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PubMed1995

Effect of stimulation on burst firing in cat primary auditory cortex.

1. Neural activity was recorded extracellularly with two independent microelectrodes aligned in parallel and advanced perpendicular to isofrequency sheets in cat primary auditory cortex. Multiunit activity was separated into single-unit spike trains using a maximum variance spike sorting algorithm. Only units that demonstrated a high quality of sorting and a minimum spontaneous firing rate of 0.2 spikes/s were considered for analysis. The primary aim of this study was to describe the effect of periodic click train and broadband noise stimulation on short-time-scale (< or = 50 ms) bursts in the spike trains of single auditory cortical units and to determine whether stimulation influenced the occurrence, spike count, and/or temporal structure of burst firing relative to a spontaneous baseline. 2. Extracellular recordings were made in 20 juvenile and adult cats from 69 single auditory cortical units during click train stimulation and silence, and from 30 single units during noise stimulation and in silence. In an additional 15 single units the effect of both click train and noise stimulation was investigated. The incidence, spike count, and temporal structure of short-time-scale burst firing in the first 100 ms following stimulus presentation was compared with burst firing in the period starting 500 ms after stimulus presentation and with spontaneous burst firing. In addition, the serial dependence of interspike intervals within a burst was tested during periods of stimulation. 3. Burst firing was present in the stimulation, poststimulation, and spontaneous conditions. Longer bursts (consisting of > or = 3 spikes) were more commonly observed in the poststimulation and spontaneous conditions than in the stimulation condition. This effect was most pronounced during click stimulation. A period of elevated firing activity was present in a subset of units 0.5-1.5 s after stimulus presentation, indicating prolonged effects of stimulation on single-unit firing behavior. 4. For both stimuli, the proportion of single-unit responses composed of bursts was significantly greater in poststimulation and spontaneous periods than during stimulation. Burst rate was higher in post-click-train stimulation and spontaneous periods than during periods of click stimulation. The isolated spike rate was significantly higher during periods of noise and click stimulation than in the poststimulation and spontaneous periods. 5. An examination of the autocorrelograms and higher-order interspike interval histograms of single-unit responses during click train stimulation indicated that 25% of single-unit spike trains contained an excess of brief first-order intervals and 14% of spike trains contained a shortage of long higher-order interspike intervals relative to a spontaneous baseline. During noise stimulation, 10% of single-unit responses contained an excess of short intervals relative to baseline. Interspike intervals of short-duration bursts were not serially dependent during periods of stimulation. 6. A comparison of the autocorrelograms and higher-order interval histograms of single-unit responses in the poststimulation and spontaneous conditions indicated that 20% of single-unit spike trains contained an excess of short first-, second-, and third-order intervals following stimulation. This subgroups of single units could not be distinguished on the basis of the age of the animal or the depth at which the recording was made. 7. The low incidence of burst firing during stimulation opposes the view that bursts serve as a mechanism to emphasize or amplify particular stimulus-related responses in the presence of ongoing spontaneous activity in the primary auditory cortex. Moreover, there is little evidence to support the notion that brief bursts represent neural codes, because intraburst intervals are not serially dependent. It is suggested that pyramidal burst firing may be an effective way to evoke postsynaptic firing in inhibitory interneurons and subsequ

Acoustic Stimulation↗
PubMed2004

A complexity-scalable software-based MPEG-2 video encoder.

With the development of general-purpose processors (GPP) and video signal processing algorithms, it is possible to implement a software-based real-time video encoder on GPP, and its low cost and easy upgrade attract developers' interests to transfer video encoding from specialized hardware to more flexible software. In this paper, the encoding structure is set up first to support complexity scalability; then a lot of high performance algorithms are used on the key time-consuming modules in coding process; finally, at programming level, processor characteristics are considered to improve data access efficiency and processing parallelism. Other programming methods such as lookup table are adopted to reduce the computational complexity. Simulation results showed that these ideas could not only improve the global performance of video coding, but also provide great flexibility in complexity regulation.

Journal Article↗
PubMed1979

A computerized rotating laminar radionuclide camera.

