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At least 1,153 records · Page 64Linked to original sources
PubMed2006

Molecular characterization of the developmental gene in eyes: through data-mining on integrated transcriptome databases.

OBJECTIVES: Our aim was to utilize publicly available and proprietary sources to discover candidate genes important for ocular development. DESIGN AND METHODS: The collated information on our 5092 non-redundant clusters was grouped and functional annotation was conducted using gene ontology (FatiGO) for categorizing them with respect to molecular function. The web-based viewer technological platform (H-InvDB) was employed for transcription analyses of in-house high quality fetal eye Expressed Sequence Tags (ESTs). Eye-specific ESTs were also analyzed across species by using EMBEST. RESULTS: According to adult eye cDNA libraries, nucleic acid binding and cell structure/cytoskeletal protein genes were the most abundant among the ESTs of fetal eyes. Using cDNA assembly in H-InvDB, 20 (80%) of the 25 most commonly expressed genes in the human eye are also expressed in extraocular tissues. The crystalline gamma S gene is highly expressed in the eye, but not in other tissues. We used EMBEST to compare human fetal eye and octopus eye ESTs and the expression similarity was low (1.6%). This indicated that our fetal eye library contains genes necessary for the developmental process and biological function of the eye, which may not be expressed in the fully developed octopus eyes. The human fetal eye cDNA library also contained highly abundant eye tissue genes, including alphaA-crystallin, eukaryotic translation elongation factor 1 alpha 1 (EEF1A1), bestrophin (VMD2), cystatin C, and transforming growth factor, beta-induced (BIGH3). CONCLUSIONS: Our annotated EST set provides a valuable resource for gene discovery and functional genomic analysis. This display will help to appreciate the strengths and weaknesses of the different technological platforms, so that in future studies the maximum amount of beneficial information can be derived from the appropriate use of each method.

Animals↗
PubMed2006

A specific database for providing local and national level of integration of clinical data in cystic fibrosis.

It has recently been stated that a database is an essential tool in the management of CF. The purpose of this work is to create a specific database allowing optimal performance of storage, search and retrieval functions on patients with CF. A specific database was developed using a Windev licence, for application via Microsoft supported platforms or Intranet system. The database allows real-time point of care data management of medical, investigational and administrative data. It is currently being used in the 6 Belgian reference centres. It represents a useful tool for gathering information on routine clinical and lab data, bacteriology, treatments, complications and specific outcomes for clinical and research purposes. The ongoing evolution of the database includes enhancements toward research data orientation including comparison of patient data between different centres and completeness of the National CF registry questionnaire. A complimentary copy of the software can be provided to multidisciplinary accredited CF centres worldwide upon request.

Belgium↗
PubMed2006

Genomic DNA as a general cohybridization standard for ratiometric microarrays.

Feature variability on ratiometric microarrays is accommodated by simultaneous cohybridization of a labeled reference standard with a labeled experimental sample. An optimal reference standard would provide full and equal representation for all array features from a given genome so that it would function on any array, would represent all features with similar signal intensity, and would be highly reproducible-both technically and biologically-from preparation to preparation and laboratory to laboratory. A low cost and a good shelf life are also highly desirable. Finally, providing for straightforward recovery of RNA prevalence information and for integration of data across multiple, initially unrelated studies would be significant advances over current methods. For virtually all ratiometric array studies published to date the reference standard has been some kind of RNA sample assembled from a number of different cell lines, tissues, or experimental time points. These RNA references fall short of the desired universality, uniformity, and reproducibility criteria, which then affect data quality and integration across studies. Also, the various mixed RNA standards cannot be used to derive RNA prevalence information from an experimental sample. In contrast, genomic DNA is a natural choice to meet all the criteria, although it has not yet been widely exploited for eukaryotic array experiments. Principal stumbling blocks have been achieving high enough absolute signals for large mammalian and plant genomes and finding a way to stabilize labeled DNA so that it can be stored and used with ease. This chapter describes two genomic DNA-labeling methods that make it possible to use genomic DNA as a universal microarray cohybridization standard. The indirect labeling method permits production of a large quantity of a stable genomic DNA standard that can then be quality tested and stored frozen. This optimizes experimental consistency and significantly improves ease of use. This chapter also shows that the genomic DNA reference standard can deliver RNA prevalence measurements from ratiometric array platforms.

Animals↗
PubMed2002

Fiber diameter distributions in the chinchilla's ampullary nerves.

