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PubMed2006

GenBank.

GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 205 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the Web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI Homepage at www.ncbi.nlm.nih.gov.

Animals↗

PubMed2007

GenBank.

GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or standalone Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage (www.ncbi.nlm.nih.gov).

Animals↗

PubMed2006

Towards a reference model for representing nursing information needs.

Information needs studies in clinical settings often face the problem of integrating and analyzing data collected using different study tools. Generally, a coding taxonomy or a model is developed to capture and code the study data. Significant efforts are required to develop a model that not only captures the study data but is also closer to the clinical domain to draw meaningful real world inferences. Further, a study-specific model limits comparative evaluation of studies across different institutions. In this paper, we propose a reference model for representing nursing information needs. We use an iterative and collaborative approach in representing the concepts in the model. The model consists of 33 information (need) concepts, 29 information sources and 7 categories of nursing tasks which were used to code 228 identified information need instances.

Hospitals, Urban↗

PubMed2004

Reexamining organizational configurations: an update, validation, and expansion of the taxonomy of health networks and systems.

OBJECTIVES: To (a) assess how the original cluster categories of hospital-led health networks and systems have changed over time; (b) identify any new patterns of cluster configurations; and (c) demonstrate how additional data can be used to refine and enhance the taxonomy measures. DATA SOURCES; 1994 and 1998 American Hospital Association (AHA) Annual Survey of Hospitals. STUDY DESIGN: As in the original taxonomy, separate cluster solutions are identified for health networks and health systems by applying three strategic/structural dimensions (differentiation, integration, and centralization) to three components of the health service/product continuum (hospital services, physician arrangements, and provider-based insurance activities). DATA EXTRACTION METHODS: Factor, cluster, and discriminant analyses are used to analyze the 1998 data. Descriptive and comparative methods are used to analyze the updated 1998 taxonomy relative to the original 1994 version. PRINCIPAL FINDINGS: The 1998 cluster categories are similar to the original taxonomy, however, they reveal some new organizational configurations. For the health networks, centralization of product/service lines is occurring more selectively than in the past. For the health systems, participation has grown in and dispersed across a more diverse set of decentralized organizational forms. For both networks and systems, the definition of centralization has changed over time. CONCLUSIONS: In its updated form, the taxonomy continues to provide policymakers and practitioners with a descriptive and contextual framework against which to assess organizational programs and policies. There is a need to continue to revisit the taxonomy from time to time because of the persistent evolution of the U.S. health care industry and the consequent shifting of organizational configurations in this arena. There is also value in continuing to move the taxonomy in the direction of refinement/expansion as new opportunities become available.

American Hospital Association↗

PubMed1991

A cognitive morphology of psychopathology.

In contrast to contemporary approaches to psychopathology that establish diagnostic taxonomies derived primarily from differences in manifest symptoms, this paper, based on an integration of cognitive and psychoanalytic developmental theory, proposes a structural cognitive morphology for understanding and assessing differences among various forms of psychopathology, from schizophrenia to the neuroses. A theoretical model based on the development of cognitive schema, consistent with clinical and research data, considers schizophrenia and paranoid schizophrenia as involving fundamental disturbances in boundary articulation and recognition constancy, and considers borderline personality disorders as involving disturbances in evocative constancy. Also, a lack of integration of object and self-schema, expressed in either a distorted and exaggerated preoccupation with interpersonal relatedness or self-definition, defines two primary personality configurations that have implications for understanding the neuroses and subtypes of depression, as well as differential response to various types of psychotherapeutic intervention.

Child↗

PubMed2003

The integration of claims to health-care: a programming approach.

The paper contributes to the use of social choice and welfare theory in health economics by developing and applying the integration of claims framework to health-care rationing. Related to Sen's critique of neo-classical welfare economics, the integration of claims framework recognises three primitive sources of claim: consequences, deontology and procedures. A taxonomy is presented with the aid of which it is shown that social welfare functions reflecting these claims individually or together, can be specified. Some of the resulting social choice rules can be regarded as generalisations of health-maximisation and all have normative justifications, though the justifications may not be universally acceptable. The paper shows how non-linear programming can be used to operationalise such choice rules and illustrates their differential impacts on the optimal provision of health-care. Following discussion of relations to the capabilities framework and the context in which rationing occurs, the paper concludes that the integration of claims provides a viable framework for modelling health-care rationing that is technically rigorous, general and tractable, as well as being consistent with relevant moral considerations and citizen preferences.

Attitude to Health↗

PubMed2000

Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes.

