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PubMed2026

High-Resolution Chromosome-Level Genome Assembly and Annotation of Triplophysa stewarti, an Endemic Plateau Loach from the Qinghai-Tibet Plateau.

The bottom-dwelling fish Triplophysa stewarti, endemic to the Qinghai-Tibet Plateau, is a valuable model for studying high-altitude adaptation in aquatic ecosystems. However, the lack of a high-quality reference genome has hindered comparative genomic and evolutionary studies within this genus. Here, we present a chromosome-level genome assembly for T. stewarti, generated using PacBio HiFi long-read sequencing and Hi-C scaffolding. The 697.9 Mb assembly is highly continuous (scaffold N50 of 253.58 Mb) and encompasses 25 chromosomes, representing 92.65% of the genome. BUSCO analysis indicated a 98.4% completeness, supporting the high quality of the assembly. We annotated 28,009 protein-coding genes, with 97.04% being functionally assigned across multiple databases (NR, UniProt, KEGG, GO, Pfam and InterPro). Additionally, repetitive elements constituted 42.47% of the genome, and we identified 52,709 non-coding RNAs. This high-quality reference genome provides a fundamental resource for exploring the adaptive evolution, population structure, and conservation genetics of T. stewarti and related species on the Qinghai-Tibet Plateau.

Animals↗
PubMed2001

Dependence in activities of daily living and cognitive impairment strongly predicted mortality in older urban residents in Brazil: a 2-year follow-up.

OBJECTIVES: To identify a set of predictors of mortality among residents in the community, before any physical, biochemical, or image examination is performed, that could be collected on a routine standardized basis, to help the clinician define a patient follow-up strategy and the health planner make decisions regarding the care of older people. DESIGN: A household follow-up study, with an evaluation at baseline and 2 years later. SETTING: Residential area, with a low rate of in- and outmigration, in Sao Paulo, a large industrialized urban center in southeastern Brazil. PARTICIPANTS: One thousand six hundred sixty-seven older urban residents in the community (65+), from different socioeconomic backgrounds, enrolled after a study area census. INTERVENTION: Structured home interview with Brazilian Older Americans Resources and Services Multidimensional Functional Assessment Questionnaire, previously validated in Portuguese. MEASUREMENTS: A logistic regression model for the risk of dying in the period was developed, having as independent variables, sociodemographic characteristics plus six other dimensions: subjective self-evaluation of health, past medical history, use of health services, dependence in activities of daily living (ADLs), mental health, and cognitive status. RESULTS: There were 146 deaths (9%) in the cohort during the follow-up interval. The variables that appeared as independent predictors of death in the final logistic regression model were: gender (relative risk (RR) = 2.8 (males)), age (RR = 2.0 (80+ vs. 65-69)), hospitalization in the previous 6 months (RR = 2.4 (at least one)), dependence in ADLs (RR = 3.0 (assistance required for 7 vs. 0 ADLs)); and cognitive impairment (RR = 1.9 (Mini-Mental State Examination 18 vs. 30)). CONCLUSION: These findings suggest that in developing countries such as Brazil, an assessment of dependence in daily living and cognitive status should be an essential part of any health evaluation of an older person, not only because these variables represent potentially high independent mortality risks, but also because they can be easily and reliably assessed, using well-validated instruments, and may be susceptible to intervention.

Activities of Daily Living↗
PubMed2001

Tanzanian midwives' views on becoming a good resource and support person for postpartum women.

