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PubMed2006

Simultaneous parallel inclined readout image technique.

Sensitivity-encoded phase undersampling has been combined with simultaneous slice excitation to produce a parallel MRI method with a high volumetric acquisition acceleration factor without the need for auxiliary stepped field coils. Dual-slice excitation was produced by modulating both spin and gradient echo sequences at +/-6 kHz. Frequency aliasing of simultaneously excited slices was prevented by using an additional gradient applied along the slice axis during data acquisition. Data were acquired using a four-channel receiver array and x4 sensitivity encoding on a 1.5 T MR system. The simultaneous parallel inclined readout image technique has been successfully demonstrated in both phantoms and volunteers. A multiplicative image acquisition acceleration factor of up to x8 was achieved. Image SNR and resolution was dependent on the ratio of the readout gradient to the additional slice gradient. A ratio of approximately 2:1 produced acceptable image quality. Use of RF pulses with additional excitation bands should enable the technique to be extended to volumetric acquisition acceleration factors in the range of x16-24 without the SNR limitations of pure partially parallel phase reduction methods.

Algorithms↗
PubMed2006

Support vector classifiers via gradient systems with discontinuous righthand sides.

Gradient dynamical systems with discontinuous righthand sides are designed using Persidskii-type nonsmooth Lyapunov functions to work as support vector machines (SVMs) for the discrimination of nonseparable classes. The gradient systems are obtained from an exact penalty method applied to the constrained quadratic optimization problems, which are formulations of two well known SVMs. Global convergence of the trajectories of the gradient dynamical systems to the solution of the corresponding constrained problems is shown to be independent of the penalty parameters and of the parameters of the SVMs. The proposed gradient systems can be implemented as simple analog circuits as well as using standard software for integration of ODEs, and in order to use efficient integration methods with adaptive stepsize selection, the discontinuous terms are smoothed around a neighborhood of the discontinuity surface by means of the boundary layer technique. The scalability of the proposed gradient systems is also shown by means of an implementation using parallel computers, resulting in smaller processing times when compared with traditional SVM packages.

Algorithms↗
PubMed2005

Cerebral pathways in processing of affective prosody: a dynamic causal modeling study.

This study was conducted to investigate the connectivity architecture of neural structures involved in processing of emotional speech melody (prosody). 24 subjects underwent event-related functional magnetic resonance imaging (fMRI) while rating the emotional valence of either prosody or semantics of binaurally presented adjectives. Conventional analysis of fMRI data revealed activation within the right posterior middle temporal gyrus and bilateral inferior frontal cortex during evaluation of affective prosody and left temporal pole, orbitofrontal, and medial superior frontal cortex during judgment of affective semantics. Dynamic causal modeling (DCM) in combination with Bayes factors was used to compare competing neurophysiological models with different intrinsic connectivity structures and input regions within the network of brain regions underlying comprehension of affective prosody. Comparison on group level revealed superiority of a model in which the right temporal cortex serves as input region as compared to models in which one of the frontal areas is assumed to receive external inputs. Moreover, models with parallel information conductance from the right temporal cortex were superior to models in which the two frontal lobes accomplish serial processing steps. In conclusion, connectivity analysis supports the view that evaluation of affective prosody requires prior analysis of acoustic features within the temporal and that transfer of information from the temporal cortex to the frontal lobes occurs via parallel pathways.

Adult↗
PubMed2002

Can valerian improve the sleep of insomniacs after benzodiazepine withdrawal?

