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Phase-constrained parallel MR image reconstruction.

A generalized method for phase-constrained parallel MR image reconstruction is presented that combines and extends the concepts of partial-Fourier reconstruction and parallel imaging. It provides a framework for reconstructing images employing either or both techniques and for comparing image quality achieved by varying k-space sampling schemes. The method can be used as a parallel image reconstruction with a partial-Fourier reconstruction built in. It can also be used with trajectories not readily handled by straightforward combinations of partial-Fourier and SENSE-like parallel reconstructions, including variable-density, and non-Cartesian trajectories. The phase constraint specifies a better-conditioned inverse problem compared to unconstrained parallel MR reconstruction alone. This phase-constrained parallel MRI reconstruction offers a one-step alternative to the standard combination of homodyne and SENSE reconstructions with the added benefit of flexibility of sampling trajectory. The theory of the phase-constrained approach is outlined, and its calibration requirements and limitations are discussed. Simulations, phantom experiments, and in vivo experiments are presented.

Algorithms↗

Self-organizing task modules and explicit coordinate systems in a neural network model for 3-D saccades.

The goal of this study was to train an artificial neural network to generate accurate saccades in Listing's plane and then determine how the hidden units performed the visuomotor transformation. A three-layer neural network was successfully trained, using back-prop, to take in oculocentric retinal error vectors and three-dimensional eye orientation and to generate the correct head-centric motor error vector within Listing's plane. Analysis of the hidden layer of trained networks showed that explicit representations of desired target direction and eye orientation were not employed. Instead, the hidden-layer units consistently divided themselves into four parallel modules: a dominant "vector-propagation" class (approximately 50% of units) with similar visual and motor tuning but negligible position sensitivity and three classes with specific spatial relations between position, visual, and motor tuning. Surprisingly, the vector-propagation units, and only these, formed a highly precise and consistent orthogonal coordinate system aligned with Listing's plane. Selective "lesions" confirmed that the vector-propagation module provided the main drive for saccade magnitude and direction, whereas a balance between activity in the other modules was required for the correct eye-position modulation. Thus, contrary to popular expectation, error-driven learning in itself was sufficient to produce a "neural" algorithm with discrete functional modules and explicit coordinate systems, much like those observed in the real saccade generator.

Algorithms↗

GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space.

GEOMETRY is a software package for the analysis of nucleotide sequences using the method of statistical geometry in sequence space. The package consists of programs performing estimation of the average geometry of sequence quartets, analysis of positional variability and computer simulation of parallel and tree-like sequence divergence with user-defined parameters. It provides an independent tool for evaluation of the reliability of conventional phylogenetic trees and calibration of the time of sequence divergence. GEOMETRY may be of interest for all scientists engaged in the study of molecular phylogeny. The package is available by anonymous FTP from ftp.bionet.nsk.su, directory /incoming/molevol/geom.exe, and will be available from EMBL file server (URL: http://@www.ebi.ac.uk)

Algorithms↗

Fourier-based forward and back-projectors in iterative fan-beam tomographic image reconstruction.

Fourier-based forward and back-projection methods can reduce computation in iterative tomographic image reconstruction. Recently, an optimized nonuniform fast Fourier transform (NUFFT) approach was shown to yield accurate parallel-beam projections. In this paper, we extend the NUFFT approach to describe an O (N2 log N) projector/backprojector pair for fan-beam transmission tomography. Simulations and experiments with real CT data show that fan-beam Fourier-based forward and back-projection methods can reduce computation for iterative reconstruction while still providing accuracy comparable to their O (N3) space-based counterparts.

Algorithms↗

[A rapid detection of motor block in patients with Parkinson disease during volitional movements of the hand].

