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At least 1,621 records · Page 90Linked to original sources
PubMed2002

Computational function assignment for potential drug targets: from single genes to cellular systems.

Biomedical science is currently undergoing an epoch-marking transition from its classical phase to the post-genome era. The outstanding success of world-wide genome sequencing efforts, evidenced by the recent publication of the draft of the human genome, together with the completion of several genomes of eukaryotic model organisms and the availability of microbial genome sequences, is opening up data sources of unprecedented scale for drug discovery. Furthermore, the elucidation of genome expression states through transcriptomic and proteomic techniques is playing a crucial role in the characterisation of disease at the molecular level. At the same time, our still very limited knowledge of the biological functions of genes and proteins at different levels of cellular organisation is preventing full exploitation of the available data. This review will discuss current computational techniques for function prediction based on the sequence-structure-function paradigm. Newly emerging approaches aimed at gaining an expanded understanding of function through integration of data from various sources and modelling of complex cellular systems will also be highlighted.

Amino Acid Sequence↗
PubMed1996

Ultraperspective and endophysics.

Ultraperspective is the capability of human beings to step into the shoes of another person. Endophysics is the science of those physical properties of the world which exist not from the outside but only form the inside. Both have in common the adoption of an 'exterior' position. In the one case, the exteriority is 'horizontal', in the other, 'vertical'. Ultraperspective is a macroscopic concept, endophysics a microscopic one. Both can be implemented in computer models. Novel experiments can be set up in either domain: animals acquiring the status of human persons, and objective features of the physical world acquiring the status of an observer-specific mirage. Mead an Levinas, and Einstein and Bohr, are the protagonists. In the age of computer-assisted enlightenment, a new look at the ethical roots of science appears justified.

Ethics↗
PubMed2000

Structural, Electrochemical, and Photophysical Properties of Gallium(III) 5,10,15-Tris(pentafluorophenyl)corrole We acknowledge support of this research from the Fund for the Promotion of Research at the Technion (Z.G.), the National Science Foundation (H.B.G.), and the Danish Natural Science Research Council for financial support under grant No. 9800549 (J.B.). We also thank Dr. H. Weihe (University of Copenhagen) for access to computing facilities, and L. M. Henling (Beckman Institute) for assistance with the crystal structure determination.

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Journal Article↗
PubMed2000

The use of instructional technology in poultry science curricula in the United States and Canada: 2. Factors contributing to the use of instructional technology.

This paper describes a study conducted in recognition of the increasingly widespread use of computers and the importance of exposure to instructional technology (IT) in all aspects of the poultry science curriculum. The study consisted of the distribution and analysis of two cross-sectional surveys. One survey was sent to departments to obtain profiles of poultry science degree programs and the availability of IT and general support for its use. The second survey was sent to faculty to obtain individual profiles of IT use and of factors which may influence IT use. Herein are reported the results and analysis of those factors that are thought to contribute to or limit the diffusion of these media among poultry science faculty. Analysis consisted of descriptive statistics and contingency table comparisons using Likelihood Ratio chi-square. Factors that appear to be most important to faculty use of IT are availability of desired IT equipment, access to adequate expert assistance, availability of knowledgeable peers willing to share their experience and expertise, and exposure to concrete examples and ideas of how to use IT. All of these factors contribute to another important factor in participation and adoption: making it as easy as possible for faculty to learn and to use advanced IT methods.

Agriculture↗
PubMed1992

The Language Research Center's Computerized Test System for environmental enrichment and psychological assessment.

In the spring of 1987, we undertook to provide environmental enrichment to nonhuman primate subjects in ways that would complement and even contribute to the bio-behaviorial science that justified the monkeys' captivity. Of course, the psychological well-being of captive primates--and indeed all research species-- has been an area of intense research activity since the 1985 amendment of the Animal Welfare Act. This mandate for researchers to ensure the psychological, as well as physical, fitness of experimental animals catalyzed the humane and scientific interests of the research community. The contemporary literature is replete with proposed means both of assaying and of providing enrichment and well-being. Notwithstanding, consensus on either assessment or intervention has yet to be reached. The paradigm we employed was modelled after successful efforts with chimpanzees. An automated test system was constructed in which subjects responded to computer tasks by manipulating a joystick. The tasks, interactive game-like versions of many of the classic testing paradigms of cognitive and comparative psychology, permitted the controlled presentation of stimuli and demands without the required presence of a human experimenter. Despite significant barriers to the success, rhesus monkeys (Macaca mulatta) and a variety of other primate species (including, of course, humans) have mastered the skills necessary for testing in this paradigm. Previous experiments have illustrated the utility of the test system for addressing questions of learning, memory, attention, perception, and motivation. Additional data have been reported to support the contention that the Language Research Center's Computerized Test System (LRC-CTS) serves its other raison d'etre--providing environmental enrichment and assessing psychological well-being. This paper is designed to augment previous descriptions of the technology and the paradigm for scientists and caretakers interested in environmental enrichment and performance assessment with primates.

Animal Welfare↗
PubMed2005

A double-dissociation in infants' representations of object arrays.

