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PubMed2004

Data mining the protein data bank: automatic detection and assignment of carbohydrate structures.

Knowledge of the 3D structure of glycans is a prerequisite for a complete understanding of the biological processes glycoproteins are involved in. However, due to a lack of standardised nomenclature, carbohydrate compounds are difficult to locate within the Protein Data Bank (PDB). Using an algorithm that detects carbohydrate structures only requiring element types and atom coordinates, we were able to detect 1663 entries containing a total of 5647 carbohydrate chains. The majority of chains are found to be N-glycosidically bound. Noncovalently bound ligands are also frequent, while O-glycans form a minority. About 30% of all carbohydrate containing PDB entries comprise one or several errors. The automatic assignment of carbohydrate structures in PDB entries will improve the cross-linking of glycobiology resources with genomic and proteomic data collections, which will be an important issue of the upcoming glycomics projects. By aiding in detection of erroneous annotations and structures, the algorithm might also help to increase database quality.

Algorithms↗
PubMed2004

The academy movement: a structural approach to reinvigorating the educational mission.

Despite its fundamental importance, the educational mission of most medical schools receives far less recognition and support than do the missions of research and patient care. This disparity is based, in part, on the predominance of discipline-based departments, which focus on the more sustainable enterprises of research and patient care. Where departmental teaching is emphasized, it tends to center on trainees directly associated with the department-leaving medical students unsupported. The authors argue that the ongoing erosion of the educational mission will never be reversed unless there are changes in the underlying structure of medical schools. Academies of medical educators are developing at a number of medical schools to advance the school-wide mission of education. The authors describe and compare key features of such organizations at eight medical schools, identified through an informal survey of the Society of Directors of Research in Medical Education, along with direct contacts with specific schools. Although these entities are relatively new, initial assessments suggest that they have already had a major impact on the recognition of teaching efforts by the faculty, fueled curricular reform, promoted educational scholarship, and garnered new resources to support teaching. The academy movement, as a structural approach to change, shows promise for reinvigorating the educational mission of academic medicine.

Academic Medical Centers↗
PubMed2005

Representing structure-function relationships in mechanistically diverse enzyme superfamilies.

The prediction of protein function from structure or sequence data remains a problem best addressed by leveraging information available from previously determined structure-function relationships. In the case of enzymes, the study of mechanistically diverse superfamilies can provide a rich source of structure-function information useful in functional determination and enzyme engineering. To access these relationships using a computational resource, several issues must be addressed regarding the representation of enzyme function, the organization of structure-function relationships in the superfamily context, the handling of misannotations, and reliability of classifications and evidence. We discuss here our approaches to solving these problems in the development of a Structure-Function Linkage Database (SFLD) (online at http://sfld.rbvi.ucsf.edu).

Amino Acid Sequence↗
PubMedDate not supplied

Our health paradigm in peril.

Health care systems are rapidly shifting attention from providing health care to producing health, profoundly altering how and which services are provided. To free up individual and collective resources for investment in activities with a greater impact on health, less care will be given. This paper posits that the current model--increased health resources make for better health care make for better health status--is too simplistic a system. Structural problems inherent in this model are being observed as the boundaries of the paradigm are pushed. Resources are limited, and health outcomes are no longer being improved despite the application of large percentages of Gross National Product. A new health paradigm is emerging, one with increased focus on health prerequisites such as housing, minimum decent income, food, education, and good social and physical environment.

Economics↗
PubMed1998

Habitat structure determines competition intensity and invasion success in gecko lizards.

Species diversity is correlated with structural complexity in many animal communities; however, experimental tests of the mechanisms underlying this important relationship are rare, especially in terrestrial communities. We manipulated physical features of the habitat of gecko lizards and measured the effect on exploitation competition for insects. Increasing both the dispersion of food resources and microhabitat topography dramatically reduced interspecific competition. Adding topographic structure reduced the advantages of the larger, faster, invasive species. Interindividual spacing decreased, but intraspecific agonistic interference increased in the more territorial, resident species. Human structural alterations of the environment facilitate invasion and competitive displacement in this system. Physical microhabitat structure can potentially affect species interactions through a variety of complex mechanisms.

Animals↗
PubMed2006

Closed-loop recycling of construction and demolition waste in Germany in view of stricter environmental threshold values.

Recycling of construction and demolition waste contributes decisively to the saving of natural mineral resources. In Germany, processed mineral construction and demolition waste from structural engineering is used nearly exclusively in civil engineering (earthwork and road construction sector) as open-loop recycling. Due to the planned stricter limit values for the protection of soil and water, however, this recycling path in civil engineering may no longer be applicable in the future. According to some new guidelines and standards adopted recently, recycled aggregates may also be used for concrete production in the structural engineering sector (closed-loop recycling). Wastes from the structural engineering sector can thus be kept in a closed cycle, and their disposal on a landfill can be avoided. The present report focuses on the determination of maximum waste volumes that may be handled by this new recycling option. Potential adverse effects on the saving of resources and climate protection have been analysed. For this purpose, materials flow analysis and ecobalancing methods have been used.