We have constructed a radionuclide camera that embodies a unique detector-collimator concept and provides a radically new approach to imaging. The heart of the instrument is a linear array of semiconductor detectors separated by thin tungsten plates that confine the field of view of each detector to one dimension. This collimator design has a higher collection efficiency than the standard parallel-hole collimator but cannot directly produce a two-dimensional image. When multiple measurements are taken as the array rotates through 180 degrees, a computerized image restoration algorithm can then produce two-dimensional images with resolution determined by the width of the detectors. A small prototype camera has produced images with resolution superior to conventional Anger cameras.

Computers↗
PubMed2000

Beam spoilers versus bolus for 6 MV photon treatment of head and neck cancers.

When parallel opposed 6-MV x-ray beams are used for treatment of head and neck tumors, superficial tissues and lymphatics at shallow depths of < or =4 to 6 mm may be at cancer risk but receive less than full radiation dose. In these cases, the use of either a beam spoiler or bolus material can increase dose to superficial tissues. The potential benefit of a beam spoiler relative to bolus is preservation of skin-sparing characteristics for cases in which the skin surface does not require full dose. In this study, we evaluate the application of a beam spoiler and compare it to bolus for standard treatments of head and neck tumors. Measurements of both depth dose in-water and in-air profiles were made with a beam spoiler for a 6-MV photon beam. The measurements were combined with Monte Carlo calculations to obtain the energy spectrum of the spoiler-generated electrons. An in-house pencil beam treatment-planning algorithm was used to calculate the dose distribution with spoiler. The dose distribution in the buildup region was then studied with and without the spoiler for a typical head and neck treatment with parallel-opposed beams. Dose distributions and partial-volume dose histograms (PVDH) demonstrate the benefits provided by spoilers for the head and neck treatments and the limitations of their use. The beam spoiler is useful in treating the superficial lymphatics in the buildup region near head and neck tumors. Guidelines for use of beam spoiler versus bolus are discussed.

Head and Neck Neoplasms↗
PubMed2004

Partial rigid-body dynamics in NPT, NPAT and NPgammaT ensembles for proteins and membranes.

A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. In this method, the symplectic integrator for rigid bodies is combined with the equations of motion for the NPT ensemble. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT (constant normal pressure and lateral surface area of membranes and constant temperature) and NPgammaT (constant normal pressure and lateral surface tension of membranes and constant temperature) ensembles. By more than 30-ns simulations of aqueous proteins and hydrated lipid bilayers, the results of the partial rigid-body method demonstrated excellent conservation of total energy and consistent behavior with the traditional constraint method in terms of structural distribution and fluctuation of proteins and lipids. The efficient implementation of the partial rigid-body method in parallel computation is presented, which is shown to work well in large-scale molecular dynamics simulations.

Algorithms↗
PubMed1994

An asymptotic solution for the contact of two biphasic cartilage layers.

This study addresses the hypothesis that interstitial fluid plays a major role in the load support mechanism of articular cartilage. An asymptotic solution is presented for two contacting biphasic cartilage layers under compression. This solution is valid for identical thin (i.e. epsilon = h'/a'0 << 1), frictionless cartilage layers, and for the 'early' time response (i.e. t' << (h')2/HAk) after the application of a step load. An equilibrium asymptotic solution is also presented (i.e.t'-->infinity). Here h' is the thickness, a'0 is a characteristic contact radius, HA is the aggregate modulus and k is the permeability of the cartilage layer. A main conclusion from this analysis is that the fluid phase of cartilage plays a major role in providing load support during the first 100-200 s after contact loading. Further, the largest component of stress in cartilage is the hydrostatic pressure developed in the interstitial fluid. For tissue fluid volume fraction (porosity) in the range 0.6 < or = phi f < or = 0.8, k = O(10(-15) m4/Ns) and HA = O(1 MPa), the peak magnitude of the principal effective (or elastic) stress may be as low as 14% of the peak hydrostatic pressure within the tissue, or the contact stress at the surface. In effect, the interstitial fluid shields the solid matrix from high normal stresses and strains. The asymptotic solution also shows that pressure-sensitive film measurements of intra-articular contact stress do not measure the elastic stress at the surface, but they rather provide a measure of the interstitial fluid pressure. Finally, this analysis provides strong support for the hypothesis that, if sudden loading causes shear failure within the cartilage-bone layer structure, this failure would take place at the cartilage-bone interface, and the plane of failure would be either parallel or perpendicular to this interface.