INTRODUCTION: An algorithm to study hand movements in patients with Parkinson's disease (PD) who experience temporary, involuntary inability to move a hand have been developed. In literature, this rather engimatic phenomenon has been described in gait, speech, handwriting and tapping, and noted as motor blocks (MB) or freezing episodes. Freezing refers to transient periods in which the voluntary motor activity being attempted by an individual is paused. It is a sudden, unplanned state of immobility that appears to arise from deficits in initiating or simultaneously and sequentially executing movements, in correcting inappropriate movements or in planning movements. The clinical evaluation of motor blocks is difficult because of a variability both within and between individuals and relationship of blocks to time of drug ingestion. In literature the terms freezing, motor block or motor freezing are used in parallel. AIM: In clinical settings classical manifestations of Parkinson's Disease (akinesia, bradykinesia, rigidity, tremor, axial motor performance and postural instability) are typically evaluated. Recently, in literature, new computerized methods are suggested for their objective assessment. We propose monitoring of motor blocks during hand movements to be integrated. For this purpose we have developed a simple method that comprises PC computer, digitizing board and custom made software. Movement analysis is "off line", and the result is the data that describe the number, duration and onset of motor blocks. METHOD: Hand trajectories are assessed during simple volitional self paced point-to-point planar hand movement by cordless magnetic mouse on a digitizing board (Drawing board III, 305 x 457 mm, GTCO Cal Comp Inc), Fig. 1. Testing included 8 Parkinsonian patients and 8 normal healthy controls, age matched, with unknown neurologic motor or sensory disorders, Table 1. Three kinematic indicators of motor blocks: 1) duration (MBT%); 2) onset (t%); and 3) number (N) of MB episodes, allow identification and quantification of motor blocks. Duration of motor blocks (MBT) is defined as the time sequence when (x,y) coordinates do not change their values and is expressed in percentage from the whole movement duration MBT% = MBT/T (%). If during some movements more than one motor block occurs (N > 1) then this movement is decomposed. The whole movement motor block (mbt) is the sum of all motor blocks MBT; during the same movement and expressed in percentage from the whole movement duration mbt% = mbt/T (%). The onset of motor block (t) is determined with the beginning of motor block and expressed in percentage from the whole movement duration: t% = t/T (%). After the determination of kinematic indicators of motor blocks (MBT, N, t) for healthy controls, their mean values are calculated. Statistical package ANOVA is applied to determine statistical significance of the difference between PD patients and mean values from age matched control healthy group. PD patients are then classified into two groups: one group consisting of PD patients with motor blocks and the other without motor blocks, similar to healthy controls. RESULTS: Acquired movements are processed and analyzed. Fig. 2 is an example of hand trajectories. Time course of (x, y) coordinates indicates motor block appearance, Fig. 3. Detailed presentation of kinematic indicators of motor block (MBT, N, t) is in Fig. 4. Intra-subject variability of these parameters is presented in Figs 5, 6 and 7 for patient #3. The results for N show that 45% of all patients #3 movements had none motor blocks (N = 0); 20% had N = 1; 15% had N = 2; 11.5% had N = 3; 5.7% had N = 4; 0.3% had N = 5; 0.7% had N = 6; 0.3% had N = 7 and 1% had N = 8 motor blocks. The results for t% show that 3% of all patients' #3 blocks started at first quarter, 17% started in the second, 36% in the third, and 44% in the last quarter of movement. The results for MBT% show that 14.5% of all movements had MBT% in the range 0-5%; 56% had MBT% 5-10%; 22% had MBT% 10-15%; 5.5% had MBT% 15-20% and 2% had MBT% 20-25%. No block lasted more than 25% from the whole movement duration. Table 2 is the summary of mean variability for kinematic indicators of motor block (N, mbt%, t%) and for the movement duration T during a 7 day-testing of patients #3. The analysis of calculated data for eight tested PD patients revealed a significant difference (p < 0.01) between healthy controls and three PD patients; data on five PD patients were not significantly different (ns). This method clustered 3 PD patients in the group that experience motor blocks, while the rest were in the group without their significant occurrence. DISCUSSION: This algorithm is an additional instrument in classical evaluation of PD patients during their clinical evaluation and treatment. It provides to clinician a rapid feedback on the changes of voluntary hand movements in everyday progress of illness. Furthermore, this method could be of assistance for developing strategies to overcome motor blocks in arm movements at their beginning, as well as for the feedback of the success of drug therapy.

Adult↗

Parallel cascade identification and kernel estimation for nonlinear systems.

