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At least 613 records · Page 34Linked to original sources
PubMed2005

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

Amino Acid Motifs↗
PubMed1989

[Marriage rate, divorce rate, and the development of the Bulgarian family].

The author examines the new forms of consensual union that are becoming increasingly prevalent in Europe and their detrimental effects on the reproduction of generations and socialization. "Using data from the sociological study conducted by the Institute of Sociology of the Bulgarian Academy of Sciences in 1977 and the data obtained in the latest population census in 1985, the development of the Bulgarian family and influence of [these] new social relations under socialism are investigated." Particular attention is given to trends in marriage and divorce rates. (SUMMARY IN ENG AND RUS)

Bulgaria↗
PubMed2005

Global landscape of recent inferred Darwinian selection for Homo sapiens.

By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The approximately 1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.

Alleles↗
PubMed2001

Evaluation of depth profiling using laser resonant desorption as a method to measure diffusion coefficients in ice.

Diffusion of gases in ice is involved in cloud, snow, and ice core chemistry, but few data exist on the relevant diffusion coefficients. A novel method to measure diffusion coefficients in ice has recently been proposed by Livingston et al. (Anal. Chem., 2000, 72, 5590-5599). It is based on depth profiling of doped ice crystals epitaxially grown on Ru(001) by laser resonant desorption (LRD). Using this method, Livingston et al. obtained a value of the diffusion coefficient of the HCl hydrate in ice at 190 K of about 5 x 10(-11) cm2/s. We argue here that this value is many orders of magnitude higher than what could be expected from literature values, which are not reported in sufficient detail by Livingston et al. We investigate the possibilities that their high value could be due to (1) diffusion in defects in the ice, which would be present in very high concentrations because of the ice growth method; and (2) the fact that diffusion of high concentrations of HCl in ice at 190 K forms an amorphous HCl:H2O solid mixture, where HCl diffusion is fast. We present new infrared spectroscopic data on solid HCl:H2O mixtures that confirm that such mixtures can indeed be formed in an amorphous state at 190 K. Our proposed interpretation is that by depositing large amounts of HCl on epitaxially grown ice, Livingston et al. created a superficial amorphous binary mixture and that fast diffusion of HCl in the ice, possibly accelerated by a high defect density, produced an amorphous HCl:H2O mixture. We conclude that the processes studied by Livingston et al. are different from those involved in the atmospheric and cryospheric sciences, and that their data, obtained by depth profiling using LRD, probably cannot be applied to those fields.

Journal Article↗
PubMed2002

Public vs. proprietary science: a fruitful tension?

The authors examine the presumption that basic scientific research is most effectively utilized when the findings of that research are openly disseminated without significant restriction, while research with more practical application should be the prerogative of private enterprise. However, many fields, including molecular biology generally and genomics in particular, lie in the intersection between basic research and application. Moreover, institutional boundaries that once reasonably sharply demarcated basic research from technological development have grown porous, with more academic research finding application in industry. The authors consider the Human Genome Project and rival industry sequencing efforts as a case in point of the new political economy of scientific research. Since the inception of the Human Genome Project, there has been general agreement among researchers that the project would be most advantageous to science if the sequence data were made publicly available, quickly and without restriction. Many of these arrangements required federal agencies and some universities to "maneuver around" the Bayh-Dole Act. In several cases, most notably genomic sequences and the SNPs (i.e., single nucleotide polymorphisms) consortium, it was the pharmaceutical industry that initiated or helped enable the project to ensure open and unencumbered access to information, the type of access that has historically been the provenance of academia and the raison d'être of academic research. The authors conclude by reasserting the value of public science as a broadly valuable and enabling social commitment, not limited simply to the products or technologies it spawns.

Cooperative Behavior↗
PubMed2005

Stories as data, data as stories: making sense of narrative inquiry in clinical education.

BACKGROUND: Narrative inquiry is a form of qualitative research that takes story as either its raw data or its product. Science and narrative can be seen as two kinds of knowing, reflected in the distinction between evidence-based medicine derived from population studies and narrative-based medicine focused upon the single case. A similar tension exists in the field of narrative inquiry between cognitive-orientated analytical methods and affective-orientated methods of synthesis. AIMS: This paper aims to make sense of narrative inquiry in clinical education through definition of 'narrative', articulation of a typology of narrative research approaches, and critical examination in particular of analytical methods, the dominant approach in the literature. The typology is illustrated by research examples, and the role of medical education in developing expertise in narrative inquiry is discussed. An argument is made that the tension between analysis of the structure of stories and empathic use of stories can be seen as productive, stimulating expertise encompassing both approaches. DISCUSSION: Analytical methods tend to lose the concrete story and its emotional impact to abstract categorizations, which may claim explanatory value but often remain descriptive. Stemming from discomfort with more integrative methods derived from the humanities, a science-orientated medical education may privilege analytical methods over approaches of synthesis. Medical education can redress this imbalance through attention to 'thinking with stories' to gain empathy for a patient's experience of illness. Such an approach can complement understanding of story as discourse - how narratives may be used rhetorically to manage both social interactions and identity.

