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PubMed2003

Recognizing the fold of a protein structure.

This paper reports a graph-theoretic program, GRATH, that rapidly, and accurately, matches a novel structure against a library of domain structures to find the most similar ones. GRATH generates distributions of scores by comparing the novel domain against the different types of folds that have been classified previously in the CATH database of structural domains. GRATH uses a measure of similarity that details the geometric information, number of secondary structures and number of residues within secondary structures, that any two protein structures share. Although GRATH builds on well established approaches for secondary structure comparison, a novel scoring scheme has been introduced to allow ranking of any matches identified by the algorithm. More importantly, we have benchmarked the algorithm using a large dataset of 1702 non-redundant structures from the CATH database which have already been classified into fold groups, with manual validation. This has facilitated introduction of further constraints, optimization of parameters and identification of reliable thresholds for fold identification. Following these benchmarking trials, the correct fold can be identified with the top score with a frequency of 90%. It is identified within the ten most likely assignments with a frequency of 98%. GRATH has been implemented to use via a server (http://www.biochem.ucl.ac.uk/cgi-bin/cath/Grath.pl). GRATH's speed and accuracy means that it can be used as a reliable front-end filter for the more accurate, but computationally expensive, residue based structure comparison algorithm SSAP, currently used to classify domain structures in the CATH database. With an increasing number of structures being solved by the structural genomics initiatives, the GRATH server also provides an essential resource for determining whether newly determined structures are related to any known structures from which functional properties may be inferred.

Algorithms↗
PubMed2003

The PEDANT genome database.

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRS data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein-protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.

Animals↗
PubMed2005

IMGT, the international ImMunoGeneTics information system.

The international ImMunoGeneTics information system (IMGT) (http://imgt.cines.fr), created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire LIGM (Universite Montpellier II and CNRS) at Montpellier, France, is a high-quality integrated knowledge resource specializing in the immunoglobulins (IGs), T cell receptors (TRs), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune systems (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT includes several sequence databases (IMGT/LIGM-DB, IMGT/PRIMER-DB, IMGT/PROTEIN-DB and IMGT/MHC-DB), one genome database (IMGT/GENE-DB) and one three-dimensional (3D) structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages (IMGT Marie-Paule page), and interactive tools. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in normal physiological and pathological situations. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow up of residual diseases) and therapeutical approaches (graft, immunotherapy and vaccinology). IMGT is freely available at http://imgt.cines.fr.

Animals↗
PubMed2006

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method.

TOPOFIT-DB (T-DB) is a public web-based database of protein structural alignments based on the TOPOFIT method, providing a comprehensive resource for comparative analysis of protein structure families. The TOPOFIT method is based on the discovery of a saturation point on the alignment curve (topomax point) which presents an ability to objectively identify a border between common and variable parts in a protein structural family, providing additional insight into protein comparison and functional annotation. TOPOFIT also effectively detects non-sequential relations between protein structures. T-DB provides users with the convenient ability to retrieve and analyze structural neighbors for a protein; do one-to-all calculation of a user provided structure against the entire current PDB release with T-Server, and pair-wise comparison using the TOPOFIT method through the T-Pair web page. All outputs are reported in various web-based tables and graphics, with automated viewing of the structure-sequence alignments in the Friend software package for complete, detailed analysis. T-DB presents researchers with the opportunity for comprehensive studies of the variability in proteins and is publicly available at http://mozart.bio.neu.edu/topofit/index.php.

Databases, Protein↗
PubMed2002

A Drosophila full-length cDNA resource.

BACKGROUND: A collection of sequenced full-length cDNAs is an important resource both for functional genomics studies and for the determination of the intron-exon structure of genes. Providing this resource to the Drosophila melanogaster research community has been a long-term goal of the Berkeley Drosophila Genome Project. We have previously described the Drosophila Gene Collection (DGC), a set of putative full-length cDNAs that was produced by generating and analyzing over 250,000 expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages. RESULTS: We have generated high-quality full-insert sequence for 8,921 clones in the DGC. We compared the sequence of these clones to the annotated Release 3 genomic sequence, and identified more than 5,300 cDNAs that contain a complete and accurate protein-coding sequence. This corresponds to at least one splice form for 40% of the predicted D. melanogaster genes. We also identified potential new cases of RNA editing. CONCLUSIONS: We show that comparison of cDNA sequences to a high-quality annotated genomic sequence is an effective approach to identifying and eliminating defective clones from a cDNA collection and ensure its utility for experimentation. Clones were eliminated either because they carry single nucleotide discrepancies, which most probably result from reverse transcriptase errors, or because they are truncated and contain only part of the protein-coding sequence.

