Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Parallel Algorithms”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,495 records · Page 83Linked to original sources

Ideal-observer performance under signal and background uncertainty.

We use the performance of the Bayesian ideal observer as a figure of merit for hardware optimization because this observer makes optimal use of signal-detection information. Due to the high dimensionality of certain integrals that need to be evaluated, it is difficult to compute the ideal observer test statistic, the likelihood ratio, when background variability is taken into account. Methods have been developed in our laboratory for performing this computation for fixed signals in random backgrounds. In this work, we extend these computational methods to compute the likelihood ratio in the case where both the backgrounds and the signals are random with known statistical properties. We are able to write the likelihood ratio as an integral over possible backgrounds and signals, and we have developed Markov-chain Monte Carlo (MCMC) techniques to estimate these high-dimensional integrals. We can use these results to quantify the degradation of the ideal-observer performance when signal uncertainties are present in addition to the randomness of the backgrounds. For background uncertainty, we use lumpy backgrounds. We present the performance of the ideal observer under various signal-uncertainty paradigms with different parameters of simulated parallel-hole collimator imaging systems. We are interested in any change in the rankings between different imaging systems under signal and background uncertainty compared to the background-uncertainty case. We also compare psychophysical studies to the performance of the ideal observer.

Algorithms↗

Plasma neurohormone levels correlate with left ventricular functional and morphological improvement in LVAD patients.

OBJECTIVE: Brain natriuretic peptide (BNP) and endothelin-1 (ET-1) have been shown to be markers of left ventricular (LV) function. To determine the feasibility of using serial assays of these neurohormones in the assessment of cardiac status in the left ventricular assist device (LVAD) setting, we examined the relationship between LV function, myocardial morphology, and plasma levels of these hormones in LVAD recipients. METHODS: Plasma BNP and ET-1 levels were serially assayed in 19 end-stage congestive heart failure (CHF) patients before and after LVAD implantation with various devices (i.e., MicroMed DeBakeyVAD/DVAD, Novacor/NVAD, TCI Heartmate/TCI, Thoratec/TVAD). Echocardiography performed correspondingly at the time points of the hormonal assays and immunohistochemical collagen staining of left ventricular tissue samples, derived from six non-failing hearts as well as from LVAD patients at the time of device insertion and removal, were then contrasted. Patients were grouped according to device used and etiology of heart disease (ischemic or dilated cardiomyopathy, ICM/DCM). RESULTS: LVAD therapy significantly improved LV ejection fraction (EF%: 21 +/- 3.8% to 28.11 +/- 3.57%), cardiac output (CO: 3.49 +/- 1.3 to 7.3 +/- 0.2 l/m), and left ventricular end-diastolic diameter (LVEDD: 6.68 +/- 0.92 versus 4.79 +/- 1.54 cm, P < 0.0001) in all patients. Absolute BNP and ET-1 plasma levels remained significantly lower in all patients after LVAD implantation (both P < 0.001). The NVAD group exhibited the most BNP reduction and EF% increase (P < 0.0004 and P < 0.038, respectively). Average collagen levels were reduced in all patients (P < 0.0005). Among the devices, the NVAD group demonstrated the most evident change (P < 0.0036), while there was comparable reduction in the DCM and ICM groups (both P < 0.03). In general, postoperative BNP and ET-1 trends exhibited a notable parallelism with both manifesting bi-phasic tendencies and an inverse proportionality to corresponding EF% measurements. CONCLUSIONS: Device selection appears to influence the cardiac morphological and neurohormonal expressive tendencies exhibited by recipients. Plasma BNP and ET-1 levels correlate with both LV function and myocardial morphological improvement. Alterations in the levels of these hormones during LVAD support may be real-time indicators of prevailing myocardial autocrine/paracrine activity and as such may be of potential use in future algorithms of cardiac assessment and therapeutic decision-making with regard to transplant urgency and/or possible device explantation.

Adult↗

Coupling ion mobility separations, collisional activation techniques, and multiple stages of MS for analysis of complex peptide mixtures.

An ion trap/ion mobility/quadrupole/collision cell/time-of-flight mass spectrometer that incorporates a differentially pumped orifice-skimmer cone region at the back of the drift tube has been developed for the analysis of peptide mixtures. The combined approach allows a variety of strategies to be employed for collisionally activating ions, and fragments can be monitored by subsequent stages of mass spectrometry in a parallel fashion, as described previously (Anal. Chem. 2000, 72, 2737). Here, we describe the overall experimental approach in detail. Applications involving different aspects of the initial mobility separation and various collisional activation and parallel sequencing strategies are illustrated by examining several simple peptide mixtures and a mixture of tryptic peptides from beta-casein. Detection limits associated with various experimental configurations and the utility for analysis of complex systems are discussed.

