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At least 613 records · Page 34Linked to original sources
PubMed1992

Computer-assisted 3D-reconstruction and statistics of the limbic system. 2. Spatial statistics of the hippocampal formation, the fornix, and the mammillary bodies.

A statistical method is described to show the distribution of neuroanatomical structures within a Cartesian coordinate system from any given number of examinations. The algorithm is based on polygons derived from the outlines of neuroanatomical structures in parallel canthomeatal-orientated cutting planes. These polygons are transformed in virtual voxels, rotated into the bicommissural coordinate system, and projected onto the three main planes of this coordinate system. Areas with the same probability for the structures examined are given in these planes. As an example this method is applied to the hippocampal formation and the results attained are shown.

Hippocampus↗
PubMed1993

The computational leech.

The local bending reflex of the leech computes a well-defined sensorimotor input-output function in which each of several unique patterns of sensory input elicits a unique pattern of motoneuron activity. Interneurons in the reflex respond to most input patterns and contribute to most motor patterns, suggesting a distributed processing mechanism for the reflex. This suggestion is supported by models in which connection strengths are adjusted by a neural network optimization algorithm to reproduce the local bending input-output function. In addition, computational parallels between the local bending network and the perceptron, a major class of artificial neural networks, brings the functional role of local bending interneurons into question and suggests new physiological experiments.

Animals↗
PubMed2004

First combined cladistic analysis of marsupial mammal interrelationships.

We combine osteological, dental, and soft tissue data with sequences from three nuclear and five mitochondrial genes, sampling all major living clades of marsupials plus several extinct taxa, to perform a simultaneous analysis of marsupial interrelationships. These data were analyzed using direct optimization and sensitivity analysis on a parallel supercomputing cluster, and compared with trees produced with conventional parsimony and likelihood algorithms using a static alignment. A major issue in marsupial phylogeny is the relationships among australidelphians. Optimal analyses using direct optimization and those based on the static alignment support the basal positions of peramelians (bandicoots) and Dromiciops ('monito del monte') within Australidelphia, and in all but one case these analyses support a monophyletic Eometatheria, a group consisting of all australidelphians excluding peramelians. Dromiciops is basal within Eometatheria in analyses that maximize congruence across partitions, including the equally weighted parameter set. The topologies resulting from direct optimization under all parameter sets show some differences, but all show a high degree of resolution. Direct optimization supports high-level clades supported by analyses of partitioned molecular (e.g., Notoryctes as sister group of Dasyuromorphia) and morphological (e.g., Diprotodontia) data.

Animals↗
PubMed2006

Last-passage Monte Carlo algorithm for mutual capacitance.

We develop and test the last-passage diffusion algorithm, a charge-based Monte Carlo algorithm, for the mutual capacitance of a system of conductors. The first-passage algorithm is highly efficient because it is charge based and incorporates importance sampling; it averages over the properties of Brownian paths that initiate outside the conductor and terminate on its surface. However, this algorithm does not seem to generalize to mutual capacitance problems. The last-passage algorithm, in a sense, is the time reversal of the first-passage algorithm; it involves averages over particles that initiate on an absorbing surface, leave that surface, and diffuse away to infinity. To validate this algorithm, we calculate the mutual capacitance matrix of the circular-disk parallel-plate capacitor and compare with the known numerical results. Good agreement is obtained.

Journal Article↗
PubMed1990

Modulation of muscle and pulmonary O2 uptakes by circulatory dynamics during exercise.

The effect of cardiovascular adjustments on the coupling of cellular to pulmonary gas exchange during unsteady states of exercise remains controversial. Computer simulations were performed to assess these influences on O2 delivery and pulmonary O2 uptake (pVO2). Algorithms were developed representing muscle and "rest-of-body" compartments, connected in parallel by arterial and venous circulations to a pump-and-lungs compartment. Exercise-induced increases in VO2 and cardiac output went to the muscle compartment. Model parameters [e.g., time constants for blood flow and muscle O2 uptake (mVO2)] could be varied independently. Simulation results demonstrated that 1) the rise in pVO2 during exercise contains three phases; 2) the contribution of changes in venous O2 stores to pVO2 kinetics and the O2 deficit occur almost entirely in phase 1; 3) under a wide variety of manipulations, the kinetics of pVO2 in phase 2 were within a couple of seconds of that assigned to mVO2 (i.e., there is not an obligatory slowing of VO2 kinetics at the lungs relative to those at the muscles; 4) by use of available estimates of blood flow adjustment, O2 delivery would not limit mVO2 after exercise onset; and 5) blood flow could limit O2 delivery in recovery, if blood flow returned to base-line levels at rates similar to those during the on-transient phase.

