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PubMed2025

Temperature and Pressure Shaped the Evolution of Antifreeze Proteins in Polar and Deep Sea Zoarcoid Fishes.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes' tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Animals↗
PubMed2003

[Implementing cardiovascular prevention in the real world: presentation of an integrated hospital-field model].

Numerous studies have documented that cardiovascular prevention in subjects at high risk has a large impact on the clinical outcomes. Data also show the efficacy of an early, intensive, well-structured, professionally expert, multidisciplinary intervention, making use of adequate behavioural and pharmacologic instruments, on the global risk. Such intervention is, however, available at present for very few healthcare users, while the majority, above all in primary prevention, receive a programme of low impact, with poor feedback between the hospital specialist and general practitioner (GP), and often limited to the simple prescription of treatment or to specialist check-ups and/or general advice on lifestyle. The project of implementation takes as its starting point this analysis and the premise that for an intervention of cardiovascular prevention to be effective, particularly in the long term, and really applicable to the broad population, it must be governed primarily by the GP--providing that s/he be adequately trained, utilize new and more dynamic caring modes, and be able to count concretely both on integration with the specialist and on the support of a multidisciplinary team for specific interventions. The paper presents the various stages of the project: from definition of the resources available (health district, GPs, hospital specialists) to the need for GP training, to the modes of operation: instruments for risk calculation, procedures followed, model of integration between GP and specialist, identification of the goals and indicators. This is a low cost project in terms of both the human and structural resources employed, utilizing what is already available in the healthcare system of our country. One of its most original aspects is the medical visit jointly conducted by the GP and hospital specialist, which realizes in concrete terms the integration of the skills: GPs can finally confront in the field the specialist of referral, acquire new skills, improve their daily mode of operating, while they will be gratified by a work more in line with their professional image, and become promoters of health. Finally, this project highlights the propositive and operative role assumed by cardiac rehabilitation and prevention, which, after developing over the years a specific know-how on the subject, now transmits these skills to other healthcare resources and creates a link with the local territory, so providing an appropriate response to the need to put into practice primary and secondary cardiovascular prevention.

Cardiac Rehabilitation↗
PubMed1998

Macroinvertebrate Community Structure Along the Longitudinal Gradient of an Agriculturally Impacted Stream

/ Lapwai Creek, an agriculturally impacted stream in northern Idaho, was sampled seasonally over a two-year period to determine if macroinvertebrate community composition changed along the longitudinal gradient and if changes followed predictions of the river continuum concept. Possible relationships between changes in food resource availability and community structure were also examined. Benthic invertebrates were collected at eight locations along the longitudinal gradient of Lapwai Creek using a Hess sampler. Random skewer analysis suggested there was no longitudinal gradient for either number of individuals or functional feeding group composition. Cluster analysis revealed that all locations, excluding a site receiving outflow from a small, eutrophic reservoir, had a similar community structure, further suggesting that invertebrate community composition remained consistent along the longitudinal gradient of the stream. The community was dominated at all sites, excluding the site below the reservoir, by functionalgrazers. Shredders were rare throughout Lapwai Creek, even in areas where healthy riparian vegetation still remained. Studies of other streams within the drainage basin show that many species found in the upper reaches of these streams, where agricultural impacts are low, were absent throughout the length of Lapwai Creek. Data collected concurrently with macroinvertebrates indicated that the input, storage, and transport of particulate organic matter was low throughout the stream, whereas periphyton abundance was high. The absence of longitudinal changes, despite flowing through three distinct geomorphological regions, and the grouping of all sites except one by cluster analysis for both dominant taxa and functional feeding groups suggest that agricultural alteration has influenced community structure of Lapwai Creek, resulting in a relatively homogeneous assemblage of macroinvertebrates capable of tolerating agricultural nonpoint source pollution. Additional support for this hypothesis is the high abundance of one food source, periphyton, and the small quantities of terrestrially derived organic matter. The abundance of the former and the rarity of the latter can be attributed to alteration of the drainage basin resulting from agricultural activities through inputs of fertilizers that generated high nutrient concentrations and the removal of riparian vegetation to clear more land for agriculture and provide increase access to the stream.KEY WORDS: Agriculture; Longitudinal patterns; Macroinvertebrates; Nonpoint source; River continuum

Journal Article↗
PubMed2006

A focus group study of factors that promote and constrain the use of satellite-derived fire products by resource managers in southern Africa.

