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PubMed2003

Automated crystallographic system for high-throughput protein structure determination.

High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.

Automation↗
PubMed1997

Three-dimensional finite-difference bidomain modeling of homogeneous cardiac tissue on a data-parallel computer.

In this paper, a data-parallel computer is used to provide the memory and reduction in computer time for solving large finite-difference bidomain problems. The finite-difference grid is mapped effectively to the processors of the parallel computer, simply by mapping one node to one (virtual) processor. Implemented on the connection machines (CM's) CM-200 and CM-5, the data-parallel finite-difference algorithm has allowed the solution of finite-difference bidomain problems with over 2 million nodes. Details on the algorithm are presented together with computational performance results.

Algorithms↗
PubMed2002

Model intestinal microflora in computer simulation: a simulation and modeling package for host-microflora interactions.

The ecology of the human intestinal microflora and its interaction with the host are poorly understood. Though more and more data are being acquired, in part using modern molecular methods, development of a quantitative theory has not kept pace with this increase in observing power. This is in part due to the complexity of the system and to the lack of simulation environments in which to test what the ecological effect of a hypothetical mechanism of interaction would be, before resorting to laboratory experiments. The MIMICS project attempts to address this through the development of a cellular automaton for simulation of the intestinal microflora. In this paper, the design and evaluation of this simulator is discussed.

Bacteria, Aerobic↗
PubMed2004

Simulation of QRST integral maps with a membrane-based computer heart model employing parallel processing.

The simulation of the propagation of electrical activity in a membrane-based realistic-geometry computer model of the ventricles of the human heart, using the governing monodomain reaction-diffusion equation, is described. Each model point is represented by the phase 1 Luo-Rudy membrane model, modified to represent human action potentials. A separate longer duration action potential was used for the M cells found in the ventricular midwall. Cardiac fiber rotation across the ventricular wall was implemented via an analytic equation, resulting in a spatially varying anisotropic conductivity tensor and, consequently, anisotropic propagation. Since the model comprises approximately 12.5 million points, parallel processing on a multiprocessor computer was used to cut down on simulation time. The simulation of normal activation as well as that of ectopic beats is described. The hypothesis that in situ electrotonic coupling in the myocardium can diminish the gradients of action-potential duration across the ventricular wall was also verified in the model simulations. Finally, the sensitivity of QRST integral maps to local alterations in action-potential duration was investigated.

Action Potentials↗
PubMed2003

Parallel pattern identification in biological sequences on clusters.

Tandem repeats are ubiquitous sequence features in both prokaryotic and eukaryotic genomes. They are known to cause several inherited neurological diseases in humans. Identifying these patterns is a highly computation-intensive process. Previous parallel implementations use straightforward domain decomposition based on existing sequential algorithms and rely on parallel machines with low-latency interconnection network and fast hardware support for processor synchronization. Our research exploits the superior cost effectiveness and flexibility achieved through low-cost clusters to speed up biological computations by designing communication-efficient parallel algorithms for pattern identification. This paper presents a low communication-overhead parallel algorithm for pattern identification in biological sequences. Given a biological sequence of length n and a pattern of length m, we conclude an algorithm with five computation/communication phases, each requiring O(n) computation time and only O(p) message units. The low communication overhead of the algorithm is essential in achieving reasonable speedups on clusters, where the inter-processor communication latency is usually higher.

Algorithms↗
PubMed2005

Cellular automata with object-oriented features for parallel molecular network modeling.

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

Algorithms↗
PubMed2004

An efficient method for computing leave-one-out error in support vector machines with Gaussian kernels.

In this paper, we give an efficient method for computing the leave-one-out (LOO) error for support vector machines (SVMs) with Gaussian kernels quite accurately. It is particularly suitable for iterative decomposition methods of solving SVMs. The importance of various steps of the method is illustrated in detail by showing the performance on six benchmark datasets. The new method often leads to speedups of 10-50 times compared to standard LOO error computation. It has good promise for use in hyperparameter tuning and model comparison

Computing Methodologies↗
PubMed2004

On the retranslation process in Zadeh's paradigm of computing with words.