We describe the 159,443-bp [corrected] sequence of the plastid chromosome of Oenothera elata (evening primrose). The Oe. elata plastid chromosome represents type I of the five genetically distinguishable basic plastomes found in the subsection Euoenothera. The genus Oenothera provides an ideal system in which to address fundamental questions regarding the functional integration of the compartmentalised genetic system characteristic of the eukaryotic cell. Its highly developed taxonomy and genetics, together with a favourable combination of features in its genetic structure (interspecific fertility, stable heterozygous progeny, biparental transmission of organelles, and the phenomenon of complex heterozygosity), allow facile exchanges of nuclei, plastids and mitochondria, as well as individual chromosome pairs, between species. The resulting hybrids or cybrids are usually viable and fertile, but can display various forms of developmental disturbance.

Base Sequence↗

PubMed1994

Agreeableness and activeness as components of conflict behaviors.

Handling social conflict is usually described in terms of 2 dimensions that either cause the behavior (concern for one's own and others' goals) or that result from it (integration and distribution). In contrast, agreeableness and activeness are common factors of modes and taxonomies of conflict behavior that do not confound independent and dependent variables. This article specifies the extent to which avoiding, accommodating, compromising, problem solving, indirect fighting, and 2 forms of direct fighting--issue fighting and outcome fighting--each positively or negatively relate to agreeableness and activeness. Systematic observations of videotaped simulations by 82 male police sargeants handling a standardized conflict with either a subordinate or a superior supported and refined this metataxonomy.

Adult↗

PubMed2005

Biology of plant rhabdoviruses.

The Rhabdoviridae, whose members collectively infect invertebrates, animals, and plants, form a large family that has important consequences for human health, agriculture, and wildlife ecology. Plant rhabdoviruses can be separated into the genera Cytorhabdovirus and Nucleorhabdovirus, based on their sites of replication and morphogenesis. This review presents a general overview of classical and contemporary findings about rhabdovirus ecology, pathology, vector relations, and taxonomy. The genome organization and structure of several recently sequenced nucleorhabdoviruses and cytorhabdoviruses is integrated with new cell biology findings to provide a model for the replication of the two genera. A prospectus outlines the exciting opportunities for future research that will contribute to a more detailed understanding of the biology, biochemistry, replication and host interactions of the plant rhabdoviruses.

Genome, Viral↗

PubMed1999

[Nursing diagnosis and interventions in a patient with multiple organ failure -- report of a case].

This study tries to identify Nursing Diagnoses and Interventions. It was done with a patient who was in critical health condition: multiple organs failure, in an Intensive Care Unit of a general hospital in Porto Alegre. The Case Study was the methodology used. Nursing Diagnoses is described mostly using NANDA Taxonomy. They are: Risk for Aspiration, Disuse Syndrome, Diarrhea, Risk for Infection, Impaired Tissue Integrity; and a Collaborative Problem was identified: Hypoglicemia. We have elaborated 34 Nursing Interventions for those diagnoses.

Aged↗

PubMed2002

Primary prevention of agricultural injuries. Use of standardized nursing diagnosis, interventions, and outcomes.

1. The use of standardized nursing language is important to the advancement of nursing knowledge and practice. The standardization of nursing diagnoses, interventions, and outcomes provides a means for collecting and analyzing large clinical databases. 2. The occupational health nurse has a clear role in developing health and safety programs. Standardized language using North American Nursing Diagnosis Association diagnoses, nursing outcomes classification, and nursing intervention classification can be incorporated into these programs. 3. The use of standardized taxonomies in the primary prevention of cumulative trauma disorders demonstrates how these systems are integrated into the documentation of the nursing process in a nursing care plan.

Accidents, Occupational↗

PubMed1995

Self-with-other representations and a taxonomy of motives: two approaches to studying persons.

This article discusses two approaches to studying persons. Part 1 describes data gathering procedures that lead to an integrated visual display of particular self-representations of an individual in various spheres of life. "Self-with-other representation" is introduced as a central unit of analysis in this research. This concept is integrated into a method that is exemplified in this article by a description of how life can be injected into static trait characterization of a person. In the context of a case study, it is shown that the method provides information about how traits are organized in terms of self-with-other working models and the conditions under which a particular working model is likely to prevail. Part 2 presents a new taxonomy of motives. This taxonomy is a product of having dipped into the area of operant conditioning and reformulating behavioral consequences into motivational causes. This intrusion into reinforcement theory has resulted in a two-dimensional classification system (referred to as PACK) that accounts for motives to keep or acquire positive experiences, and to cure or prevent negative experiences. After the taxonomy is described, it is used to organize motivational concepts in the area of goal-directed behaviors, and it is applied to purpose statements of individuals in different age groups.

Adult↗

PubMed2005

Atlas - a data warehouse for integrative bioinformatics.

BACKGROUND: We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. DESCRIPTION: The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. CONCLUSION: The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Computational Biology↗

PubMed2000

Phylogenetic analysis of members of the genus Rickettsia using the gene encoding the outer-membrane protein rOmpB (ompB).