We consider the representation and identification of nonlinear systems through the use of parallel cascades of alternating dynamic linear and static nonlinear elements. Building on the work of Palm and others, we show that any discrete-time finite-memory nonlinear system having a finite-order Volterra series representation can be exactly represented by a finite number of parallel LN cascade paths. Each LN path consists of a dynamic linear system followed by a static nonlinearity (which can be a polynomial). In particular, we provide an upper bound for the number of parallel LN paths required to represent exactly a discrete-time finite-memory Volterra functional of a given order. Next, we show how to obtain a parallel cascade representation of a nonlinear system from a single input-output record. The input is not required to be Gaussian or white, nor to have special autocorrelation properties. Next, our parallel cascade identification is applied to measure accurately the kernels of nonlinear systems (even those with lengthy memory), and to discover the significant terms to include in a nonlinear difference equation model for a system. In addition, the kernel estimation is used as a means of studying individual signals to distinguish deterministic from random behaviour, in an alternative to the use of chaotic dynamics. Finally, an alternate kernel estimation scheme is presented.

Algorithms↗

Detection, classification and 3D reconstruction of biological macromolecules on hypercube computers.

In this work we present results of the mapping on hypercube computers of some of the key steps involved in the procedure for 3D structural determination from transmission electron microscopy images. The goal is the introduction of parallel processing tools in the field of electron microscopy image processing. We show how the rich topology of the hypercube, combined with an efficient programming strategy, allows for order-of-magnitude increase in computational capacity for such time-consuming tasks as calculation of multidimensional FFT's, cross-correlation coefficients, fuzzy partitioning functionals and the filtered back-projection 3D reconstruction method.

Algorithms↗

Photon migration in turbid media with anisotropic optical properties.

We analyse properties of photon migration in reflectance measurements made on a semi-infinite medium bounded by a plane, in which optical parameters may vary in directions neither parallel to, nor perpendicular to the bounding plane. Our aim in doing this is to develop the formulae necessary to deduce parameters of directionality from both time-gated and continuous wave measurements. The mathematical development is based on a diffusion picture, in which the bounding plane is regarded as being totally absorbing so that all photons reaching the surface contribute to the reflectance.

Algorithms↗

Recombination factors for the cylindrical FC65-G ionization chamber in pulsed photon beams and the plane-parallel Roos ionization chamber in pulsed electron beams.

The use of ionization chambers in linac radiotherapy dosimetry requires various corrections to the measured charges, one of these being the recombination correction. The recombination correction factor (k(s)) is generally estimated from the two-voltage analysis (TVA) for each beam quality. However, it is possible that the ionization chamber above some threshold polarizing voltage does not follow the accepted Boag theory very well. Secondly the TVA is time-consuming as the chamber needs to stabilize after each polarizing voltage change and since it must be performed for each beam quality. Another approach consists in using the fact that k(s) is predicted to depend linearly on dose per pulse by Boag theory: determining this relationship once and for all using a multi-voltage analysis (MVA), one also checks the range validity of the Boag theory for the chamber considered. This work presents a thorough analysis of k(s) dependence on dose per pulse of FC65-G (cylindrical) and Roos (plane-parallel) ionization chambers in pulsed photon and electron beams, respectively. Within the uncertainties, the recombination factors are found to be independent of beam quality, and no deviation from the Boag theory is observed within the tested range of polarizing voltages. Before adapting the equations given using the MVA other users should check that their ionization chambers show the same dose per pulse dependence using the TVA for a few beam qualities.

Algorithms↗

Activation analysis of concrete and graphite in the experimental reactor RUS.

