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PubMed2004

The RESID Database of Protein Modifications as a resource and annotation tool.

The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications and cross-links including pre-, co-, and post-translational modifications. The database provides: systematic and alternate names, atomic formulas and masses, enzymatic activities that generate the modifications, keywords, literature citations, Gene Ontology (GO) cross-references, protein sequence database feature table annotations, structure diagrams, and molecular models. This database is freely accessible on the Internet through resources provided by the European Bioinformatics Institute (http://www.ebi.ac.uk/RESID), and by the National Cancer Institute--Frederick Advanced Biomedical Computing Center (http://www.ncifcrf.gov/RESID). Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries. As an Internet resource, the RESID Database assists researchers in high-throughput proteomics to search monoisotopic masses and mass differences and identify known and predicted protein modifications.

Databases, Factual↗
PubMed1990

Mental health in older spouses: the dynamic interplay of resources, depression, quality of the marital relationship, and social participation.

This study demonstrates a conceptual linkage between exchange theory and psychoanalytic theory of depression. The effects of diminished resources and the dynamic relationships between depression, quality of the marital relationship, and social participation were investigated with a sample of 229 community residing, married older people (Duke Longitudinal Study) using a combined structural and measurement model with linear structural relations (LISREL) analysis. Findings are that some resources have direct effects on depression, marital quality, and social participation. However, it is through the pathway of depressive moods that ill health, retirement, and stress have their negative effects on the marital relationship. Depressive moods do affect social participation, but psychosomatic symptoms of depression do not affect the amount of social participation nor the marital relationship. Recognizing depressive moods as intervening variables is important because older people tend to deny feeling depressed. Without a conceptual linkage of exchange and depression theories, this pathway would not have been identified.

Aged↗
PubMed1990

Physician payment and cost-containment strategies in West Germany: suggestions for Medicare reform.

The West German health care system pays ambulatory care physicians on a fee-for-service basis but employs a national relative value scale and regional capitation-based revenue pools to achieve expenditure controls on total physician reimbursement. Physician-controlled organizations manage these pools and conduct utilization reviews on their own members. The capitation rates are determined by negotiations between the physician associations and health insurers. The West German government has been able to exert some influence on the outcome of these negotiations through a quasi-governmental advisory body. Aspects of this structure could be adopted by Medicare in order to determine conversion factors for resource-based relative value scales or to create expenditure control and incentive structures for Medicare-participating physicians.

Ambulatory Care↗
PubMed2006

A resource-based view of partnership strategies in health care organizations.

The distribution of management structures in health care has been shifting from independent ownership to interorganizational relationships with other firms. A shortage of resources has been cited as one cause for such collaboration among health care entities. The resource- based view of the firm suggests that organizations differentiate between strategic alliances and acquisition strategies based on a firm's internal resources and the types of resources a potential partner organization possesses. This paper provides a review of the literature using the resource-based theory of the firm to understand what conditions foster different types of health care partnerships. A model of partnership alliances using the resource-based view is presented, strategic linkages are presented, managerial implications are outlined, and directions for future research are given.

Cooperative Behavior↗
PubMed2003

Activity-based costing: a practical model for cost calculation in radiotherapy.

PURPOSE: The activity-based costing method was used to compute radiotherapy costs. This report describes the model developed, the calculated costs, and possible applications for the Leuven radiotherapy department. METHODS AND MATERIALS: Activity-based costing is an advanced cost calculation technique that allocates resource costs to products based on activity consumption. In the Leuven model, a complex allocation principle with a large diversity of cost drivers was avoided by introducing an extra allocation step between activity groups and activities. A straightforward principle of time consumption, weighed by some factors of treatment complexity, was used. The model was developed in an iterative way, progressively defining the constituting components (costs, activities, products, and cost drivers). RESULTS: Radiotherapy costs are predominantly determined by personnel and equipment cost. Treatment-related activities consume the greatest proportion of the resource costs, with treatment delivery the most important component. This translates into products that have a prolonged total or daily treatment time being the most costly. The model was also used to illustrate the impact of changes in resource costs and in practice patterns. CONCLUSION: The presented activity-based costing model is a practical tool to evaluate the actual cost structure of a radiotherapy department and to evaluate possible resource or practice changes.

Accounting↗
PubMed1991

Determination of nurse adequacy in rural areas.

The examination of the adequacy of nursing resources requires an analysis of a variety of factors. Because registered nurses primarily provide their services as employees of organized health care delivery structures, the number, size and type of these structures in an area are key to the nursing resources required and the nurse supply.

Data Collection↗
PubMed2004

Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.

