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PubMed2005

Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.

MOTIVATION: In a liquid chromatography-mass spectrometry (LC-MS)-based expressional proteomics, multiple samples from different groups are analyzed in parallel. It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance. RESULTS: We have developed an algorithm for spectrum deconvolution. A two-step alignment algorithm is proposed for recognizing peaks generated by the same peptide but detected in different samples. The quality of LC-MS data is evaluated using statistical tests and alignment quality tests. AVAILABILITY: Xalign software is available upon request from the author.

Algorithms↗
PubMed2005

Genetic-based fuzzy image filter and its application to image processing.

In this paper, we propose a Genetic-based Fuzzy Image Filter (GFIF) to remove additive identical independent distribution (i.i.d.) impulse noise from highly corrupted images. The proposed filter consists of a fuzzy number construction process, a fuzz filtering process, a genetic learning process, and an image knowledge base. First, the fuzzy number construction process receives sample images or the noise-free image and then constructs an image knowledge base for the fuzzy filtering process. Second, the fuzzy filtering process contains a parallel fuzzy inference mechanism, a fuzzy mean process, and a fuzzy decision process to perform the task of noise removal. Finally, based on the genetic algorithm, the genetic learning process adjusts the parameters of the image knowledge base. By the experimental results, GFIF achieves a better performance than the state-of-the-art filters based on the criteria of Peak-Signal-to-Noise-Ratio (PSNR), Mean-Square-Error (MSE), and Mean-Absolute-Error (MAE). On the subjective evaluation of those filtered images, GFIF also results in a higher quality of global restoration.

Algorithms↗
PubMed2005

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

SUMMARY: Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. AVAILABILITY: The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Algorithms↗
PubMed2001

Value of flow diagrams in reports of randomized controlled trials.

CONTEXT: Diagrams of the flow of participants through a clinical trial are recommended in the Consolidated Standards for Reporting of Trials (CONSORT) statement, but it is unclear whether such flow diagrams improve the quality of trial reports. OBJECTIVE: To examine the information contributed by flow diagrams and the completeness of reporting overall in reports of randomized controlled trials (RCTs) published in 5 general and internal medicine journals. DESIGN AND SETTING: Analysis of 270 reports of RCTs published in 1998 in the Annals of Internal Medicine (AIM; n = 19), BMJ (n = 42), JAMA (n = 45), The Lancet (n = 81), and The New England Journal of Medicine (NEJM; n = 83). MAIN OUTCOME MEASURES: Proportion of reports that included a flow diagram, information provided in flow diagrams, and completeness of reporting about flow of participants overall in flow diagrams or text. RESULTS: A total of 139 reports (51.5%) of RCTs included a flow diagram, but this varied widely among journals (AIM, 21.0%; BMJ, 38.1%; JAMA, 80.0%; The Lancet, 93.8%; and NEJM, 8.4%). Diagrams generally provided useful information, but only 73 (52.5%) included the number of participants who received allocated interventions and only 32 (23.0%) included the number of participants included in the analysis. In logistic regression analysis, overall completeness of reporting about flow of study participants was associated with publication of a flow diagram. CONCLUSIONS: Flow diagrams are associated with improved quality of reporting of randomized controlled trials. However, the structure of current flow diagrams is less than ideal. We propose a revised flow diagram that includes all important counts through the stages of parallel group trials.

Algorithms↗
PubMed2005

Videomicroscopy, image processing, and analysis of whole histologic sections of the human brain.