Algorithms↗

Methodological aspects of the genetic dissection of gene expression.

MOTIVATION: Dissection of the genetics underlying gene expression utilizes techniques from microarray analyses as well as quantitative trait loci (QTL) mapping. Available QLT mapping methods are not tailored for the highly automated analyses required to deal with the thousand of gene transcripts encountered in the mapping of QTL affecting gene expression (sometimes referred to as eQTL). This report focuses on the adaptation of QTL mapping methodology to perform automated mapping of QTL affecting gene expression. RESULTS: The analyses of expression data on > 12,000 gene transcripts in BXD recombinant inbred mice found, on average, 629 QTL exceeding the genome-wide 5% threshold. Using additional information on trait repeatabilities and QTL location, 168 of these were classified as 'high confidence' QTL. Current sample sizes of genetical genomics studies make it possible to detect a reasonable number of QTL using simple genetic models, but considerably larger studies are needed to evaluate more complex genetic models. After extensive analyses of real data and additional simulated data (altogether > 300,000 genome scans) we make the following recommendations for detection of QTL for gene expression: (1) For populations with an unbalanced number of replicates on each genotype, weighted least squares should be preferred above ordinary least squares. Weights can be based on repeatability of the trait and the number of replicates. (2) A genome scan based on multiple marker information but analysing only at marker locations is a good approximation to a full interval mapping procedure. (3) Significance testing should be based on empirical genome-wide significance thresholds that are derived for each trait separately. (4) The significant QTL can be separated into high and low confidence QTL using a false discovery rate that incorporates prior information such as transcript repeatabilities and co-localization of gene-transcripts and QTL. (5) Including observations on the founder lines in the QTL analysis should be avoided as it inflates the test statistic and increases the Type I error. (6) To increase the computational efficiency of the study, use of parallel computing is advised. These recommendations are summarized in a possible strategy for mapping of QTL in a least squares framework. AVAILABILITY: The software used for this study is available on request from the authors.

Algorithms↗

MR volumetry for monitoring intramuscular bromocriptine treatment in macroprolactinomas.

OBJECTIVE: To assess volumetric changes of pituitary prolactinomas, we applied a threshold-based segmentation algorithm in two patients during intramuscular bromocriptine treatment. MATERIALS AND METHODS: Tumor volumes were calculated from contiguous slices of a 3D GE sequence and from conventional SE images. RESULTS: After a single 50 mg i.m. bromocriptine administration, the prolactinoma volumes decreased by 25 and 35% within 7 and 11 days, respectively. Volume calculations from 3D GE images were more accurate than calculations from 3 mm 2D SE images, especially for smaller tumors. A decrease of prolactinoma size was paralleled by a decrease of serum prolactin levels and correlated with an improvement of visual field and endocrine function in both patients. The end of the bromocriptine effect was indicated by a reincreasing tumor volume, which was observed after 30 days in the first patients and after 43 days in the second patient. CONCLUSION: Our results suggest that MR volumetry represents a useful tool to monitor changes of prolactinoma volume during bromocriptine treatment and may improve the clinical management of these patients.

Adult↗

Fast fully 3-D image reconstruction in PET using planograms.

We present a method of performing fast and accurate three-dimensional (3-D) backprojection using only Fourier transform operations for line-integral data acquired by planar detector arrays in positron emission tomography. This approach is a 3-D extension of the two-dimensional (2-D) linogram technique of Edholm. By using a special choice of parameters to index a line of response (LOR) for a pair of planar detectors, rather than the conventional parameters used to index a LOR for a circular tomograph, all the LORs passing through a point in the field of view (FOV) lie on a 2-D plane in the four-dimensional (4-D) data space. Thus, backprojection of all the LORs passing through a point in the FOV corresponds to integration of a 2-D plane through the 4-D "planogram." The key step is that the integration along a set of parallel 2-D planes through the planogram, that is, backprojection of a plane of points, can be replaced by a 2-D section through the origin of the 4-D Fourier transform of the data. Backprojection can be performed as a sequence of Fourier transform operations, for faster implementation. In addition, we derive the central-section theorem for planogram format data, and also derive a reconstruction filter for both backprojection-filtering and filtered-backprojection reconstruction algorithms. With software-based Fourier transform calculations we provide preliminary comparisons of planogram backprojection to standard 3-D backprojection and demonstrate a reduction in computation time by a factor of approximately 15.