Amino Acid Sequence↗
PubMed1990

Enhancing social work influence in the hospital: identifying sources of power.

Social workers need to develop interest and skills in hospital politics. Turbulent health care systems, combined with the unique organizational attributes of health care organizations, create environments where political skills are essential to achieve social work goals and objectives. This article identifies sources of social work power within the hospital. Power resides not only in the political acumen of the individual but also in the structural attributes associated with the work group. Discussion focuses on resource control and network centrality as structural sources of social work power.

Humans↗
PubMed2006

Perceptions of empowerment and respect: effect on nurses' organizational commitment in nursing homes.

This study tested Kanter's theory of structural empowerment in a sample of nurses employed in nursing homes throughout Ontario by examining relationships between nurses' perceptions of structural and psychological empowerment, respect, and organizational commitment. A random sample of 79 RNs (response rate 64%) and 75 RPNs (response rate 60%) were used. Both groups reported moderate levels of empowerment, respect, and commitment. RNs perceived higher levels of empowerment and respect than RPNs. Access to opportunity was the most empowering factor for nurses in this study, and access to resources the least empowering. Structural empowerment, psychological empowerment, and respect explained 48% of the variance in affective commitment for RNs and 40% for RPNs. Results of this study provide support for the use of Kanter's theory in LTC nurse populations.

Aged↗
PubMed2006

Structure-guided recombination creates an artificial family of cytochromes P450.

Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising 3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, is a valuable resource for sequence-structure-function studies. Logistic regression analysis of the multiple sequence alignment identifies key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2.

Amino Acid Sequence↗
PubMed1996

Effect of feedback on resource use and morbidity in hip and knee arthroplasty in an integrated group practice setting.

OBJECTIVE: To assess the effect of a structured program of feedback about resource utilization and morbidity on resource consumption and complications in an orthopedic surgical practice. DESIGN: We prospectively analyzed use and outcomes before and after an intervention (departmental data presentation). MATERIAL AND METHODS: Feedback on resource utilization and morbidity for 2,820 patients who underwent a primary total hip or knee arthroplasty for a diagnosis of osteoarthritis between Jan. 1, 1990, and Dec. 31, 1992, was provided to members of the orthopedic department of an academic medical center. Data were adjusted for severity of disease. RESULTS: On reassessment 18 months after the beginning of the feedback program, total charges and length of hospital stay for hip or knee arthroplasty were significantly reduced. Interpractitioner variability was also reduced but not significantly. The feedback process was instrumental in identifying a specific complication--pulmonary embolism after bilateral total knee replacement--which was significantly reduced by addition of warfarin prophylaxis. CONCLUSION: The intervention was successful in reducing resource use (length of hospital stay) and complications (pulmonary embolism). In addition, total charges for hip and knee arthroplasty declined significantly at a time when medical center charges overall were increasing. Efforts to maintain continuous improvement will primarily focus on the development of critical pathways.

Critical Pathways↗
PubMed1999

[The study of the distribution of Chinese surnames and the diversity of genetic population structure in the Song dynasty].

Surname in China, as a cultural genetic factor, is a very huge and remarkable human population study resource. The transmission feature of surname has been proved to be similar to that of the genetic markers on Y chromosome of males. It, therefore, has been applied in the population genetic studies since 1965's. In the present study, we have analyzed a group of Chinese surname data of the Song dynasty (AD. 960-1179). The distribution of the present surname data is corresponded with the Karlin-McGregor's neutral allele model. The surname abundance alpha and the migration rate parameter v in the Song dynasty in 16 provincial regions reflected degrees of migration and admixture at that time. Surname phylogenetic dendrogram analysis demonstrated that the Han Chinese had been segregated into North and South two parts in Song dynasty of 1000 years ago. Wuyi and Nanling Mountains divided Northern and Southern Han populations into the two major parts of Han Chinese. The results also showed that the surname distribution of Song dynasty 1000 years ago was quite similar to the present model. The 100 high frequency surnames in Song dynasty were well corresponded with the current surname distribution. This phenomenon suggests that Chinese surnames have been steadily transmitted from ancient to the present. The present study improved that the Chinese surname is a very important genetic resource for the studies of structure of the Chinese populations, migration, and affinities among different populations.