Serial histologic sections of a whole human brain may have extensions of up to 130 x 130 mm within the coronal plane around the temporal lobe. To date, however, technology has not provided a bright field microscope that is able to shift the object holder continuously in the x- and y-direction over such distances and still possess the same optical capabilities as comparable devices. We developed a new light microscope to continuously quantify such sections. We also developed the computing environment for controlling the device and for analyzing the data produced. In principle, we are now able to quantify each neuron of a human brain. The data ultimately will provide the most detailed structural information about the human brain ascertained thus far. Such detailed information of the spatial distribution of neurons is essential to develop realistic models for simulation of large-scale neuronal networks and to investigate the significance of neuronal arrangements with respect to neuronal signal processing in the CNS. After preprocessing of the data produced by the new microscope, we are able to detect lamination patterns in the spatial distribution of gravity centers of cells. Furthermore, morphological features like size of the projection area and mean staining intensity are visualized as a particle process. The particle process presents the sizes and staining intensity of perikaryons and allows a distinction of gray matter and white matter. These results provide evidence that the system works correctly and can be applied to a systematic analysis of a larger sequence of serial histologic sections. The objective of this study is to introduce the very large section analyzing microscope (VLSAM) and to present the initial data produced by the system. Moreover, we will discuss workload and future developments of the parallel image analysis system that are associated with the microscope.

Aged↗
PubMed2006

Encoding and reconstruction in parallel MRI.

The advent of parallel MRI over recent years has prompted a variety of concepts and techniques for performing parallel imaging. A main distinguishing feature among these is the specific way of posing and solving the problem of image reconstruction from undersampled multiple-coil data. The clearest distinction in this respect is that between k-space and image-domain methods. The present paper reviews the basic reconstruction approaches, aiming to emphasize common principles along with actual differences. To this end the treatment starts with an elaboration of the encoding mechanisms and sampling strategies that define the reconstruction task. Based on these considerations a formal framework is developed that permits the various methods to be viewed as different solutions of one common problem. Besides the distinction between k-space and image-domain approaches, special attention is given to the implications of general vs lattice sampling patterns. The paper closes with remarks concerning noise propagation and control in parallel imaging and an outlook upon key issues to be addressed in the future.

Algorithms↗
PubMed1989

A low-cost single-board solution for real-time, unsupervised waveform classification of multineuron recordings.

We describe a low-cost single-board system for unsupervised, real-time spike sorting of recordings from a number of neurons on a single microelectrode. The maximum number of spike classes depends on the quality of the recording; it will typically be between 2 and 5. The spike sorter communicates with a conventional microcomputer through a standard serial port (RS232). For typical firing rates as measured in the mammalian central nervous system, this set-up will accommodate up to some 10 parallel spike sorters for as many separate microelectrodes.

Algorithms↗
PubMed2004

Magnetoencephalographic gamma-band responses to illusory triangles in humans.

Electroencephalography studies have suggested that the perception of illusory figures is associated with increases in gamma-band activity putatively reflecting the formation of synchronously firing neuronal assemblies. Here we assessed magnetoencephalographic gamma-band activity, which has been shown to be topographically more focal than in electroencephalogram. In line with functional brain imaging findings, we hypothesized gamma-band activity over ventral visual stream areas. In addition, we expected that the analysis of oscillatory activity would provide information on the time courses and connectivity patterns of these activations. Following a paradigm previously assessed with electroencephalography, 16 adults were presented four types of stimuli at equal probabilities: illusory (Kanizsa) triangles, real triangles, no-triangle stimuli with rotated inducer disks, and curved illusory triangles serving as targets that subjects had to respond to. Induced oscillatory responses were compared between illusory triangles and no-triangle stimuli and between illusory and real triangles using a statistical probability mapping method. Illusory triangles were distinguished from no-triangles by increased activity at around 70 Hz over midline occipital cortex peaking at 240 ms after stimulus onset. This was followed by activations over bilateral lateral occipital areas at 430 ms. Illusory triangles differed from real triangles by increased spectral activity at 90 Hz over posterior parietal cortex between 100 and 450 ms after stimulus onset, suggesting an involvement of visual dorsal stream regions. Coherence analysis showed increased connectivity between posterior parietal and lateral occipital cortex. These findings suggest that illusory triangles are encoded in parallel by networks along the visual ventral and dorsal streams.