To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel "full-length" enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new "full-length" cDNA sequences, raising the number of annotated genes with a corresponding "full-length" cDNA sequence to about 14,000. Detailed comparisons between these "full-length" cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by "full-length" cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation.

Arabidopsis↗
PubMed2006

ADSA Foundation Scholar Award: Implementing waste solutions for dairy and livestock farms.

Water quality in the United States is threatened by contamination with nutrients, primarily nitrogen (N) and phosphorus (P). Animal manure can be a valuable resource for farmers, providing nutrients, improving soil structure, and increasing vegetative cover to reduce erosion potential. At the same time, application of manure nutrients in excess of crop requirements can result in environmental contamination. Concentrated animal agriculture has been identified as a significant source of nutrient contamination of surface water, nitrogen contamination of groundwater, and ammonia emission. Areas facing the dilemma of an economically important livestock industry concentrated in an environmentally sensitive area have few options. If agricultural practices continue as they have in the past, despite the significant changes in agricultural intensity and changing environmental conditions, continued damage to water resources and a loss of fishing and recreational activity are inevitable. If agricultural productivity is reduced, however, the maintenance of a stable farm economy, a viable rural economy, and a reliable domestic food supply are seriously threatened. The identification and implementation of solutions to the generation of excess manure in confined animal feeding operations are necessary to enable such agricultural operations to thrive in environmentally sensitive areas such as the Chesapeake Bay Watershed. This paper will review an innovative collaborative approach to the development of a manure and litter solutions strategy by a diverse array of potential problem-solvers.

Agriculture↗
PubMed2006

Teaching anatomy: cadavers vs. computers?

Our study was aimed to show if cadaver dissections are still important in the Anatomy Course for medical students or whether computerized resources could replace them. We followed three groups, one of them (698 students) proceeded through the Anatomy Course in a traditional way, meaning, with cadaver material enough to observe all the regions and structures; the second group (330 students) used many technological resources but not cadaver dissections; and the third group (145 students) followed the course, recently, with the same program but with both practical resources. Theoretical contents were developed in the same way and by the same professor. The traditional teaching group obtained better results than the technologically supported group, evaluated by the number of students that passed their exams. The third group results were better than the others, with regard to passed exams and marks. Even when computerized improvements have developed a new area giving students a lot of elements to facilitate their approach to imaging structures, the possibility of direct contact with tissues and anatomical elements cannot yet be replaced. We are demonstrating that the best possibility is the correct association of all these resources to complement one another.

Anatomy↗
PubMed2000

Project 2000: a study of expected and experienced stressors and support reported by students and qualified nurses.

The present study was conducted in the light of major reforms to nurse education which have taken place in the United Kingdom since 1989. The study aimed to identify initially perceived stressors and coping resources and subsequently, to compare these with actually reported stressors and available resources, during a critical period in nurses' careers. Three groups of nurses participated who were undertaking, or had recently completed, the first Project 2000 course at a university in the south of England. Participants were given an open-ended questionnaire and asked to describe potential difficulties, and the coping resources they anticipated using, in a subsequent 6-month period. Following analysis of the descriptors a structured questionnaire was developed to measure actually experienced difficulties and coping resources that were reported; this was completed by the three groups 6 months after the initial phase of the study. Both student and staff nurse groups reported fewer stressors and more resources than they had predicted. Students anticipated difficulties with competence but actually reported financial difficulties. They experienced support from mentors although this was not anticipated. Newly qualified staff nurses experienced fewer difficulties with meeting personal expectations of the role than they had anticipated. They reported more use of emotion-focused coping and less professional support than the student groups. The results are discussed in relation to training needs.

Adolescent↗
PubMed1999

Human epidermal differentiation complex in a single 2.5 Mbp long continuum of overlapping DNA cloned in bacteria integrating physical and transcript maps.

Terminal differentiation of keratinocytes involves the sequential expression of several major proteins which can be identified in distinct cellular layers within the mammalian epidermis and are characteristic for the maturation state of the keratinocyte. Many of the corresponding genes are clustered in one specific human chromosomal region 1q21. It is rare in the genome to find in such close proximity the genes belonging to at least three structurally different families, yet sharing spatial and temporal expression specificity, as well as interdependent functional features. This DNA segment, termed the epidermal differentiation complex, contains 27 genes, 14 of which are specifically expressed during calcium-dependent terminal differentiation of keratinocytes (the majority being structural protein precursors of the cornified envelope) and the other 13 belong to the S100 family of calcium binding proteins with possible signal transduction roles in the differentiation of epidermis and other tissues. In order to provide a bacterial clone resource that will enable further studies of genomic structure, transcriptional regulation, function and evolution of the epidermal differentiation complex, as well as the identification of novel genes, we have constructed a single 2.45 Mbp long continuum of genomic DNA cloned as 45 p1 artificial chromosomes, three bacterial artificial chromosomes, and 34 cosmid clones. The map encompasses all of the 27 genes so far assigned to the epidermal differentiation complex, and integrates the physical localization of these genes at a high resolution on a complete NotI and SalI, and a partial EcoRI restriction map. This map will be the starting resource for the large-scale genomic sequencing of this region by The Sanger Center, Hinxton, U.K.

