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PubMed2000

Molecular modelling and drug design.

Drug design is a creative act of the same magnitude as composing, sculpting, or writing. The results can touch the lives of millions, but the creator is rarely one scientist and the rewards are distributed differently in the arts than in the sciences. The mechanisms of creativity are the same, i.e., incremental (plodding from darkness to dawn) or sudden (the "Eureka" effect) realization, but both are poorly understood. Creativity remains a human characteristic, but it is directly related to the tools available, especially computer software and hardware. While modelling software continues to mature, very little new has evolved in terms of hardware. Here, we discuss the history of molecular modelling and describe two novel modelling tools, a haptic device and a program, SCULPT, to generate solid molecular models at atomic resolution.

Databases, Factual↗
PubMed2002

VERIDOS: a new tool for quality assurance for intensity modulated radiotherapy.

BACKGROUND: The use of intensity modulated radiation fields needs an extended quality assurance concept. This consists of a linac related part and a case related part. Case related means the verification of an individual treatment plan, optimized on a CT data set of an individual patient and prepared for the treatment of this patient. This part of the quality assurance work is usually time consuming, delivers only partially quantitative results and is uncomfortable without additional help. It will be shown in this paper how the software VERIDOS will improve the optimization of the case related part of the quality assurance work. MATERIAL AND METHODS: The main function of the software is the quantitative comparison of the calculated dose distribution from the treatment planning software with the measured dose distribution of an irradiated phantom. Several additional functions will be explained. Two self-developed phantoms made of RW3 (solid water) and GAFCHROMIC films or Kodak EDR2 films for the measurement of the dose distributions were used. VERIDOS was tested with the treatment planning systems Helay-TMS and Brainscan. RESULTS: VERIDOS is a suitable tool for the import of calculated dose matrices from the treatment planning systems Helax-TMS and Brainscan and of measured dose matrices exported from the dosimetry software Mephysto (PTW). The import from other treatment planning systems and scanning software applications for film dosimetry is generally possible. In such case the import function has to be adapted to the special header of the import matrix. All other functions of this software tool like normalization (automatically, manually), working with corrections (ground substraction, factors), overlay/comparison of dose distributions, difference matrix, cutting function (profiles) and export functions work reliable. CONCLUSIONS: VERIDOS improves the optimization of the case related part of the quality assurance work for intensity modulated radiation therapy (IMRT). The diverse functions of the software offer the radiation physicist a wide base to verify the IMRT plan independent from the mode of its delivery (compensator technology or MLC technology).

Dose Fractionation, Radiation↗
PubMed2003

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics.

Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/.

Alleles↗
PubMed2003

probeBase: an online resource for rRNA-targeted oligonucleotide probes.

Ribosomal RNA-(rRNA)-targeted oligonucleotide probes are widely used for culture-independent identification of microorganisms in environmental and clinical samples. ProbeBase is a comprehensive database containing more than 700 published rRNA-targeted oligonucleotide probe sequences (status August 2002) with supporting bibliographic and biological annotation that can be accessed through the internet at http://www.probebase.net. Each oligonucleotide probe entry contains information on target organisms, target molecule (small- or large-subunit rRNA) and position, G+C content, predicted melting temperature, molecular weight, necessity of competitor probes, and the reference that originally described the oligonucleotide probe, including a link to the respective abstract at PubMed. In addition, probes successfully used for fluorescence in situ hybridization (FISH) are highlighted and the recommended hybridization conditions are listed. ProbeBase also offers difference alignments for 16S rRNA-targeted probes by using the probe match tool of the ARB software and the latest small-subunit rRNA ARB database (release June 2002). The option to directly submit probe sequences to the probe match tool of the Ribosomal Database Project II (RDP-II) further allows one to extract supplementary information on probe specificities. The two main features of probeBase, 'search probeBase' and 'find probe set', help researchers to find suitable, published oligonucleotide probes for microorganisms of interest or for rRNA gene sequences submitted by the user. Furthermore, the 'search target site' option provides guidance for the development of new FISH probes.

Base Sequence↗
PubMed1988

Use of computers in dysmorphology.

