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At least 397 records · Page 22Linked to original sources
PubMed2006

Mapping data elements to terminological resources for integrating biomedical data sources.

BACKGROUND: Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration. METHODS: We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings. RESULTS: 82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed. CONCLUSION: Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.

Abstracting and Indexing↗
PubMed2001

[Hypno-analysis: On the integration of hypnotic elements in individual uncovering psychotherapy in patients with anxiety disorder].

Following a short history of the development of the therapeutic techniques of psychoanalysis as derived from the basic rules of hypnosis, the apparent contradictions between the two approaches are called into question, with particular reference to the importance and efficacy of suggestion and suggestibility in both methods. How the integration of hypnotic interventions can both intensify and at the same time shorten the process of analytic therapy is demonstrated by two vignettes. The range of indications for the use of hypnosis as a complementary measure is currently restricted to the analysis of resistance and of the making conscious of past traumatic experiences that are involved in the psychogenesis of anxiety disorders. Particular importance is attached to the careful establishment of the indication and then psychoanalytic working-through of the accompanying transference-countertransference-dynamics following the completion of the hypno-analytic phase and in the course of the ongoing uncovering therapeutic process.

Adult↗
PubMed2003

Stable propagation of 'selfish' genetic elements.

Extrachromosomal or chromosomally integrated genetic elements are common among prokaryotic and eukaryotic cells. These elements exhibit a variety of 'selfish' strategies to ensure their replication and propagation during the growth of their host cells. To establish long-term persistence, they have to moderate the degree of selfishness so as not to imperil the fitness of their hosts. Earlier genetic and biochemical studies together with more recent cell biological investigations have revealed details of the partitioning mechanisms employed by low copy bacterial plasmids. At least some bacterial chromosomes also appear to rely on similar mechanisms for their own segregation. The 2 mm plasmid of Saccharomyces cerevisiae and related yeast plasmids provide models for optimized eukaryotic selfish DNA elements. Selfish DNA elements exploit the genetic endowments of their hosts without imposing an undue metabolic burden on them. The partitioning systems of these plasmids appear to make use of a molecular trick by which the plasmids feed into the segregation pathway established for the host chromosomes.

Cell Cycle Proteins↗
PubMed2001

PROSPECT improves cis-acting regulatory element prediction by integrating expression profile data with consensus pattern searches.

Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data.

5' Untranslated Regions↗
PubMed1991

Integration of cultural elements in the therapeutic milieu of a psychiatric day care unit.

For comprehensive understanding of a patient's mental crisis, a thorough knowledge of his cultural context is valuable, as this affords reciprocal translation of the patient's and therapist's codes. Elucidation of the cultural context belongs to the domain of clinical anthropology. In our Day Care Unit we utilize an ethno-psychiatric approach. The anthropologist employs the life-cycle method and a health/illness questionnaire. The former consists of a chronological narration of the patient's life events as rendered by him. Integration of this anthropological material with the anamnestic data is time saving, in that it furnishes the therapist with the opportunity to determine the focus of dynamic therapy already in an early phase of the treatment. The aim of the health/illness questionnaire is to discover the patient's conception of sickness in general and of his mental illness in particular. The information gathered by this anthropological tool guides the therapist in planning the appropriate treatment strategy, while at the same time it may predict the patient's compliance.

Adult↗
PubMed2006

A novel ICE in the genome of Shewanella putrefaciens W3-18-1: comparison with the SXT/R391 ICE-like elements.

A novel R391-like ICE (integrating conjugative element) has been detected in the 4.2 MB genome of Shewanella putrefaciens W3-18-1 located on three different contigs. Assembly of the ICE encoding contigs based on similarity with R391 revealed a mosaic element of plasmid, phage and transposon-like sequences typical of SXT/R391 ICE-like elements. The element, which is 110 057 bp in length, was highly similar to R391 sequences, with most related ORFs showing >96% amino acid sequence identity. The element, designated ICESpuPO1, contained a number of inserts determining resistance to copper and other heavy metals and a broad-spectrum RND efflux pump similar to antibiotic efflux systems. The element was integrated into the Shewanella prfC gene in a manner similar to related ICE-like elements. The chromosomal element junctions contained a 17-bp SXT/R391-like attL and attR site and an unannotated ORF between attL and the ICE integrase encoding a putative recombinational directional factor necessary for excision, with 100% amino acid identity to the R391 ORF4 product.

Bacterial Proteins↗
PubMed2004

Microfluidic routing of aqueous and organic flows at high pressures: fabrication and characterization of integrated polymer microvalve elements.

This paper presents the first systematic engineering study of the impact of chemical formulation and surface functionalization on the performace of free-standing microfluidic polymer elements used for high-pressure fluid control in glass microsystems. System design, chemical wet-etch processes, and laser-induced polymerization techniques are described, and parametric studies illustrate the effects of polymer formulation, glass surface modification, and geometric constraints on system performance parameters. In particular, this study shows that highly crosslinked and fluorinated polymers can overcome deficiencies in previously-reported microvalve architectures, particularly limited solvent compatibility. Substrate surface modification is shown effective in reducing the friction of the polymer-glass interface and thereby facilitating valve actuation. A microchip one-way valve constructed using this architecture shows a 2 x 10(8) ratio of forward and backward flow rates at 7 MPa. This valve architecture is integrated on chip with minimal dead volumes (70 pl), and should be applicable to systems (including chromatography and chemical synthesis devices) requiring high pressures and solvents of varying polarity.

Journal Article↗
PubMed2006

Identification of a unique Alu-based polymorphism and its use in human population studies.