OBJECTIVES: to explore midwives' views in relation to the provision of systematic postpartum care. DESIGN: qualitative focus group study using grounded theory approach. SETTING: Dar es Salaam, Tanzania. PARTICIPANTS: 49 nurse/midwives in five focus group discussions, each having 9-11 participants. FINDINGS: eight categories were identified: 'reflecting', 'getting ready', 'defining abilities', 'networking', 'integrating', 'balancing', 'dealing with reality', and 'caring'. The identified core category that integrated and encapsulated all other categories was 'becoming a good resource and support person for postpartum woman'. The mediating factors found to have potential for influencing how a midwife can function in order to become a good resource and support person were: a) the structure and approach in maternal and child health services, b) midwives' knowledge, attitude and skills, c) informal sources of knowledge to parents, and d) cultural beliefs and practices. CONCLUSION: the findings of this study provide an understanding of the way midwives feel and think about the provision of postpartum care. The findings demonstrate that midwives need support in their efforts to achieve what they consider necessary for postpartum care. Interventions for educating and supporting midwives should be targeted at enabling them to deal with all the factors that influence their role and help them to identify and use better strategies to provide quality care.

Anecdotes as Topic↗
PubMed2001

A new paradigm for practice education.

This paper explores the complex nature of professional practice. It suggests that educating for all practice disciplines is about to undergo a paradigm shift whereby the value of practical education and experience will be better understood, more rigorously analyzed and integrated with propositional knowledge in the construction of personal professional knowledge and identity. It relates this cross disciplinary position to the present problems of skills deficits which are evident in nurses at the point of registration and demonstrates how routinization and internalization of process and tacit knowledge can create problems for students and newly qualified staff nurses. It also suggests how this can be addressed. It discusses the present culture of 'clinical education by default', unavailability of mentors and resources, and general lack of formal collaborative structures between education and service institutions and suggests that the present system cannot sustain the complex demands, expectations and pace of the clinical context and the evolution of nursing practice. Clinical credibility is an issue as is the current heavy clinical workload of staff nurse mentors, and several collaborative clinical education models are outlined which ensure that staff nurses or resident clinical educators are available and can make clinical teaching their priority. History and the present crisis in nursing suggest that there is a case for mandatory collaborative education/service structures to ensure adequate funding and to monitor the effectiveness of selected models so that staff nurse mentors can work with lecturer colleagues to articulate and teach the complexities of clinical practice through related research. It is predicted that this collaborative approach is capable of addressing both the skills deficits and the wider intellectual challenge of developing a new paradigm of practice education and providing an integrated base for continuing professional development.

Clinical Competence↗
PubMed2001

Beyond pharmaceutical manufacturer assistance: broadening the scope of an indigent drug program.

A medication assistance program at a university medical center is described. The program was implemented in July 1999 by the ambulatory care pharmacy at the University of Illinois at Chicago Medical Center (UICMC). A full-time pharmacist and a full-time social worker run the program, along with support from technicians and a student extern. The program functions like a clinic, with both scheduled appointments and drop-ins. Patients are referred by UICMC providers or may self-refer. Sources of assistance include Medicaid, Medicare Part B, several state programs, manufacturers' programs, drug samples, private insurance plans and HMOs, and the patients themselves in the form of small payments. Patients receive medications at UICMC's expense only as a last resort. The medication assistance program helped 231 patients in the six months from July to December 1999. Program costs totaled $110,537, but $237,985 was saved. Only 13% of the savings came from pharmaceutical companies; 63% came from Medicaid. Experience with the program suggests that medication assistance initiatives should be structured to tap the full spectrum of resources for indigent patients, that programs be staffed by personnel with relevant experience, that program staff be prepared to work closely with patients and to follow up, and that the institution's charitable goods and services be restricted to patients for whom there are no other resources. A highly proactive medication assistance program at a university medical center improves the access of indigent patients to medications and is cost-effective.

Academic Medical Centers↗
PubMed2005

Dynamics of leaf and root growth: endogenous control versus environmental impact.

