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At least 1,405 records · Page 78Linked to original sources
PubMed2004

A method of improving overall resolution in ultrasonic array imaging using spatio-temporal deconvolution.

In this paper a beamforming method for ultrasonic array imaging is presented that performs both spatial and temporal deconvolution based on a minimum mean square error (MMSE) criteria. The presented MMSE receive mode beamformer performs a regularized inversion of the propagation operator for the ultrasonic array system at hand. The MMSE beamformer accounts for the transmit and receive processes, defined in terms of finite array element sizes, transmit focusing laws and electrical transducer characteristics. The MMSE beamformer is compared to the traditional delay-and-sum (DAS) beamformer with respect to both resolution and signal-to-noise ratio. The two algorithms are compared using both simulated and measured data. The simulated data was obtained using ultrasonic field simulations and the measured data was acquired using a linear phased array imaging wire targets in water. The results show that the MMSE beamformer has superior temporal and lateral resolution compared to DAS. It is also shown that the MMSE beamformer can be expressed as a filter bank, which enables parallel processing at high frame rates.

Journal Article↗
PubMed2000

Effect of electron beam parameters on simulated CBED patterns from edge-on grain boundaries.

Convergent beam electron diffraction (CBED) at vertical grain boundaries (parallel to the electron beam) can be applied to determine the symmetry of bicrystals. It can also be used to investigate the structure of the boundary region itself when subnanometre probe sizes are employed. In this paper it is shown that (sub)nanometre-probe CBED patterns are largely influenced by the electron-beam geometry. In particular, simulations of coherent CBED patterns based on the multislice algorithm show that the CBED pattern of an edge-on interface depends on the defocus distance between the probe position and the specimen midplane, the probe size and the beam-convergence angle. The pattern symmetry may be lower than the theoretically predicted symmetry in case of large spherical aberration. This effect increases with smaller accelerating voltages. An increase in the beam-convergence angle also increases the possibility of a non-optimum symmetry due to spherical aberration of a coherent probe. Thus, for the determination of an interface structure using subnanometre (coherent) probes, the imaging conditions play an important role.

Microscopy, Electron↗
PubMed1990

Principles of management of shotgun wounds.

As an instrument of close range combat, the shotgun has no parallel. At short distances, its destructive capacity parallels that seen from high velocity missile injury. In this study, the history of the shotgun, wound ballistics, principles of initial therapy and special management problems related to shotgun wounds of specific sites are reviewed. An analysis of pooled data on abdominal shotgun wounds is presented. A subset of patients who do not require abdominal exploration exists. Specific problems encountered in defining this subset are enumerated. Three algorithms are presented that summarize our current management approach to shotgun wounds of the torso and extremities.

Abdominal Injuries↗
PubMed2006

Shear wave group velocity inversion in MR elastography of human skeletal muscle.

In vivo quantification of the anisotropic shear elasticity of soft tissue is an appealing objective of elastography techniques because elastic anisotropy can potentially provide specific information about structural alterations in diseased tissue. Here a method is introduced and applied to MR elastography (MRE) of skeletal muscle. With this method one can elucidate anisotropy by means of two shear moduli (one parallel and one perpendicular to the muscle fiber direction). The technique is based on group velocity inversion applied to bulk shear waves, which is achieved by an automatic analysis of wave-phase gradients on a spatiotemporal scale. The shear moduli are then accessed by analyzing the directional dependence of the shear wave speed using analytic expressions of group velocities in k-space, which are numerically mapped to real space. The method is demonstrated by MRE experiments on the biceps muscle of five volunteers, resulting in 5.5+/-0.9 kPa and 29.3+/-6.2 kPa (P<0.05) for the medians of the perpendicular and parallel shear moduli, respectively. The proposed technique combines fast steady-state free precession (SSFP) MRE experiments and fully automated processing of anisotropic wave data, and is thus an interesting MRI modality for aiding clinical diagnosis.

Adult↗
PubMed2005

The SIMRI project: a versatile and interactive MRI simulator.

