and typical antipsychotic action, as well as negative symptoms of schizophrenia and atypical antipsychotic action.

Animals↗
PubMed2006

National outpatient medication profiling: medications associated with outpatient fractures in community-dwelling elderly veterans.

AIMS: The primary objective of this retrospective case-control study in an elderly veteran population was to assess the impact of specific medications with recognized side-effects that increase the risk of a fall and were prescribed prior to fractures treated in the outpatient setting compared with patients treated for nonspecific chest pain. METHODS: Two national Veterans Health Administration (VHA) databases were used to identify 17 273 unique patients, aged > or =65 years, treated in outpatient settings with a fracture in fiscal year 2005, and for whom we could link to all of their outpatient prescriptions (809 536). For comparison, we identified other elderly patients with outpatient clinic visits for nonspecific chest pain (N = 62 331) for whom we could link with their 2 987 394 outpatient prescriptions. We categorized the fall-related medications as drugs that primarily affect the cardiovascular (CVS), the central nervous (CNS) or the muscular skeletal system (MSS). RESULTS: Significant differences in the two patient groups occurred in the CNS category. Approximately 41% of the patients with fracture-coded encounters were prescribed CNS drugs compared with 31% of the patients in the comparison group (P < 0.0003). Finally, the use of muscle relaxants in the MSS category was significantly higher in the fracture group than in the nonspecific chest pain group. CONCLUSIONS: Studies using administrative data can foster the development of more proactive pharmacovigilance systems and assist in formulary refinement, particularly in countries with national healthcare systems that have integrated patient data. Particular attention and monitoring of elderly patients taking CNS medications may be important for injury prevention.

Accidental Falls↗
PubMed2025

PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data.

Bacteria showcase remarkable metabolic diversity and traits, even among strains of the same species. In recent years, a large number of bacterial genomes have been sequenced, leading to the elucidation and documentation of genomic differences and commonalities across and within species. Genome-scale metabolic reconstructions, which are often defined and curated using data from phenotype microarrays, elucidate the differences in metabolic traits resulting from genomic diversity. These microarrays measure cellular respiration on a variety of carbon, nitrogen, phosphorus, and sulfur sources and various stressors and inhibitors over a period of time to determine the metabolic activity of a given strain. Despite their popularity in measuring bacterial metabolic activity and traits, no public databases that allow researchers to warehouse, access, and analyze this information currently exist. Additionally, there are no publicly available tools that allow researchers to view the variance of these metabolic traits across bacterial strains. To address this need, we present Phenotype Microarray Knowledgebase (PMkbase [version 1.0], https://pmkbase.com/), an interactive database that acts as a repository of phenotype microarray (PM) data with integrated sequence information. Binarized activity calls, along with associated kinetic parameters, are made for all metabolic substrates and inhibitors. Users can upload their own data for analysis and visualization and to perform quality checks on their experiments. PMkbase will address an unmet need to track and view bacterial metabolic traits and provide researchers with valuable information to develop metabolic models, enrich pangenomic analyses, and design new experiments.IMPORTANCEBacterial species can be differentiated by their metabolic profiles or the type of nutrients they consume. Interestingly, strains within the same species also display differences in nutrient consumption. Phenotype microarrays are a high-throughput, widely used technology to measure which substrates can be metabolized by various microbial strains and the extent to which inhibitors can affect it. Despite their widespread use, public databases to parse and access this data type at scale do not exist. PMkbase, which contains 9,024 data points for nitrogen substrate utilization, 41,664 data points for carbon substrate utilization, 8,448 data points for phosphorus/sulfur substrate utilization, and 27,264 data points on various antibiotics across three species (Escherichia coli, Pseudomonas putida, and Staphylococcus aureus), has been developed to allow researchers to freely access PM data, along with enriching the data with sequence information.

Bacteria↗
PubMed2005

FACT--a framework for the functional interpretation of high-throughput experiments.

BACKGROUND: Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel. It is usually a matter of extensive testing and unknown beforehand, which of the possible approaches for the functional analysis will be the most informative. RESULTS: To address this problem, we have developed the Flexible Annotation and Correlation Tool (FACT). FACT allows for detection of important patterns in large data sets by simplifying the integration of heterogeneous data sources and the subsequent application of different algorithms for statistical evaluation or visualization of the annotated data. The system is constantly extended to include additional annotation data and comparison methods. CONCLUSION: FACT serves as a highly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at http://www.factweb.de.

Algorithms↗
PubMed2004

Control of yeast filamentous-form growth by modules in an integrated molecular network.

On solid growth media with limiting nitrogen source, diploid budding-yeast cells differentiate from the yeast form to a filamentous, adhesive, and invasive form. Genomic profiles of mRNA levels in Saccharomyces cerevisiae yeast-form and filamentous-form cells were compared. Disparate data types, including genes implicated by expression change, filamentation genes known previously through a phenotype, protein-protein interaction data, and protein-metabolite interaction data were integrated as the nodes and edges of a filamentation-network graph. Application of a network-clustering method revealed 47 clusters in the data. The correspondence of the clusters to modules is supported by significant coordinated expression change among cluster co-member genes, and the quantitative identification of collective functions controlling cell properties. The modular abstraction of the filamentation network enables the association of filamentous-form cell properties with the activation or repression of specific biological processes, and suggests hypotheses. A module-derived hypothesis was tested. It was found that the 26S proteasome regulates filamentous-form growth.

Cell Cycle↗
PubMed1998

Toward a general model for the description of multimedia clinical data.

The patient folder integrates information originating from heterogeneous sources. For this reason computerized tools for patient data management should exploit the advantages of multimediality and offer an integrated environment for data presentation, and image and biosignal visualization. Object-oriented modeling is the best approach for designing systems for multimedia patient folder management. We propose an object-oriented model, able to define the entities constituting the patient folder and their logical organization. This model has sufficient flexibility to adapt to the most varied clinical environments. It allows the physician to structure the information needed for his/her patient folder without employing a programming language.

Computer Simulation↗
PubMed2001

High-throughput interpretation of pathways and biology.

The genomics revolution is opening many diverse pathways in science. In the midst of the tidal wave of information being generated by the new "omics" disciplines, bioinformatics is meeting the challenge to decipher and organize the data mountain. The endeavor to integrate diverse biological data into a common vocabulary will be an essential part of the "biotechnological age" leading to a new understanding of complex biological systems. This potential promises to revolutionize medicine as knowledge is translated into novel therapies. The Integrated Bioinformatics meeting held in Zurich January 2426, 2001, provided an insight into the cutting edge of bioinformatics and its central role in the genomics revolution. The evolution of bioinformatics will act as a guide in 21st century biological sciences.

Journal Article↗
PubMed1994

Quality assurance for interventions in clinical trials. Multicenter data monitoring, data management, and analysis.

Quality assurance for the management of multicenter clinical trials requires timely patient and data accrual and consistency with design parameters. Data from central pathology review, treatment modality, and follow-up as well as trial end points direct the selection of appropriate compliance measures. To integrate these data to monitor group performance on a specific protocol, to monitor discipline performance, or to monitor an institution's performance is a formidable task. This is especially true for a group such as the Pediatric Oncology Group, where there are a large number of protocols, many diseases, and widely differing protocol requirements. Quality assurance methods for the Pediatric Oncology Group are discussed.

Clinical Trials as Topic↗