Conservation of Natural Resources↗
PubMed2000

Optimal intraguild foraging and population stability.

This article explores effects of adaptive intraguild predation on species coexistence and community structure in three species' food webs. Two Lotka-Volterra models that assume a trade-off between competition and predation strength are considered in detail. The first model does not explicitly model resource dynamics and is considered with both nonadaptive and adaptive intraguild predation; in the latter case predators choose their diet in order to maximize their instantaneous population growth rate. The second model includes resource population dynamics. Effects of adaptive intraguild predation on the community structure along a gradient in environment productivity are analyzed and compared with some experimental results of protist food webs. Conditions under which intraguild predation is adaptive are discussed for both models. It is proved that if intraguild predators are perfect optimizers then intraguild predation should decrease with increasing environmental productivity and adaptive intraguild predation is a stabilizing factor provided environmental productivity is high enough.

Adaptation, Biological↗
PubMed1998

Syntactic facilitation in agrammatic sentence production.

Recently, proposals have been made to relate processing difficulties in aphasic language performance to limitations in resources for grammatical processing (Carpenter et al., 1994; Hagiwara, 1995; Kolk, 1995; Martin & Romani, 1994). Such proposals may account for a defining characteristic of agrammatic sentence production: reduced syntactic complexity. Syntactic structures that require deep hierarchical processing or reversals of canonical word order make demands exceeding limited resources. In the present study, we investigate the possibility of counteracting hypothesized resource limitations by increasing the availability of relatively complex sentences (i.e., datives and passives). The phenomenon of "syntactic priming" has been observed in a number of studies with healthy adults (e.g., Bock, 1986). With respect to Broca's aphasia, we hypothesized that increased availability of a syntactic structure, due to syntactic priming, results in a lesser demand on (limited) resources for sentence production. We elicited speech from 12 Broca's aphasics and 12 control subjects in three different conditions: spontaneous speech, picture description without priming, and picture description with priming. In addition, we varied instructions, in order to determine the role of strategies. The main findings were that (a) Brocas show stronger syntactic priming effects than controls; (b) the effects are automatic rather than strategic; and (c) in conditions with priming, Brocas produce relatively complex sentences (e.g., passives). We discuss these results in relation to capacity theories.

Adult↗
PubMed2004

Exploring comprehensibility and manageability in palliative home care: an interview study of dying cancer patients' informal carers.

The presence of an informal carer is often a prerequisite for successful palliative home care, and the staff's ability to support informal carers' coping in such situations is important. Recent research has revealed that it is possible to achieve positive psychological states in palliative care despite the burdening situation. As there is a lack of theory-based coping studies, the aim of this study was to describe, within the context of palliative home care, two concepts in Antonovsky's theory of Sense of Coherence: comprehensibility (a perception that the challenge is understood) and manageability (a perception that the resources to cope are available). Tape-recorded semi-structured interviews with 19 informal carers during ongoing palliative home care were transcribed and analysed with a qualitative hermeneutic approach. Elements that facilitated comprehensibility included open information, symbolic information, basic life assumptions and previous knowledge. These were important for creating a congruent inner reality (as opposed to chaos). Resources contributing to manageability dealt with power, support, competence and accessibility, which on a more abstract level resulted in a feeling of togetherness (as opposed to isolation). The findings are discussed in relation to the complexity of communication between staff and carers within palliative care.

Adaptation, Psychological↗
PubMed2025

Toward an integrated resource for pharmacogenomics (PGx): Survey findings from the genomic medicine communities.

PURPOSE: Pharmacogenomics (PGx) is a critical component of precision health care that aims to improve drug efficacy and reduce adverse events. Terminologies and standards have not always aligned between PGx and broader genomic medicine communities, which is a barrier to PGx implementation. An updated assessment of community barriers, needs, and perspectives is critical to enable more standardized terminologies and interpretation frameworks. METHODS: The Clinical Genome Resource's PGx Interpretation Committee (PGxIC, formerly referred to as the PGx Working Group, PGxWG) conducted 2 surveys targeting the PGx and genomic medicine communities (n = 508) to evaluate perspectives on PGx clinical validity and actionability frameworks, as well as other barriers to PGx implementation. Surveys were tailored toward self-reported familiarity with PGx. Data primarily consisted of free text, which were analyzed using qualitative content analysis methods. RESULTS: Survey responses indicated conflation of terminology across disciplines, including confusion around differing definitions of terms in PGx and non-PGx contexts. Data also indicated broad support for leveraging existing PGx guidelines and framework structures alongside the standardization of approaches and centralization of resources. CONCLUSION: These novel survey results demonstrate broad consensus on the importance of integrating PGx into clinical practice, including support for development of gene-drug response clinical validity and actionability frameworks aligned with Clinical Genome Resource's frameworks for gene-disease relationships.