This paper gives an overview of SIMRI, a new 3D MRI simulator based on the Bloch equation. This simulator proposes an efficient management of the T2* effect, and in a unique simulator integrates most of the simulation features that are offered in different simulators. It takes into account the main static field value and enables realistic simulations of the chemical shift artifact, including off-resonance phenomena. It also simulates the artifacts linked to the static field inhomogeneity like those induced by susceptibility variation within an object. It is implemented in the C language and the MRI sequence programming is done using high level C functions with a simple programming interface. To manage large simulations, the magnetization kernel is implemented in a parallelized way that enables simulation on PC grid architecture. Furthermore, this simulator includes a 1D interactive interface for pedagogic purpose illustrating the magnetization vector motion as well as the MRI contrasts.

Algorithms↗
PubMed1999

Where the abstract feature maps of the brain might come from.

Three types of neuronal organization can be called 'brain maps': sets of feature-sensitive cells, ordered projections between neuronal layers and ordered maps of abstract features. The latter are most intriguing as they reflect the central properties of an organism's experiences and environment. It is proposed that such feature maps are learned in a process that involves parallel input to neurons in a brain area and adaptation of neurons in the neighborhood of the cells that respond most strongly to this input. This article presents a new mathematical formulation for such adaptation and relates it to physiological functions.

Algorithms↗
PubMed1992

Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis.

It is widely accepted that parallel computers, which have the ability to execute different parts of a program simultaneously, will offer dramatic speed-up for many time-consuming biological computations. The paper describes how the use of the machine-independent parallel programming language, Linda, allows parallel programs to run on an institution's network of workstations. In this way, an institution can harness existing hardware, which is often either idle or vastly underutilized, as a powerful 'parallel machine' with supercomputing capability. The paper illustrates this very general paradigm by describing the use of Linda to parallelize three widely used programs for genetic linkage analysis, a mathematical technique used in gene mapping. The paper then discusses a number of technical, administrative and social issues that arise when creating such a computational resource.

Algorithms↗
PubMed1992

Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison.

A platform program that performs biological sequence comparison provides a case study to compare the relative advantages of a machine-independent approach to parallel computation versus a machine-specific approach. The program consists of two routines: (i) PSCANLIB, which compares a single biological sequence against a database of sequences, and (ii) PCOMPLIB, which compares a database of sequences against another database of sequences, or against itself. The program was first parallelized to run on the Intel Hypercube parallel computer using native Hypercube commands to coordinate the parallel computation. The parallelization logic of the program was then translated into a machine-independent parallel programming language, Linda. These two approaches to parallelization are contrasted in terms of: (i) the expressive power of the logic that coordinates the parallel computation, (ii) the portability of the machine-independent version to other parallel machines and (iii) the relative efficiency of the two versions of the program. In the benchmark tests reported, the benefits of the machine-independent approach were achieved with only a modest sacrifice in efficiency.

Algorithms↗
PubMed2001

Parallel FD-TD simulation of radiobase antennae.

The rigorous characterisation of the behaviour of a radiobase antenna for wireless communication systems is a hot topic both for antenna or communication system design and for radioprotection-hazard reasons. Such a characterisation deserves a numerical solution, and the use of a finite-difference time-domain (FD-TD) approach is an attractive candidate. Unfortunately, it has strong memory and CPU-time requirements. Numerical complexity can be successfully afforded by using parallel computing. The parallel implementation of the FD-TD code, individuating the theoretical lower bound for its parallel execution time are discussed and the findings achieved on the APE/Quadrics massively parallel systems are presented. Results obtained from the simulation of actual radiobase antennae, clearly demonstrate that massively parallel processing is a viable approach to solving electromagnetic problems, allowing the simulation of radiating devices which could not be modelled through conventional computing systems. The tests showed a sustained computational speed equal to 17% of the theoretical maximum.

Algorithms↗
PubMed2000

Actively contracting bundles of polar filaments.

We introduce a phenomenological model to study the properties of bundles of polar filaments which interact via active elements. The stability of the homogeneous state, the attractors of the dynamics in the unstable regime, and the tensile stress generated in the bundle are discussed. We find that the interaction of parallel filaments can induce unstable behavior and is responsible for active contraction and tension in the bundle. The interaction between antiparallel filaments leads to filament sorting. Our model could apply to simple contractile structures in cells such as stress fibers.

Actins↗
PubMed2001

Using meta computing tools to facilitate large-scale analyses of biological databases.