The decommissioning and dismantling of nuclear installations after their service life involves the necessary disassembling, handling and disposing of a large amount of radioactive equipment and structures. In particular, the concrete that has been used as a biological reactor shield and graphite that has been used as a moderator-reflector represent the majority of waste, requiring geological disposal. To reduce this undesirable volume to the minimum and to successfully plan the dismantling and disposal of radioactive materials to storage facilities, the activations of the structures should be accurately evaluated. In the framework of the decommissioning and the dismantling of the experimental reactor of the University of Strasbourg, detailed activation estimates have been conducted to characterise the graphite and the structural materials present in the reactor environment. For this purpose, the chemical compositions of fresh graphite samples and different types of concrete have been determined by activation analysis in the research reactors OSIRIS and ORPHEE of CEA Saclay (France). Then, the activations of graphite, concrete and other materials have been calculated in the whole reactor, as a function of the three main nuclear data libraries, i.e. ENDF, JEF and JENDL. In parallel, the activations of representative graphite and concrete samples have been measured experimentally. The comparison of theoretical predictions with experimental values validates the approach and the methodology used in the present study and tests the consistency and the reliability of the nuclear data used for activation analysis. We believe that a similar approach could also be used for the decommissioning of industrial nuclear reactors.

Algorithms↗

Insect motion perception.

The first step in this work of reconstruction of a theory of insect vision was to demonstrate that visual behaviour relies on scanning by self-motion and apparently involves measurement of angular velocities of contrasts moving across the eye. The next step was to demonstrate that parallax is also significant as a way of segmenting the visual scene into separate objects. There followed a series of experiments to rule out the existing theory that motion perception depends on autocorrelation, and at the same time an alternative theory was developed. The new theory assumes that at the level of the optic medulla there are numerous parallel channels on each visual axis, representing different neurons, all looking out for their specific combination of signals. The combinations are formed by positive, negative or no-change temporal contrasts at two adjacent visual axes at two successive times, forming 3(4) = 81 possible templates. Simulation of this highly parallel system shows that it can represent the moving image in a compact form that would be adequate to explain what is known for motion and form vision (but not colour vision) in insects. Form, like colour, would be seen as the ratio of numbers of responses of particular templates, in the same way that colours are seen as ratios of responses of receptors for different wavelengths.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

Public health monitoring tools for multiple data streams.

INTRODUCTION: In concert with increased concerns regarding both biologic terrorism and new natural infectious disease threats (e.g., severe acute respiratory syndrome [SARS] and West Nile virus), as a result of advances in medical informatics, various data sources are available to epidemiologists for routine, prospective monitoring of public health. The synthesis of this evidence requires tools to find anomalies within various data stream combinations while maintaining manageable false alarm rates. OBJECTIVES: The objectives of this report are to establish statistical hypotheses to define the compound multivariate problem of surveillance systems, present statistical methods for testing these hypotheses, and examine results of applying these methods to simulated and actual data. METHODS: Canonical problems of parallel monitoring and consensus monitoring are considered in this report. Modified Bonferroni methods are examined for parallel monitoring. Both multiple univariate and multivariate methods are applied for consensus monitoring. A multivariate adaptation of Monte Carlo trials, using the injection of epidemic-curve-like signals in the multiple data streams of interest, is presented for evaluation of the various tests. RESULTS: The Monte Carlo test results demonstrate that the multiple univariate combination methods of Fisher and Edgington provide the most robust detection performance across the scenarios tested. As the number of data streams increases, methods based on Hotelling's T2 offer added sensitivity for certain signal scenarios. This potential advantage is clearer when strong correlation exists among the data streams. CONCLUSION: Parallel and consensus monitoring tools must be blended to enable a surveillance system with distributed sensitivity and controlled alert rates. Whether a multiple univariate or multivariate approach should be used for consensus monitoring depends on the number and distribution of useful data sources and also on their covariance structure and stationarity. Strong, consistent correlation among numerous sources warrants the examination of multivariate control charts.

Algorithms↗

Assessment of the vasomotility of epicardial coronary arteries with quantitative coronary angiography.