Algorithms↗

Single- and multifrequency models for bioelectrical impedance analysis of body water compartments.

The 1994 National Institutes of Health Technology Conference on bioelectrical impedance analysis (BIA) did not support the use of BIA under conditions that alter the normal relationship between the extracellular (ECW) and intracellular water (ICW) compartments. To extend applications of BIA to these populations, we investigated the accuracy and precision of seven previously published BIA models for the measurement of change in body water compartmentalization among individuals infused with lactated Ringer solution or administered a diuretic agent. Results were compared with dilution by using deuterium oxide and bromide combined with short-term changes of body weight. BIA, with use of proximal, tetrapolar electrodes, was measured from 5 to 500 kHz, including 50 kHz. Single-frequency, 50-kHz models did not accurately predict change in total body water, but the 50-kHz parallel model did accurately measure changes in ICW. The only model that accurately predicted change in ECW, ICW, and total body water was the 0/infinity-kHz parallel (Cole-Cole) multifrequency model. Use of the Hanai correction for mixing was less accurate. We conclude that the multifrequency Cole-Cole model is superior under conditions in which body water compartmentalization is altered from the normal state.

Adult↗

Micromechanical resonator array for an implantable bionic ear.

In this paper we report on a multi-resonant transducer that may be used to replace a traditional speech processor in cochlear implant applications. The transducer, made from an array of micro-machined polymer resonators, is capable of passively splitting sound into its frequency sub-bands without the need for analog-to-digital conversion and subsequent digital processing. Since all bands are mechanically filtered in parallel, there is low latency in the output signals. The simplicity of the device, high channel capability, low power requirements, and small form factor (less than 1 cm) make it a good candidate for a completely implantable bionic ear device.

Algorithms↗

New management strategies in the treatment of status epilepticus.

Status epilepticus is a neurologic emergency associated with high mortality and long-term disability. Recent advances in our understanding of the pathophysiological mechanisms involved in the initiation and perpetuation of seizure activity have revealed that status epilepticus is a dynamic and evolving process. Alterations at the cellular level parallel physiological, physical, and electrical changes at the bedside. Loss of cerebral autoregulation and neuronal damage begin after 30 minutes of continuous seizure activity. This understanding has led to changes in treatments of status epilepticus, which must be multidisciplinary and occur simultaneously in many different areas. The goals of pharmacological therapy are to terminate seizures early and prevent recurrence. Two recent large clinical studies have shown the benefit of early administration of benzodiazepines to control status epilepticus. Pharmacological algorithms designed to focus medical management have trended toward earlier and more aggressive treatment. The hope is that continued exploration into the basic mechanisms involved in status epilepticus and future controlled clinical trials defining optimal medical management will produce further advances.

Anticonvulsants↗

Bradykinin modulation of tumor vasculature: II. activation of nitric oxide and phospholipase A2/prostaglandin signaling pathways synergistically modifies vascular physiology and morphology to enhance delivery of chemotherapeutic agents to tumors.

Intravenous infusions of the bradykinin agonist Cereport (labradimil, formerly RMP-7) enhance delivery of concomitantly administered hydrophilic chemotherapeutic agents to solid tumors. The enhanced delivery produces greater in vivo efficacy of chemotherapeutic agents, manifested as suppressed tumor growth and increased survival in tumor-bearing rats. Here we elucidate the mechanisms of action involved with this unique phenomenon, at both the physical and biochemical levels. At the physical level we demonstrate that Cereport modifies the tumor vasculature in several important ways, including transient 1) reductions in interstitial fluid pressure within the tumor, 2) increases in pore size of the vasculature, and 3) increases in total vascular surface area. All three of these changes modify tumor-specific characteristics of the vasculature known to impede drug delivery to the tumor interstitium. Biochemically, we demonstrate that the activation of both of bradykinin's major signaling pathways, the nitric oxide and phospholipase A2/prostaglandin E2 are necessary events. Although pharmacologically blocking either pathway greatly reduced the effects of Cereport, stimulation of either pathway alone did not enhance delivery. However, simultaneous stimulation of both pathways (without exogenous bradykinin B2 receptor stimulation) produced a nearly 2-fold increase in delivery of carboplatin to the tumor. Thus, stimulation of endogenous bradykinin B2 receptors induces at least two parallel biochemical cascades that act synergistically to uniquely modify the tumor vasculature in ways that increase delivery and efficacy of chemotherapeutic agents.