Semi-structured focus group interviews were employed to examine factors that affect the likelihood that resource managers in southern Africa will use information on vegetation fires provided by two satellite-derived products: an active fire product and a burned area product. The two products are updated regularly and aim to deliver the state-of-the-art in the global monitoring of fires from satellite remote-sensing. Both products are derived from data transmitted by the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors carried onboard NASA's Aqua and Terra satellites. The active fire product can be accessed for free via the internet and on media by users working anywhere in the world; the burned area product will be accessible in a similar manner in 2006. The MODIS fire products provide systematic, near-global coverage and are freely available; as such, they give resource managers new opportunities to obtain or supplement information they need to manage vegetation fires effectively. However, the availability of these products does not mean that resource managers will use them, and many other factors are involved. To understand factors that affect whether southern African resource managers will use the two products, two focus groups were held with members of the Southern African Fire Network (SAFNet) in Malawi, Africa, August 2004. Analysis of the group discussions reveals a number of factors that influence whether they will use the products. The qualitative, in depth nature of the group discussions revealed 12 main factors that influence product use; not least the low international internet bandwidths for African countries outside of South Africa. Analysis of the group discussions also suggests how the uptake of MODIS fire products by resource managers in southern Africa might be enhanced by affecting specific changes to how MODIS products are packaged and delivered.

Africa, Southern↗
PubMed1999

[Effective use of medical-scientific internet resources].

PROBLEM: The Internet is not structured hierarchically and therefore it distinguishes from today's common knowledge sources. The rapidly growing number of medical websites offers comprehensive but not easy to find information resources and continuing education opportunities for ophthalmologists. METHODS AND RESULTS: The efficiency of an Internet search is related to knowledge about existing search strategies. Several search systems are described (search engines, catalogs, databases, indices, etc.). Additional advice about efficient usage (Meta-Search, use of Boolean operators, phrase search, etc.) is provided. The suggested search strategies are evaluated regarding their specific results, update status, and the usability of search engines used. New applications such as SemioMap and Intelligent Agents are described. CONCLUSION: Today the Internet provides practitioners and scientists who are able to use efficient search strategies with easy and fast to use information resources. The total number of scientific-medical documents on the Web is growing very quickly. More and more, their content is related to current problems in patient treatment and future trends in clinical research.

Education, Medical, Continuing↗
PubMed1996

Audit in the therapy professions: some constraints on progress.

AIMS: To ascertain views about constraints on the progress of audit experienced by members of four of the therapy professions: physiotherapy, occupational therapy, speech and language therapy, and clinical psychology. METHODS: Interviews in six health service sites with a history of audit in these professions. 62 interviews were held with members of the four professions and 60 with other personnel with relevant involvement. Five main themes emerged as the constraints on progress: resources; expertise; relations between groups; organisational structures; and overall planning of audit activities. RESULTS: Concerns about resources focused on lack of time, insufficient finance, and lack of access to appropriate systems of information technology. Insufficient expertise was identified as a major constraint on progress. Guidance on designing instruments for collection of data was the main concern, but help with writing proposals, specifying and keeping to objectives, analysing data, and writing reports was also required. Although sources of guidance were sometimes available, more commonly this was not the case. Several aspects of relations between groups were reported as constraining the progress of audit. These included support and commitment, choice of audit topics, conflicts between staff, willingness to participate and change practice, and concerns about confidentiality. Organisational structures which constrained audit included weak links between heads of professional services and managers of provider units, the inhibiting effect of change, the weakening of professional coherence when therapists were split across directorates, and the ethos of regarding audit findings as business secrets. Lack of an overall plan for audit meant that while some resources were available, others equally necessary for successful completion of projects were not. CONCLUSION: Members of four of the therapy professions identified a wide range of constraints on the progress of audit. If their commitment to audit is to be maintained these constraints require resolution. It is suggested that such expert advice, but also that these are directed towards the particular needs of the four professions. Moreover, a forum is required within which all those with a stake in therapy audit can acknowledge and resolve the different agendas which they may have in the enterprise.