Adult↗
PubMed2003

Exploratory data analysis using set operations and ordinal mapping.

Exploratory data analysis requires the ability to issue ad hoc queries to filter and summarise data sets. As the sizes of health data sets grow, traditional methods of processing data have difficulty in providing acceptable response times for such queries. An alternative method is described which combines complete vertical partitioning of data with set operations on ordinal mappings (SOOM). An initial implementation of the technique provides significantly better performance than a conventional SQL database on typical exploratory data analysis queries. The use of parallel, distributed computation to further increase the performance of the technique appears to be feasible.

Algorithms↗
PubMed2001

A model of oxidative phosphorylation in mammalian skeletal muscle.

A dynamic computer model of oxidative phosphorylation in oxidative mammalian skeletal muscle was developed. The previously published model of oxidative phosphorylation in isolated skeletal muscle mitochondria was extended by incorporation of the creatine kinase system (creatine kinase plus phosphocreatine/creatine pair), cytosolic proton production/consumption system (proton production/consumption by the creatine kinase-catalysed reaction, efflux/influx of protons), physiological size of the adenine nucleotide pool and some additional minor changes. Theoretical studies performed by means of the extended model demonstrated that the CK system, which allows for large changes in P(i) in relation to isolated mitochondria system, has no significant influence on the kinetic properties of oxidative phosphorylation, as inorganic phosphate only slightly modifies the relationship between the respiration rate and [ADP]. Computer simulations also suggested that the second-order dependence of oxidative phosphorylation on [ADP] proposed in the literature refers only to the ATP synthesis flux, but not to the oxygen consumption flux (the difference between these two fluxes being due to the proton leak). Next, time courses of changes in fluxes and metabolite concentrations during transition between different steady-states were simulated. The model suggests, in accordance with previous theoretical predictions, that activation of oxidative phosphorylation by an increase in [ADP] can (roughly) explain the behaviour of the system only at low work intensities, while at higher work intensities parallel activation of different steps of oxidative phosphorylation is involved.

Adenosine Diphosphate↗
PubMed2002

Parallel computing in microwave heating analysis.

The use of parallel computing in the finite element analysis of microwave heating applicators is discussed. Numerical results for a multiple feed cavity at 896 MHz and a cavity with a mode stirrer at 2.45 GHz are presented, and it is shown that for the two structures parallelism is most effectively introduced at different levels in the analysis.

Algorithms↗
PubMed2003

Dynamics of deterministic and stochastic paired excitatory-inhibitory delayed feedback.

We examine the effects of paired delayed excitatory and inhibitory feedback on a single integrate-and-fire neuron with reversal potentials embedded within a feedback network. These effects are studied using bifurcation theory and numerical analysis. The feedback occurs through modulation of the excitatory and inhibitory conductances by the previous firing history of the neuron; as a consequence, the feedback also modifies the membrane time constant. Such paired feedback is ubiquitous in the nervous system. We assume that the feedback dynamics are slower than the membrane time constant, which leads to a rate model formulation. Our article provides an extensive analysis of the possible dynamical behaviors of such simple yet realistic neural loops as a function of the balance between positive and negative feedback, with and without noise, and offers insight into the potential behaviors such loops can exhibit in response to time-varying external inputs. With excitatory feedback, the system can be quiescent, can be periodically firing, or can exhibit bistability between these two states. With inhibitory feedback, quiescence, oscillatory firing rates, and bistability between constant and oscillatory firing-rate solutions are possible. The general case of paired feedback exhibits a blend of the behaviors seen in the extreme cases and can produce chaotic firing. We further derive a condition for a dynamically balanced paired feedback in which there is neither bistability nor oscillations. We also show how a biophysically plausible smoothing of the firing function by noise can modify the existence and stability of fixed points and oscillations of the system. We take advantage in our mathematical analysis of the existence of an invariant manifold, which reduces the dimensionality of the dynamics, and prove the stability of this manifold. The novel computational challenges involved in analyzing such dynamics with and without noise are also described. Our results demonstrate that a paired delayed feedback loop can act as a sophisticated computational unit, capable of switching between a variety of behaviors depending on the input current, the relative strengths and asymmetry of the two parallel feedback pathways, and the delay distributions and noise level.