Adhesiveness↗
PubMed2006

Assigning solid-state NMR spectra of aligned proteins using isotropic chemical shifts.

A method for assigning solid-state NMR spectra of membrane proteins aligned in phospholipid bicelles that makes use of isotropic chemical shift frequencies and assignments is demonstrated. The resonance assignments are based on comparisons of 15N chemical shift differences in spectra obtained from samples with their bilayer normals aligned perpendicular and parallel to the direction of the applied magnetic field.

Algorithms↗
PubMed2000

The design and applications of a recursive molecular modeling framework.

In this paper, we present a recursive molecular model suitable for multiresolution analysis in a variety of application areas. Our approach allows ease of use by computer scientists and biologists by proposing a software interface for molecular analysis that hides programming details. We demonstrate that our design is flexible enough for use in desktop analytical applications, in large-scale parallel simulations, and as a server for remote molecular analysis across wide-area networks.

Algorithms↗
PubMed2006

High-resolution mutation mapping reveals parallel experimental evolution in yeast.

Understanding the genetic basis of evolutionary adaptation is limited by our ability to efficiently identify the genomic locations of adaptive mutations. Here we describe a method that can quickly and precisely map the genetic basis of naturally and experimentally evolved complex traits using linkage analysis. A yeast strain that expresses the evolved trait is crossed to a distinct strain background and DNA from a large pool of progeny that express the trait of interest is hybridized to oligonucleotide microarrays that detect thousands of polymorphisms between the two strains. Adaptive mutations are detected by linkage to the polymorphisms from the evolved parent. We successfully tested our method by mapping five known genes to a precision of 0.2-24 kb (0.1-10 cM), and developed computer simulations to test the effect of different factors on mapping precision. We then applied this method to four yeast strains that had independently adapted to a fluctuating glucose-galactose environment. All four strains had acquired one or more missense mutations in GAL80, the repressor of the galactose utilization pathway. When transferred into the ancestral strain, the gal80 mutations conferred the fitness advantage that the evolved strains show in the transition from glucose to galactose. Our results show an example of parallel adaptation caused by mutations in the same gene.

Algorithms↗
PubMed1999

[Research highlight of image reconstruction today].

In today's image processing researches, image reconstruction is a highlight. It includes the following several aspects: (1) reducing noise before reconstruction or after reconstruction under time-frequency constraints; (2) researches for reconstruction of motion organ; (3) image reconstruction from incomplete projection data; (4) direct volume reconstruction and 3-D image rendering; (5) researches for non-X-ray CT; (6) researches for parallel processing system of CT. In this paper, an introduction to these aspects is given.

Algorithms↗
PubMed2001

[Effect of electric field on exciton energy level width in quantum well].

By using concept as quasi-classical particles, the particles which move in a large range of space in solid state are described. Applying the derived formula of energy uncertainty and exciton model of classical mechanics to GaAs/GaAIAs quantum well in electric field, the calculation results of exciton energy level width arc in agreement with measured results. The great different effects of perpendicular-field and parallel-field on exciton optical absorption in the quantum well can be explained clearly and simply.

Algorithms↗
PubMed1991

Dose in bone and tissue near bone-tissue interface from electron beam.