As a consequence of the increasing power and decreasing cost of digital computers, dysmorphologists have begun to explore a wide variety of computerised applications in clinical genetics. Of considerable interest are developments in the areas of syndrome databases, expert systems, literature searches, image processing, and pattern recognition. Each of these areas is reviewed from the perspective of the underlying computer principles, existing applications, and the potential for future developments. Particular emphasis is placed on the analysis of the tasks performed by the dysmorphologist and the design of appropriate tools to facilitate these tasks. In this context the computer and associated software are considered paradigmatically as tools for the dysmorphologist and should be designed accordingly. Continuing improvements in the ability of computers to manipulate vast amounts of data rapidly makes the development of increasingly powerful tools for the dysmorphologist highly probable.

Computers↗
PubMed2004

FlexX-Scan: fast, structure-based virtual screening.

We present a new software module, FlexX-Scan, for high-throughput, structure-based virtual screening. FlexX-Scan was developed with the aim to further speed up the virtual screening process. Based on the incremental construction docking tool FlexX (Rarey et al., J Mol Biol 1996;261:470-489), a compact descriptor for representing favorable protein interaction spots within the protein binding site has been developed. The descriptor is calculated using special-purpose clustering techniques applied to the usual interaction points created by FlexX. The algorithm automatically detects a small set of interaction spots in the binding site for positioning ligand functional groups. The parametrizations of the base placement and incremental construction algorithms have been adapted to the new interaction model. We tested the software tool on a diverse set of 200 protein-ligand complexes from the protein database (PDB) (Kramer et al., Proteins 1999;37:228-241). On average, the algorithm proposes about 90 interaction spots per binding site compared to about 1000 interaction dots in FlexX. We observe that the docking solutions of FlexX-Scan have a root-mean-square deviation from the crystal structure similar to the deviation of docking solutions of standard FlexX. For further validation we also performed virtual screening experiments for cyclin-dependent kinase 2, thrombin, angiotensin-converting enzyme, and dihydrofolat reductase. In these experiments, we screened a set of 34,000 random compounds and a number of known actives for each target. With FlexX-Scan, we achieved comparable enrichments to standard FlexX, with an averaged computing time of 5-10 s per compound, depending on parametrization.

Algorithms↗
PubMed2006

Sources of error in computerized neuropsychological assessment.

Computerized neuropsychological assessment has integrated slowly into research and practice since the introduction of the personal computer. Though initial integration of technology to the laboratory and clinical setting utilized specialized hardware and software, newer generation assessment tools are integrated with "off-the-shelf" operating systems. Further, neuropsychological assessment is beginning to find Internet-based application for remote assessment. As these applications are more broadly applied, it is essential to understand potential errors that can be created both in test administration and in reaction time measurement due to hardware and software interactions. In this article, user considerations are specifically addressed for resident and Internet-enabled assessment software. Potential hardware and software conflicts are defined and potential remediation is suggested. Computerized assessment is a valuable tool for neuropsychologists as long as it is used responsibly with an understanding of the potential technical complications.

Diagnosis, Computer-Assisted↗
PubMed2004

REDCAT: a residual dipolar coupling analysis tool.

Recent advancements in the utilization of residual dipolar couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT's algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.

Algorithms↗
PubMed2006

Applying FSL to the FIAC data: model-based and model-free analysis of voice and sentence repetition priming.

This article presents results obtained from applying various tools from FSL (FMRIB Software Library) to data from the repetition priming experiment used for the HBM'05 Functional Image Analysis Contest. We present analyses from the model-based General Linear Model (GLM) tool (FEAT) and from the model-free independent component analysis tool (MELODIC). We also discuss the application of tools for the correction of image distortions prior to the statistical analysis and the utility of recent advances in functional magnetic resonance imaging (FMRI) time series modeling and inference such as the use of optimal constrained HRF basis function modeling and mixture modeling inference. The combination of hemodynamic response function (HRF) and mixture modeling, in particular, revealed that both sentence content and speaker voice priming effects occurred bilaterally along the length of the superior temporal sulcus (STS). These results suggest that both are processed in a single underlying system without any significant asymmetries for content vs. voice processing.

Brain Mapping↗
PubMed1990

Computer-assisted analysis of transrectal ultrasound images.