AIMS: Production of biomass and yield in natural and agronomic conditions depend on the endogenous growth capacity of plants and on the environmental conditions constraining it. Sink growth drives the competition for carbon, nutrients and water within the plant, and determines the structure of leaves and roots that supply resources to the plant later on. For their outstanding importance, analyses of internal growth mechanisms and of environmental impact on plant growth are long-standing topics in plant sciences. SCOPE: Recent technological developments have made it feasible to study the dynamics of plant growth in temporal and spatial scales that are relevant to link macroscopic growth with molecular control. These developments provided first insights into the truly dynamic interaction between environment and endogenous control of plant growth. CONCLUSIONS: Evidence is presented in this paper that the relative importance of endogenous control versus the impact of the dynamics of the environment depends on the frequency pattern of the environmental conditions to which the tissue is exposed. It can further be speculated that this is not only relevant within individual plants (hence leaves versus roots), but also crucial for the adaptation of plant species to the various dynamics of their environments. The following are discussed: mechanisms linking growth and concentrations of primary metabolites, and differences and homologies between spatial and temporal patterns of root and leaf growth with metabolite patterns.

Environment↗
PubMed2002

LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures.

A database comprising all ligand-binding sites of known structure aligned with all related protein sequences and structures is described. Currently, the database contains approximately 50000 ligand-binding sites for small molecules found in the Protein Data Bank (PDB). The structure-structure alignments are obtained by the Combinatorial Extension (CE) program (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998) and sequence-structure alignments are extracted from the ModBase database of comparative protein structure models for all known protein sequences (Sanchez et al., Nucleic Acids Res., 28, 250-253, 2000). It is possible to search for binding sites in LigBase by a variety of criteria. LigBase reports summarize ligand data including relevant structural information from the PDB file, such as ligand type and size, and contain links to all related protein sequences in the TrEMBL database. Residues in the binding sites are graphically depicted for comparison with other structurally defined family members. LigBase provides a resource for the analysis of families of related binding sites.

Binding Sites↗
PubMed1994

Genes conserved in yeast and humans.

Evolutionary conservation of homologous gene products from distantly related organisms provides an information resource of great value for elucidating protein structure and function. Sequence similarities also serve as molecular cross-references between diverse organisms that offer different, or complementary, experimental approaches for analyzing gene expression and biochemistry in normal and abnormal states. There are now countless examples of information about a protein from one species contributing to the understanding of biological phenomena or disease in another species. Such connections are often unanticipated and surprising, but there is an opportunity to make them more systematically as concerted genome sequencing projects progress. In the present review we focus on connections between yeast and human proteins and their functional implications. We present several 'case studies' as well as survey results derived from comprehensive sequence comparisons among all yeast and human proteins currently present in the public databases.

Conserved Sequence↗
PubMed1998

The Eukaryotic Promoter Database EPD.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of experimentally characterised eukaryotic POL II promoters. The underlying definition of a promoter is that of a transcription initiation site. All information presented in EPD results from an independent evaluation of primary experimental data shown in the biological literature. Sequences flanking transcription initiation sites are indirectly given by pointers to EMBL sequences. The annotation part of a promoter entry includes description of the promoter-defining evidence, cross-references to other databases, and bibliographic references. Being designed as a resource for comparative sequence analysis, EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets. The database is available through the World Wide Web at URL http://cmpteam4.unil.ch

Animals↗
PubMed2001

iProClass: an integrated, comprehensive and annotated protein classification database.

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200,000 non-redundant PIR and SWISS-PROT proteins organized with more than 28,000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetown.edu/iproclass/.

Databases, Factual↗
PubMed1998

Deinstitutionalization and schizophrenia in Finland: I. Discharged patients and their care.

Finland has experienced one of the most rapid psychiatric deinstitutionalization processes in the world. Since 1980, the use of psychiatric beds has decreased about one-third. The effects of this deinstitutionalization were studied in the national Discharged Schizophrenia Patient Project. The study used three representative samples of patients with schizophrenia who were discharged from mental hospitals in 1982, 1986, and 1990, and followed them for 3 years. Patients with schizophrenia discharged at the beginning of the 1990s were older and more disturbed, and had been ill for a longer time than patients discharged at the beginning of the 1980s. The use of outpatient care increased and that of hospital care decreased, but because of the increased residential outpatient care, the total amount of residential care did not change during the study period. However, readmissions to the hospital increased. In patients with a long duration of illness, the increase in readmissions was exceptionally high; these patients also seemed to be losing their share of the residential outpatient services. On the whole, from the point of view of the psychiatric treatment system, deinstitutionalization seemed to have proceeded fairly successfully. The system proved able to redirect and use the available resources more effectively and to modify the structure of services according to the changing needs of patients discharged from hospitals. The well-developed social services have also supported this adaptation to the decreasing use of mental hospital beds.