This work has quantitatively studied the variation of dose both within bone and in unit density tissue near bone-tissue interfaces. Dose upstream of a bone-tissue interface is increased because of an increase in the backscattered electrons from the bone. The magnitude of this effect was measured using a thin parallel-plate ionization chamber upstream of a polymethyl methacrylate (PMMA)-hard bone interface. The electron backscatter factor (EBF) increased rapidly with bone thickness until a full EBF was achieved. This occurred at approximately 3.5 mm at 2 MeV and 6 mm at 13.1 MeV. The full EBF at the interface ranged from approximately 1.018 at 13.1 MeV to 1.05 at 2 MeV. It was also observed that the EBF had a dependence on the energy spectrum at the interface. The penetration of the backscattered electrons in the upstream direction of PMMA was also measured. The dose penetration fell off rapidly in the upstream direction of the interface. Dose enhancement to unit density tissue in bone was measured for an electron beam by placing thermoluminescent dosimeters (TLDs) in a PMMA-bone-PMMA phantom. The maximum dose enhancement in bone was approximately 7% of the maximum dose in water. However, the pencil-beam algorithm of Hogstrom et al. predicted an increase of only 1%, primarily owing to the inverse-square correction. Film was also used to measure the dose enhancement in bone. The film plane was aligned either perpendicular or parallel to the central axis of the beam. The film data indicated that the maximum dose enhancement in bone was approximately 8% for the former film alignment (which was similarly predicted by the TLD measurements) and 13% for the latter film alignment. These results confirm that the X ray film is not suitable to be irritated "edge on" in an inhomogeneous phantom without making perturbation corrections resulting from the film acting as a long narrow inhomogeneous cavity within the bone. In addition, the results give the radiotherapist a basis for clinical judgment when electron beams are used to treat lesions behind bone or near bony structures. We feel these data enhance the ability to recognize the shortcomings of the current dose calculation algorithm used clinically.

Bone and Bones↗
PubMed2005

Controlled protein precipitation in combination with chip-based nanospray infusion mass spectrometry. An approach for metabolomics profiling of plasma.

Liquid chromatography-mass spectrometry (LC-MS) is a common method for profiling biological samples in metabolomics. However, LC-MS data of metabolomic studies are often affected by high noise levels, retention time shifts, and high variability in signal intensities. With a new chip-based nanoelectrospray source it becomes possible to directly infuse complex biological samples such as plasma without any chromatographic separation beforehand. In combination with highly diluted samples and long data acquisition times, the parallel analysis of hundreds of compounds is now possible. In a proof-of-concept study, 10 human plasma samples from females and males were analyzed with the intention to separate the two groups by their different metabolomes. The reproducibility was so high that statistical analysis of the data could be performed without prior normalization. Two groups of female and male samples were separated by a supervised machine learning algorithm, principal component analysis, and hierarchical clustering. Peaks contributing to the group separation were characterized by accurate mass measurement and MS-MS fragmentation and by spiking experiments. The feasibility of direct sample infusion using the new chip-based nanoelectrospray device opens a new dimension for the rapid parallel analysis of complex biological mixtures.

Adult↗
PubMed2000

Adaptive optics based on analog parallel stochastic optimization: analysis and experimental demonstration

Wave-front distortion compensation using direct system performance metric optimization is studied both theoretically and experimentally. It is shown how different requirements for wave-front control can be incorporated, and how information from different wave-front sensor types can be fused, within a generalized gradient descent optimization paradigm. In our experiments a very-large-scale integration (VLSI) system implementing a simultaneous perturbation stochastic approximation optimization algorithm was applied for real-time adaptive control of multielement wave-front correctors. The custom-chip controller is used in two adaptive laser beam focusing systems, one with a 127-element liquid-crystal phase modulator and the other with beam steering and 37-control channel micromachined deformable mirrors. The submillisecond response time of the micromachined deformable mirror and the parallel nature of the analog VLSI control architecture provide for high-speed adaptive compensation of dynamical phase aberrations of a laser beam under conditions of strong intensity scintillations. Experimental results demonstrate improvement of laser beam quality at the receiver plane in the spectral band up to 60 Hz.

Journal Article↗
PubMed2001

Socket: a program for identifying and analysing coiled-coil motifs within protein structures.