Humans↗
PubMedDate not supplied

Mass-casualty, terrorist bombings: epidemiological outcomes, resource utilization, and time course of emergency needs (Part I).

INTRODUCTION: This article characterizes the epidemiological outcomes, resource utilization, and time course of emergency needs in mass-casualty, terrorist bombings producing 30 or more casualties. METHODS: Eligible bombings were identified using a MEDLINE search of articles published between 1996 and October 2002 and a manual search of published references. Mortality, injury frequency, injury severity, emergency department (ED) utilization, hospital admission, and time interval data were abstracted and relevant rates were determined for each bombing. Median values for the rates and the inter-quartile ranges (IQR) were determined for bombing subgroups associated with: (1) vehicle delivery; (2) terrorist suicide; (3) confined-space setting; (4) open-air setting; (5) structural collapse sequela; and (6) structural fire sequela. RESULTS: Inclusion criteria were met by 44 mass-casualty, terrorist bombings reported in 61 articles. Median values for the immediate mortality rates and IQRs were: vehicle-delivery, 4% (1-25%); terrorist-suicide, 19% (7-44%); confined-space 4% (1-11%); open-air, 1% (0-5%); structural-collapse, 18% (5-26%); structural fire 17% (1-17%); and overall, 3% (1-14%). A biphasic pattern of mortality and unique patterns of injury frequency were noted in all subgroups. Median values for the hospital admission rates and IQRs were: vehicle-delivery, 19% (14-50%); terrorist-suicide, 58% (38-77%); confined-space, 52% (36-71%); open-air, 13% (11-27%); structural-collapse, 41% (23-74%); structural-fire, 34% (25-44%); and overall, 34% (14-53%). The shortest reported time interval from detonation to the arrival of the first patient at an ED was five minutes. The shortest reported time interval from detonation to the arrival of the last patient at an ED was 15 minutes. The longest reported time interval from detonation to extrication of a live victim from a structural collapse was 36 hours. CONCLUSION: Epidemiological outcomes and resource utilization in mass-casualty, terrorist bombings vary with the characteristics of the event.

Emergencies↗
PubMed2005

The design and implementation of the immune epitope database and analysis resource.

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, "The Immune Epitope Database and Analysis Resource." We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.

Animals↗
PubMed1982

Declining public social service resources: a managerial problem.

Declining budget conditions in many social service settings suggest that education must provide future graduates with very different managerial skills. When human service organizations are perceived as evolving political structures, populated with a variety of individuals who represent diverse values and claims, resource scarcity often results in growing conflict and a preoccupation with individual and subunit survival. This changing organizational context will require increasing political skill on the part of managers as well as an ability to harmonize new approaches with prior service values in achieving consensus around solutions to service delivery problems.

Budgets↗
PubMed2001

Using Internet technology to deliver a behavioral weight loss program.

CONTEXT: Rapid increases in access to the Internet have made it a viable mode for public health intervention. No controlled studies have evaluated this resource for weight loss. OBJECTIVE: To determine whether a structured Internet behavioral weight loss program produces greater initial weight loss and changes in waist circumference than a weight loss education Web site. DESIGN: Randomized, controlled trial conducted from April to December 1999. SETTING AND PARTICIPANTS: Ninety-one healthy, overweight adult hospital employees aged 18 to 60 years with a body mass index of 25 to 36 kg/m(2). Analyses were performed for the 65 who had complete follow-up data. INTERVENTIONS: Participants were randomly assigned to a 6-month weight loss program of either Internet education (education; n = 32 with complete data) or Internet behavior therapy (behavior therapy; n = 33 with complete data). All participants were given 1 face-to-face group weight loss session and access to a Web site with organized links to Internet weight loss resources. Participants in the behavior therapy group received additional behavioral procedures, including a sequence of 24 weekly behavioral lessons via e-mail, weekly online submission of self-monitoring diaries with individualized therapist feedback via e-mail, and an online bulletin board. MAIN OUTCOME MEASURES: Body weight and waist circumference, measured at 0, 3, and 6 months, compared the 2 intervention groups. RESULTS: Repeated-measures analyses showed that the behavior therapy group lost more weight than the education group (P =.005). The behavior therapy group lost a mean (SD) of 4.0 (2.8) kg by 3 months and 4.1 (4.5) kg by 6 months. Weight loss in the education group was 1.7 (2.7) kg at 3 months and 1.6 (3.3) kg by 6 months. More participants in the behavior therapy than education group achieved the 5% weight loss goal (45% vs 22%; P =.05) by 6 months. Changes in waist circumference were also greater in the behavior therapy group than in the education group at both 3 months (P =.001) and 6 months (P =.005). CONCLUSIONS: Participants who were given a structured behavioral treatment program with weekly contact and individualized feedback had better weight loss compared with those given links to educational Web sites. Thus, the Internet and e-mail appear to be viable methods for delivery of structured behavioral weight loss programs.