Bacteria↗
PubMed1999

Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities.

The deduced primary sequence (cbbL and cbbS) of form I ribulose 1, 5-bisphosphate carboxylase/oxygenase (rubisco) from Bradyrhizobium japonicum places this enzyme within the Type IC subgroup of red-like rubisco enzymes. In addition, B. japonicum appears to organize most of the structural genes of the Calvin-Benson-Bassham (CBB) pathway in at least one major operon. Functional expression and characterization of the B. japonicum and Xanthobacter flavus enzymes from this group revealed that these molecules exhibit diverse kinetic properties despite their relatively high degree of sequence relatedness. Of prime importance was the fact that these closely related enzymes exhibited CO2 and O2 substrate specificities that varied from relatively low values [tau = (VcKo)/(VoKc) = 45] to values that approximated those obtained for higher plants (tau = 75). These results, combined with the metabolic and genetic versatility of the organisms from which these enzymes were derived, suggest a potential rich resource for future biological selection and structure-function studies aimed at elucidating structural features that govern key enzymological properties of rubisco.

Amino Acid Sequence↗
PubMed2005

[Effects of land use structure change on regional ecological health--taking Shapingba County as an example].

Land resource is the carrier for the exchange of matter, energy and information flows, while the change velocity and the intensity of land use has strong effects on the ecological processes such as matter circulation, energy flow, and biologic diversity. Land use structure change will alter the type, area, and spatial distribution of ecosystem, and in the meantime, result in the changes of regional ecological health. Employing the principles and methods of landscape ecology, and through endowing relative ecological value to land use type, this paper analyzed the charaeteristics of recent 10 years land use change in Shapingba County of Chongqing, and discussed the effects of land use change on regional ecological health, aimed to provide scientific references for land use planning and sustainable land resource utilization. The results indicated that transformation often occurred among different land use types, and the land use structure in each transformation phase differed quite obviously. Under different land use structure, there was a great disparity in relative ecological value of sub-ecosystems, which played various roles in regional ecological health. In general, the regional relative ecological value embodied both increase and decrease. In the future, the relative ecological value of sub-ecosystem would represent three tendencies, i.e., increase first and decrease then, continuous decrease, and continuous increase. The situation of regional ecological health would gradually become better.

Biodiversity↗
PubMed2005

Organelle DB: a cross-species database of protein localization and function.

To efficiently utilize the growing body of available protein localization data, we have developed Organelle DB, a web-accessible database cataloging more than 25,000 proteins from nearly 60 organelles, subcellular structures and protein complexes in 154 organisms spanning the eukaryotic kingdom. Organelle DB is the first on-line resource devoted to the identification and presentation of eukaryotic proteins localized to organelles and subcellular structures. As such, Organelle DB is a strong resource of data from the human proteome as well as from the major model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans and Mus musculus. In particular, Organelle DB is a central repository of yeast data, incorporating results--and actual fluorescent imagesfrom ongoing large-scale studies of protein localization in S.cerevisiae. Each protein in Organelle DB is presented with its sequence and, as available, a detailed description of its function; functions were extracted from relevant model organism databases, and links to these databases are provided within Organelle DB. To facilitate data interoperability, we have annotated all protein localizations using vocabulary from the Gene Ontology consortium. We also welcome new data for inclusion in Organelle DB, which may be freely accessed at http://organelledb.lsi.umich.edu.

Animals↗
PubMed2003

[A research review on "fertile islands" of soils under shrub canopy in arid and semi-arid regions].