China↗
PubMed2004

PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation.

PhosphoSite is a curated, web-based bioinformatics resource dedicated to physiologic sites of protein phosphorylation in human and mouse. PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. Links are also provided to a number of external resources for protein sequences, structure, post-translational modifications and signaling pathways, as well as sources of phospho-specific antibodies and probes. As the amount of information in the underlying knowledgebase expands, users will be able to systematically search for the kinases, phosphatases, ligands, treatments, and receptors that have been shown to regulate the phosphorylation status of the sites, and pathways in which the phosphorylation sites function. As it develops into a comprehensive resource of known in vivo phosphorylation sites, we expect that PhosphoSite will be a valuable tool for researchers seeking to understand the role of intracellular signaling pathways in a wide variety of biological processes.

Animals↗
PubMed2000

[A survey on drug-related service by homehelper in the Japanese home care system].

The purposes of this study are a) to determine whether homehelpers attend to drug-related service of elder care-recipients at home and b) to determine what cooperating human resources were utilized. A structured questionnaire survey was conducted in 1997 with 403 homehelpers who provided in home care to dependent elderly person. Of the total, 19% subjects did deal with care recipients' medication. Regarding the type of service, the highest proportion of subjects had assisted by picking up medicine from pharmacy and talking it to the care recipients' home. Results showed that physicians and home visiting nurses were the most depended upon human resources in the home health care system among health, medical and welfare facilities. Results also suggested that many homehelpers are not aware that pharmacists are readily available resources for providing home health care. Hence we conclude that the respondents tend to rely on physicians or home visiting nurses to respond to care recipients care, and pharmacists should be made aware of the necessity of providing the appropriate drug-related information to physicians or home visiting nurses.

Adult↗
PubMed2004

CHOP proteins into structural domain-like fragments.

We developed a method CHOP dissecting proteins into domain-like fragments. The basic idea was to cut proteins beginning from very reliable experimental information (PDB), proceeding to expert annotations of domain-like regions (Pfam-A), and completing through cuts based on termini of known proteins. In this way, CHOP dissected more than two thirds of all proteins from 62 proteomes. Analysis of our structural domain-like fragments revealed four surprising results. First, >70% of all dissected proteins contained more than one fragment. Second, most domains spanned on average over approximately 100 residues. This average was similar for eukaryotic and prokaryotic proteins, and it is also valid-although previously not described-for all proteins in the PDB. Third, single-domain proteins were significant longer than most domains in multidomain proteins. Fourth, three fourths of all domains appeared shorter than 210 residues. We believe that our CHOP fragments constituted an important resource for functional and structural genomics. Nevertheless, our main motivation to develop CHOP was that the single-linkage clustering method failed to adequately group full-length proteins. In contrast, CLUP-the simple clustering scheme CLUP introduced here-succeeded largely to group the CHOP fragments from 62 proteomes such that all members of one cluster shared a basic structural core. CLUP found >63,000 multi- and >118,000 single-member clusters. Although most fragments were restricted to a particular cluster, approximately 24% of the fragments were duplicated in at least two clusters. Our thresholds for grouping two fragments into the same cluster were rather conservative. Nevertheless, our results suggested that structural genomics initiatives have to target >30,000 fragments to at least cover the multimember clusters in 62 proteomes.

Amino Acids↗
PubMed2005

Provision of information for cancer patients: an appraisal and review.

This article is based on an appraisal of Cancer Information and Support Services in Britain supported by the UK-based charity Macmillan Cancer Relief. Commissioned in 2002, the appraisal formed part of a wider review aimed at extending knowledge about Cancer Information and Support Services. It was also designed to ensure that the Macmillan Cancer Information and Support Service Model continues to reflect the needs of people whose lives are affected by cancer. The individual services reviewed for the appraisal vary widely in terms of resources, staffing and organizational structure, but many common themes emerge. The importance of outreach and networking are highlighted, along with the problem of isolation. Many post-holders saw a need to include a hospital base, while the role played by volunteers is widely acknowledged. A key aim of the review was to start to identify the factors that contribute to the success of a service, and a number of these emerge from the study. The creation of a culture that enables such a service to thrive appears to be as important as securing financial and other resources. The contribution made by Macmillan is explored, and ways in which the organization can support the dissemination of knowledge are put forward.