The coiled coil is arguably the simplest protein-structure motif and probably the most ubiquitous facilitator of protein-protein interactions. Coiled coils comprise two or more alpha-helices that wind around each other to form "supercoils". The hallmark of most coiled coils is a regular sequence pattern known as the heptad repeat. Despite this apparent simplicity and relatedness at the sequence level, coiled coils display a considerable degree of structural diversity: the helices may be arranged parallel or anti-parallel and may form a variety of oligomer states. To aid studies of coiled coils, we developed SOCKET, a computer program to identify these motifs automatically in protein structures. We used SOCKET to gather a set of unambiguous coiled-coil structures from the RCSB Protein Data Bank. Rather than searching for sequence features, the algorithm recognises the characteristic knobs-into-holes side-chain packing of coiled coils; this proved to be straightforward to implement and was able to distinguish coiled coils from the great majority of helix-helix packing arrangements observed in globular domains. SOCKET unambiguously defines coiled-coil helix boundaries, oligomerisation states and helix orientations, and also assigns heptad registers. Structures retrieved from the Protein Data Bank included parallel and anti-parallel variants of two, three and four-stranded coiled coils, one example of a parallel pentamer and a small number of structures that extend the classical description of a coiled coil. We anticipate that our structural database and the associated sequence data that we have gathered will be of use in identifying principles for coiled-coil assembly, prediction and design. To illustrate this we give examples of sequence and structural analyses of the structures that are possible using the new data bases, and we present amino acid profiles for the heptad repeats of different motifs.

Algorithms↗
PubMed1988

Tracking multiple independent targets: evidence for a parallel tracking mechanism.

There is considerable evidence that visual attention is concentrated at a single locus in the visual field, and that this locus can be moved independent of eye movements. Two studies are reported which suggest that, while certain aspects of attention require that locations be scanned serially, at least one operation may be carried out in parallel across several independent loci in the visual field. That is the operation of indexing features and tracking their identity. The studies show that: (a) subjects are able to track a subset of up to 5 objects in a field of 10 identical randomly-moving objects in order to distinguish a change in a target from a change in a distractor; and (b) when the speed and distance parameters of the display are designed so that, on the basis of some very conservative assumptions about the speed of attention movement and encoding times, the predicted performance of a serial scanning and updating algorithm would not exceed about 40% accuracy, subjects still manage to do the task with 87% accuracy. These findings are discussed in relation to an earlier, and independently motivated model of feature-binding--called the FINST model--which posits a primitive identity maintenance mechanism that indexes and tracks a limited number of visual objects in parallel. These indexes are hypothesized to serve the function of binding visual features prior to subsequent pattern recognition.

Algorithms↗
PubMed2004

Grid powered nonlinear image registration with locally adaptive regularization.

Multi-subject non-rigid registration algorithms using dense deformation fields often encounter cases where the transformation to be estimated has a large spatial variability. In these cases, linear stationary regularization methods are not sufficient. In this paper, we present an algorithm that uses a priori information about the nature of imaged objects in order to adapt the regularization of the deformations. We also present a robustness improvement that gives higher weight to those points in images that contain more information. Finally, a fast parallel implementation using networked personal computers is presented. In order to improve the usability of the parallel software by a clinical user, we have implemented it as a grid service that can be controlled by a graphics workstation embedded in the clinical environment. Results on inter-subject pairs of images show that our method can take into account the large variability of most brain structures. The registration time for images of size 256 x 256 x 124 is 5 min on 15 standard PCs. A comparison of our non-stationary visco-elastic smoothing versus solely elastic or fluid regularizations shows that our algorithm converges faster towards a more optimal solution in terms of accuracy and transformation regularity.

Algorithms↗
PubMed2004

Using molecular sizes of simple sequence repeats vs. discrete binned data in assessing probability of ancestry: application to maize hybrids.

Most inferential methods for profiling genotypes based upon the use of DNA fragments use molecular-size data transcribed into discrete bins, which are intervals of DNA fragment sizes. Categorizing into bins is labor intensive with inevitable arbitrariness that may vary between laboratories. We describe and evaluate an algorithm for determining probabilities of parentage based on raw molecular-size data without establishing bins. We determine the standard deviation of DNA fragment size and assess the association of standard deviation with fragment size. We consider a pool of potential ancestors for an index line that is a hybrid with unknown pedigree. We evaluate the identification of inbred parents of maize hybrids with simple sequence repeat data in the form of actual molecular sizes received from two laboratories. We find the standard deviation to be essentially constant over the molecular weight. We compare these results with those of parallel analyses based on these same data that had been transcribed into discrete bins by the respective laboratories. The conclusions were quite similar in the two cases, with excellent performance using either binned or molecular-size data. We demonstrate the algorithm's utility and robustness through simulations of levels of missing and misscored molecular-size data.

Algorithms↗