Given the high rate at which biological data are being collected and made public, it is essential that computational tools be developed that are capable of efficiently accessing and analyzing these data. High-performance distributed computing resources can play a key role in enabling large-scale analyses of biological databases. We use a distributed computing environment, Legion, to enable large-scale computations on the Protein Data Bank (PDB). In particular, we employ the Feature program to scan all protein structures in the PDB in search for unrecognized potential cation binding sites. We evaluate the efficiency of Legion's parallel execution capabilities and analyze the initial biological implications that result from having a site annotation scan of the entire PDB. We discuss four interesting proteins with unannotated, high-scoring candidate cation binding sites.

Algorithms↗
PubMed2005

Aligning multiple protein structures by deterministic annealing.

Protein structure alignment plays a key role in protein structure prediction and fold family classification. An efficient method for multiple protein structure alignment in a mathematical manner is presented, based on deterministic annealing technique. The alignment problem is mapped onto a nonlinear continuous optimization problem (NCOP) with common consensus chain, matching assignment matrices and atomic coordinates as variables. At each step in the annealing procedure, the NCOP is decomposed into as many sub-problems as the number of protein chains, each of which is actually an independent pairwise structure alignment between a protein chain and the consensus chain and hence can be efficiently solved by the parallel computation technique. The proposed method is robust with respect to choice of iteration parameters for a wide range of proteins, and performs well in both multiple and pairwise structure alignment cases, compared with existing alignment methods.

Algorithms↗
PubMed2005

Development, parallelization, and automation of a gas-inducing milliliter-scale bioreactor for high-throughput bioprocess design (HTBD).

A novel milliliter-scale bioreactor equipped with a gas-inducing impeller was developed with oxygen transfer coefficients as high as in laboratory and industrial stirred-tank bioreactors. The bioreactor reaches oxygen transfer coefficients of >0.4 s(-1). Oxygen transfer coefficients of >0.2 s(-1) can be maintained over a range of 8- to 12-mL reaction volume. A reaction block with integrated heat exchangers was developed for 48-mL-scale bioreactors. The block can be closed with a single gas cover spreading sterile process gas from a central inlet into the headspace of all bioreactors. The gas cover simultaneously acts as a sterile barrier, making the reaction block a stand-alone device that represents an alternative to 48 parallel-operated shake flasks on a much smaller footprint. Process control software was developed to control a liquid-handling system for automated sampling, titration of pH, substrate feeding, and a microtiter plate reader for automated atline pH and atline optical density analytics. The liquid-handling parameters for titration agent, feeding solution, and cell samples were optimized to increase data quality. A simple proportional pH-control algorithm and intermittent titration of pH enabled Escherichia coli growth to a dry cell weight of 20.5 g L(-1) in fed-batch cultivation with air aeration. Growth of E. coli at the milliliter scale (10 mL) was shown to be equivalent to laboratory scale (3 L) with regard to growth rate, mu, and biomass yield, Y(XS).

Aerobiosis↗
PubMed1987

Continuous, real-time, noninvasive monitor of blood pressure: Penaz methodology applied to the finger.

The finger blood pressure monitor measures blood pressure continuously and noninvasively by means of a technique described by J. Penaz. The size of the artery is measured when its internal pressure (arterial pressure) equals the external pressure. (At this point, transmural pressure equals zero and the arterial wall is said to be "unloaded.") This unloaded condition is maintained by continuous, automatic adjustments of external pressure on the artery, adjustments that are made simultaneously with and parallel to intraarterial pressure variations. The external pressure then constantly equals internal pressure (arterial blood pressure) and is reported by the monitor as values for systolic, mean, and diastolic pressure. A finger cuff with a built-in light source and detector is used to measure finger artery size, and an inflatable bladder is used to apply the external pressure to the artery. The monitor is microprocessor based; algorithms determine the unloaded artery size approximately every minute and automatically correct for changes possibly induced by smooth muscle contraction or relaxation, and a high-speed electropneumatic servo control system enables automatic calibration and adjustment.

Blood Pressure Determination↗
PubMed2005

Caco-2 permeability of weakly basic drugs predicted with the double-sink PAMPA pKa(flux) method.