Ancillary Services, Hospital↗
PubMed1995

A purchaser perspective of managing new drugs: interferon beta as a case study.

Many new drugs in the future will be very expensive and have major resource implications. Given current structures and legislation covering the prescribing of drugs, there are no clear means of controlling the use of these drugs to avoid diverting money away from other health care services and into drug treatment. This paper considers what mechanisms might be used by a purchaser to manage the introduction of an expensive new drug and uses interferon beta-1b for treating multiple sclerosis as an example. The most likely mechanism is the prescribing of the drug by a general practitioner on the advice of a neurologist. This would achieve a good benefit for the resources invested but would not control total expenditure. Devolving a limited budget for the drug to a specialist centre so that neurologists may prescribe it directly would be preferable, as this would link clinical, prescribing, and budgetary responsibility. These issues need to be addressed urgently by purchasers if major disruptions of services are to be avoided.

Drug Approval↗
PubMedDate not supplied

Stepwise approach to developing point-of-care testing services in the community/ambulatory pharmacy setting.

OBJECTIVE: To provide a stepwise approach to development and implementation of a point-of-care testing (POCT) patient care service. SETTING: Community and ambulatory care pharmacy practice. PRACTICE DESCRIPTION: To provide community and ambulatory pharmacists with the steps involved in integrating POCT services into their pharmacy practice site. PRACTICE INNOVATION: Authors used various resources to detail the process of implementing pharmaceutical care in community or ambulatory pharmacy settings in combination with individual practice experiences. The five steps involved in developing a POCT service include conducting a needs assessment, researching and organizing information, developing program materials, implementing the service, and evaluating the service. The narrative description of each step is illustrated by a case study example. INTERVENTIONS: Not applicable. MAIN OUTCOME MEASURES: Not applicable. RESULTS/CONCLUSION: POCT patient care services are a valuable addition to a pharmacy's services, benefiting patients, health care providers, and the pharmacy. This article presents a structured, deliberate approach with resources that can be used to develop a successful POCT service within a community or ambulatory pharmacy setting.

Ambulatory Care↗
PubMedDate not supplied

[Community psychiatry in Latin America].

Present trends of communitary Psychiatry are considered, with an assessment of their measurable parameters and degrees of feasibility. Three models are set forth, taking into account their principal factors: primary mental health agents, actual resources, socio-political structures, geographical setting, cultural patterns, possible strategies, and community participation. Model I is a traditional one, it relies on decisions taken from the administration, which endows both scientific authority and normative power. Participation of the community is not called for, and has neither a place nor a function. The stress is on secondary and tertiary prevention. Model II is more focused on community needs and primary prevention. Programs are conceived after the community is consulted. They use primarily the health efectors within the community itself. Model III stresses active participation of community leaders and members at all levels of decision, and implementation, as well as the use of community's own resources for promoting health. Assistential centers and personnel are only the specialized supports and supervisors of actions, mainly carried out by the protagonists themselves. All three models are analyzed from several standpoints, including theoretical conception, feasbility of implementation, efficacity, vulnerability, cost-benefit ratios and foreseeable outlooks.

Community Psychiatry↗
PubMed2004

Bacterial competition in activated sludge: theoretical analysis of varying solids retention times on diversity.

A mechanistic model for activated sludge sewage treatment was developed to predict exploitative competition of six aerobic heterotrophic bacterial species competing for three essential resources. The central hypothesis of the model is that in a multispecies/limiting resource system the number of coexisting bacterial species, N, exceeds the number of limiting resources, K, available for them. The explanation for this is that for certain species combinations, the dynamics of the competition process generate oscillations in the abundances of species, and these oscillations allow the coexistence of greater number of species than the number of limiting resources ( N > K). This result is a direct contradiction of an existing activated sludge steady state competition theory, "the principle of competitive exclusion," which states that the competition process proceeds to equilibrium, allowing only N </= K species to coexist. The model was used to investigate the effect of varying solids retention times on the diversity of species using the conventional, completely mixed activated sludge configuration. The results of model simulations showed that for a certain range of solids retention times (2.28-5.66 days) the competition of six species for three essential resources produces oscillations within the structure of the bacterial community allowing for the sustained growth of more than three species on three resources.

Bacterial Physiological Phenomena↗