Allied Health Occupations↗
PubMed1989

"Desktop knowledge": a new focus for medical education and decision support.

Physicians today are faced with "data overload" and, paradoxically, "information underload"--the inability to locate pertinent, needed knowledge in a sea of data with which they are inundated. Increasingly, the professional functions of the physician are becoming focused on the desktop workstation, in terms of its ability to provide "windows" into local databases and knowledge resources, and to serve as an access port to other networked resources. A challenge we now face is to develop means for structuring the vast potentially available knowledge resources in such a manner that access to pertinent knowledge can be facilitated, and to develop acceptable interfaces to the knowledge resources so that a user can effectively navigate through them. The complexity of this task is due to the nature of the knowledge resources--knowledge can be in a variety of forms, ranging from textual and pictorial material, to structured representations, to more dynamic embodiments in the form of procedures. In the Decision Systems Group we have focused on the development of a prototype desktop knowledge management environment known as Explorer-2, with the objective of providing a consistent interface for access to a wide variety of knowledge. Our accomplishments to date encompass the incorporation into the Explorer-2 environment of adaptations of textbook chapters and books, image data bases, simulations, and expert systems. Navigational aids are provided by a semantic net browser using both MeSH and augmented taxonomies and by a graphical overview map.(ABSTRACT TRUNCATED AT 250 WORDS)

Artificial Intelligence↗
PubMed2003

Gender-specific floral and physiological traits: implications for the maintenance of females in gynodioecious Lobelia siphilitica.

A common gender dimorphism in angiosperms is gynodioecy, in which hermaphrodites and females co-occur. Females are at an inherent disadvantage because they can transmit their genes only through ovule production. One mechanism by which females can compensate for the loss of male function is by producing more seeds than hermaphrodites. As such, females should: (1) increase resource uptake to support higher seed production; and (2) allocate resources saved by the loss of male function to seed production. To test this hypothesis, we measured physiological and floral traits of gynodioecious Lobelia siphilitica, controlling for both environmental and genetic variation through a comparison of greenhouse-grown siblings. Pre-reproductive females had 14% higher area-based (Z=2.14; P=0.04) and 32% higher mass-based (Z=1.96; P=0.05) photosynthetic rate than hermaphrodites, suggesting that they have increased carbon acquisition by altering photosynthetic physiology. Female L. siphilitica produced flowers with 4-8% smaller corollas than hermaphrodites (all P<0.05), suggesting that females allocate resources away from floral structures used for pollinator attraction. The genetic correlation between genders for four floral and four physiological traits was significantly less than one but greater than zero, indicating that the evolution of gender dimorphism in response to sex-differential selection will be constrained. The allocation of resources saved by the loss of male function has been viewed as the most important mechanism allowing females of gynodioecious species to support higher seed production. Our data suggest that increased resource acquisition by females at pre-reproductive stages can also contribute to the maintenance of gender dimorphism in gynodioecious species.

Analysis of Variance↗
PubMed2001

Hydrosolidarity intergenerational challenges: long-term commitment for long-term issues.

The year 2000 Young Professionals Seminar focused on long-term intergenerational challenges. Water related problems are symptoms of complex and ultimately societal problems linked to human behaviour, political support and managerial and institutional structures. Although integrated water resources management is presented as a solution, it is not always well understood, and can create a sense of hopelessness among professionals. To make it operational requires long-term commitments among various professionals and the involvement of new actors. A number of key topics crystallised as needing further attention, including ethical dimensions in policy making, the development of a framework for a "Future Generation Impact Assessment" (FGIA), and efforts to achieve true dialogue among stakeholders. Young water professionals must become more involved in political processes and take active part in institutional changes. Such engagement will require changes in the working environment facing many young professionals that causes frustration due to inefficient and conservative hierarchical structures and the lack of transparency.

Conservation of Natural Resources↗
PubMedDate not supplied

Political, administrative, and economic resources for the control of poliomyelitis.

Control of any major childhood disease in developing countries is dependent on the ability of health services to reach the susceptible population and to administer appropriate therapy or preventive action. Both of these needs are addressed by the development of primary health-care services. The vaccine-preventable diseases, including poliomyelitis, are likely to be controlled only through programs that are executed through the primary health-care system. The implications of the technical aspect of poliomyelitis control on economic resources are secondary to the administrative capability of the programs to manage these technical facilities effectively. The first prerequisite of any health program is the political will on the part of the decision makers to carry it through effectively. This will be reflected in the strength of the administrative structures and the economic resources made available. At present poliomyelitis, with its clinical visibility and its appeal to humanitarian instincts, has an importance as a leader for immunization programs and thus, for primary health care.