A morphometric study of the chinchilla's ampullary nerves was conducted to produce an unbiased accounting of the diameter distribution of their constituent fibers. Diameter analyses were determined from 1 microm plastic-embedded nerve sections taken at a plane immediately proximal to the sensory epithelium. We found these nerves to be composed of 2094+/-573 fibers, having diameters that ranged from 0.5 to 8 microm. The distributions of diameters were positively skewed, where approximately 75% of the fibers were found to have diameters less than 3.5 microm. An analysis of the spatial distribution of diameters within the nerve section revealed that the lateralmost areas of the nerve contained larger fractions of fibers within the smallest diameter quintiles, and the central area harbored greater proportions of the larger diameter quintiles. However, significant fractions of all quintiles were found in all areas. These data were integrated with available data of Fernandez et al. (1998) to produce diameter estimates of calyx, dimorphic, and bouton morphology subpopulations. In view of a general relationship between diameter, innervation locus, and an afferent's physiologic characteristics, these data provide the basis for developing a perspective for the in situ distribution of afferent response dynamics.

Animals↗
PubMed1999

Performing cost-effectiveness analysis by integrating randomized trial data with a comprehensive decision model: application to treatment of acute ischemic stroke.

A recent national panel on cost-effectiveness in health and medicine has recommended that cost-effectiveness analysis (CEA) of randomized controlled trials (RCTs) should reflect the effect of treatments on long-term outcomes. Because the follow-up period of RCTs tends to be relatively short, long-term implications of treatments must be assessed using other sources. We used a comprehensive simulation model of the natural history of stroke to estimate long-term outcomes after a hypothetical RCT of an acute stroke treatment. The RCT generates estimates of short-term quality-adjusted survival and cost and also the pattern of disability at the conclusion of follow-up. The simulation model incorporates the effect of disability on long-term outcomes, thus supporting a comprehensive CEA. Treatments that produce relatively modest improvements in the pattern of outcomes after ischemic stroke are likely to be cost-effective. This conclusion was robust to modifying the assumptions underlying the analysis. More effective treatments in the acute phase immediately following stroke would generate significant public health benefits, even if these treatments have a high price and result in relatively small reductions in disability. Simulation-based modeling can provide the critical link between a treatment's short-term effects and its long-term implications and can thus support comprehensive CEA.

Acute Disease↗
PubMed2001

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms.

With the massive amount of sequence and structural data being produced, new avenues emerge for exploiting the information therein for applications in several fields. Fold distributions can be mapped onto entire genomes to learn about the nature of the protein universe and many of the interactions between proteins can now be predicted solely on the basis of the genomic context of their genes. Furthermore, by utilising the new incoming data on single nucleotide polymorphisms by mapping them onto three-dimensional structures of proteins, problems concerning population, medical and evolutionary genetics can be addressed.

Apolipoproteins E↗
PubMed2002

[SIMS REIN: a multi-source information system for end-stage renal disease].

In France, the prevalence of End-Stage Renal Disease (ESRD) is not precisely known. The sources of information are scattered and not coordinated. Consequently, care is ill adapted to meet the demand. The Multi-Source Information System is the basis of the Renal Epidemiology and Information Network (REIN). It is dedicated to improve and organise our medical and epidemiological knowledge of ESRD and to aid public health decision-making in this area. The proposed approach is based on the datawarehouses. This model allows a unified vision of scattered data into distinct databases, for a better management, be it particular (patient follow-up) or global (regional follow-up), with a finality of aid in decision-making. Several categories of problems were considered: the global conception of the information system, the organisation of the datawarehouse, which offers different viewpoints of the data, the integration of heterogeneous data coming from different sources, data exchange and definition of a specific ontology.

Computer Communication Networks↗
PubMed1998

Integration of haemodynamic and electrocardiographic waveform data with DICOM images.

The cardiac catheterization procedure involves acquisition of haemodynamic and electrocardiographic waveforms, as well as X-ray angiographic images. The DICOM standards is being extended to address robust interchange of this waveform data together with the image data, so as to present an integrated data set for the procedure. The proposed waveform information object definition is one of the new generation of DICOM extensions, and uses controlled vocabularies and coded entry sequences to represent clinically significant aspects of the data acquisition. This enables a generic waveform object to be specialized for disparate uses, e.g., haemodynamics, electrocardiograms, phonocardiograms, and electrophysiological data.

Cardiac Catheterization↗
PubMed2002

Sequencing of endocrine therapies in breast cancer--integration of recent data.