Cardiac Output↗
PubMed2000

PepTool and GeneTool: platform-independent tools for biological sequence analysis.

Although we are unable to discuss all of the functionality available in PepTool and GeneTool, it should be evident from this brief review that both packages offer a great deal in terms of functionality and ease-of-use. Furthermore, a number of useful innovations including platform-independent GUI design, networked parallelism, direct internet connectivity, database compression, and a variety of enhanced or improved algorithms should make these two programs particularly useful in the rapidly changing world of biological sequence analysis. More complete descriptions of the programs, algorithms and operation of PepTool and GeneTool are available on the BioTools web site (www.biotools.com), in the associated program user manuals and in the on-line Help pages.

Amino Acid Sequence↗
PubMed2000

Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors.

MOTIVATION: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware. RESULTS: A fast implementation of the Smith-Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel's latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith-Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.

Algorithms↗
PubMed1994

Apparent cerebral cytochrome aa3 reduction during cardiopulmonary bypass in hypoxaemic children with congenital heart disease. A critical analysis of in vivo near-infrared spectrophotometric data.

The purpose of this analysis was critically to examine the changes of cerebral cytochrome oxidase as detected by near-infrared spectrophotometry (NIRS) during induction of cardiopulmonary bypass (CPB) in fourteen children undergoing open heart surgery. Five children were hypoxaemic (arterial oxygen saturation 49%-84%) before the switch to CPB and nine children were not. In the hypoxaemic children, the total cerebral hemoglobin concentration [tHb] decreased rapidly and markedly, reaching a plateau after 2 min. Surprisingly, cytochrome aa3 concentration in its oxygenated form [CytO2] decreased in parallel while the cerebral haemoglobin oxygenation index [HbO2]-[Hb] increased gradually. In the eight normoxaemic children, changes in the NIRS signals were insignificant. When a standard NIRS algorithm was used, the magnitude of the change in [CytO2] was closely associated with the magnitude of the change in [tHb] (p < 0.0001), the time courses of the [CytO2] and [tHb] signals were parallel in 11 of the 14 children and the error of fit in the NIRS multicomponent analysis increased 10- to 100-fold over system noise. A new NIRS algorithm, using wavelength specific optical pathlengths, did not improve the error of fit but produced smaller estimates of [CytO2] changes, which were unrelated to the [tHb] changes. In our opinion the interesting possibility of monitoring cytochrome oxidation by NIRS requires further validation.

Algorithms↗
PubMed2004

Intelligent decision making in disassembly process based on fuzzy reasoning petri nets.

Practical disassembly process planning is extremely important for efficient material recycling and components reuse. The research work for the process planning in literature focuses on the generation of optimal sequences based on the predictive information of products. The used products, unfortunately, exhibit high uncertainty since products may experience very different conditions during their use stage. The indeterminate characteristics associated to used products often makes the predetermined plan unrealistic. Their disassembly process has to be decided dynamically adaptive to the products' specific status. To be able to deal with uncertainty in a dynamic decision making process, this paper presents a fuzzy reasoning Petri net (FRPN) model to represent related decision making rules in disassembly process. Using the proposed fuzzy reasoning algorithm based on the FRPN model, the multicriterion disassembly rules can be considered in the parallel way to make the decision automatically and quickly. Instead of producing the disassembly sequences before disassembling a whole product, the proposed method makes intelligent decisions based on dynamically updated status of components in the product at each disassembly step. Therefore, it is adaptive to the changes that arise during the process. Finally, an example is used to illustrate the application of the proposed methodology.

Algorithms↗
PubMed2006

Efficient partitioning technique for computing the dynamics of intramolecular processes: radiationless transitions in pyrazine.

An efficient QP partitioning algorithm to compute the eigenvalues, eigenvectors, and the dynamics of large molecular systems of a particular type is presented. Compared to straightforward diagonalization, the algorithm displays favorable scaling (proportional to N(T)2) as a function of N(T), the size of the Hamiltonian matrix. In addition, the algorithm is trivially parallelizable, necessitating no "cross-talk" between nodes, thus enjoying the full linear speedup of parallelization. Moreover, the method requires very modest storage space, even for extremely large matrices. The method has also been enhanced through the development of a coarse-grained approximation, enabling an increase of the basis set size to unprecedented levels (10(8)-10(10) in the current application). The QP algorithm is applied to the dynamics of electronic internal conversion in a 24 vibrational-mode model of pyrazine. A performance comparison with other dynamical methods is presented, along with results for the decay dynamics of pyrazine and a discussion of resonance line shapes.