Alu elements represent a family of short interspersed DNA elements (SINEs) found in primate genomes. These are members of a group of transposable elements that integrate into the genome by the process of retrotransposition. Recent integrations of Alu elements within the human genome have generated presence/absence variants useful as DNA markers in human population studies as well as in forensic and paternity analyses. Besides the ease of use, this type of marker is unique because the absence of the Alu represents the ancestral form. We have identified an Alu-based polymorphism that consists of four alleles in which we can predict the evolutionary order. Additionally, we have developed a simple PCR plus restriction endonuclease assay to readily distinguish the four alleles. We have thus far analyzed DNA from a small set of samples comprising ten different ethnic groups. The three populations of African descent exhibited a relatively low frequency of the absence allele in contrast to the other populations, as well as being the only populations in which all four alleles were identified. One presence allele was not found in both European Caucasian and South American populations that were sampled, whereas a different presence allele was not observed among the sampled Asian populations. Additionally, the four-allele system identified variations among populations not observed by simply scoring as presence/absence variants. Therefore, extending beyond the two-allele dimorphic Alu system further elucidates population variations. These features afford this marker as a unique tool in the study of both global and regional analyses of human populations.

Alleles↗
PubMed1999

Chromatography and electrophoresis on chips: critical elements of future integrated, microfluidic analytical systems for life science.

Liquid chromatography and electrophoresis played a major role in the life-science revolution, most strikingly in protein purification, peptide fractionation and sequencing, amino acid analysis, and DNA sequencing. The objective of this article is to examine the potential role of separation systems in the continuing evolution of biochemistry, biotechnology and molecular biology. Very small chip-based systems may change how chemical analyses in biology, medical research and health care evolve over the next decade.

Biological Science Disciplines↗
PubMed2003

Accessibility, continuity and appropriateness: key elements in assessing integration of perinatal services.

A trend toward the reduction in the length of hospital stays has been widely observed. This increasing shift is particularly evident in perinatal care. A stay of less than 48 hours after delivery has been shown to have no negative effects on the health of either the mother or the baby as long as they receive an adequate follow-up. This implies a close integration between hospital and community health services. The present article addresses the following questions: To what extent are postnatal services accessible to mothers and neonates? Are postnatal services in the community in continuity with those of the hospital? Are the services provided by the appropriate source of care? The authors conducted a telephone survey among 1158 mothers in a large urban area in the province of Quebec, Canada. The results were compared to clinical guidelines widely recognised by professionals. The results show serious discrepancies with these guidelines. The authors found a low accessibility to services: less than half of the mothers received a home visit by a nurse. In terms of continuity of care, less than 10% of the mothers received a follow-up telephone call within the recommended time frame and only 18% benefited from a home visit within the recommended period. Finally, despite guidelines to the contrary, hospitals continue to intervene after discharge. This results in a duplication of services for 44.7% of the new-borns. On the other hand, 40.7% are not seen in the recommended period after hospital discharge at all. These results raise concerns about the integration of services between agencies. Following earlier work, the present authors have grouped explanatory factors under four dimensions: the strategic dimension, particularly leadership; the structural dimension, including the size of the network; the technological dimension, with respect to information transmission system; and the cultural dimension, which concerns the collaboration process and the development of relationships based on trust.

Continuity of Patient Care↗
PubMed1999

Site-specific recombination of temperate Myxococcus xanthus phage Mx8: genetic elements required for integration.

Like most temperate bacteriophages, phage Mx8 integrates into a preferred locus on the genome of its host, Myxococcus xanthus, by a mechanism of site-specific recombination. The Mx8 int-attP genes required for integration map within a 2.2-kilobase-pair (kb) fragment of the phage genome. When this fragment is subcloned into a plasmid vector, it facilitates the site-specific integration of the plasmid into the 3' ends of either of two tandem tRNAAsp genes, trnD1 and trnD2, located within the attB locus of the M. xanthus genome. Although Int-mediated site-specific recombination occurs between attP and either attB1 (within trnD1) or attB2 (within trnD2), the attP x attB1 reaction is highly favored and often is accompanied by a deletion between attB1 and attB2. The int gene is the only Mx8 gene required in trans for attP x attB recombination. The int promoter lies within the 106-bp region immediately upstream of one of two alternate GTG start codons, GTG-5208 (GTG at bp 5208) and GTG-5085, for integrase and likely is repressed in the prophage state. All but the C-terminal 30 amino acid residues of the Int protein are required for its ability to mediate attP x attB recombination efficiently. The attP core lies within the int coding sequence, and the product of integration is a prophage in which the 3' end of int is replaced by host sequences. The prophage intX gene is predicted to encode an integrase with a different C terminus.

Amino Acid Sequence↗
PubMed1995

The wind-evoked escape behavior of the cricket Gryllus bimaculatus: integration of behavioral elements

The wind-evoked escape behavior of freely ranging crickets (Gryllus bimaculatus) was studied using high-speed video and film analysis. The escape response can be of three types: a turn, a jump or a turn + jump. Any of these can be followed by running. The turn is similar to that of the cockroach, in terms of the details of body and leg movements. A jump occurs only when the cricket has its back to the wind, either because the stimulus came approximately from behind or because the cricket had first turned away from the wind and then jumped. The jump, like that of locust, requires some form of energy storage and quick release to obtain the necessary power. Locusts use long-term co-activation of antagonistic leg motor neurons to produce mechanical energy storage. By contrast, crickets do not appear to co-activate antagonistic leg motor neurons. Possible alternative energy storage and release mechanisms are discussed.

Journal Article↗