Action Potentials↗
PubMed2001

Photophysical characterization of natural cis-carotenoids.

By means of steady-state fluorescence spectroscopy we explore the photophysics of two lowest lying singlet excited states in two natural 15-cis-carotenoids, namely phytoene and phytofluene, possessing three and five conjugated double bonds (N), respectively. The results are interpreted in relation to the photophysics of all-transcarotenoids with varying N. The fluorescence of phytofluene is more Stokes-shifted relative to that of phytoene, and is ascribed to the forbidden S1-->S0 transition, with its first excited singlet state (S1) lying 3340 cm-1 below the dipole allowed second excited singlet state (S2), at 77 K. For phytoene the S2 and S1 potential surfaces are closer in energy, probably giving rise to the mixed S2 and S1 fluorescence characteristics. The origin of phytoene fluorescence is discussed and is suggested to be due to the S1-->S0 transition; with the S1 state located 1100 cm-1 below S2 at 77 K. The dependence of the fluorescence quantum yield on temperature and viscosity shows that large amplitude molecular motions are involved in the radiationless relaxation process of phytoene. The transition dipole moment of absorption and emission are parallel in phytoene and nonparallel in phytofluene.

Algorithms↗
PubMed1988

Refined evaluation of the exponential curve parameters and initial exchange rate constant for 22Na+ washout in cultured human skin fibroblasts.

A technique is proposed to evaluate the exponential curve parameters and the initial exchange rate constant (kie) for 22Na+ washout from cultured human skin fibroblasts. After loading with the isotope, the cells were subjected to cold washing and warming steps. A desaturation curve for 22Na+ washout was developed including the activity in the warming medium that corresponded to t = 0 min. Using nonlinear regression analysis, a general three exponential function adequately described the 22Na+ washout in the time interval of 0-70 min. A back extrapolation was performed to estimate the initial time (ti; a negative number) when the total activity was present in the cells. The ti was substituted into the first derivative function of the three exponents to yield the kie. Calculated from the equilibrium distribution of 22Na+ and the specific activity of the medium, the concentration of Na+ (in mM; mean +/- SD) for fibroblasts of two individuals were 13.3 +/- 2.3, n = 3, and 19.0 +/- 5.2, n = 4. This indicates that the washout originated mainly or exclusively from the cellular milieu. Therefore, the kie represents the equilibrium exchange rate constant for Na+ washout from an inhomogeneous cell-related space. Multiple experiments demonstrated that the kie value for the two subjects were significantly higher than the initial slopes of the washout curves (kA), a commonly used parameter to characterize Na+ washout, and significantly lower than the slopes of the fastest exponential components (k3): kie = 0.531 +/- 0.017, kA = 0.502 +/- 0.019, and k3 = 0.557 +/- 0.017 min-1 (n = 3) for one subject, and kie = 0.567 +/- 0.065, kA = 0.479 +/- 0.031, and k3 = 0.667 +/- 0.094 min-1 (n = 6) for the other subject. The respective equilibrium exchange rates for these cells, namely the products of kie and cellular Na+ contents, were 1.10 +/- 0.16 and 1.19 +/- 0.24 nmole/10(5) cells. Using the exponential curve parameters, analytical solutions of a serial model and a parallel model with three compartments were performed. According to these analyses the major portion of the cellular Na+ comprises a fast exchangeable cellular compartment. The relative size of this compartment (expressed as a fraction of total cellular Na+ content) for fibroblasts of the two subjects was 96.2 and 89.2% for the serial model and 96.1 and 89.3% according to the parallel model.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed2006

On-axis sensitivity and resolution of a slit-slat collimator.

