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At least 1,207 records · Page 67Linked to original sources
PubMed2005

From single genes to co-expression networks: extracting knowledge from barley functional genomics.

The paper reports an 'in silico' approach to gene expression analysis based on a barley gene co-expression network resulting from the study of several publicly available cDNA libraries. The work is an application of Systems Biology to plant science: at the end of the computational step we identified groups of potentially related genes. The communities of co-expressed genes constructed from the network are remarkably characterized from the functional point of view, as shown by the statistical analysis of the Gene Ontology annotations of their members. Experimental, lab-based testing has been carried out to check the relationship between network and biological properties and to identify and suggest effective strategies of information extraction from the network-derived data.

Computational Biology↗
PubMed1996

The clinical workstation as a means of improving laboratory use.

Driven to make timely decisions, doctors may act with less than all of the relevant patient data. Sub-optimal use of clinical laboratory resources can result. Our clinicians' workstation (CWS) is meant to provide doctors and nurses ready access to laboratory results in a form that makes the data easy to review and use. In addition, the workstation provides immediate feedback regarding blood orders, to encourage appropriate clinical practice. Feedback is based on the medical staff's clinical guidelines that have been incorporated into an embedded expert system. CWS also helps blood bank physicians to monitor, review and control requests for special needs such as irradiated products. Challenges to system acceptance await those trying to bring functional decision support to the clinical environment. Among these are barriers to understanding and cooperation posed by departmental boundaries and interacting professional cultures as well as the politics of hospital-based information systems.

Chemistry, Clinical↗
PubMed1983

Quantitative analysis of cyclic AMP waves mediating aggregation in Dictyostelium discoideum.

We have previously reported the detection of cAMP waves within monolayers of aggregating Dictyostelium discoideum cells (K. J. Tomchik and P.N. Devreotes, 1981, Science 212, 443-446). The computer-assisted analysis presented here of the fluorographic images of the cAMP waves reveals (1) all the waves have a consistent width and height; (2) cAMP concentrations within centers of concentric aggregation territories oscillate periodically while at spiral centers the concentration builds up to a plateau value within 2 mm; (3) cells within the region of intersection of two oppositely directed cAMP waves are stimulated to produce more cAMP than those responding to a single wave; (4) cells start to move when the cAMP level begins to increase and cease movement when the peak cAMP concentration reaches the cell.

Computers↗
PubMedDate not supplied

Cognitive neurotoxicology: a luxury or necessity?

Impaired psychological test performance is often observed at concentrations of a neurotoxicant below those producing harmful effects on other organ systems. The importance of this distinctive susceptibility lies in the opportunity it provides for the early detection of dysfunction. From this perspective, it is essential to evolve sensitive psychological methods for studying these states of marginal toxicity. It is argued that a cognitive approach provides the necessary degree of sensitivity and specificity for characterizing these states. Given the growing interest in using cognitive models to assess minor dysfunction in areas outside neurotoxicology, it is further argued that theoretically motivated methods can no longer be considered a luxury for neurotoxicological work. It is concluded that there are at least two advantages to this approach. First, it provides a theoretical framework for organising data. Second, establishing and developing links to substantive areas of cognitive investigation outside neurotoxicology will allow cross-fertilization to occur on a scientific level and provide a more convincing basis for action on a regulatory level.

Behavior↗
PubMedDate not supplied

The Automated Cognitive Test (ACT) system.

The ACT system is a key-press, menu-driven system for selecting, administering, and storing raw data from a series of specially designed psychological tasks. Associated task analysis programs process the raw data and store the resulting summary data for later statistical analysis. The system utilizes a cognitive approach to assessments of marginal toxicity by employing multiple performance parameters to specify a profile of deficits that, on the basis of a task's internal structure, can be related to functionally discrete cognitive systems. The tasks have been developed from a consideration of current cognitive theory and the areas of cognition include those of learning, memory, attention, reasoning, verbal, and spatial abilities. The ACT system is described in terms of its four major components: the cognitive tasks, the stimulus materials, the analysis methods, and the process of saving and combining summary data into files suitable for transfer to statistical analysis programs. The system thus automates the data collection to statistical analysis process.

Cognition↗
PubMed2026

FusionTarget: Computational framework for drug repurposing against modeled fusion protein structures from genomic breakpoints.

Many fusion genes have been recognized as biomarkers and therapeutic targets. However, the lack of knowledge on protein structures and targeting approaches made it challenging to develop effective targeting therapeutics. To fill this, we developed a computational pipeline, FusionTarget, which annotates the genomic DNA breakage to RNA and protein sequences, predicts the 3D structures of fusion proteins, and performs comparative virtual screening, comparative molecular dynamics simulation, and quantitative analyses to identify the fusion protein-selective small molecules by selecting drugs with consistent high-fold binding affinity between fusion and wild-type proteins in multiple isoforms. We applied our pipeline to EWSR1::FLI1 in Ewing sarcoma and KMT2A::AFF1 in infant acute lymphoblastic leukemia. Further cell assay experiments confirmed that cells expressing individual fusion genes were more sensitive to the suggested drugs, and the key downstream genes were affected by our drugs. FusionTarget provides a unique foundation for developing therapeutics targeting fusion proteins.

applied computing in medical science↗
PubMed2004

Can Tai Chi improve vestibulopathic postural control?