Quantitative in vivo analysis of the vasomotility of epicardial coronary arteries is based on the measurement of changes of the vessel diameters. Vessel contours can be determined with the help of a precision caliper by the investigator or with computer-assisted geometrical analysis systems applying a contour detection algorithm; the variability of the results from repeated coronary diameter measurements in the identical film frame is comparably low with all systems (less than or equal to 0.12 mm standard deviation). When investigating the influence of an intervention on coronary vasomotility the variability of the measurements can only be kept low by careful standardization of the entire method. Repeated coronary angiograms are performed in identical angiographic projections (mono- or biplane) with standardization of the inspiratory status of the patient and of the rate of contrast material injection (automatic injection pump). For quantitative analysis all coronary segments with a diameter greater than 1 mm which are clearly outlined, free from overlaps, and mainly run parallel to the image plane, are selected by the investigator in preferably end-diastolic cineframes. Whereas with a caliper and with most of the semi-automatic edge detection systems the segment diameter can only be measured at particular sites defined by the investigator, few systems are able to analyze and average the diameter over the entire segment length. The variability of measurements of the minimal diameters of coronary stenoses in different cine frames is particularly high; therefore, only distinct changes of this parameter (e.g. with the CAAS-system greater than 0.24 mm) may be considered significant.(ABSTRACT TRUNCATED AT 250 WORDS)

Cineangiography↗

High-throughput techniques for analyzing complex bacterial communities.

A more complete understanding of microbial diversity and the environmental processes they control will require much more than a biotic inventory. It will require a deeper understanding of the basic features of systems organization and inter-population interactions. Communities, not total biomass, control net process rates driving the biogeochemical cycles sustaining the biosphere. Although the general patterns of macroorganismal diversity are relatively well known, spatial and temporal patterns of microorganismal diversity are essentially unknown. Having tools capable of resolving these patterns is a prerequisite to developing an understanding of the relationship between community structure and function. This talk discusses conceptual and technical developments that now provide the framework for systematically resolving temporal and spatial patterns of microorganisms and relating those patterns to processes at local and system levels. Of particular emphasis will be ongoing studies using highly parallel analyses with DNA microarrays for intensive monitoring of microbial populations in environmental systems. Although microarray technology is reasonably well established for studies of model organisms in well-defined laboratory settings, the application of this technology to environmental systems of uncharacterized diversity imposes additional demands on implementation; in particular, the requirement for optimized discrimination between target and non-target nucleic acids in complex, and undefined, mixtures. To increase the resolving power (information content) of our DNA microarray format, we are investigating the use of thermal dissociation of hybrids immobilized on individual array elements to resolve target and non-target sequences that differ by a single nucleotide. These studies, combined with specialized algorithms for optimizing the readout of the microarray should serve for informed environmental application. Initial studies have validated the general approach for analyses of sediment systems.

Bacteria↗

Combination (multiple) testing for myocardial infarction using myoglobin, creatine kinase-2 (mass), and troponin T.

We retrospectively determined the mass concentrations of myoglobin, creatine kinase-2 (CK-2), and troponin T in serial samples from 80 patients with confirmed myocardial infarction (MI) and 60 non-MI patients. Results from receiver operating characteristic curve analyses show that all three tests are comparable in their diagnostic utility within the first 12 h of infarction. Decision thresholds were selected at a constant rule-in specificity of 95% and rule-out sensitivities of 95% at, respectively, 3-6, 6-9, and 9-12 h intervals after the onset of symptoms. Test sensitivities and specificities were compared for each, used as: a single test; two-test parallel combination; three-test parallel combination; two-test series combination; and three-test series combination. Our results from combination testing indicate what for the early diagnosis of MI, a single serum myoglobin measurement has diagnostic utility at 3 h after the onset of symptoms, and myoglobin and CK-2 (mass) in combination later than 3 h following the onset of symptoms. Serum troponin T is diagnostically similar to CK-2 (mass), although it has superior cardiac-tissue specificity, but it is not as yet commercially available as a "stat" test. Therefore, we recommend using troponin T as a confirmatory test 9 h after the onset of MI. Based on our findings, we suggest a testing algorithm for the early biochemical diagnosis of MI.

Adult↗

Optimal contrast agents for vascular imaging on computed tomography: iodixanol versus iohexol.