Health Policy↗
PubMed1998

Standardization in the field of medical image management: the contribution of the MIMOSA model.

This paper deals with the development of standards in the field of medical imaging and picture archiving and communication systems (PACS's), and notably concerning the interworking between PACS's and hospital information systems (HIS). It explains, in detail, how a conceptual model of the management of medical images, such as the medical image management in an open system architecture (MIMOSA) model, can contribute to the development of standards for medical image management and PACS's. This contribution is twofold: 1) Since the model lists and structures the concepts and resources involved to make the images available to the users when and where they are required, and describes the interactions between PACS components and HIS, the MIMOSA work helps by defining a reference architecture which includes an external description of the various components of a PACS, and a logical structure for assembling them. 2) The model and the implementation of a demonstrator based on this model allow the relevance of the Digital Imaging and Communications in Medicine (DICOM) standard with respect to image management issues to be assessed, highlighting some current limitations of this standard and proposing extensions. Such a twofold action is necessary in order both to bring solutions, even partial, in the short term, and to allow for the convergence, in the long term, of the standards developed by independent standardization groups in medical informatics (e.g., those within Technical Committee 251 of CEN: Comité Européen de Normalisation).

Diagnostic Imaging↗
PubMed2003

Population dynamics of prey exhibiting inducible defenses: the role of associated costs and density-dependence.

The effect of antipredator behavior on the dynamics of a resource-consumer model was analyzed in relation to the magnitude of associated costs, and the strength of density-dependence. For this purpose, I present a deterministic continuous resource-consumer model that exhibits biomass conversion, structural homogeneity, and competition for renewable and fixed resources as separate processes. Antipredator behavior is incorporated as an inducible response to consumer density, and has metabolic and feeding costs. By means of numerical methods, I show: (1) that antipredator behavior is stabilizing for certain parameter ranges, where other stabilizing forces do not dominate the dynamics; (2) intraspecific competition for both fixed and renewable resources have a stabilizing role; (3) metabolic cost is always stabilizing, and feeding cost can be stabilizing or destabilizing, depending on the relative strength of the two competition forces.

Animals↗
PubMed2005

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.

Databases, Protein↗
PubMed2006

VIPERdb: a relational database for structural virology.

VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.

Capsid↗
PubMed2004

The factors facilitating and inhibiting effective clinical decision-making in nursing: a qualitative study.

BACKGROUND: Nurses' practice takes place in a context of ongoing advances in research and technology. The dynamic and uncertain nature of health care environment requires nurses to be competent decision-makers in order to respond to clients' needs. Recently, the public and the government have criticized Iranian nurses because of poor quality of patient care. However nurses' views and experiences on factors that affect their clinical function and clinical decision-making have rarely been studied. METHODS: Grounded theory methodology was used to analyze the participants' lived experiences and their viewpoints regarding the factors affecting their clinical function and clinical decision-making. Semi-structured interviews and participant observation methods were used to gather the data. Thirty-eight participants were interviewed and twelve sessions of observation were carried out. Constant comparative analysis method was used to analyze the data. RESULTS: Five main themes emerged from the data. From the participants' points of view, "feeling competent", "being self-confident", "organizational structure", "nursing education", and "being supported" were considered as important factors in effective clinical decision-making. CONCLUSION: As participants in this research implied, being competent and self-confident are the most important personal factors influencing nurses clinical decision-making. Also external factors such as organizational structure, access to supportive resources and nursing education have strengthening or inhibiting effects on the nurses' decisions. Individual nurses, professional associations, schools of nursing, nurse educators, organizations that employ nurses and government all have responsibility for developing and finding strategies that facilitate nurses' effective clinical decision-making. They are responsible for identifying barriers and enhancing factors within the organizational structure that facilitate nurses' clinical decision-making.

Journal Article↗
PubMed2006

Children enrolled in public pre-K: the relation of family life, neighborhood quality, and socioeconomic resources to early competence.

