Human resources management and structures: CEO perceptions and practices.
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Administrative Personnel↗
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Results for “resource structure”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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Structure and organizational resource allocation.
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Centralized Hospital Services↗
Task-evoked pupillary responses, processing load, and the structure of processing resources.
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Attention↗
Streamlining our structure, focusing our resources.
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Humans↗
The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology.
The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.
Amino Acid Sequence↗
Using benchmarking practices for the learning resource center.
Structured ongoing and systematic evaluation is required to ensure up-to-date resources and continuous quality improvement plans to meet the learning needs of the diverse student population and the complex needs of patients. Using benchmarking to achieve evaluation goals in the learning resource center has great merit as schools of nursing respond to consumer demand for improvement, rapid changes resulting from changing patient needs, and the technology explosion.
Benchmarking↗
Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly.
Stochastic niche theory resolves many of the differences between neutral theory and classical tradeoff-based niche theories of resource competition and community structure. In stochastic niche theory, invading species become established only if propagules can survive stochastic mortality while growing to maturity on the resources left unconsumed by established species. The theory makes three predictions about community structure. First, stochastic niche assembly creates communities in which species dominate approximately equally wide "slices" of the habitat's spatial heterogeneity. These niche widths generate realistic distributions of species relative abundances for which, contrary to neutral theory but consistent with numerous observations, there are strong correlations among species traits, species abundances, and environmental conditions. Second, slight decreases in resource levels are predicted to cause large decreases in the probability that a propagule would survive to be an adult. These decreases cause local diversity to be limited by the inhibitory effects of resource use by established species on the establishment (recruitment) of potential invaders. If resource pulses or disturbance allowed invaders to overcome this recruitment limitation, many more species could indefinitely coexist. Third, the low invasibility of high diversity communities is predicted to result not from diversity per se, but from the uniformly low levels of resources that occur in high-diversity communities created by stochastic competitive assembly. This prediction provides a potential solution to the invasion paradox, which is the tendency for highly diverse regions to be more heavily invaded.
Computer Simulation↗
MODBASE: a database of annotated comparative protein structure models and associated resources.
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on MODELLER for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, and improvements in the software for calculating the models. MODBASE currently contains 3 094 524 reliable models for domains in 1 094 750 out of 1 817 889 unique protein sequences in the UniProt database (July 5, 2005); only models based on statistically significant alignments and models assessed to have the correct fold despite insignificant alignments are included. MODBASE also allows users to generate comparative models for proteins of interest with the automated modeling server MODWEB (http://salilab.org/modweb). Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally defined binary domain interfaces (PIBASE, http://salilab.org/pibase) as well as predictions of ligand binding sites, interactions between yeast proteins, and functional consequences of human nsSNPs (LS-SNP, http://salilab.org/LS-SNP).
Binding Sites↗
MODBASE, a database of annotated comparative protein structure models, and associated resources.
MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).
Amino Acid Sequence↗
Resource variation and the structure of British bird communities.
Data on the foraging microhabitats of British birds are reanalyzed with the aim of understanding how fluctuations in resource abundance affect niche relationships and community structure. At Marley Wood, overlap in the foraging sites of resident bird species increased during the late spring and summer and decreased during the fall and winter. Among bird species coexisting in the pine forests at Thetford Chase, spatial overlap and spatial niche widths were positively correlated with food abundance over a 4-year period. These results suggest that in variable environments similarity in spatial niches is an inverse function of the intensity of competition for food. As food supplies drop, consumer species must apparently occupy increasingly different foraging areas in order to coexist. In less variable environments, however, resource stability may allow finer partitioning of the available foraging space and greater spatial overlap within a given foraging area. The results of this paper also suggest a reinterpretation of MacArthur's study of resource partitioning among warbler species in the boreal forests of New England. Rather than providing an instance of niche segregation in order to avoid intense competition, MacArthur's warblers may actually represent another example of increased spatial similarity when food resources are abundant and competition is reduced.
Journal Article↗
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants.
Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The Swiss-Prot protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the Swiss-Prot Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly Swiss-Prot release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The Swiss-Prot variant pages are accessible from the NiceProt view of a Swiss-Prot entry on the ExPASy server (www.expasy.org/), via a hyperlink created for the stable and unique identifier FTId of each human SAP.
Amino Acid Substitution↗
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds. This extended CATH protein family database contains 616,470 domain sequences classified into 23,876 sequence families. This results in the significant expansion of the CATH HMM model library to include models built from the CATH sequence relatives, giving a 10% increase in coverage for detecting remote homologues. An improved Dictionary of Homologous superfamilies (DHS) (http://www.biochem.ucl.ac.uk/bsm/dhs/) containing specific sequence, structural and functional information for each superfamily in CATH considerably assists manual validation of homologues. Information on sequence relatives in CATH superfamilies, GenBank and completed genomes is presented in the CATH associated DHS and Gene3D resources. Domain partnership information can be obtained from Gene3D (http://www.biochem.ucl.ac.uk/bsm/cath/Gene3D/). A new CATH server has been implemented (http://www.biochem.ucl.ac.uk/cgi-bin/cath/CathServer.pl) providing automatic classification of newly determined sequences and structures using a suite of rapid sequence and structure comparison methods. The statistical significance of matches is assessed and links are provided to the putative superfamily or fold group to which the query sequence or structure is assigned.
