Supercomputer docking with a large number of degrees of freedom.

Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful in prediction of compound activity. Despite many success stories, there are challenges, in particular, handling with a large number of degrees of freedom in solving the docking problem. Here, we show that SOL-P, the docking program based on the new Tensor Train algorithm, is capable to dock successfully oligopeptides having up to 25 torsions. To make the study comparative we have performed docking of the same oligopeptides with the SOL program which uses the same force field as that utilized by SOL-P and has common features of many docking programs: the genetic algorithm of the global optimization and the grid approximation. SOL has managed to dock only one oligopeptide. Moreover, we present the results of docking with SOL-P ligands into proteins with moveable atoms. Relying on visual observations we have determined the common protein atom groups displaced after docking which seem to be crucial for successful prediction of experimental conformations of ligands.

A brief history of liquid computers.

A substrate does not have to be solid to compute. It is possible to make a computer purely from a liquid. I demonstrate this using a variety of experimental prototypes where a liquid carries signals, actuates mechanical computing devices and hosts chemical reactions. We show hydraulic mathematical machines that compute functions based on mass transfer analogies. I discuss several prototypes of computing devices that employ fluid flows and jets. They are fluid mappers, where the fluid flow explores a geometrically constrained space to find an optimal way around, e.g. the shortest path in a maze, and fluid logic devices where fluid jet streams interact at the junctions of inlets and results of the computation are represented by fluid jets at selected outlets. Fluid mappers and fluidic logic devices compute continuously valued functions albeit discretized. There is also an opportunity to do discrete operation directly by representing information by droplets and liquid marbles (droplets coated by hydrophobic powder). There, computation is implemented at the sites, in time and space, where droplets collide one with another. The liquid computers mentioned above use liquid as signal carrier or actuator: the exact nature of the liquid is not that important. What is inside the liquid becomes crucial when reaction-diffusion liquid-phase computing devices come into play: there, the liquid hosts families of chemical species that interact with each other in a massive-parallel fashion. I shall illustrate a range of computational tasks, including computational geometry, implementable by excitation wave fronts in nonlinear active chemical medium. The overview will enable scientists and engineers to understand how vast is the variety of liquid computers and will inspire them to design their own experimental laboratory prototypes. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Medical Devices; Hematology and Pathology Devices; Classification of Blood Establishment Computer Software and Accessories. Final rule.

The Food and Drug Administration (FDA, Agency, or we) is issuing a final rule to classify blood establishment computer software (BECS) and BECS accessories (regulated under product code MMH) into class II (special controls). FDA has identified special controls for BECS and BECS accessories that are necessary to provide a reasonable assurance of safety and effectiveness. FDA is also giving notice that the Agency does not intend to exempt BECS and BECS accessories from premarket notification requirements of the Federal Food, Drug, and Cosmetic Act (FD&C Act).

User settings on dive computers: reliability in aiding conservative diving.

INTRODUCTION: Divers can make adjustments to diving computers when they may need or want to dive more conservatively (e.g., diving with a persistent (patent) foramen ovale). Information describing the effects of these alterations or how they compare to other methods, such as using enriched air nitrox (EANx) with air dive planning tools, is lacking. METHODS: Seven models of dive computer from four manufacturers (Mares, Suunto, Oceanic and UWATEC) were subjected to single square-wave compression profiles (maximum depth: 20 or 40 metres' sea water, msw), single multi-level profiles (maximum depth: 30 msw; stops at 15 and 6 msw), and multi-dive series (two dives to 30 msw followed by one to 20 msw). Adjustable settings were employed for each dive profile; some modified profiles were compared against stand-alone use of EANx. RESULTS: Dives were shorter or indicated longer decompression obligations when conservative settings were applied. However, some computers in default settings produced more conservative dives than others that had been modified. Some computer-generated penalties were greater than when using EANx alone, particularly at partial pressures of oxygen (PO2) below 1.40 bar. Some computers 'locked out' during the multi-dive series; others would continue to support decompression with, in some cases, automatically-reduced levels of conservatism. Changing reduced gradient bubble model values on Suunto computers produced few differences. DISCUSSION: The range of possible adjustments and the non-standard computer response to them complicates the ability to provide accurate guidance to divers wanting to dive more conservatively. The use of EANx alone may not always generate satisfactory levels of conservatism.

Consejos y trucos en OsiriX / Tips and tricks in OsiriX

No disponible

[HYGIENIC REGULATION OF THE USE OF ELECTRONIC EDUCATIONAL RESOURCES IN THE MODERN SCHOOL].

We studied the effect of academic studies with the use a notebook computer and interactive whiteboard on the functional state of an organism of schoolchildren. Using a complex of hygienic and physiological methods of the study we established that regulation of the computer activity of students must take into account not only duration but its intensity either. Design features of a notebook computer were shown both to impede keeping the optimal working posture in primary school children and increase the risk offormation of disorders of vision and musculoskeletal system. There were established the activating influence of the interactive whiteboard on performance activities and favorable dynamics of indices of the functional state of the organism of students under keeping optimal density of the academic study and the duration of its use. There are determined safety regulations of the work of schoolchildren with electronic resources in the educational process.