RATIONALE AND OBJECTIVES: Dimeric nonionic iodinated contrast has a lower osmolality than monomeric nonionic iodinated contrast but is available at lower iodine concentrations. Less dilution of intravascular fluid by influx from the extravascular space is proposed to occur with decreasing osmolality. The purpose of this study was to determine if a dimeric nonionic iso-osmolar contrast agent (iodixanol) gives equal vascular enhancement compared with a monomeric nonionic hyperosmolar contrast agent (iohexol). MATERIALS AND METHODS: A dynamic single-level computed tomography (CT) scan was performed of the abdominal aorta of 12 sedated rabbits using a four-row multidetector CT scanner following injection of 1.5 mL contrast/kg body weight at 2 mL/sec. The rabbits were injected with the dimeric contrast agent iodixanol (Visipaque 320; Amersham Health) or the monomeric contrast agent iohexol (Omnipaque 350; Amersham Health). The order of the type of contrast media injected was randomized for each rabbit, and the interval between injections was 2 weeks. Using the 2.5-mm detectors, four contiguous 3-mm contrast-enhanced scans were obtained at a single level every 5 seconds for 120 seconds (total of 24 scans) with a kVp of 120, mA.s of 110, field of view of 106 mm, and soft tissue reconstruction algorithm. A single level was chosen to measure the attenuation of the abdominal aorta at 5-second intervals. The mean attenuation and standard deviation values were recorded for the whole aorta, for the central half of the vessel, and for the peripheral half of the vessel. A log-log transformation of the data was performed and regression analysis was done on the outcomes of interest (e.g., mean, standard deviation) on time for each region. RESULTS: There was no statistically significant difference in mean attenuation for the whole aorta for iodixanol and iohexol (P = .918) even though the iodine content was 9.3% less with the dimeric iodixanol. The time-attenuation curve of iodixanol paralleled that of iohexol for all time points. The mean attenuation values of the central half of the aorta (P = .354) and peripheral half of the aorta (P = .758) were also not statistically different for the two contrast agents. CONCLUSION: The vascular attenuation provided by a 9.3% lower iodine concentration of iso-osmolar iodixanol is equal to that given by hyperosmolar iohexol. This suggests that there is less intravascular dilution of iso-osmolar contrast. The enhancement across the cross section of the vessel is also similar for both contrast agents. This suggests the vascular studies with iodixanol and iohexol are of equal quality even when a lower dose of iodine is given with iodixanol. It is relevant for patients with borderline or diminished renal function in whom less volume of contrast may be administered.

Animals↗

Optimization of ion-exchange displacement separations. II. Comparison of displacement separations on various ion-exchange resins.

A variety of stationary-phase materials are currently available for the chromatographic purification of biomolecules. However, the effect of various resin characteristics on the performance of displacement chromatography has not been studied in depth. In Part I, a novel iterative scheme was presented for the rapid optimization of displacement separations in ion-exchange systems. In this article, the optimization scheme is employed to identify the optimum operating conditions for displacement separations on various ion-exchange resin materials. In addition, the effect of different classes of separation problems (e.g., diverging, converging or parallel affinity lines) on the performance of displacement separations is also presented. The solid film linear driving force model is employed in concert with the Steric Mass Action isotherm to describe the chromatographic behavior in these systems. The results presented in this article provide insight into the effects of resin capacity and efficiency as well as the type of separation problem on the performance of various ion-exchange displacement systems.

Algorithms↗

FFC: a scalable FASTA compressor.

SUMMARY: FASTA is a widely used text-based format for storing nucleotide and protein sequences. The existing FASTA compressors usually focus on (slightly) improving the compression ratio, not on practical performance. We present FFC, a scalable FASTA compressor that achieves average compression speeds 4.7&#xd7; and 11.4&#xd7; higher than two high-performance compressors, zstd and NAF, respectively, across a benchmark set of seven single genomes. It also delivers average decompression speeds 3.5&#xd7; and 2.7&#xd7; higher than zstd and NAF, respectively. Although a chunk-based zstd variant with parallel decompression, pzstd, almost matches FFC speed, its compression ratio is on average by 23% worse than FFC's. For the experiment, a 14-core workstation and a RAM disk (to reduce the impact of I/O) were used. AVAILABILITY AND IMPLEMENTATION: FFC is freely available at github.com/kowallus/ffc and also as a Zenodo repository at 10.5281/zenodo.18892353, and the used datasets at 10.5281/zenodo.18873744.

Data Compression↗