PURPOSE: The authors studied the sleep of patients with insomnia who complained of poor sleep despite chronic use of benzodiazepines (BZDs). The sample consisted of 19 patients (mean age 43.3+/-10.6 years) with primary insomnia (DSM-IV), who had taken BZDs nightly, for 7.1+/-5.4 years. The control group was composed of 18 healthy individuals (mean age 37+/-8 years). Sleep electroencephalogram (EEG) of the patients was analyzed with period amplitude analysis (PAA) and associated algorithms, during chronic BZD use (Night 1), and after 15 days of a valerian placebo trial (initiated after washout of BZD, Night 2). Sleep of control subjects was monitored in parallel. RESULTS: Valerian subjects reported significantly better subjective sleep quality than placebo ones, after BZD withdrawal, despite the presence of a few side effects. However, some of the differences found in sleep structure between Night 1 and Night 2 in both the valerian and placebo groups may be due to the sleep recovery process after BZD washout. Example of this are: the decrease in Sleep Stage 2 and in sigma count; the increase in slow-wave sleep (SWS), and delta count, which were found to be altered by BZD ingestion. There was a significant decrease in wake time after sleep onset (WASO) in valerian subjects when compared to placebo subjects; results were similar to normal controls. Nonetheless, valerian-treated patients also presented longer sleep latency and increased alpha count in SWS than control subjects. CONCLUSIONS: The decrease in WASO associated with the mild anxiolytic effect of valerian appeared to be the major contributor to subjective sleep quality improvement found after 2-week of treatment in insomniacs who had withdrawn from BDZs. Despite subjective improvement, sleep data showed that valerian did not produce faster sleep onset; the increase in alpha count compared with normal controls may point to residual hyperarousabilty, which is known to play a role in insomnia. Nonetheless, we lack data on the extent to which a sedative drug can improve alpha sleep EEG. Thus, the authors suggest that valerian had a positive effect on withdrawal from BDZ use.

Adult↗
PubMed2005

Free energies of ligand binding for structurally diverse compounds.

The one-step perturbation approach is an efficient means to calculate many relative free energies from a common reference compound. Combining lessons learned in previous studies, an application of the method is presented that allows for the calculation of relative binding free energies for structurally rather diverse compounds from only a few simulations. Based on the well known statistical-mechanical perturbation formula, the results do not require any empirical parameters, or training sets, only limited knowledge of the binding characteristics of the ligands suffices to design appropriate reference compounds. Depending on the choice of reference compound, relative free energies of binding rigid ligands to the ligand-binding domain of the estrogen receptor can be obtained that show good agreement with the experimental values. The approach presented here can easily be applied to many rigid ligands, and it should be relatively easy to extend the method to account for ligand flexibility. The free-energy calculations can be straightforwardly parallelized, allowing for an efficient means to understand and predict relative binding free energies.

Algorithms↗
PubMed2006

An alternative proof of Bukhgeim and Kazantsev's inversion formula for attenuated fan-beam projections.

An inversion formula was developed by Bukhgeim and Kazantsev for attenuated fan-beam projections [Russian Academy of Science Siberian Branch: The Sobolev Institute of Mathematics (2002)]. The inversion formula was obtained by relating the attenuated fan-beam projections to unattenuated fan-beam projections and by trickily processing the unattenuated fan-beam projections. We show in this paper that the inversion formula can be readily obtained from Novikov's inversion formula for the two-dimensional (2D) attenuated radon transform. The derivation provides an alternative proof of Bukhgeim and Kazantsev's inversion formula by the use of transformation between parallel-beam coordinates and fan-beam coordinates and thus is quite elementary.

Algorithms↗
PubMedDate not supplied

[Optic methods for measurements of muscle fiber birefringence].

An optical method for measuring the birefringence of muscle fibers was developed, which is realized on an automated Linnick interferometer microscope equipped with a laser. It was shown that the method has some advantages over the methods based on measurements of the intensity of light passing through a crossed polarizer, an analyzer, and a fiber (light polarized microscopy). The method involves direct phase measurements of optical path length at the parallel and perpendicular orientations of the polarization plane of probing radiation. The phase image is reconstructed automatically from interferograms with the use of the four-frame phase-shifting algorithm. The phase images of one and the same central part of the fiber at different orientations of the polarization plane represent two-dimensional numerical maps of the optical path length. The subtraction of these images gives a two-dimensional map of the phase shift, which includes information about the birefringence of the fiber. A formula for birefringence measurements was deduced, which has a certain advantage in comparison to that used earlier in that it does not take into account the thickness of a fiber that depends on the measurement point. The birefringence is normalized to a value of the half sum of phases, which are measured separately in the course of the experiment.

Algorithms↗
PubMed2003

Reorganization of water distribution system of Greater Jammu using computer software OPT DIS.