Journal Article↗
PubMed2003

Edge encoding mechanisms in the parallel L4 neuron array of the fly (Musca domestica).

The current model of fly's cartridge termed Olson's Algorithm employs seven photoreceptors (R1-R6, Rref) to encode edge orientation. The models provide a sinusoidal output for an edge rotated about the reference photoreceptor. Although the model is powerful in providing insight into a fly's visual apparatus, it has several shortcomings. The model: does not respond to horizontal edges, does not provide Gaussian overlapped weighting of the photoreceptors which provides hyperacuity capability, and does not provide for a unique encoding of edge information. We are currently working on modifications to the model to remedy these issues. These issues must be resolved prior to pursuing object segmentation, tracking, and identification. In this paper we will investigate enhancements to the model and what they provide in solving some of the issues.

Algorithms↗
PubMed2001

Glycaemic control in type 1 diabetic patients using optimised insulin aspart or human insulin in a randomised multinational study.

Insulin aspart (IAsp), is a rapid-acting analogue of human insulin (HI), for use in the meal related treatment of diabetes mellitus. The degree of glycaemic control achieved by IAsp in comparison with HI after algorithm-driven dose optimisation was tested over 3 months. The prospective, multicentre, randomised, open-label study with parallel groups was performed in 48 centres in 11 countries and included 423 basal-bolus treated patients with Type 1 diabetes. Main outcome measures were blood glucose control assessed by HbA1c, nine-point self-monitored blood glucose profiles, insulin dose, quality of life, hypoglycaemia and adverse events. An algorithm-driven increase occurred in the dose and number of daily injections of basal insulin, particularly in the IAsp group. After 12 weeks of treatment, HbA1c was significantly lower in IAsp compared to HI treated subjects by 0.17 (95% CI 0.30-0.04) (P<0.05). Comparison of the blood glucose profiles showed lower blood glucose levels with IAsp after breakfast (mean 8.4 vs 10.1 mmol/l; P<0.0001) and dinner (8.2 vs 9.3 mmol/l; P<0.01). There were no differences between treatments in the incidence of hypoglycaemic episodes or in the adverse event profiles. The WHO Diabetes Treatment Satisfaction Questionnaire score for perceived hyperglycaemia was lower with Iasp (P=0.005), and patients found the insulin aspart treatment more flexible (P=0.022). The current study underlines the need for optimising the basal insulin regimen in order to take full advantage of the pharmacodynamics of IAsp.

Adult↗
PubMed2006

Parallel imaging in cardiovascular MRI: methods and applications.

Cardiovascular MR imaging (CVMR) has become a valuable modality for the non-invasive detection and characterization of cardiovascular diseases. CVMR requires high imaging speed and efficiency, which is fundamentally limited in conventional cardiovascular MRI studies. With the introduction of parallel imaging, alternative means for increasing acquisition speed beyond these limits have become available. In parallel imaging some image data are acquired simultaneously, using RF detector coil sensitivities to encode simultaneous spatial information that complements the information gleaned from sequential application of magnetic field gradients. The resulting improvements in imaging speed can be used in various ways, including shortening long examinations, improving spatial resolution and/or anatomic coverage, improving temporal resolution, enhancing image quality, overcoming physiological constraints, detecting and correcting for physiologic motion, and streamlining work flow. Examples of each of these strategies will be provided in this review. First, basic principles and key concepts of parallel MR are described. Second, practical considerations such as coil array design, coil sensitivity calibrations, customized pulse sequences and tailored imaging parameters are outlined. Next, cardiovascular applications of parallel MR are reviewed, ranging from cardiac anatomical and functional assessment to myocardial perfusion and viability to MR angiography of the coronary arteries and the large vessels. Finally, current trends and future directions in parallel CVMR are considered.

Algorithms↗
PubMed2006

Highly accelerated MRI by skipped phase encoding and edge deghosting with array coil enhancement (SPEED-ACE).