We have developed a microcomputer based system with an application specific software package which permits the direct digitization and analysis of transrectal ultrasound (TRUS) images. The system is highly flexible and enables access to a wide range of image analysis tools through relatively simple software modifications, which cannot be implemented using a standard ultrasound instrument. We have demonstrated the capability of the system by an analysis of a number of morphometric parameters and by a correlation of these measurements with the presence of prostatic cancer. We found that the measurement of the ratio of the anterior-posterior axis to transverse axis and the presumed circular area ratio (PCAR) were significant predictors of prostatic cancer. The sensitivity of the PCAR measurement was 93%, the specificity was 50%, the positive predictive value was 57%, and the negative predictive value was 91%. The high negative predictive values of these parameters may provide objective criteria to allow for selective biopsy of patients. This system provides researchers with an efficient, economical, and flexible method to aid in the analysis of TRUS images in a quantitative manner.

Humans↗
PubMed1986

Computer software for the professional. Its evolution and current status.

The development of software during the past 30 years has been just as dramatic in many respects as that of hardware. Whereas future developments in hardware technology can be expected to provide smaller, cheaper, and more powerful computers as has been the case during the past 25 years, future developments in software technology can be expected to play the equally important role of expanding the user base for computers, thus making it economically feasible to exploit new technologies on the hardware side. Although today's computer software offerings are very broad indeed in terms of the variety of tasks they perform, one can reasonably expect that entirely new uses will be found for computers, through the development of new types of software, in the future. By exploiting the huge memory capacities of today's newer computers, future software will be much easier to use and will be capable of carrying out several tasks simultaneously. It will also be much more forgiving, adapting itself automatically to the work style (and probably also to the mistakes) of the user. By incorporating at least a part of what constitutes the stock of knowledge in particular applications, so-called "expert systems," one may expect future software, particularly in areas such as financial and statistical analysis, to enable the computer to work more as a partner or colleague than as an unintelligent (albeit very fast) tool. Perhaps to an even greater extent in the future than has been true to date, the evolution of the computer as a useful tool will depend on software, rather than hardware, innovation. The hardware advances necessary to place hearing, speaking, seeing, and even thinking computers on everyone's desktop, each of which would be able to provide ready access to truly mind-boggling quantities of information, is at hand. Only the software really remains to be developed.

Computers↗
PubMedDate not supplied

A flexible and stable numerical method for simulating the thermal decomposition of wood particles.

The objective of this paper is to present a flexible and stable simulation method to predict the thermal conversion of wood particles. A combination of several subprocesses such as heating-up, drying, pyrolysis, gasification and combustion of fuel particles of different properties and sizes represents the global process of thermal conversion. This approach allows for simultaneous processes e.g. reactions in time and covers the entire range between transport-limited (shrinking core) and kinetically limited (reacting core) reaction regimes. Thus, the model is applicable to simulate sufficiently accurate the thermal decomposition of each particle in a packed bed, of which the entire conversion is regarded as the sum of all particle processes. Effects such as fragmentation, swelling, homogeneous reactions e.g. ignition outside a particle are excluded as a tradeoff between complexity and calculation time. However, a description of the particle processes by one-dimensional and transient differential conservation equations for mass and energy is feasible to represent the above mentioned subprocesses. The particles are coupled to the gas phase by heat and mass transfer taking into account the Stefan correction due to the gas outflow during conversion. A general formulation of the conservation equations allows the geometry of a fuel particle to be treated as a plate, cylinder or sphere. In order to achieve a high degree of flexibility, the method distinguishes between data, such as kinetics or material properties and the conversion process, for which relevant data are stored in a data base for easy access and extension. The resulting modules of this subdivision are encapsulated into separate software units cast in a hierarchy of well-defined classes in Tools of Object-oriented Software for Continuum-Mechanics Applications (TOSCA) by object-oriented techniques.

Journal Article↗
PubMedDate not supplied

Computer-based tutorial in MR imaging.