Due to the inclemency of climate and soil conditions and the intense disturbance of human beings, the soil resources heterogeneity in arid and semi-arid grassland ecosystems worldwide was gradually increased during the last century. The interaction between soil heterogeneity and shrubs induced the autogenic development of "fertile islands" and the increasing spread of shrubs in the grassland ecosystems. The development of "fertile islands" around individual shrubs could change the vegetation composition and structure, as well as the distribution patterns of soil resources, and thus, reinforced the changes of the ecosystem function and structure from a relative stable grassland ecosystem to a quasi-stable shrubland ecosystem. The study of "fertile islands" phenomenon would help us to understand the causes, consequences and processes of desertification in arid and semi-arid areas. In this paper, the causes of "fertile islands", its study methods and significance and its relationship with shrub spreading as well as the responses of vegetation to it were summarized. The problems which might occur in the study of this phenomenon were also pointed out. Our aim was to offer some references to the study of land desertification processes and vegetation restoration in the arid and semi-arid regions.

Desert Climate↗
PubMed2005

Open book tests: assessment of academic learning in clerkships.

An examination of an open-book testing approach in a family medicine clerkship seeks to determine whether this method more closely mirrors the discipline of family medicine, where practitioners refer daily to written resource materials in order to make clinical decisions without compromising the learning and assessment process. Student scores on the multiple-choice test were analysed by year, by quarter and by site using ANOVA. Students in the experimental site were interviewed to determine preparation style, use of text during test, as well as attitudes toward open-book testing. Analysis of variance showed that the interaction of site and year was significant at p = 0.03. The mean score of 88.2 for Maine students in 2002 was significantly different from the other three mean scores. The desired qualitative outcomes of the intervention were confirmed: reducing the anxiety of students, wider reading of the textbook, knowing the structure of the textbook as a learning resource, and deeper understanding of concepts and principles rather than time spent on memorization. While the difference in scores did reach statistical significance, it is important to note that the difference in mean score was only four points on a 100-point scale. Given the percentage of the total grade represented by the test score, it is unlikely that this difference represents any real difference in grade for students in Maine compared with Vermont. The students appeared to approach the textbook and therefore, perhaps, the body of knowledge as a whole with the orientation of a generalist. The MMC Clerkship Director recommended the implementation of the open-book approach to the Family Practice clerkship at all sites and the University of Vermont Medical School accepted the proposal. This recommendation supports advising students on the preparation for an open-book test and on tactics for the best use of the textbook during the test.

Attitude of Health Personnel↗
PubMed2001

A Web-based classification system of DNA-binding protein families.

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The family of DNA-binding proteins is one of the most populated and studied amongst the various genomes of bacteria, archaea and eukaryotes and the Web-based system presented here is an approach to their classification. The DnaProt resource is an annotated and searchable collection of protein sequences for the families of DNA-binding proteins. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes. The database is freely available for online search of a library containing specific patterns of the identified DNA-binding protein classes and retrieval of individual entries from our WWW server (http://kronos.biol.uoa.gr/~mariak/dbDNA.html).

Amino Acid Motifs↗
PubMed2005

[New pathways in undergraduate medical education - first experiences with the cross section speciality emergency and intensive care medicine].

OBJECTIVE: On October 1 (st) 2003 Emergency Medicine was recognised for the first time as an independent cross section speciality in the new German "Approbationsordnung fuer Aerzte" (Medical Licensing Regulations). These amendments were made not only to increase the amount of small group teaching sessions but also to encourage a multidisciplinary and rather practical approach to the related topics. This article portrays the realisation of these objectives in form of a multidisciplinary module, as it has been established at University of Göttingen Medical School since the summer semester of 2004. We present the new curriculum, calculate the associated personnel resources and demonstrate the results of the structured evaluation given by the participating students. METHODS: We linked the fields of emergency and intensive care medicine by splitting them up into submodules which the students had to run through according to a set rota. 162 students were allocated to 27 small groups. Every student received a total of 38.5 hours of teaching, with the workshops coming to 46.8 %. The workshops comprised of nine sessions, three in Emergency Medicine, four in Intensive Care Medicine and two at human patient simulators. In addition we scheduled a seminar and an accompanying lecture. The final examination was performed as an Objective Structured Clinical Evaluation (OSCE). RESULTS: The realisation of the new module required a total of 1290 working hours for medical staff and 130 for our student aids. Compared to all other modules of Goettingen University Medical School the module here presented obtained the highest overall evaluation score by the medical students. Lessons with a high amount of practical involvement (i. e. Emergency Medicine and simulator-based workshops) were significantly better evaluated than rather formal teaching techniques, such as the lectures and the seminar. According to the students' self-assessment the simulator-based workshops were seen particularly valuable for the facilitation of knowledge transfer into clinical practice. CONCLUSION: The determined realisation of the new German Medical Licensing Regulations requires considerable time resources. However, its evaluation by the medical students is strikingly positive.

Anesthesiology↗