Databases, Nucleic Acid↗
Exploring organizational characteristics associated with practice changes following a mentored online educational module.
INTRODUCTION: Studies of health professionals' perceptions of barriers to and facilitators of research utilization in clinical practices suggest that structural and resource characteristics of service provider organizations are key determinants of the capacity of individual practitioners to provide evidence-based practices. In this pilot study, we compare health professionals' self-reported practice changes with characteristics of the structures and resources available to support research use at 4 hospitals. METHODS: Data on the self-reported practice changes of stroke rehabilitation professionals at Ontario hospitals were analyzed following their participation in a mentored online educational intervention, the Rehabilitation Education Program for Stroke (REPS). In-depth interviews with a purposefully drawn subsample of REPS mentors and managers of stroke rehabilitation programs examined the participating hospitals' structural and resource characteristics. The interview data on hospital characteristics were coded descriptively and thematically, quantified, and then compared with the percentage of individual REPS participants who reported positive practice changes in each hospital. RESULTS: Hospitals with higher percentages of participants reporting improved practices following REPS provided better computer access, paid time to participate in REPS, had established specialized units of stroke care, strong teamwork, and were previously committed to implementing best practices. They also conducted program audits or evaluations and engaged in "bottom-up" program decision making. DISCUSSION: Continuing educators should consider the capacity of hospitals to support practice changes when planning educational interventions for rehabilitation professionals. Larger studies employing objective measures are needed to examine relationships between practice improvements and organizational characteristics following educational interventions.
Education, Medical, Continuing↗
The PRESAGE database for structural genomics.
The PRESAGE database is a collaborative resource for structural genomics. It provides a database of proteins to which researchers add annotations indicating current experimental status, structural predictions and suggestions. The database is intended to enhance communication among structural genomics researchers and aid dissemination of their results. The PRESAGE database may be accessed at http://presage.stanford.edu/
Databases, Factual↗
Age, attention, expertise, and time-sharing performance.
Time-sharing efficiency and resource allocation from a group of pilots with expertise in time-sharing and a group of nonpilots (ages 20-79 years) were examined. Participants performed 5 dual tasks that represented different degrees of structural similarity as characterized by the structure-specific resource model. Age, expertise, and structural similarity were found to interactively affect time-sharing performance through attentional resources. Age-related deficits in time-sharing were evident under conditions of intense attentional demands and when precise control was required. Modest expertise modulation of the age effects is likely to increase with more domain-specific time-sharing. The structure-specific resource model provided a useful framework for interpreting the relationship between aging and time-sharing performance.
Adult↗
Teaching resources. Protein domains that interact with receptor tyrosine kinases: structural aspects.
This Teaching Resource provides lecture notes and slides for a class covering insights gained from structural analysis of the regulation of receptor tyrosine kinases and is part of the course "Cell Signaling Systems: A Course for Graduate Students." The lecture begins with an overview of the many protein domains thus far implicated in cell signaling and then describes in detail the phosphotyrosine-binding domain (PTB). The application of structural information to rational drug design by targeting protein interaction domains is also covered.
Audiovisual Aids↗
Seq2Struct: a resource for establishing sequence-structure links.
UNLABELLED: Several methods for establishing cross-links between Protein Data Bank (PDB) structures or Structural Classification of Proteins (SCOP) domains and Swiss-Prot + TrEMBL sequences (or vice versa) rely on database annotations. Alternatively, sequence alignment procedures can be used. In this study, we describe Seq2Struct, a web resource for the identification of sequence-structure links. The resource consists of an exhaustive collection of annotated links between Swiss-Prot + TrEMBL and PDB + SCOP database entries. Links are based on pre-established highly reliable thresholds and stored in a relational database, which has been enhanced using annotations derived from Swiss-Prot, PDB, SCOP, GOA and DSSP databases. The Seq2Struct database contents, supported by a WWW web interface, can be queried both online and downloaded. AVAILABILITY: The Seq2Struct resource, with related documentation, is available at http://surface.bio.uniroma2.it/seq2struct/ CONTACT: seq2struct@cbm.bio.uniroma2.it.
Database Management Systems↗
The biology of nonfrugivorous tephritid fruit flies.
This review is the first comprehensive treatment of the biology of nonfrugivorous fruit flies of the family Tephritidae. Feeding habits of destructive and useful species, morphology of immature stages, and hypotheses regarding structural homology and the evolutionary biology of nonfrugivorous tephritids are reviewed, including zoogeography and theories involving resource heterogeneity, guild structure, resource partitioning, resource utilization, facultative niche exploitation, extrinsic and intrinsic factors, host associations, seasonal distribution and phenology, aggregative and circumnatal life history strategies, voltinism, diapause, aestivation, oviposition site, clutch size, and supernumerary oviposition.
Journal Article↗