Water supply in old Jammu city is not evenly distributed due to undulating terrain and increase in population density. A study was undertaken to suggest measures for improvement to the distribution system. The paper presents results of analysis carried out using computer package OPT DIS developed at NEERI for optimal design of distribution sytem including system augmentation and reorganization measures needed for the design year 2021. The analysis of zone 1 of the distribution network indicates that seven pipes need alteation to cater to the demand for the year 2006 and fifteen pipes need replacement for the year 2021. New pipelines (13 nos.) are to be provided in parallel to the existing pipes in Upper Reach and 28 pipes in Lower Reach to ensure the service standards of 225 lpcd with minimum residual head of 17 m. Efficient algorithm for augmentations of water supply systems comprising combination of dead-end and loop network are having much wider application in developing countries. The software OPT DIS developed at NEERI was found to be extremely powerful and user friendly for addressing such systems with varying demand pattern, peaking factor, pipe condition, water supply modes and design horizones.

Algorithms↗
PubMed1991

Cone-beam transmission computed tomography for nonuniform attenuation compensation of SPECT images.

This paper develops and tests cone-beam transmission computed tomography (CB-CT) for attenuation compensation of SPECT images. CB-CT was implemented on a rotating gamma camera with a point source (1-2 mCi) of 99mTc, and a light-weight aluminum source holder. A cone-beam collimator may be used but is not required. Since the point source is either located at the collimator focal point, or the camera is uncollimated, CB-CT has excellent sensitivity (at least 150 times that of a parallel-hole, high-resolution collimator). The predicted resolution is equal to the intrinsic gamma camera resolution (3-4 mm), which is much higher than for a high-resolution, parallel-hole collimator (10-20 mm). In the present study, CB-CT provided low noise, high-resolution attenuation maps for use in a nonuniform attenuation-weighted backprojection algorithm. The attenuation compensation accuracy was tested using basic geometries of line sources and nonuniform density models. For the appropriate scaling of the attenuation map, the attenuation compensation was accurate and removed the SPECT image distortion associated with nonuniform attenuation. Attenuation maps acquired either with cone beam collimator or without any collimator were both successful. Using CB-CT, SPECT can thus be made much more accurate without adding unduly to the imaging time, complexity, or cost.

Algorithms↗
PubMed1996

Instantiating and monitoring skeletal treatment plans.

Current emphasis on protocol-based care has stirred interest in planning research as applied to clinical medicine. However, many assumptions made in designing traditional planners and plan-execution algorithms do not hold in medical domains. The problems include the unpredictable nature of the domain, uncertainty and the variability in the utility of available actions, and the need for parallel and continuous execution of treatment plans. In the context of our research on intelligent monitoring and control, we developed an approach for plan instantiation and execution which takes advantage of readily available treatment protocols. The system, named SPIN, instantiates treatment protocols based on current context, executes plans and closed-loop control actions, monitors the execution of plans and actions, and modifies plan execution as necessitated by patient response. The system is incorporated in the Guardian system for intensive-care patient monitoring and control. We address the strengths and limitations of the representation and the execution framework and discuss how the methodology may be improved and used in clinical practice.

Artificial Intelligence↗
PubMedDate not supplied

Biologically based validation of PC electrophysiology data collection systems utilizing the Good Automated Laboratory Practices.

Since there was a scientific need to conduct electrophysiology measurements to detect possible ocular (electroretinography, ERG), central neurotoxic (quantitative electroencephalography, qEEG), and cardiac (electrocardiography, ECG) effects in animals used in certain regulatory studies, the acquisition of suitable automated PC software systems were required. This article describes the process by which these systems were validated to ensure that they met the scientific requirements, while also addressing the principles of Good Automated Laboratory Practices (GALP). After a thorough search of existing commercial packages, a plan was developed specific for each PC-based collection system selected for evaluation. The common elements of each plan included consideration of both scientific and GALP elements, such as necessary biological response variables, raw data acquisition and identification, acceptance criteria, security, protection, storage media, data integrity, audit requirements and standard operating procedures. The authors' approach to validation for each electrophysiology system was to determine scientific needs for accuracy, precision, and detection limit of biological effects concurrent with GALP requirements. The selected software systems were employed in separate scientific GLP studies conducted in dogs, rats, and mini-pigs to demonstrate the ability to detect cholinesterase effects due to multiple infusions of physostigmine, based on parallel measurement of cholinesterase biomarkers. Since the systems were designed for human usage, certain adaptations were necessary. A critical assumption to be tested was the ability of the system's algorithms to adequately capture and assimilate the data in an accurate fashion. Concomitantly, the related GALP needs, such as data integrity, security, CD-ROM archive, and personnel training requirements were evaluated, implemented, and defined to accommodate the application and process needs. The biological approach to validation of these PC-based electrophysiology systems met the necessary scientific acceptance criteria as well as compliance requirements in order to be used in regulatory studies.