A wide range of endocrine therapies has demonstrated activity in the treatment of hormone receptor-positive metastatic breast cancer and sequential tumor responses to sequential hormonal therapies are common. However, the optimal sequence of the hormonal therapies has not yet been determined. The selection of endocrine therapies in women with hormone receptor-positive breast cancer is strongly influenced by the menopausal status of the patient. For premenopausal women, tamoxifen alone or combined with ovarian suppression using a luteinizing hormone-releasing hormone (LHRH) agonist - such as goserelin or leuprolide - is an appropriate first-line hormonal therapy. Ovarian ablation or megestrol acetate is an appropriate second-line hormonal therapy for premenopausal women treated with tamoxifen as first-line therapy, or ovarian ablation plus an aromatase inhibitor (AI) or megestrol acetate for women treated with first-line tamoxifen plus an LHRH agonist. For postmenopausal women, the non-steroidal AIs anastrozole and letrozole now represent the preferred first-line hormonal treatment for metastatic breast cancer, based upon both efficacy and toxicity considerations. For second-line therapy in postmenopausal women, a number of options now exist, including tamoxifen, the steroidal AI exemestane, and the new agent fulvestrant. Fulvestrant, a novel estrogen receptor (ER) antagonist that downregulates the ER and has no known agonist effects, has been demonstrated to be at least as effective as anastrozole in postmenopausal women whose tumors progress on tamoxifen. The establishment of the optimal sequence of the endocrine therapies should offer significant benefits to women with hormone-sensitive metastatic breast cancer.

Antineoplastic Agents, Hormonal↗
PubMed2001

Personality and recovery: integrating personality assessment data to facilitate the recovery process.

The relatively enduring and persistent nature of personality traits means that they will likely continue to impact the course of psychiatric recovery after Axis I symptoms are stabilized. These traits can significantly impact the choices that recovering persons make and the quality of interpersonal relationships with care providers who are trying to facilitate the recovery process. Despite this, they are often inadequately assessed and considered in providing psychiatric care. This manuscript reviews the common combinations of personality traits that have emerged across a variety of clinical samples. The implications of these personality features for the provision of care in an inpatient setting to facilitate recovery are discussed.

Convalescence↗
PubMed2006

Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae.

In Saccharomyces cerevisiae, the heme-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration. Thus, overexpression of HAP4 has been shown to result in a 10% increase in the respiratory capacity. Here the physiology of a HAP4-deleted S. cerevisiae strain was investigated, and we found that the hap4delta S. cerevisiae exhibited poor growth on ethanol, although the growth rate on glucose was indifferent from the wild type in aerobic as well as anaerobic cultures. Moreover, it exhibited a large (75%) reduction in the critical glucose uptake rate at which fermentative metabolism is onset, indicating a substantial reduction in respiratory capacity. We also performed whole genome transcription analysis for the hap4delta and the wild type, grown in carbon-limited chemostat cultures operated at a dilution rate of 0.05 h(-1). Although both strains exhibited respiratory metabolism, there was significant change in expression of many genes in the hap4delta strain. These genes are involved in several different parts of the metabolism, including oxidative stress response, peroxisomal functions, and energy generation. This study strongly indicates that Hap4 activation only occurs at intermediate specific growth rates, below which the transcription of genes responsible for respiration is dependent on the Hap2/3/5 complex and above which the Hap4 protein augments the transcription. Furthermore, statistical analysis of the transcription data and integration of the data with a genome scale metabolic network provided new insight and evidence for the role of Hap4 in transcriptional regulation of mitochondrial respiration.

Biomass↗
PubMed2005

Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions.

We report an extensive proteome analysis of rice etioplasts, which were highly purified from dark-grown leaves by a novel protocol using Nycodenz density gradient centrifugation. Comparative protein profiling of different cell compartments from leaf tissue demonstrated the purity of the etioplast preparation by the absence of diagnostic marker proteins of other cell compartments. Systematic analysis of the etioplast proteome identified 240 unique proteins that provide new insights into heterotrophic plant metabolism and control of gene expression. They include several new proteins that were not previously known to localize to plastids. The etioplast proteins were compared with proteomes from Arabidopsis chloroplasts and plastid from tobacco Bright Yellow 2 cells. Together with computational structure analyses of proteins without functional annotations, this comparative proteome analysis revealed novel etioplast-specific proteins. These include components of the plastid gene expression machinery such as two RNA helicases, an RNase II-like hydrolytic exonuclease, and a site 2 protease-like metalloprotease all of which were not known previously to localize to the plastid and are indicative for so far unknown regulatory mechanisms of plastid gene expression. All etioplast protein identifications and related data were integrated into a data base that is freely available upon request.

Amino Acid Sequence↗
PubMedDate not supplied

Integration of chemical data using XML.

Internet resources for the toxicological and pharmacological communities offer considerable information, however, the data is generally not amenable to machine-driven reuse. Adoption of XML standards by these (and related) communities will revolutionize the process of sharing information, promoting collaboration and discovery.

Environmental Pollutants↗
PubMed2005

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling.

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.

Animals↗