Adolescent↗
PubMed1999

The Visible Human Project: a resource for education.

Throughout recorded history, the relationships between biological structure and function have been central to the understanding of health and disease. For many centuries, the anatomy illustrations originally created during the medieval period formed the basis for the study of medicine. But learning and understanding anatomic structures is limited by the fundamentally two-dimensional images traditionally used to teach them. The digital computer now allows scientists to acquire, store, manipulate, and display complex images. In 1989, the National Library of Medicine (NLM) began a project to use computer technologies to build a prototype digital image library of data representing a complete normal adult human male and female. In this paper, the author describes the beginnings of this project, the Visible Human Project (VHP), the digital images currently available in the VHP database, ongoing research and development, and plans for the future of the VHP.

Adult↗
PubMed2002

360 degrees: planning a new pediatric clerkship.

OBJECTIVE: Mount Sinai School of Medicine is midway through a major curriculum revision. The immediate goal for the core third-year clerkships was to create a modular schedule with varied and integrated clinical experiences. Some clerkships were lengthened; others, blended. Clerkship directors were asked to find ways to ally with those also in their 12-week module. Content material, only presented at Mount Sinai, was to be delivered at all affiliate sites. Each clerkship had one year to prepare. DESCRIPTION: Core pediatrics faced multiple challenges. Once an eight-week clerkship, pediatrics was condensed into a six-week block and paired with ob-gyn at the same affiliate sites. Material presented during weekly, lecture-based didactic sessions at Mount Sinai was to be delivered at all sites, some of which were considerable distances away. To enable students to have both content and clinical experiences at the same site, new teaching formats and techniques had to be utilized and faculty retrained to implement their new roles. Three approaches met both conditions: (1) interactive case-based learning of clerkship content objectives, (2) use of Web-based instruction to provide resources to all sites, and (3) the identification and training core educators to deliver this new content material. Generalist and specialist pediatricians prepared clinical cases. Each author was given a case-writing template, so that all cases included objectives, references, a case presentation, and guiding questions. Cases were written with extended answers to each of eight standard questions, including key teaching points, to create a teacher's manual. Three faculty members reviewed each case to assure that the content matched the objectives for the module and that cases were written at an appropriate level for third-year medical students. Weekly seminars are now interactive, small-group, and Web-based. Cases use multimedia resources and integrate multiple clinical disciplines. The structure of the seminars, modeled on adult learning theory, include review of the basic approach to patients, organization of data, and generation of a prioritized differential diagnosis. The seminars also review basic management principles for a variety of common pediatric conditions. Core educators were designated to facilitate the cases at each clinical site. They were given instructions for case facilitation, a detailed teacher's manual, and a multimedia CD-ROM. The teacher's manual contains the course syllabus as well as extended case discussions. The accompanying CD-ROM contains photographic images, growth charts, x-rays, microscopy, and sound files. Computers are available at each site and are linked to WEB-CT, the program supporting the Mount Sinai undergraduate online curriculum. DISCUSSION: We have not yet reached 360 degrees in revising our clerkship. Feedback from both students and clinician educators has been extremely positive. Future plans include further enhancement of the cases to incorporate clinical pathology, genetics, laboratory medicine, radiology, and evidence-based medicine. We will also develop and implement a faculty development program to equip our faculty with tools for effective, time-efficient, case facilitation. Starting anew with a few core organizing principles and a multidisciplinary approach has enhanced the learning for both faculty and students.

Child↗
PubMed1991

Codependency: management and administrative policy implications.