Clinical Medicine↗
PubMed2004

Assessing precollege science education outreach initiatives: a funder's perspective.

We describe an assessment of the collective impact of 35 grants that the Howard Hughes Medical Institute (HHMI) made to biomedical research institutions in 1999 to support precollege science education outreach programs. Data collected from funded institutions were compared with data from a control group of institutions that had advanced to the last stage of review but had not been funded. The survey instrument and the results reveal outcomes and impacts that HHMI considers relevant for these programs. The following attributes are considered: ability to secure additional, non-HHMI funding; institution buy-in as measured by gains in dedicated space and staff; enhancement of the program director's career; number and adoption of educational products developed; number of related publications and awards; percentage of programs for which teachers received course credit; increase in science content knowledge; and increase in student motivation to study science.

Academies and Institutes↗
PubMed1999

Developmental assessment. Its role in comprehensive psychiatric assessment of young children.

The psychiatric assessment of young children is a multifaceted endeavor, and developmental assessment, formal or informal, is an integral component. Sound developmental assessment, however, is a thoughtful process that requires specialized knowledge of young children, appropriate assessment methods, and the interpretation and integration of psychiatric and developmental data. The art and science of developmental assessment have improved significantly over the past century. Despite technologic advances in instruments, clinicians must be as astute and mindful as ever of what constitutes sound diagnostic formulation and treatment planning. Although many limitations and potential abuses certainly exist, results of developmental evaluations play a unique and often essential role in the comprehensive psychiatric assessment of young children.

Child, Preschool↗
PubMed1998

Topic selection in undergraduate medical education and relevance to general practice.

Most patients who have possibly malignant diseases are first seen by physicians not specifically trained in oncology. The cancer education that undergraduate medical students receive is frequently dominated by basic science topics, detailed staging data, pharmacology of cancer drugs, and treatment protocols. This is not in accordance with the needs in general practice. In pre-course information and correspondence with reference to the International Summer School "Oncology for Medical Students," held in Groningen, The Netherlands, it is emphasized that the Summer School focuses on cancer care in general practice. As part of the education program participants are required to prepare abstracts and posters on oncologic topics in general health care in their own countries. Despite the emphasis on cancer care in general practice and despite suggestions for topics, some students have first sent in abstracts describing basic sciences research projects. Evidently during their medical training the relevancy of cancer education to the reality of daily practice had not been taught or had already been lost. In teaching undergraduate medical students, it should be realized that the vast majority will choose non-oncology disciplines. Thus, cancer education of these students should focus mainly on clinical cancer issues that are relevant in general practice.

Abstracting and Indexing↗
PubMed1994

[Data for the assessment of the 1850 population census in Transylvania].

"Having reviewed the population figures of historical Transylvania the study analyses from three aspects the reliability of data of the population census in 1850.... Through the analysis of 100 settlements in county Haromszek the author has found that population figure pointed out in 1784 must be doubled, however, the number of those left out varies significantly from settlement to settlement." (SUMMARY IN ENG AND RUS)

Censuses↗
PubMed1999

Challenge of Goodness II: new humanitarian technology, developed in croatia and bosnia and Herzegovina in 1991-1995, and applied and evaluated in Kosovo 1999.

This paper presents improvements of the humanitarian proposals of the Challenge of Goodness project published earlier (1). In 1999 Kosovo crisis, these proposals were checked in practice. The priority was again on the practical intervention - helping people directly - to prevent, stop, and ease suffering. Kosovo experience also prompted us to modify the concept of the Challenge of Goodness. It should include research and education (1. redefinition of health, 2. confronting genocide, 3. university studies and education, and 4. collecting experience); evaluation (1. Red Cross forum, 2. organization and technology assessment, 3. Open Hand - Experience of Good People); activities in different stages of war or conflict in: 1. prevention (right to a home, Hate Watch, early warning), 2. duration (refugee camps, prisoners-of-war camps, global hospital, minorities), 3. end of conflict (planned, organized, and evaluated protection), 4. post conflict (remaini ng and abandoned populations, prisoners of war and missing persons, civilian participation, return, and renewal). Effectiveness of humanitarian intervention may be performed by politicians, soldiers, humanitarian workers, and volunteers, but the responsibility lies on science. Science must objectively collect data, develop hypotheses, check them in practice, allow education, and be the force of good, upon which everybody can rely. Never since the World War II has anybody in Europe suffered in war and conflict so much as peoples in Croatia, Bosnia and Herzegovina, and Kosovo. We should search for the meaning of their suffering, and develop new knowledge and technology of peace.