We discuss Zadeh's paradigm of computing with words and indicate the three important stages. We focus on the retranslation process, selecting a term from our prescribed vocabulary to express information represented using fuzzy sets. A number of criteria of concern in this retranslation process are introduced. Some of these criteria can be seen to correspond to a desire to accurately reflect the given information. Other criteria may correspond to a desire, on the part of the provider of the information, to give a particular perception or "spin." These types of criteria can be of particular importance in many types of information warfare. We discuss some methods for combining these criteria to evaluate potential retranslations.

Algorithms↗
PubMed2004

Enhancing prototype reduction schemes with recursion: a method applicable for "large" data sets.

Most of the prototype reduction schemes (PRS), which have been reported in the literature, process the data in its entirety to yield a subset of prototypes that are useful in nearest-neighbor-like classification. Foremost among these are the prototypes for nearest neighbor classifiers, the vector quantization technique, and the support vector machines. These methods suffer from a major disadvantage, namely, that of the excessive computational burden encountered by processing all the data. In this paper, we suggest a recursive and computationally superior mechanism referred to as adaptive recursive partitioning (ARP)_PRS. Rather than process all the data using a PRS, we propose that the data be recursively subdivided into smaller subsets. This recursive subdivision can be arbitrary, and need not utilize any underlying clustering philosophy. The advantage of ARP_PRS is that the PRS processes subsets of data points that effectively sample the entire space to yield smaller subsets of prototypes. These prototypes are then, in turn, gathered and processed by the PRS to yield more refined prototypes. In this manner, prototypes which are in the interior of the Voronoi spaces, and thus ineffective in the classification, are eliminated at the subsequent invocations of the PRS. We are unaware of any PRS that employs such a recursive philosophy. Although we marginally forfeit accuracy in return for computational efficiency, our experimental results demonstrate that the proposed recursive mechanism yields classification comparable to the best reported prototype condensation schemes reported to-date. Indeed, this is true for both artificial data sets and for samples involving real-life data sets. The results especially demonstrate that a fair computational advantage can be obtained by using such a recursive strategy for "large" data sets, such as those involved in data mining and text categorization applications.

Algorithms↗
PubMed2004

Parallel and distributed methods for incremental frequent itemset mining.

Traditional methods for data mining typically make the assumption that the data is centralized, memory-resident, and static. This assumption is no longer tenable. Such methods waste computational and input/output (I/O) resources when data is dynamic, and they impose excessive communication overhead when data is distributed. Efficient implementation of incremental data mining methods is, thus, becoming crucial for ensuring system scalability and facilitating knowledge discovery when data is dynamic and distributed. In this paper, we address this issue in the context of the important task of frequent itemset mining. We first present an efficient algorithm which dynamically maintains the required information even in the presence of data updates without examining the entire dataset. We then show how to parallelize this incremental algorithm. We also propose a distributed asynchronous algorithm, which imposes minimal communication overhead for mining distributed dynamic datasets. Our distributed approach is capable of generating local models (in which each site has a summary of its own database) as well as the global model of frequent itemsets (in which all sites have a summary of the entire database). This ability permits our approach not only to generate frequent itemsets, but also to generate high-contrast frequent itemsets, which allows one to examine how the data is skewed over different sites.

Algorithms↗
PubMed2005

Recent findings with computerized methods for scalp hair growth measurements.