Health care practitioners may exhibit behaviors that are considered dysfunctional for personal well-being. These behaviors, feelings, and thoughts could affect the manager-employee relations, as well as the implementation of patient care. This discussion focuses on the relevance of codependency in human resource management. Implications of codependency for organizational structure, standards of care, and managerial roles are pointed out. Specific strategies are outlined in recognizing manifestations of codependency. Finally, administrative interventions such as the Employee Assessment and Counseling Programs are suggested to prevent the negative outcomes of codependency which can affect job performance.

Adaptation, Psychological↗
PubMedDate not supplied

Nurse staffing patterns and quality of care in nursing homes.

Using the structure-process-outcome framework and the resource-based view of the firm, this study considers both direct and indirect effects of registered nurse staffing patterns on the quality of patient care outcomes. Consistent with theory, registered nurse staffing patterns were found to affect quality of patient care both directly and indirectly through their positive effect on the processes of delivering care.

Diagnosis-Related Groups↗
PubMed2007

Effects of teamwork training on adverse outcomes and process of care in labor and delivery: a randomized controlled trial.

OBJECTIVE: To evaluate the effect of teamwork training on the occurrence of adverse outcomes and process of care in labor and delivery. METHODS: A cluster-randomized controlled trial was conducted at seven intervention and eight control hospitals. The intervention was a standardized teamwork training curriculum based on crew resource management that emphasized communication and team structure. The primary outcome was the proportion of deliveries at 20 weeks or more of gestation in which one or more adverse maternal or neonatal outcomes or both occurred (Adverse Outcome Index). Additional outcomes included 11 clinical process measures. RESULTS: A total of 1,307 personnel were trained and 28,536 deliveries analyzed. At baseline, there were no differences in demographic or delivery characteristics between the groups. The mean Adverse Outcome Index prevalence was similar in the control and intervention groups, both at baseline and after implementation of teamwork training (9.4% versus 9.0% and 7.2% versus 8.3%, respectively). The intracluster correlation coefficient was 0.015, with a resultant wide confidence interval for the difference in mean Adverse Outcome Index between groups (-5.6% to 3.2%). One process measure, the time from the decision to perform an immediate cesarean delivery to the incision, differed significantly after team training (33.3 minutes versus 21.2 minutes, P=.03). CONCLUSION: Training, as was conducted and implemented, did not transfer to a detectable impact in this study. The Adverse Outcome Index could be an important tool for comparing obstetric outcomes within and between institutions to help guide quality improvement. CLINICAL TRIAL REGISTRATION: (www.ClinicalTrials.gov), NCT00381056 LEVEL OF EVIDENCE: I.

Delivery, Obstetric↗
PubMed2005

Indirect effects and spatial scaling affect the persistence of multispecies metapopulations.

Quantifying the role of space and spatial scale on the population dynamics of ecological assemblages is a contemporary challenge in ecology. Here, we evaluate the role of metapopulation dynamics on the persistence and dynamics of a multispecies predator-prey assemblage where two prey species shared a common natural enemy (apparent competition). By partitioning the effects of increased resource availability from the effects of metapopulation structure on regional population persistence we show that space has a marked impact on the dynamics of apparent competition in multispecies predator-prey assemblages. Further, the role of habitat size and stochasticity are also shown to influence the dynamics and persistence of this multispecies interaction. The broader consequences of these processes are discussed.

Computer Simulation↗
PubMed2006

Generic entanglement and standard form for N-mode pure Gaussian states.

We investigate the correlation structure of pure N-mode Gaussian resources which can be experimentally generated by means of squeezers and beam splitters, whose entanglement properties are generic. We show that those states are specified (up to local unitaries) by N(N-1)/2 parameters, corresponding to the two-point correlations between any pair of modes. Our construction yields a practical scheme to engineer such generic-entangled N-mode pure Gaussian states by linear optics. We discuss our findings in the framework of Gaussian matrix product states of harmonic lattices, raising connections with entanglement frustration and the entropic area law.

Journal Article↗