PURPOSE: To test the effectiveness of customized software as a teaching tool to help the novice understand basic physics concepts underlying the creation of MR images via various pulse sequences. METHODS: The authors have developed animating graphic and highly interactive electronic MR audiovisual software for the Macintosh computer in the C programming language, and have integrated it into the classroom setting for teaching MR imaging physics concepts such as T1, T2, T2*, proton density, RF excitation, TR, TE, TI, flip angle, static magnetic field strength, gradient magnetic fields, section thickness, number of phase-encoding gradients, number of excitations, field of view, intersection gap, receiver bandwidth, contrast agent(s), etc. The program interactively demonstrates the effects of these variables upon such imaging objectives as voxel dimensions, section quantity, total scanned volume, signal-to-noise ratio, contrast, contrast-to-noise ratios, resolving power, and scan acquisition time. Partial saturation, gradient echo, inversion recovery, and fat-saturation imaging techniques are included. Written posttests on the syllabus covered in our basic MR course were administered to three groups: 43 student professionals (technologist/physicist/radiologist) (control professional group) before, 149 student professionals (exposed professional group) after the addition of the tutorial software into the MR course as an integral part of the teaching process, and a group of 200 pharmaceutical sales staff with little to no prior MR or scientific background (exposed pharmaceutical group). The scores were then evaluated and compared among the groups. One hundred ten students exposed to this software also anonymously rated the software on a 1 to 5 scale (harmful to very helpful, respectively) as to their feeling regarding its role in their MR educational experience and the ease with which they were able to understand the material covered in the basic MR course curriculum. RESULTS: Mean test scores were statistically significantly lower in the Control Professional Group (60%, +/- 2.59 standard error of the mean (SEM)) than in either the Exposed Pharmaceutical (73% +/- 0.75 SEM) or Exposed Professional Groups (77% +/- 0.99 SEM). The mean subjective assessment score regarding the software was 4.8 (scale 1 to 5). CONCLUSION: This custom-developed interactive MR tutorial software is demonstrated to be effective in assisting even those new to MR imaging in understanding the concepts underlying MR imaging physics in a manner that is felt to be significantly more palatable than lectures, articles, and/or textbooks alone.

Computer-Assisted Instruction↗
PubMed2004

4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin - poor tracks.

BACKGROUND: The dynamics of nuclear organization, nuclear bodies and RNPs in particular has been the focus of many studies. To understand their function, knowledge of their spatial nuclear position and temporal translocation is essential. Typically, such studies generate a wealth of data that require novel methods in image analysis and computational tools to quantitatively track particle movement on the background of moving cells and shape changing nuclei. RESULTS: We developed a novel 4-D image processing platform (TIKAL) for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software. With this new tool, we studied the dynamics of two different types of nuclear particles, namely nuclear bodies made from GFP-NLS-vimentin and microinjected 0.1 mum - wide polystyrene beads, by live cell time-lapse microscopy combined with single particle tracking and mobility analysis. We now provide a tool for the automatic 3-D analysis of particle movement in parallel with the acquisition of chromatin density data. CONCLUSIONS: Kinetic analysis revealed 4 modes of movement: confined obstructed, normal diffusion and directed motion. Particle tracking on the background of stained chromatin revealed that particle movement is directly related to local reorganization of chromatin. Further a direct comparison of particle movement in the nucleoplasm and the cytoplasm exhibited an entirely different kinetic behaviour of vimentin particles in both compartments. The kinetics of nuclear particles were slightly affected by depletion of ATP and significantly disturbed by disruption of actin and microtubule networks. Moreover, the hydration state of the nucleus had a strong impact on the mobility of nuclear bodies since both normal diffusion and directed motion were entirely abolished when cells were challenged with 0.6 M sorbitol. This effect correlated with the compaction of chromatin. We conclude that alteration in chromatin density directly influences the mobility of protein assemblies within the nucleus.

Adenosine Triphosphate↗
PubMed2005

Automated software supported versus manual aorto-iliac diameter measurements in CT angiography of patients with abdominal aortic aneurysms: assessment of inter- and intraobserver variation.