Altruism↗
PubMed2002

Teaching neuroscience through Web adventures: adolescents reconstruct the history and science of opioids.

New technological and cultural developments surrounding adolescents' use of the World Wide Web offer an opportunity for turning aspects of the Internet gaming phenomenon to the advantage of neuroscience education. Specifically, an experimental project to transmit aspects of problem-based learning and the National Science Standards through an interactive Web adventure is reported here. The Reconstructors is an episodic Web-based adventure series entitled Medicinal Mysteries from History. It is funded by the National Institute on Drug Abuse, and the first series focuses on opioids. It was created with the input of middle school students and teachers. Through the use of multimedia technologies, middle school students enter a futuristic world in which they become "reconstructors," members of an elite scientific unit charged with recovering lost medical knowledge about analgesic drugs. Two of the four episodes have been evaluated through a comprehensive review process involving middle school students, teachers, neuroscience researchers, and clinicians. Analysis of the pretest and posttest scores demonstrated significant knowledge gain that validly can be attributed to use of the game. These data provide evidence that science content can be transmitted through innovative online techniques without sacrificing compelling content or effective pedagogical strategies.

Adolescent↗
PubMed2005

Survey of clustering algorithms.

Data analysis plays an indispensable role for understanding various phenomena. Cluster analysis, primitive exploration with little or no prior knowledge, consists of research developed across a wide variety of communities. The diversity, on one hand, equips us with many tools. On the other hand, the profusion of options causes confusion. We survey clustering algorithms for data sets appearing in statistics, computer science, and machine learning, and illustrate their applications in some benchmark data sets, the traveling salesman problem, and bioinformatics, a new field attracting intensive efforts. Several tightly related topics, proximity measure, and cluster validation, are also discussed.

Algorithms↗
PubMed1983

Health science libraries in the United States: I. Overview of the post-World War II years.

Data from three surveys of health sciences libraries in the United States (1969, 1973, and 1979) were analyzed within the context of scientific, technological, and sociopolitical developments. Findings included decrease in the number of separately administered libraries, growth of some, decline or discontinuation of others, and geographic movement. Overall, the aggregate resources are increasing, as is cooperation among libraries.

Libraries, Medical↗
PubMed1999

What should we be teaching residents about behavioral science? Opinions of practicing family physicians.

BACKGROUND AND OBJECTIVES: A behavioral science curriculum in family practice residency education encompasses a wide range of topics. Time limitations reduce the number of topics that can be emphasized. This study presents the opinions of practicing family physicians regarding the prioritization of behavioral science topics for residency education. METHODS: We mailed a questionnaire to 633 practicing family physicians. Respondents provided demographic data and rated 28 behavioral science topics according to priority to be given in residency education. RESULTS: A total of 447 questionnaires were returned, for a response rate of 71%. On a 4-point scale, the average ratings of the 28 topics ranged from 3.79 (depression) to 2.40 (enuresis/encopresis). Female physicians and physicians with a behaviorist in their practice provided significantly higher overall average ratings. CONCLUSIONS: Practicing family physicians identify specific behavioral science topics to be given high priority during residency education. The list of prioritized topics may provide a useful guide to help family medicine educators decide which topics to emphasize in the behavioral science curriculum.

Behavioral Sciences↗
PubMedDate not supplied

[An analysis of the scientific publications of the A. A. Bogomolets Institute of Physiology of the Academy of Sciences of Ukraine].

Scientific publications from three sectors of the Institute have analyzed for the period since 1979 till 1988 inclusive. The analysis is based on data of annual reference books Science Citation Index (SCI) and lists of publications of each researcher of the Institute. It is shown that with almost equal numerical strength of researchers and similar number of publications the sector of molecular physiology contributed 43.6% to cited works 48.2% of these works are included into database of SCI. Such indices for the sectors of neurophysiology and physiology of visceral systems accounted for 33%, 33.4% and 23.4, 18.4% respectively. It is of interest that 47.5% of references to the cited works of the molecular physiology sector were made by foreign scientists and self-citation constituted 17.4%, while for the other sectors such indices had a reverse relationship. The problem on objectification of estimation of research is under discussion.

Academies and Institutes↗
PubMed1978

Management data for collection analysis and development.

Sound management data are needed to evaluate the collections of health sciences libraries. This study reports the utilization of computer data bases to compare the libary collections of The University of Texas Health Science Center at San Antonio. The University of Texas Medical Branch, and the National Library of Medicine's CATLINE data base. The imprint dates of the records of two libraries are compared to measure acquisitions rates. Subject profiles for the Q and W classes demonstrate the similarity of the collections. Reasons for the variances are considered.

Analysis of Variance↗