Sensitive tools have been developed in order to monitor hair loss and treatment responses. Recently the Tricho-Scan was presented (by RH) as such a method which combines epiluminescence microscopy (ELM) with automatic digital image analysis. Herewith new TrichoScan data obtained from 10 women and 21 men with androgenetic hair loss after 6 mo of treatment with 5%-minoxidil are presented. Even in this small cohort of patients, we noticed a significant increase of hair density, cumulative hair thickness and terminal hair counts. Alternative methods were developed during a human alopecia investigation and research technology (HAIR Technology) programme at Skinterface. This involves contrast-enhancement, image acquisition, and processing by qualified technicians followed by computer-assisted image analysis. The specific identification of exogen hair, further adds to this very refined non-invasive investigative method for hair follicle function investigation. Regional variations of hair growth dynamics do exist in the human scalp such as in female patients complaining of hair loss, scalp hair density and growth on top of the head differs significantly from the occipital site. Finally, from transversal studies and from detailed monitoring of subsequent hair cycles during longitudinal studies, data were obtained that support the fact that shortening of hair cycle, slowing down of growth rates and thinning of hair shafts are heralding hair miniaturisation. In the workshop the TrichoScan, the method of Canfield and Skinterface have been shown.

Adult↗
PubMed2005

Object identification in preschool children and adults.

We introduce computer-based methodologies for investigating object identification in 3- to 5-year-old children. In two experiments, preschool children and adults indicated when they could identify degraded pictures of common objects as those pictures either gradually improved or degraded in clarity. Clarity transformations were implemented in four ways: blurring, decreasing the picture's physical size, decreasing the pixel signal-to-noise ratio, and cropping. In Experiment 1, all age groups correctly identified objects at a more degraded state when those objects began moderately, as opposed to very, degraded and then clarified. This finding supports the notion that previous perceptual hypotheses interfere with object identification (i.e. the perceptual interference effect). In Experiment 2, children, but not adults, overestimated their ability to recognize objects in a degraded state when the object's identity was given to them beforehand. This suggests that for young children knowledge of the object's true identity cannot be ignored when evaluating their current perceptions. This is the first demonstration of the perceptual interference effect in children. We discuss both methodological and theoretical implications of the findings for research on object perception and theory of mind.

Adult↗
PubMed1984

Simultaneous measurement of 2':3' cyclic-nucleotide 3' phosphodiesterase and RNase activities in sera and spinal fluids of multiple sclerosis patients.

The enzymes 2':3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) and RNase were simultaneously measured in the sera and CSF of multiple sclerosis (MS) and non-MS patients. No evidence of increased activity for these enzymes could be found regardless of pathology in either fluid source. Discrepancies between the present results and those from two previous studies that reported significant increases in CNPase activity in the CSF of patients with MS were carefully analyzed. It was concluded that the apparent increased CNPase activity correlated with MS in both previous studies was most probably the result of methodological and computational difficulties.

2',3'-Cyclic-Nucleotide Phosphodiesterases↗
PubMed2004

Computerized calculation scheme for toric intraocular lenses.

BACKGROUND AND PURPOSE: While a number of intraocular lens (IOL) power prediction formulae are well established for determination of spherical lenses, no common strategy has been published for the computation of toric IOLs. The purpose of this study is to describe a paraxial computing scheme for tracing an axial pencil of rays through the 'optical system eye' containing astigmatic refractive surfaces with their axes at random. The capabilities of this computing scheme are demonstrated with clinical examples. METHODS: Based on a schematic model eye with spherocylindric surfaces, we use two alternative notations for description of vergences or prescriptions: (1) standard notation (refraction in both cardinal meridians and axis), and (2) component notation (spherical equivalent and cylindric component in 0 degrees and 45 degrees. Refractive surfaces are added to the vergence in component notation, whereas the transformation of the vergence through media is performed in the standard notation for both cardinal meridians. For calculation of the toric lens implant, a pencil of rays is traced through the spectacle and the cornea to the estimated lens position as well as backwards from the retina to the estimated lens position. For calculation of residual spectacle refraction, a pencil of rays is traced backwards from the retina through the toric lens implant and the cornea to the spectacle plane. RESULTS: In example 1 we calculate a 'thin toric lens' for compensation of a corneal astigmatism to achieve a spherical target refraction. In example 2 we compute a 'thick toric lens', which has to compensate for an oblique corneal astigmatism and rotate the spectacle cylinder to the against the rule position to enhance near vision. In example 3 we estimate the residual refraction at the corneal plane after implantation of a thick toric lens, when the cylinder of the lens implant is compensating the corneal cylinder in part and the axis of implantation is not fully aligned with the axis of the corneal astigmatism. CONCLUSION: This novel mathematical concept for computation of toric IOLs or prediction of the refractive outcome with a toric implant in place is a straightforward, computer-based approach, which may substitute for more or less empirical methods of determining toric IOL implants.