UNLABELLED: A slit-slat collimator combines a slit along the axis of rotation with a set of axial septa, offering both magnification in the transaxial direction and complete sampling with just a circular orbit. This collimator has a sensitivity that increases for points near the aperture slit. The literature treats this collimator as having the same sensitivity as a single-pinhole collimator, ignoring the effect of the axial septa. Herein, the sensitivity and resolution of this collimator are reevaluated. METHODS: Experimental and Monte Carlo methods are used to determine the sensitivity and resolution in both the transaxial and axial directions as a function of distance from the slit (h). Eight configurations are tested, varying the slit width, septal spacing, and septal height. RESULTS: Both the experimental and the Monte Carlo sensitivities agree reasonably with an analytic form that is the geometric mean of the pinhole and parallel-beam formulas, disagreeing with previous literature. Transaxial resolution is consistent with the pinhole-resolution formula. Axial resolution is consistent with the parallel-beam resolution formula. CONCLUSION: The sensitivity of this collimator is proportional to h(-1) and has resolution in the transaxial direction that is consistent with pinhole resolution and in the axial direction that is consistent with parallel-beam resolution.

Algorithms↗
PubMed2003

Compression assessment based on medical image quality concepts using computer-generated test images.

Compression algorithms are widely used in medical imaging systems for efficient image storage, transmission, and display. In the acceptance of lossy compression algorithms in the clinical environment, important factors are the assessment of 'visually lossless' compression thresholds, as well as the development of assessment methods requiring fewer data and time than observer performance based studies. In this study a set of quantitative measurements related to medical image quality parameters is proposed for compression assessment. Measurements were carried out using region of interest (ROI) operations on computer-generated test images, with characteristics similar to radiographic images. As a paradigm, the assessment of the lossy Joint Photographic Expert Group (JPEG) algorithm, available in a telematics application for healthcare, is presented. A compression ratio of 15 was found as the visually lossless threshold for the JPEG lossy algorithm, in agreement with previous observer performance studies. Up to this ratio low contrast discrimination is not affected, image noise level is decreased, high contrast line-pair amplitude is decreased by less than 3%, and input/output gray level differences are minor (less than 1%). This type of assessment provides information regarding the type of loss, offering cost and time benefits, in parallel with the advantages of test image adaptation to the requirements of a certain imaging modality and clinical study.

Algorithms↗
PubMed2003

Accelerating comparative genomics using parallel computing.

In the past decade there has been an increase in the number of completely sequenced genomes due to the race of multibillion-dollar genome-sequencing projects. The enormous biological sequence data thus flooding into the sequence databases necessitates the development of efficient tools for comparative genome sequence analysis. The information deduced by such analysis has various applications viz. structural and functional annotation of novel genes and proteins, finding gene order in the genome, gene fusion studies, constructing metabolic pathways etc. Such study also proves invaluable for pharmaceutical industries, such as in silico drug target identification and new drug discovery. There are various sequence analysis tools available for mining such useful information of which FASTA and Smith-Waterman algorithms are widely used. However, analyzing large datasets of genome sequences using the above codes seems to be impractical on uniprocessor machines. Hence there is a need for improving the performance of the above popular sequence analysis tools on parallel cluster computers. Performance of the Smith-Waterman (SSEARCH) and FASTA programs were studied on PARAM 10000, a parallel cluster of workstations designed and developed in-house. FASTA and SSEARCH programs, which are available from the University of Virginia, were ported on PARAM and were optimized. In this era of high performance computing, where the paradigm is shifting from conventional supercomputers to the cost-effective general-purpose cluster of workstations and PCs, this study finds extreme relevance. Good performance of sequence analysis tools on a cluster of workstations was demonstrated, which is important for accelerating identification of novel genes and drug targets by screening large databases.

Algorithms↗
PubMed2005

ABACUS, a direct method for protein NMR structure computation via assembly of fragments.

The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.

Algorithms↗