Algorithms↗
PubMed1998

Pinhole SPECT imaging in normal and morbid ankles.

UNLABELLED: Pinhole SPECT can generate sectional nuclear images of a normal and morbid ankle and hindfoot with remarkably enhanced resolution by portraying the topography and pathological alterations in great detail. METHODS: Pinhole SPECT was performed using a commercially available single-head, rotating gamma camera system by replacing the parallel-hole collimator used for planar SPECT with a pinhole collimator. The images were reconstructed in the same way as in planar SPECT by using the filtered back-projection algorithm and a Butterworth filter. First, we compared the scan resolution between the planar and pinhole SPECT images of a thyroid phantom and a normal ankle and hindfoot by working out pinhole SPECT anatomy with CT validation. Second, the clinical usefulness was assessed in one case each of fracture, reflex sympathetic dystrophy syndrome and rheumatoid arthritis of the ankle with radiographic correlation. The resolution of the pinhole SPECT and planar pinhole images was compared for these diseases. RESULTS: The resolution of the pinhole SPECT of a thyroid phantom and of a normal ankle and hindfoot was significantly enhanced compared to the planar SPECT although image distortion was seen in the periphery of the field-of-view. The pinhole SPECT resolution was such that most of the anatomical landmarks were sharply delineated in the ankle and hindfoot and some useful diagnostic signs in the diseased ankle were visible. CONCLUSION: Pinhole SPECT can be performed using a single-head gamma camera system and filtered back-projection algorithm. It generates sectional scan images of both normal and morbid ankle and hindfoot with enhanced resolution portraying many anatomical landmarks and pathological signs in useful detail.

Adult↗
PubMed1999

Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.

We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.

Algorithms↗
PubMed2005

Intensity-modulated radiotherapy technique for three-field breast treatment.

PURPOSE: To develop a simplified intensity-modulated radiotherapy (IMRT) algorithm for three-field breast treatment using a single isocenter setup. The algorithm aims to deliver a uniform dose throughout the breast volume. Special attention was paid to the highly divergent nature of the beam configuration. METHODS AND MATERIALS: Computed tomography (CT) image setup of the patient was acquired. On each CT slice, the computer automatically generated lines parallel to the posterior edge of the tangent field. The mid-point of each line segment that intersected the breast was determined and the dose from an open field calculated. The intensity of the divergent pencil beam corresponding to the mid-point was set to be inversely proportional to the open field dose to the mid-point. Forward dose calculation was then performed using this intensity distribution. RESULTS: A total of 15 breast cancer patients undergoing three-field IMRT who underwent planning and treatment with this algorithm were included in this study. Compared with standard wedged pair tangents, the IMRT plan produced statistically significant better dose distributions in terms of target coverage and target dose uniformity, as well as reduced dose to the contralateral breast and reduced hot spots to the ipsilateral lung. CONCLUSION: Since March 2004, the new IMRT algorithm has been used for planning and treatment of > 20 patients undergoing three-field treatment, as well as >200 patients undergoing regular two-field tangent treatment, all with excellent dose distributions throughout the breast volume.

Algorithms↗
PubMed1995

Order and disorder in auditory cortical maps.

Recent physiological experiments suggest that several basic receptive field properties of neurons show non-uniform spatial distributions in the primary auditory cortex of cats and primates. The spatial distribution patterns of some of these receptive field parameters are suggestive of a parallel coding scheme for processing sound information onto several superimposed cortical 'maps'. The representations of these parameters in the auditory cortex are compatible with general features of self-organizing mapping algorithms, as the spatial representations exhibit global parameter gradients with overlaid functional patchiness. Recent studies have also revealed that within a 'representational' map, the degree of local coherence varies over a wide range and that the map can contain a substantial degree of disorder in its parametric representation of sounds. Although the causes and consequences of this representational disorder are not known, it may reflect yet unresolved organizational principles in the auditory cortex.