The fast MRI method of skipped phase encoding and edge deghosting (SPEED) is further developed with array coil enhancement, and thus is termed SPEED-ACE. In SPEED-ACE, k space is sparsely sampled with skipped phase encoding at every Nth step using a set of receiver coils simultaneously, similar to SENSE, leading to sensitivity-weighted images with up to N layers of overlapping aliasing ghosts. The ghosted images are edge enhanced by a differential filter to yield ghosted edge maps, in which the ghost overlapping layers are greatly reduced since the sparseness of edges reduces the chance of ghost overlapping. Typical ghosted edge maps can be adequately modeled with a double-layer structure. By using data from at least three coils through least-square-error minimization, a deghosted edge map is obtained and inverse-filtered into a final deghosted image. In this way, SPEED-ACE partially samples k space with a skip size of N by using multiple receiver coils in parallel, and obtains a fairly good deghosted image with an undersampling factor of N. SPEED-ACE is not limited to the double-layer ghost model, but can be generalized to include more layers of ghosts for more flexible and improved performance. As a new parallel imaging method, SPEED-ACE was tested using in vivo data to demonstrate the possibility of achieving undersampling factors even greater than the number of receiver coils, which is so far not achievable by other parallel imaging methods.

Algorithms↗
PubMed2006

A transversely isotropic viscoelastic constitutive equation for brainstem undergoing finite deformation.

The objective of this study was to define the constitutive response of brainstem undergoing finite shear deformation. Brainstem was characterized as a transversely isotropic viscoelastic material and the material model was formulated for numerical implementation. Model parameters were fit to shear data obtained in porcine brainstem specimens undergoing finite shear deformation in three directions: parallel, perpendicular, and cross sectional to axonal fiber orientation and determined using a combined approach of finite element analysis (FEA) and a genetic algorithm (GA) optimizing method. The average initial shear modulus of brainstem matrix of 4-week old pigs was 12.7 Pa, and therefore the brainstem offers little resistance to large shear deformations in the parallel or perpendicular directions, due to the dominant contribution of the matrix in these directions. The fiber reinforcement stiffness was 121.2 Pa, indicating that brainstem is anisotropic and that axonal fibers have an important role in the cross-sectional direction. The first two leading relative shear relaxation moduli were 0.8973 and 0.0741, respectively, with corresponding characteristic times of 0.0047 and 1.4538 s, respectively, implying rapid relaxation of shear stresses. The developed material model and parameter estimation technique are likely to find broad applications in neural and orthopaedic tissues.

Animals↗
PubMed1993

Use of transputers for real time dose calculation and presentation for three-dimensional radiation treatment planning.

PURPOSE: Real-time 3-dimensional dose calculation will allow display of isodose contours and other metrics for a planner to assess plan effectiveness during plan development, facilitating optimization. METHODS AND MATERIALS: Parallel processing provides an effective means to calculate 3-dimensional dose distribution in real-time while plan parameters are being chosen and adjusted. An array of 20 transputers and a high performance graphics workstation have demonstrated the feasibility of real-time 3-dimensional beam parameter specification, dose calculation, and dose-distribution presentation for evaluation. A mesh connected set of processors using surface processors to generate and terminate rays, and ray processors to calculate ray attenuation and dose distribution has been developed to efficiently utilize large numbers of processors and provide good load sharing, even for small beams that intersect only a small part of the volume. RESULTS: Our feasibility study has calculated dose distribution by the Effective Path Length method in about one second per beam for a treatment volume of 56,400 voxels. We expect to reduce the total time for computation, communication, and display, with even larger volumes, to less than one second. The number of processors can easily be increased for larger treatment volumes or more accurate and computation-intensive dose-calculation algorithms. Transputers provide an elegant and economical method for harnessing up to hundreds of powerful general-purpose processors for computational tasks including dose calculation and isodose contour generation. The same distributed-memory parallel-processing configuration is also suitable for calculation of isodose contours and dose-volume histograms for plan evaluation, automatic calculation of apertures and filters as beam parameters are manipulated, and more accurate dose calculation algorithms that incorporate the effects of scatter. CONCLUSION: Parallel processors can efficiently provide real-time calculation of the information necessary to evaluate treatment plans as they are developed allowing the planner to optimize the plan based on dose distribution and its effects on tumor control and complications.

Humans↗
PubMed1997

ECG recording by a microdot thermal printer.

Recently high quality ECG records have been obtained by means of microdot thermal printers, because of their numerous advantages. Usually they contain a shift register in the thermal head and the fast control of the dot locations to be heated is an important software problem. We implemented the TLP 480Z-N Gotemba thermal printer (made in Japan) in our ECG instruments, and elaborated two algorithms for lengthwise and crosswise printing on the paper. They use 'black and white' strips loaded into the shift register by 1-byte parallel data organization. The lengthwise mode can operate in real time, while the crosswise one is intended for memorized signals.

Algorithms↗