Aged↗
PubMed2006

Corneal optics after reading, microscopy and computer work.

PURPOSE: To compare lid-induced changes in corneal optics following reading, microscopy and computer work. METHODS: Nine subjects with normal ocular health were recruited for the study. Five subjects were myopic, two were emmetropic, one was astigmatic and one was hyperopic. Corneal topography was measured before and after 60 mins of reading a novel, performing a blood cell counting task on a microscope and Internet searching. Corneal topography data were used to derive the corneal wavefront Zernike coefficients up to the fourth order. A meridian analysis of instantaneous corneal power along the upper 90-degree semi-meridian was performed to examine local changes caused by eyelid pressure. Digital photography was used to capture body posture and eyelid position during the tasks. RESULTS: Each of the three tasks showed systematically different effects on both the characteristics and location of corneal topography changes. Reading and microscopy generally exhibited larger and more centrally located changes compared with the computer task. Differences in wavefront aberration characteristics between the three tasks were apparent in both lower and higher order aberrations. The location of corneal distortions differed significantly between microscopy and computer work, with microscopy causing distortions to occur closer to the videokeratoscope measurement axis compared with computer work (p = 0.015). CONCLUSIONS: Reading, microscopy and computer work have different effects on corneal aberrations. The results are in agreement with the hypothesis that lid-induced corneal aberrations may play a role in myopia development.

Adult↗
PubMed2002

Ca(2+)-activated Cl(-) current in rabbit sinoatrial node cells.

The Ca(2+)-activated Cl(-) current (I(Cl(Ca))) has been identified in atrial, Purkinje and ventricular cells, where it plays a substantial role in phase-1 repolarization and delayed after-depolarizations. In sinoatrial (SA) node cells, however, the presence and functional role of I(Cl(Ca)) is unknown. In the present study we address this issue using perforated patch-clamp methodology and computer simulations. Single SA node cells were enzymatically isolated from rabbit hearts. I(Cl(Ca)) was measured, using the perforated patch-clamp technique, as the current sensitive to the anion blocker 4,4'-diisothiocyanostilbene-2,2'-disulphonic acid (DIDS). Voltage clamp experiments demonstrate the presence of I(Cl(Ca)) in one third of the spontaneously active SA node cells. The current was transient outward with a bell-shaped current-voltage relationship. Adrenoceptor stimulation with 1 microM noradrenaline doubled the I(Cl(Ca)) density. Action potential clamp measurements demonstrate that I(Cl(Ca)) is activate late during the action potential upstroke. Current clamp experiments show, both in the absence and presence of 1 microM noradrenaline, that blockade of I(Cl(Ca)) increases the action potential overshoot and duration, measured at 20 % repolarization. However, intrinsic interbeat interval, upstroke velocity, diastolic depolarization rate and the action potential duration measured at 50 and 90 % repolarization were not affected. Our experimental data are supported by computer simulations, which additionally demonstrate that I(Cl(Ca)) has a limited role in pacemaker synchronization or action potential conduction. In conclusion, I(Cl(Ca)) is present in one third of SA node cells and is activated during the pacemaker cycle. However, I(Cl(Ca)) does not modulate intrinsic interbeat interval, pacemaker synchronization or action potential conduction.

4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid↗