Algorithms↗

Dynamic autocalibrated parallel imaging using temporal GRAPPA (TGRAPPA).

Current parallel imaging techniques for accelerated imaging require a fully encoded reference data set to estimate the spatial coil sensitivity information needed for reconstruction. In dynamic parallel imaging a time-interleaved acquisition scheme can be used, which eliminates the need for separately acquiring additional reference data, since the signal from directly adjacent time frames can be merged to build a set of fully encoded full-resolution reference data for coil calibration. In this work, we demonstrate that a time-interleaved sampling scheme, in combination with autocalibrated GRAPPA (referred to as TGRAPPA), allows one to easily update the coil weights for the GRAPPA algorithm dynamically, thereby improving the acquisition efficiency. This method may update coil sensitivity estimates frame by frame, thereby tracking changes in relative coil sensitivities that may occur during the data acquisition.

Algorithms↗

Apparent response incompatibility effects on P3 latency depend on the task.

Ten young women were tested with an ERP paradigm that used the words 'left,' 'right,' 'LEFT,' 'RIGHT' as stimuli. The stimulus sequence was presented as several separate runs with varying response instructions. Subjects were instructed to respond according to the meaning of the stimulus in the (WORD task), to the case in which the stimulus was written (CASE task), or to both the case and meaning of the stimulus (CASE/WORD) task. In each task, half the trials called for a response that was incompatible with the stimulus. For the WORD task, compatible and incompatible trials were presented as separate blocks of trials. For all 3 tasks an additional stimulus sequence was presented in which the words were degraded with superimposed visual random noise. Reaction time (RT) in the CASE/WORD task was more than 100 msec later than in the other tasks. In the WORD and CASE/WORD tasks, RT was delayed more than 100 msec when the response was incompatible with the stimulus. Degrading the stimulus additionally delayed RT by about 100 msec. In the WORD and CASE tasks, error RTs were earlier than correct RTs. P3 latency was measured with a single-trial latency adjustment algorithm. P3 latency was delayed in the CASE/WORD task compared to the other 2 tasks. P3 was delayed by degrading the stimuli. Contrary to some previous reports, P3 was delayed by about 70 msec when incompatible responses were required, but only in the WORD task. Taken together with error and RT data, these P3 latency data are consistent with the notion that the task causes subjects to adopt different strategies and hence different types of processing (i.e., serial vs. parallel). Depending on the type of processing, P3 may appear to be affected by response incompatibility.

Adult↗

Evaluation and management of pituitary incidentalomas--revisiting an acquaintance.

Incidentalomas of the pituitary gland have been described with increasing frequency, paralleling the advances in diagnostic imaging modalities. Several approaches have been proposed in order to appropriately evaluate their impact on patients, some recommending extensive investigations, while others advocate a more focused and potentially more cost-effective approach. The first part of this article will review current data about the prevalence, natural history and potential morbidity associated with these tumors. The second part will focus on imaging and hormonal evaluation of the incidental mass and suggest an updated management algorithm.

Adenoma↗

Reconstruction of 2D PET data with Monte Carlo generated system matrix for generalized natural pixels.

In discrete detector PET, natural pixels are image basis functions calculated from the response of detector pairs. By using reconstruction with natural pixel basis functions, the discretization of the object into a predefined grid can be avoided. Here, we propose to use generalized natural pixel reconstruction. Using this approach, the basis functions are not the detector sensitivity functions as in the natural pixel case but uniform parallel strips. The backprojection of the strip coefficients results in the reconstructed image. This paper proposes an easy and efficient way to generate the matrix M directly by Monte Carlo simulation. Elements of the generalized natural pixel system matrix are formed by calculating the intersection of a parallel strip with the detector sensitivity function. These generalized natural pixels are easier to use than conventional natural pixels because the final step from solution to a square pixel representation is done by simple backprojection. Due to rotational symmetry in the PET scanner, the matrix M is block circulant and only the first blockrow needs to be stored. Data were generated using a fast Monte Carlo simulator using ray tracing. The proposed method was compared to a listmode MLEM algorithm, which used ray tracing for doing forward and backprojection. Comparison of the algorithms with different phantoms showed that an improved resolution can be obtained using generalized natural pixel reconstruction with accurate system modelling. In addition, it was noted that for the same resolution a lower noise level is present in this reconstruction. A numerical observer study showed the proposed method exhibited increased performance as compared to a standard listmode EM algorithm. In another study, more realistic data were generated using the GATE Monte Carlo simulator. For these data, a more uniform contrast recovery and a better contrast-to-noise performance were observed. It was observed that major improvements in contrast recovery were obtained with MLEM when the correct system matrix was used instead of simple ray tracing. The correct modelling was the major cause of improved contrast for the same background noise. Less important factors were the choice of the algorithm (MLEM performed better than ART) and the basis functions (generalized natural pixels gave better results than pixels).