Adult↗
PubMed2003

The HEDIS performance NAVIGATOR for controlling high blood pressure: a resource to assist health plans improve patient adherence.

This article describes how the resources in the Health Plan Employer and Data Information Set (HEDIS; a registered trademark of the National Committee for Quality Assurance) Performance NAVIGATOR for Controlling High Blood Pressure (HEDIS NAVIGATOR) developed by Merck & Co., Inc. assist managed care organizations in understanding and encouraging the active involvement of their members in adhering to a treatment plan developed in partnership by physicians and patients. (HEDIS is a set of standardized performance measures that enable purchasers and consumers to make informed decisions regarding the quality of managed care organizations.) The discussion uses the Health Belief and Transtheoretical Models as a framework to better understand patient behavior change. Targeted strategies to facilitate adherence are also addressed. Examples of structured programs using nationally recommended guidelines and HEDIS NAVIGATOR resources are included to illustrate coordinated efforts to assist patients with high blood pressure adhere to their treatment plan and help managed care organizations improve patient outcomes and HEDIS scores.

Data Collection↗
PubMed1986

A contribution to the geographical interpretation of biological change.

"Geography" has traditionally been assigned the role of handmaiden in evolutionary studies. In this work a different understanding of the relationship between biological change and locational setting is developed: evolution as a dynamic form of spatial interaction. In the causal model presented, adaptive change is portrayed as a negative feedback response contributing to a general spatial-temporal process of resource cycle tightening involving exchanges between the two fundamental structural sectors ("abiotic" and "biotic") of the earth's surface system. As such, it is rejected as "evolution" per se. This position makes it possible to circumvent the "adaptation yields adaptation" circularity, and to view locational circumstances as being evolutionarily causal, yet not deterministic with respect to population-level change. A parallel interpretation of the relation between range and range change and evolution is also implicit; the individualistic hypothesis is thereby superceded by a model of community evolution allowing for individualistic rates of population (adaptive and) range change, but operating on the principle that populations should tend to change range in common directions (as a response to spatially-varying degrees of efficiency of turnover of resources vital to biotic sector function). This in turn leads to the possibility of normative biogeographic modelling. Comment is also made on the relationship of the present understanding to disequilibrium and dynamic equilibrium interpretations of evolutionary change, and to human cultural evolution.

Animals↗
PubMed2006

Habitat shape, metapopulation processes and the dynamics of multispecies predator-prey interactions.

1. The effects of habitat shape, connectivity and the metapopulation processes of persistence and extinction are explored in a multispecies resource-consumer interaction. 2. The spatial dynamics of the indirect interaction between two prey species (Callosobruchus chinensis, Callosobruchus maculatus) and a predator (Anisopteromalus calandrae) are investigated and we show how the persistence time of this interaction is altered in different habitat configurations by the presence of an apparent competitor. 3. Habitat structure has differential effects on the dynamics of the resource-consumer interaction. Across all habitat types, the pairwise interaction between C. chinensis and A. calandrae is highly prone to extinction, while the interaction between C. maculatus and A. calandrae shows sustained long-term fluctuations. Contrary to expectations from theory, habitat shape has no significant effect on persistence time of the full, three-species resource-consumer assemblage. 4. A stochastic metapopulation model for a range of habitat configurations, incorporating different forms of regulatory processes, highlights that it is the spatially explicit population dynamics rather than the shape of the metapopulation that is the principal determinant of interaction persistence time.

Animals↗
PubMedDate not supplied

A search tool based on 'encapsulated' MeSH thesaurus to retrieve quality health resources on the internet.

In the year 2001, the Internet has become a major source of health information for the health professional and the Netizen. The objective of Doc' CISMeF (D'C) was to create a powerful generic search tool based on a structured information model which 'encapsulates' the MeSH thesaurus to index and retrieve quality health resources on the Internet. To index resources, D'C uses four sections in its information model: 'meta-term', keyword, subheading, and resource type. Two search options are available: simple and advanced. The simple search requires the end-user to input a single term or expression. If this term belongs to the D'C information structure model, it will be exploded. If not, a full-text search is performed. In the advanced search, complex searches are possible combining Boolean operators with meta-terms, keywords, subheadings and resource types. D'C uses two standard tools for organising information: the MeSH thesaurus and the Dublin Core metadata format. Resources included in D'C are described according to the following elements: title, author or creator, subject and keywords, description, publishers, date, resource type, format, identifier, and language.

Abstracting and Indexing↗