The aim of this study was to analyze pH-dependent permeability of cationic drugs in Caco-2 cell monolayers using the pK(a)(flux) method and to correlate the results with those obtained in PAMPA (parallel artificial membrane permeability assay). The pH-dependent permeability of verapamil and propranolol was studied in Caco-2 cell monolayers. The data were subsequently processed using software developed for the PAMPA pK(a)(flux) method. Literature values for an additional nine cationic drugs were also analyzed. Double-Sink PAMPA data were also obtained for the same cationic drugs, to compare with the Caco-2 data. The Algorithm Builder program was then used to develop a predictive model of Caco-2 permeability based on PAMPA permeability and calculated Abraham molecular descriptors. From the relationship between permeability and pH it was shown that in PAMPA only the uncharged form of the drugs permeated across the membrane barrier, while charged and ionized forms of the drugs were significantly permeable in Caco-2. The charged-form permeability, P(i), was therefore determined and subsequently subtracted from all permeability coefficients in Caco-2 prior to the comparison with PAMPA. The resulting intrinsic permeability coefficients (P(o)) obtained in Caco-2 were successfully related to those derived from the PAMPA model. In this study we have shown that permeability coefficients obtained in PAMPA can predict the passive transcellular permeability in Caco-2.

Caco-2 Cells↗
PubMed1992

[Neoplastic involvement of pulmonary fissures. Diagnostic possibility of high resolution x-ray computed tomography].

Acknowledging fissure invasion by pulmonary tumors located in contact with or in the vicinity of a fissure is an important piece of information for the therapeutic choice, especially in patients whose functional respiratory impairments are a contraindication of pneumonectomy. Fifteen patients with pulmonary neoplasms adjacent to a fissure were studied with standard computed tomography (10 mm sections), completed by high-resolution CT. The findings of the CT studies were compared with those operative reports. On surgery, the oblique fissure was infiltrated in 12 patients, unharmed in 2 others, while the horizontal fissure was infiltrated in 3 patients. Standard CT allowed diagnosing the involvement of the oblique fissure in 4 patients. Thin sections with high-resolution reconstruction algorithms allowed detecting the involvement of the oblique fissure in 13 cases, including one false-positive result. On thin sections, the fissures appear as well-delineated, dense lines. This allows an accurate study of the relationships between the tumor and the fissure, thus increasing the sensitivity of CT for the detection of tumoral extension across the fissures. The orientation of the horizontal fissure, which is almost parallel to the plane of section, makes the study of its relationships with an adjacent mass difficult, even in high-resolution CT.

Humans↗
PubMed2006

Minimum-norm reconstruction for sensitivity-encoded magnetic resonance spectroscopic imaging.

In this work we propose minimum-norm reconstruction as a means to enhance the spatial response behavior in parallel spectroscopic MRI. By directly optimizing the shape of the spatial response function (SRF), the new method accounts for coil sensitivity variation across individual voxels and their side lobes. In this fashion, it mitigates the signal contamination and side-lobe aliasing, to which previous techniques are susceptible at low resolution. Although the computational burden is higher, minimum-norm reconstruction is shown to be feasible using an iterative algorithm. Benefits in terms of SRF shape and artifact suppression are demonstrated.

Algorithms↗
PubMed2006

Somatosensory-evoked potentials indicate increased unpleasantness of noxious stimuli in response to increasing stimulus intensities in the rat.

Recently, it has been shown in rats that specific characteristics of somatosensory-evoked potentials (SEPs) recorded from different sites on the scalp correlate differently to the amount of unpleasantness experienced by the animal following noxious stimulation. It was shown that the SEP recorded from vertex (Vx-SEP) did correlate with the unpleasantness, whereas the SEP recorded from the primary somatosensory cortex (SI-SEP) did not. In the present study, we further investigated the relationship between the Vx-SEP, SI-SEP and the unpleasantness of noxious stimuli. Therefore, different groups of rats were subjected to a SEP fear-conditioning paradigm in which the unconditioned stimulus (US), represented by noxious stimuli applied to evoke SEPs, was paired to a conditioned stimulus (CS) represented by a tone. Different stimulus intensities of the US were applied in the different groups. After CS-US presentation, CS-induced fear-conditioned behaviour was analysed in relation to the characteristics of the Vx- and SI-SEP during CS-US presentation. Results showed that increasing stimulus intensities led to increased SEP amplitudes, which were paralleled by an increased amount of CS-induced fear-conditioned behaviour. No differences between Vx-SEP and SI-SEP were found. The increase in the SEPs in parallel with the increased amount of fear-induced behaviour further supports the SEP to be a potentially valuable tool for studying acute pain and analgesia in animals.

Algorithms↗