OBJECTIVES: To evaluate the rationale and scientific support for Tai Chi as an intervention for vestibulopathy and to offer recommendations for future studies. DATA SOURCES: A computer-aided search, including MEDLINE and Science Citation Index, to identify original Tai Chi studies published in English; relevant references cited in the retrieved articles were also included. STUDY SELECTION: A preliminary screening selected all randomized controlled trials (RCTs), non-RCTs, case-control studies, and case series that included Tai Chi as an intervention and had at least 1 outcome variable relevant to postural stability. DATA EXTRACTION: Authors critically reviewed studies and summarized study designs and outcomes in a summary table. DATA SYNTHESIS: Twenty-four Tai Chi studies met screening criteria. No studies specifically studying Tai Chi for vestibulopathy were found. Collectively, the 24 studies provide sometimes contradictory but generally supportive evidence that Tai Chi may have beneficial effects for balance and postural impairments, especially those associated with aging. Ten RCTs were found, of which 8 provide support that Tai Chi practiced alone, or in combination with other therapies, can reduce risk of falls, and/or impact factors associated with postural control, including improved balance and dynamic stability, increased musculoskeletal strength and flexibility, improved performance of activities of daily living (ADLs), reduced fear of falling, and general improvement in psychologic well-being. Studies using other designs support the results observed in RCTs. CONCLUSIONS: At present, few data exist to support the contention that Tai Chi specifically targets the impairments, functional limitations, disability, and quality of life associated with peripheral vestibulopathy. There are, however, compelling reasons to further investigate Tai Chi for vestibulopathy, in part because Tai Chi appears useful for a variety of nonvestibulopathy etiologic balance disorders, and is safe. Especially needed are studies that integrate measures of balance relevant to ADLs with other psychologic and cognitive measures; these might help identify specific mechanisms whereby Tai Chi can remedy balance disorders.

Humans↗
PubMed2003

Evaluating the use of streaming video to support student learning in a first-year life sciences course for student nurses.

Streaming video was used to support the learning of first year student nurses on a Life Sciences module, as one of many innovations designed to increase the range of resources and support available to students. This paper describes the background to this innovation, the procedures adopted and the results of extensive evaluation. The use of streaming video was evaluated in three applications in the module. A total of 656 students used online directed-learning sessions that incorporated streamed video. Just over half of these students actually viewed the video streams. Their feedback showed that 32% found access easy, 59% enjoyed using the resources, and 25% were very confident that they learned from them. Different types of video were used, and embedded in diverse ways, but the results were consistent across the three applications. They suggest that streamed video can contribute to useful resources to support learning by student nurses but, for a variety of reasons, it may not appeal or be adequately accessible to all students at present.

Biological Science Disciplines↗
PubMed1999

Computerized physiologic monitoring.

Computers can offer significant enhancement to the monitoring of the critically ill. Their value is derived from improved vigilance, better charting, and an opportunity to assess practitioner compliance with unit protocols. However, their true value can only be attained when they are integrated into a total information system.

Computer Systems↗
PubMed2001

Beyond the genome: turning data into knowledge.

Since the publication of the draft sequence of the human genome in April 2001 (1,2), the pressure on life scientists to annotate and gain useful knowledge from the millions of As, Gs, Cs and Ts, is ever increasing. Now that the initial hype has passed, the life sciences field demands the technologies and computer power that can produce and analyze data in a high-throughput manner for drug discovery and disease diagnosis. Cambridge Healthtech Institute's Beyond Genome 2001 conference(1) (17-22 June 2001, San Francisco, CA, USA) brought together the latest research in these technologies in a 'tri-conference' that encompassed the 10th Annual Conference of Bioinformatics and Genome Research, the 3rd Annual Conference of In Silico Biology and the 5th Annual Conference of Proteomics.

Journal Article↗
PubMed2005

A grid-enabled lightweight computational steering client: a .NET PDA implementation.

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world. These grid resources comprise specialized distributed three-dimensional visualization environments through to massive computational systems. The scientist usually accesses these resources from reasonably high-end desktop computers. Even though most modern desktop computers are provided with reasonably powerful three-dimensional graphical hardware, not all scientific applications require high-end three-dimensional visualization because the data of interest is essentially numerical or two-dimensional graphical data. For these applications, a much simpler two-dimensional graphical displays can be used. Since large jobs can take many hours to complete the scientist needs access to a technology that will allow them to still monitor and control their job while away from their desks. This paper describes an effective method of monitoring and controlling a set of chained computer simulations by means of a lightweight steering client based on a small personal digital assistant (PDA). The concept of using a PDA to steer a series of computational jobs across a supercomputing resource may seem strange at first but when scientists realize they can use these devices to connect to their computation wherever there is a wireless network (or cellular phone network) the concept becomes very compelling. Apart from providing a much needed easy-to-use interface, the PDA-based steering client has the benefit of freeing the scientist from the desktop. It is during this monitoring stage that the hand-held PDA client is of particular value as it gives the application scientist greater freedom to leave his or her desk but still communicate with their simulation, with the proviso that they remain within the range of a wireless network.

Computer Graphics↗
PubMed2005

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids.

During the last 2.5 years, the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational Grids. Since smoothly working production Grids are not yet available, we have been able to substantially influence the direction of software and Grid deployment within the project. In this paper, we review our results from large-scale three-dimensional lattice Boltzmann simulations performed over the last 2.5 years. We describe how the proactive use of computational steering, and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organization of liquid cubic mesophases.

Computer Graphics↗
PubMed2003

Interaction potentials for soft and hard ellipsoids.

Using results from colloid science we derive interaction potentials for computer simulations of mixtures of soft or hard ellipsoids of arbitrary shape and size. Our results are in many respects reminicent of potentials of the Gay-Berne type but have a well-defined microscopic interpretation and no adjustable parameters. Since our potentials require the calculation of similar variables, the modification of existing simulation codes for Gay-Berne potentials is straightforward. The computational performance should remain unaffected.

Journal Article↗