BACKGROUND: Open surgical or endovascular abdominal aortic aneurysm (AAA) relies on precise preprocedual imaging. Purpose of this study was to assess inter- and intraobserver variation of software-supported automated and manual multi row detector CT angiography (MDCTA) in aortoiliac diameter measurements before AAA repair. PATIENTS AND METHODS: Thirty original MDCTA data sets (4 x 2mm collimation) of patients scheduled for endovascular AAA repair were studied on a dedicated software capable of creating two-dimensional reformatted planes orthogonal to the aortoiliac center-line. Measurements were performed twice with afour-week interval between readings. Data were analysed by two blinded readers at random order Two different measurement methods were performed: reader-assisted freehand wall-to-wall measurement and semi-automatic measurement. RESULTS: Aortoiliac diameters were significantly underestimated by the semi-automatic method as compared to reader-assisted measurements (p < 0.0031). Intraobserver variability of AAA diameter calculation was not significant (p > 0. 15) for reader-assisted measurements except for the diameter of the left common iliac artery in reader 2 (p = 0.0045) and it was not significant (p > 0. 14) using the semi-automatic method. Interobserver variability was not significant for AAA diameter measurements using the reader-assisted method and for proximal neck analysis with the semiautomatic method (p > 0.27). Relevant interobserver variation was observed for semi-automatic measurement of maximum AAA (p = 0.0007) and iliac artery diameters (p = 0.024). CONCLUSIONS: Dedicated MDCTA software provides a useful tool to minimize aortoiliac diameter measurement variation and to improve imaging precision before AAA repair. For reliable AAA diameter analysis the reader-assisted freehand measurement method is recommended to be applied to a set of reformatted CT data as provided by the software used in this study.

Aged↗
PubMed1997

Early detection of visual field progression in glaucoma: a comparison of PROGRESSOR and STATPAC 2.

AIM: To compare the performance of PROGRESSOR (pointwise linear regression) and STATPAC 2 (comparison with baseline values) in detecting early deterioration in the visual fields of glaucoma patients. METHODS: Visual field series from 19 untreated normal tension glaucoma eyes which were deteriorating on clinical grounds were analysed by PROGRESSOR and STATPAC 2. Progression criteria for PROGRESSOR were (1) inner points: slope < -1 dB/year, p < 0.05 and (2) edge points: slope < -2 dB/year, p < 0.05. Criteria for STATPAC 2 were p < 0.05 change probability for any point on three consecutive fields. Detection time was defined as the time interval between the initial field and the first field in which at least one progressing point was identified. Detection times produced by the two techniques were compared. RESULTS: PROGRESSOR and STATPAC 2 agreed on progression in all 19 eyes. Mean detection time for PROGRESSOR was 1.077 (SD 0.985) years and for STATPAC 2 was 2.161 (1.357) years. PROGRESSOR detected progression sooner than STATPAC 2 in 18 eyes (p < 0.01), Wilcoxon matched pairs signed rank test). PROGRESSOR detected progression earlier by a mean of 1.085 (0.936) years. CONCLUSIONS: PROGRESSOR consistently detected progression earlier than STATPAC 2. The PROGRESSOR software is a useful tool for the early detection of visual field deterioration in glaucoma.

Algorithms↗
PubMed2002

A simple, spreadsheet-based, food safety risk assessment tool.

The development and use of a simple tool for food safety risk assessment is described. The tool is in spreadsheet software format and embodies established principles of food safety risk assessment, i.e., the combination of probability of exposure to a food-borne hazard, the magnitude of hazard in a food when present, and the probability and severity of outcomes that might arise from that level and frequency of exposure. The tool requires the user to select from qualitative statements and/or to provide quantitative data concerning factors that that will affect the food safety risk to a specific population, arising from a specific food product and specific hazard, during the steps from harvest to consumption. The spreadsheet converts the qualitative inputs into numerical values and combines them with the quantitative inputs in a series of mathematical and logical steps using standard spreadsheet functions. Those calculations are used to generate indices of the public health risk. Shortcomings of the approach are discussed, including the simplifications and assumptions inherent in the mathematical model, the inadequacy of data currently available, and the lack of consideration of variability and uncertainty in the inputs and outputs of the model. Possible improvements are suggested. The model underpinning the tool is a simplification of the harvest to consumption pathway, but the tool offers a quick and simple means of comparing food-borne risks from diverse products, and has utility for ranking and prioritising risks from diverse sources. It can be used to screen food-borne risks and identify those requiring more rigorous assessment. It also serves as an aid to structured problem solving and can help to focus attention on those factors in food production, processing, distribution and meal preparation that most affect food safety risk, and that may be the most appropriate targets for risk management strategies.

Food Contamination↗