Practicing evidence based medicine at the bedside: a randomized controlled pilot study in undergraduate medical students assessing the practicality of tablets, smartphones, and computers in clinical life.

BACKGROUND: Practicing evidence-based medicine is an important aspect of providing good medical care. Accessing external information through literature searches on computer-based systems can effectively achieve integration in clinical care. We conducted a pilot study using smartphones, tablets, and stationary computers as search devices at the bedside. The objective was to determine possible differences between the various devices and assess students' internet use habits. METHODS: In a randomized controlled pilot study, 120 students were divided in three groups. One control group solved clinical problems on a computer and two intervention groups used mobile devices at the bedside. In a questionnaire, students were asked to report their internet use habits as well as their satisfaction with their respective search tool using a 5-point Likert scale. RESULTS: Of 120 surveys, 94 (78.3%) complete data sets were analyzed. The mobility of the tablet (3.90) and the smartphone (4.39) was seen as a significant advantage over the computer (2.38, p < .001). However, for performing an effective literature search at the bedside, the computer (3.22) was rated superior to both tablet computers (2.13) and smartphones (1.68). No significant differences were detected between tablets and smartphones except satisfaction with screen size (tablet 4.10, smartphone 2.00, p < .001). CONCLUSIONS: Using a mobile device at the bedside to perform an extensive search is not suitable for students who prefer using computers. However, mobility is regarded as a substantial advantage, and therefore future applications might facilitate quick and simple searches at the bedside.

Pharmacist computer skills and needs assessment survey.

BACKGROUND: To use technology effectively for the advancement of patient care, pharmacists must possess a variety of computer skills. We recently introduced a novel applied informatics program in this Canadian hospital clinical service unit to enhance the informatics skills of our members. OBJECTIVE: This study was conducted to gain a better understanding of the baseline computer skills and needs of our hospital pharmacists immediately prior to the implementation of an applied informatics program. METHODS: In May 2001, an 84-question written survey was distributed by mail to 106 practicing hospital pharmacists in our multi-site, 1500-bed, acute-adult-tertiary care Canadian teaching hospital in Vancouver, British Columbia. RESULTS: Fifty-eight surveys (55% of total) were returned within the two-week study period. The survey responses reflected the opinions of licensed BSc and PharmD hospital pharmacists with a broad range of pharmacy practice experience. Most respondents had home access to personal computers, and regularly used computers in the work environment for drug distribution, information management, and communication purposes. Few respondents reported experience with handheld computers. Software use experience varied according to application. Although patient-care information software and e-mail were commonly used, experience with spreadsheet, statistical, and presentation software was negligible. The respondents were familiar with Internet search engines, and these were reported to be the most common method of seeking clinical information online. Although many respondents rated themselves as being generally computer literate and not particularly anxious about using computers, the majority believed they required more training to reach their desired level of computer literacy. Lack of familiarity with computer-related terms was prevalent. Self-reported basic computer skill was typically at a moderate level, and varied depending on the task. Specifically, respondents rated their ability to manipulate files, use software help features, and install software as low, but rated their ability to access and navigate the Internet as high. Respondents were generally aware of what online resources were available to them and Clinical Pharmacology was the most commonly employed reference. In terms of anticipated needs, most pharmacists believed they needed to upgrade their computer skills. Medical database and Internet searching skills were identified as those in greatest need of improvement. CONCLUSIONS: Most pharmacists believed they needed to upgrade their computer skills. Medical database and Internet searching skills were identified as those in greatest need of improvement for the purposes of improving practice effectiveness.

A tool for software and hardware evaluation.

The proliferation of information technology has enormously eased the burden of computing for medical users. However, it has also created a confusing, difficult problem in evaluation and selection of appropriate software and hardware components. This paper presents an easy to use software tool based on Anderson's Ranking Methodology implemented in Excel 5 that enables one an objective evaluation and selection.

[Computerized planning of radiotherapy]. / Sistema kompíuternogo planirovaniia luchevoi terapii.

The hypophysis was studied by MR tomography in 148 patients with the most prevalent diseases of the hypothalamohypophyseal system and in 13 ones with primary hypothyrosis. The findings evidence a great variety of changes in the MRT picture in the examinees. The method permits a reliable diagnosis of hypophyseal macroadenoma and of an 'empty' sella turcica. Qualitative and quantitative criteria for MRT diagnosis of these conditions are suggested. The diagnostic value of MRT for the detection of macroadenomas is still to be researched. The method was effectively used for a dynamic follow-up of the hypophyseal status in the course of pathogenetic therapy; the formation of an 'empty' sella turcica is possible against the background of dopamine agonist therapy and substitution therapy of primary hypothyrosis.

Selecting a processor for computations in molecular biophysics.

A number of relatively low-cost processors are now available which employ architectural features previously found only on very expensive supercomputers. The speed of these computers makes it possible to reduce the time to solution of certain problems and to resolve large problems that previously were too time consuming to perform locally. A brief overview of this type of processor is given and the implications for computations in molecular biophysics are discussed in reference to the results of a benchmark that uses the refinement of a protein structure from X-ray crystallographic data.