To confirm the phylogenetic analysis previously inferred by comparison of the citrate synthase and rOmpA gene sequences (gitA and ompA, respectively), the rOmpB gene (ompB) of 24 strains of the genus Rickettsia was amplified and sequenced. rOmpB is an outer-membrane protein of high molecular mass, the presence of which can be demonstrated in most rickettsiae by immunological cross-reactivity in Western blots. No PCR amplification was obtained with Rickettsia bellii or Rickettsia canadensis. For the other rickettsiae, phylogenetic analysis was inferred from the comparison of both the gene and derived protein sequences by using parsimony, maximum-likelihood and neighbour-joining methods which gave the same organization. All nodes were well supported (>86% bootstrap values), except in the cluster including Rickettsia africae strain S and Rickettsia parkeri, and this analysis confirmed the previously established phylogeny obtained from combining results from gltA and ompA. Based on phylogenetic data, the current classification of the genus Rickettsia is inappropriate, specifically its division into two groups, typhus and spotted fever. Integration of phenotypic, genotypic and phylogenetic data will contribute to the definition of a polyphasic taxonomy as has been done for other bacterial genera.

Bacterial Outer Membrane Proteins↗

PubMed1983

Conservation of genetic linkage in nonisogenic isolates of Candida albicans.

A number of laboratories are now engaged in the genetic analysis of Candida albicans. This diploid yeast, the major fungal pathogen of humans, is imperfect. Parasexual techniques have been devised for complementation and recombination analysis in this organism. This paper attempts to address the question of the extent to which nonisogenic strains of C. albicans have conserved a common genetic map. This analysis is a prerequisite for the integration of work done in different laboratories and may also provide useful information on the taxonomy of the genus Candida. The paper also reports the analysis of an interspecific hybrid between C. albicans and Candida stellatoidea. The method employed in these studies was the analysis of the mitotic recombination relationships of a group of linked genes and their centromere. Strains carrying linked auxotrophic mutations were fused with isogenic and nonisogenic complementary strains to form tetraploids. The mitotic recombination analyses of these tetraploids suggest that in the isolates studied the genetic map is conserved. A comparison of tetraploid and diploid mitotic recombination analyses is also presented.

Adenine↗

PubMed1999

[Risk factors for pressure ulcer: suggestions for prevention].

Pressure ulcers is one of the most severe complication in the spinal cord injured patients begin the prevention aspects and the early identification of the risk factors are imperative action for the nursing assistance of these patients. This study evaluated the nursing care plans for these patients that at the time of the study were already included in the rehabilitation program in order to identify the risk factors for the pressure ulcer development by analysing the nursing documentation adapting the Taxonomy of NANDA. Evaluate the nursing procedures proposed to the diagnosis risk for impaired skin integrity. The identified risk factors are referred to the physical alterations determinate by the neurologic lesion, wound's history and initial lesions. The proposed nursing procedures were sixteen (16) that emphasized patient and family's instructions on body cleaning, position on bed and wheel chair based on the diagnosis established.

Humans↗

PubMed2005

Ensuring the Quality of Aggregated General Practice Data: Lessons from the Primary Care Data Quality Programme (PCDQ).

BACKGROUND: There are large numbers of schemes that collect and aggregate data from primary care computer systems into large databases. These data are then used for market and academic research. How the data is aggregated, cleaned and processed is usually opaque. Making the method transparent allows researchers to compare methods, and users of the output to better understand the strengths and weaknesses of the data.Objectives To define the stages of the process of aggregating, processing and cleaning clinical data from multiple data sources. METHODS: Identify errors in design, collection, staging, integration and analysis. RESULTS: An eight step process defined: (1) Design (2) DATA: entry, (3) Extraction, (4) Migration, (5) Integration, (6) Cleaning, (7) Processing, and (8) Analysis. CONCLUSIONS: This eight step method provides a taxonomy to enable researchers to compare their methods of data process and aggregation.

Computer Systems↗

PubMed1992

Integration of the big five and circumplex approaches to trait structure.

To integrate the 5-dimensional simple-structure and circumplex models of personality, the Abridged Big Five Dimensional Circumplex (AB5C) taxonomy of personality traits was developed, consisting of the 10 circumplexes that can be formed by pitting each of the Big Five factors against one another. The model maps facets of the Big Five dimensions as blends of 2 factors. An application to data consisting of 636 self-ratings and peer ratings on 540 personality trait adjectives yielded 34 well-defined facets out of a possible 45. The AB5C solution is compared with simple-structure and lower dimensional circumplex solutions, and its integrative and corrective potential are discussed, as well as its limitations.

Adult↗