Previous studies show that infants can compute either the total continuous extent (e.g. Clearfield, M.W., & Mix, K.S. (1999). Number versus contour length in infants' discrimination of small visual sets. Psychological Science, 10(5), 408-411; Feigenson, L., & Carey, S. (2003). Tracking individuals via object-files: evidence from infants' manual search. Developmental Science, 6, 568-584) or the numerosity (Feigenson, L., & Carey, S. (2003). Tracking individuals via object-files: evidence from infants' manual search. Developmental Science, 6, 568-584) of small object arrays. The present experiments asked whether infants can compute both extent and number over a given array. Experiment 1 used a habituation procedure to show that 7-month-old infants can compute numerosity when the objects in the array contrast in color, pattern, and texture. Experiment 2 revealed that, with these heterogeneous arrays, infants no longer represent the array's total continuous extent. Since previous work shows that infants compute continuous extent but not numerosity when objects have identical rather than contrasting properties, these results form a double dissociation. Infants computed number but not extent over representations of contrasting objects, and computed extent but not number over representations of identical objects.

Cognition↗
PubMed2006

Development and use of behavior and social interaction software installed on Palm handheld for observation of a child's social interactions with the environment.

In settings in developing countries, children often socialize with multiple socializing agents (peers, siblings, neighbors) apart from their parents, and thus, a measurement of a child's social interactions should be expanded beyond parental interactions. Since the environment plays a role in shaping a child's development, the measurement of child-socializing agents' interactions is important. We developed and used a computerized observational software Behavior and Social Interaction Software (BASIS) with a preloaded coding scheme installed on a handheld Palm device to record complex observations of interactions between children and socializing agents. Using BASIS, social interaction assessments were conducted on 573 preschool children for 1 h in their natural settings. Multiple screens with a set of choices in each screen were designed that included the child's location, broad activity, state, and interactions with child-socializing agents. Data were downloaded onto a computer and systematically analyzed. BASIS, installed on Palm OS (M-125), enabled the recording of the complex interactions of child-socializing agents that could not be recorded with manual forms. Thus, this tool provides an innovative and relatively accurate method for the systematic recording of social interactions in an unrestricted environment.

Activities of Daily Living↗
PubMed2003

Craniofacial computed tomography scanning: technology, applications and future trends.

OBJECTIVES: Craniofacial imaging in three dimensions depends on computed tomography (CT) and related technologies. This paper explains the state-of-the-art for medical and dedicated craniofacial cone-beam CT scanners. METHOD: Current medical CT scanners are surveyed, especially the recently announced 16 simultaneous slice models with subsecond source-detector rotation times and spiral/helical third generation geometry. The medical scanner technology is contrasted with dedicated low-cost craniofacial cone-beam CT scanners to delineate the relevant technologies and clarify the differences. RESULTS: CT scanners performance in any task is determined by their detectors and reconstruction algorithm primarily and to a lesser extent by the X-ray source, dose utilization, computational and display electronics, and software for post-processing. Each of these components differs between medical and low-cost cone-beam scanners, and the differences are tabulated and explained. CONCLUSION: Low-cost craniofacial CT scanners are significantly different from general purpose medical CT scanners, with compromises in technical performance. Despite their limitations, these instruments are remarkably useful for their intended application domain and should improve as computers continue to increase their performance.

Algorithms↗
PubMed2004

Data-driven computer simulation of human cancer cell.

Using the Diagrammatic Cell Language trade mark, Gene Network Sciences (GNS) has created a network model of interconnected signal transduction pathways and gene expression networks that control human cell proliferation and apoptosis. It includes receptor activation and mitogenic signaling, initiation of cell cycle, and passage of checkpoints and apoptosis. Time-course experiments measuring mRNA abundance and protein activity are conducted on Caco-2 and HCT 116 colon cell lines. These data were used to constrain unknown regulatory interactions and kinetic parameters via sensitivity analysis and parameter optimization methods contained in the DigitalCell computer simulation platform. FACS, RNA knockdown, cell growth, and apoptosis data are also used to constrain the model and to identify unknown pathways, and cross talk between known pathways will also be discussed. Using the cell simulation, GNS tested the efficacy of various drug targets and performed validation experiments to test computer simulation predictions. The simulation is a powerful tool that can in principle incorporate patient-specific data on the DNA, RNA, and protein levels for assessing efficacy of therapeutics in specific patient populations and can greatly impact success of a given therapeutic strategy.

Apoptosis↗
PubMed2000

OBSERVE: a multimedia course on the observational analysis of behavior.

OBSERVE is a preliminary release of a multimedia course for teaching undergraduate and graduate students how and why to study behavior by direct observation. The instructional text and commentary and the self-test and examination materials are built around a series of exercises in which the student observes and categorizes film clips of the behavior of several different species in several different ways. Incorporation of elements from The Observer software for computer recording and video analysis implements fully computerized continuous recording. At present, the text, together with check sheets that the program generates, enables a comparison between one-zero, instantaneous, and continuous sampling of the same behavioral excerpts. Matrices are printed out for an exercise in calculating interobserver reliability. Another section supports carrying out and writing up a small observational project on human behavior in the field. Plans for the future development of OBSERVE are briefly described.