Acoustic Stimulation↗
PubMed2006

Inducing NNC-Trees with the R4-rule.

An NNC-Tree is a decision tree (DT) with each non-terminal node containing a nearest neighbor classifier (NNC). Compared with the conventional axis-parallel DTs (APDTs), the NNC-Trees can be more efficient, because the decision boundary made by an NNC is more complex than an axis-parallel hyperplane. Compared with single-layer NNCs, the NNC-Trees can classify given data in a hierarchical structure that is often useful for many applications. This paper proposes an algorithm for inducing NNC-Trees based on the R4-rule, which was proposed by the author for finding the smallest nearest neighbor based multilayer perceptrons (NN-MLPs). There are mainly two contributions here. 1) A heuristic but effective method is given to define the teacher signals (group labels) for the data assigned to each nonterminal node. 2) The R4-rule is modified so that an NNC with proper size can be designed automatically in each nonterminal node. Experiments with several public databases show that the proposed algorithm can produce NNC-Trees effectively and efficiently.

Algorithms↗
PubMed2002

Increasing myocardial contraction and blood pressure in C57BL/6 mice during early postnatal development.

Knowledge of the developmental changes of cardiovascular parameters in the genetic background of a mouse strain is important for understanding phenotypic changes in transgenic or knockout mouse models for heart disease. We studied arterial blood pressure and myocardial contractility in mice of the common background strain C57BL/6, aged 21 days [postnatal day 21 (P21)] to 580 days. Heart rate increased during maturation from 396 beats/min at P21 to 551 beats/min at postnatal day 50 (P50), and mean arterial blood pressure increased in parallel from 86 to 110 mmHg and remained constant afterward. Echocardiographically determined left ventricular myocardial wall dimensions (R = 0.79, P < 0.0001) and left ventricular mass calculated using the area-length algorithm correlated strongly with histomorphometrical measurements (R = 0.93, P < 0.001). Sarcomere shortening records from isolated ventricular myocytes used as a measure for myocardial contractility revealed a negative shortening-frequency relation under a pacing frequency of 2 Hz and a positive relation above 2 Hz. Shortening amplitudes recorded from P21 myocytes were smaller, and the shortening-frequency relation was less steep than in adult myocytes. A stimulation pause was followed by a negative "staircase" at pacing frequency of < or =6 Hz and a positive staircase at > or =6 Hz. P21 myocytes developed positive staircases at 8 and 10 Hz, and adult myocytes also developed them at 6 Hz. Blood pressure increase during maturation until P50 may originate from increasing single cardiomyocyte contractility.

Aging↗
PubMed1999

A simple method for Emax trend evaluation: in vitro and in vivo results.

The aim of this study is the evaluation of end systolic ventricular elastance trend (as a measure of heart contractility) by hemodynamic variables available in intensive care units or during heart surgery: heart rate, cardiac output, left atrial, mean and diastolic arterial pressure. Its basic assumption is the description of ejection as the interaction between variable left ventricular and arterial compliances (reciprocal of the corresponding elastances) connected in parallel. As pressure is the same in each compliance at systole beginning and ending, ventricular elastance can be estimated by assuming that energy variation is the same on both compliances. The algorithm has been tested on a numerical simulator of the circulatory system and on six sheep at basal conditions and during drug infusion. Correlation function in numerical simulation, between true and computed ventricular elastance (range 0.45 divided by 5 mm Hg-cm(-3)), yields 0.985. In vivo comparison between computed ventricular elastance trend and ventricular dp/dt trend yields a correlation function ranging between 0.87 and 0.99. The result of the algorithm cannot be assumed to be Emax value. However, it can be considered a contractility index as it closely follows any change in dp/dt. It can be computed by simple calculations and needs no variables other than those usually measured in intensive care . It allows the extrapolation of useful information for evaluating the trend in heart contractility and for setting up a control strategy for mechanical or pharmacological assistance during heart recovery.

Algorithms↗