Algorithms↗

Detection of multiple sclerosis with visual evoked potentials--an unsupervised computational intelligence system.

This paper describes the application of a novel unsupervised pattern recognition system to the classification of the Visual Evoked Potentials (VEP's) of normal and multiple sclerosis (MS) patients. The method combines a traditional statistical feature extractor with a fuzzy clustering method, all implemented in a parallel neural network architecture. The optimization routine, ALOPEX, is used to train the network while decreasing the likelihood of local solutions. The unsupervised system includes a feature extraction and clustering module, trained by the optimization routine ALOPEX. Through maximization of the output variance of each node, and an architecture which excludes redundancy, the feature extraction network retains the most significant Karhunen-Loeve expansion vectors. The clustering module uses a modification to the Fuzzy c-Means (FCM) clustering algorithms, where ALOPEX adjusts a set of cluster centers to minimize an objective error function. The result combines the power of the FCM algorithms with the advantage of a more global solution from ALOPEX. The new pattern recognition system is used to cluster the VEP's of 13 normal and 12 MS subjects. The classification with this technique can, without supervision, separate the patient population into two groups which largely correspond to the MS and control subject groups. A suitable threshold can be chosen so that the recognizer chooses no false negatives. The use of multiple stimulation patterns appears to improve the reliability of the decision. The reasoning of most neural networks in their decision making cannot easily be extracted upon the completion of training. However, due to the linearity of the network nodes, the cluster prototypes of this unsupervised system can be reconstructed to illustrate the reasoning of the system. In this application, this analysis hints at the usefulness of previously unused portions of the VEP in detecting MS. It also indicates a possible use of the system as a training aide.

Adult↗

Seven-pinhole tomography--a technical description.

A single-photon emission tomography system was developed and studied. Based upon a seven-pinhile-collimated Anger camera, interfaced to a digital minicomputer, this imaging configuration yielded seven independent, nonoverlapping projection images of the radioactivity in a commonly viewed volume. The computer was used to implement an iterative algorithm that processed these projections to yield a three-dimensional reconstruction of the soruce distribution. The algorithm provudes a nonlinear first approximation to the reconstruction, then use a single iteration technique to reduce errors resulting from that approximation. Point spread functions (PSF) at various distances from the collimator face, and point-source sensitivity (PSS) at a location in the middle of the reconstruction volume were determined. The system was used for thallium-201 imaging, where it was shown to reduce imaging time and increase sensitivity without loss in specificity when compared with standard parallel-hole-collimated imaging. Seven-pinhole tomography is a practical three-dimensional imaging system that has been demonstrated to be useful in the emission cardiology setting.

Heart↗

PROPELLER-EPI with parallel imaging using a circularly symmetric phased-array RF coil at 3.0 T: application to high-resolution diffusion tensor imaging.

A technique integrating multishot periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) and parallel imaging is presented for diffusion echo-planar imaging (EPI) at high spatial resolution. The method combines the advantages of parallel imaging to achieve accelerated sampling along the phase-encoding direction, and PROPELLER acquisition to further decrease the echo train length (ETL) in EPI. With an eight-element circularly symmetric RF coil, a parallel acceleration factor of 4 was applied such that, when combined with PROPELLER acquisition, a reduction of geometric distortions by a factor substantially greater than 4 was achieved. The resulting phantom and human brain images acquired with a 256 x 256 matrix and an ETL of only 16 were visually identical in shape to those acquired using the fast spin-echo (FSE) technique, even without field-map corrections. It is concluded that parallel PROPELLER-EPI is an effective technique that can substantially reduce susceptibility-induced geometric distortions at high field strength.

Adult↗

Data analysis of alternative splicing microarrays.

The importance of alternative splicing in drug and biomarker discovery is best understood through several example genes. For most genes, the identification, detection and particularly quantification of isoforms in different tissues and conditions remain to be carried out. As a result, the focus in drug and biomarker development is increasingly on high-throughput studies of alternative splicing. Initial strategies for the parallel analysis of alternative splicing by microarrays have been recently published. The design specificities and goals of alternative splicing microarrays, in terms of identification and quantification of multiple mRNAs from one gene, are promoting the development of novel methods of analysis.

Algorithms↗