Behavioral Sciences↗
PubMed1986

Computer systems to support census geography.

The development of computer systems that support the geography of the census in Canada is described. The authors "present proposals for the 1991 Census that increase the level of automation, whether the geography changes or not. In addition, opportunities for change and improvement, should the geography change, are outlined. To minimize the risks involved, it is important to give these different proposals serious consideration early in the planning of a census."

Americas↗
PubMed1999

Audit of cervical screening and colposcopy in HIV-positive women at a central London teaching hospital.

The purpose of this audit was to assess the prevalence of cervical pathology and clinical outcome in HIV-infected women as well as adherence to local screening guidelines. As there are no national screening guidelines for HIV-positive patients, recommendations vary widely. At St Stephen's Centre, these included annual cytology and a baseline colposcopy. We audited this recommendation by a clinical notes review using a computer database. Analysis was performed using Statistical Package for Social Sciences (SPSS). Two hundred and twenty-two patients were eligible for analysis, their mean age was 33.6 years, median CD4 count was 239 and median viral load was 7836 RNA copies. Cytology was undocumented in 72 women (32.4%), while overall 42 (28%) smears of the remaining 150 patients were abnormal: borderline 17.3%, mild dyskaryosis 4.6%, moderate dyskaryosis 4%, severe dyskaryosis 2%. The results were normal in 64% and unsatisfactory in 4.6%. Colposcopy was offered to 93 (42%) women who attended at least once in 71 cases (32%). Thirty-one women had biopsies taken (43.6% of all colposcopies). Twenty-four (77.4%) had a histology more severe than HPV and 15 (48.4%) more severe than cervical intraepithelial neoplasia (CIN)-1. Overall, 49.7% had management not complying with the guidelines. This audit led to a critical literature review and of local screening guidelines. A computer aided reminder program has now been installed and re-auditing of the management of HIV-positive women is planned.

Adolescent↗
PubMed1999

Awareness of the earth and possibilities for new science education in the Internet age.

The internet as "the nervous system of global size" and multimedia technology have changed our global experience radically and suggests possibilities of entirely new approaches to the conventional education of sciences and the environment. They are not merely the changes where printed text books are converted into dynamic things with vivid appeal to our senses and information about the world's museums and art galleries, digitalized and shared by all. If the seismic activities occurring every day in various parts of the world can be seen in real form directly through the internet by all the people of the world, how will children's views of the earth change and how will their scientific understanding improved? If there was a system whereby one could monitor, in real time, how one member or others of the world net surf the global home pages, and if one could follow the "moving" process on the internet, children would certainly appreciate the presence of the internet as a global network of information. The web site "Sensorium" (http://www.sensorium.org) was created by us in an effort to put these live experiences of the internet into design. Sensorium is not a site merely to digitalize and list the existing knowledge and data. It is an experiment for the Digital Museum as a new "forum" where we may experience and share a moment. It is also an attempt to create tools for science and environment education which are only available on the network.

Child↗
PubMed2000

Using lateral capillary forces to compute by self-assembly.

Investigations of DNA computing have highlighted a fundamental connection between self-assembly (SA) and computation: in principle, any computation can be performed by a suitable self-assembling system. In practice, exploration of this connection is limited by our ability to control the geometry and specificity of binding interactions. Recently, a system has been developed that uses surface tension to assemble plastic tiles according to shape complementarity and likeness of wetting [Bowden, N., Terfort, A., Carbeck, J. & Whitesides, G. M. (1997) Science 276, 233-235]. Here the capacity of this system to compute by SA is explored. Tiles were prepared to test the system's ability to generate three structures of increasing complexity: a periodic checkerboard tiling, an aperiodic Penrose tiling, and a computational tiling that simulates a one-dimensional cellular automaton. Matching rules for these tilings were enforced by coating tiles with patterns of hydrophobic and hydrophilic patches or wetting codes. Energetic, kinetic, and mechanistic details of SA explain differences between experimental structures and mathematically ideal ones. In particular, the growth mechanism observed appears incompatible with computations that make use of a chosen input.

Journal Article↗
PubMed2002

Structuring the universe of proteins.

High-throughput sequencing of human genomes and those of important model organisms (mouse, Drosophila melanogaster, Caenorhabditis elegans, fungi, archaea) and bacterial pathogens has laid the foundation for another "big science" initiative in biology. Together, X-ray crystallographers, nuclear magnetic resonance (NMR) spectroscopists, and computational biologists are pursuing high-throughput structural studies aimed at developing a comprehensive three-dimensional view of the protein structure universe. The new science of structural genomics promises more than 10,000 experimental protein structures and millions of calculated homology models of related proteins. The evolutionary underpinnings and technological challenges of automating target selection, protein expression and purification, sample preparation, NMR and X-ray data measurement/analysis, homology modeling, and structure/function annotation are discussed in detail. An informative case study from one of the structural genomics centers funded by the National Institutes of Health and the National Institute of General Medical Sciences (NIH/NIGMS) demonstrates how this experimental/computational pipeline will reveal important links between form and function in biology and provide new insights into evolution and human health and disease.

Amino Acid Sequence↗