This article presents data on the family and social environments of 501 children enrolled in public sponsored pre-K in 5 states and tests the relation of these resources to child competence. Structured interviews and questionnaires provide information from parents about the family's social and economic status. Direct assessments and teacher reports provide data on children's literacy, numeracy, and behavioral problems. A majority of the children served in public pre-K lived in poverty and showed decrements in language but not in other domains. A socioeconomic resource factor consisting of parental education, household income, and material need predicted all domains of children's functioning. Children from households high in socioeconomic resources entered pre-K with more well developed language and math skill but fewer behavioral problems than their disadvantaged peers. Neighborhood quality status was related to language competence and mother's marital status to math competence. Neighborhood quality and income level may have their impact on child competence through their relation to dyadic quality and the health and the psychological well-being of the parents.

Aptitude↗
PubMed2001

Salivary cortisol levels and work-related stress among emergency department nurses.

The objective of this study was to assess and compare the self-perceived work-related stress of emergency department (ED) and general ward (GW) nurses and to assess the relationship between self-perceived stress and salivary cortisol levels in these groups of nurses. Seventy-three female ED (n = 23) and GW (n = 50) nurses from a general hospital completed a self-administered questionnaire. A modified mental health professional stress scale (PSS) was used to measure self-perceived work-related stress. Salivary samples were collected at the start and end of morning shiftwork. An enzyme-linked immunosorbent assay method was used to determine the salivary cortisol concentration (nmol/L). ED nurses perceived that nursing was more stressful (mean, 1.58; 95% confidence interval [CI], 1.35 to 1.81) than did GW nurses (mean, 1.30; 95% CI, 1.18 to 1.40). On the PSS subscales, scores of organizational structure and process, lack of resources, and conflict with other professionals were higher in ED nurses (all P < 0.01). The morning cortisol was significantly lower in ED (geometric mean, 9.10; 95% CI, 6.62 to 12.42 nmol/L) than in GW (geometric mean, 15.45; 95% CI, 11.86 to 20.14 nmol/L) nurses. Log morning salivary cortisol was negatively correlated with PSS (r = -0.255), scores of organizational structure and process, and conflict with other professionals (all P < 0.05). The difference between morning and afternoon cortisol concentration in ED nurses (geometric mean, 6.35; 95% CI 4.14 to 9.93 nmol/L) was lower than in GW nurses (geometric mean, 12.42; 95% CI, 9.38 to 16.28 nmol/L). The log value of the difference correlated marginally with PSS (r = -0.21, P = 0.07) and significantly with scores of organizational structure and process, lack of resources, and conflict with other professionals (all P < 0.05). There was no difference between the two groups in afternoon salivary cortisol level. ED nurses perceived more stress compared with GW nurses. Morning salivary cortisol concentration is better correlated with PSS compared with the morning-afternoon salivary cortisol difference. The result raises the possibility of using a single morning salivary cortisol sample to reflect self-perceived stress.

Adult↗
PubMed1999

BOLD--a biological O-linked glycan database.

Glycans can be O-linked to proteins via the hydroxyl group of serine, threonine, tyrosine, hydroxylysine or hydroxyproline. Sometimes the glycan is O-linked to the hydroxyl group via a phosphodiester bond. The core monosaccharide residue may be N-acetylgalactosamine, N-acetylglucosamine, galactose, glucose, fucose, mannose, xylose or arabinose. These O-linked glycans can remain as a monosaccharide, but often a complex structure is built up by stepwise addition of monosaccharides. Monosaccharides known to be added include galactose, N-acetylglucosamine, fucose, N-acetylneuraminic acid, N-glycolylneuraminic acid and 2-keto-3-deoxynonulosonic acid. O-linked glycans can also contain sulfate and phosphate residues. This leads to the possibility of the existence of numerous O-glycan structures. The biological O-linked database (BOLD) is a relational database that contains information on O-linked glycan structures, their biological sources (with a link to the SWISS-PROT protein database), the references in which the glycan was described (with a link to MEDLINE), and the methods used to determine the glycan structure. The database provides a valuable resource for glycobiology researchers interested in O-linked oligosaccharide structures that have been previously described on proteins from different species and tissues.

Carbohydrate Conformation↗