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Phase function measurements on nonspherical scatterers using a two-axis goniometer.

We present a two-axis goniometer for measuring the phase function of scattering media with an angular resolution of about 0.2 deg having 12 decades of dynamic range and covering almost the full solid angle. The setup is evaluated with polystyrene spheres and with perpendicularly and obliquely illuminated thin glass cylinders. The scattering pattern and its intensity distribution are in excellent agreement with analytical theory. A multiple scattering configuration composed of two parallel cylinders is also examined. Finally, the phase function of dentin slabs is measured and its dependence on the dental microstructure is discussed.

Algorithms↗

Optoelectronic implementation of neural networks.

The performance of electronic neural networks will eventually be limited by the capacity of their interconnections as operating speeds are increased. The use of optical connections to link electronic elements offers a way to overcome this problem. In particular, spatial optic techniques are especially suited to neural systems because of their parallel structure. Three experimental optoelectronic networks are described that employ holographic components and arrays of high-speed optical modulators. These of a network to 64 x 8 connections with optical fan-out. A hybrid networks have been used to demonstrate operation at 50 MHz, novel training algorithms and the expansion technique for integrating optoelectronic systems is also being developed.

Algorithms↗

Nonlinear analysis of EEG signals at different mental states.

BACKGROUND: The EEG (Electroencephalogram) is a representative signal containing information about the condition of the brain. The shape of the wave may contain useful information about the state of the brain. However, the human observer can not directly monitor these subtle details. Besides, since bio-signals are highly subjective, the symptoms may appear at random in the time scale. Therefore, the EEG signal parameters, extracted and analyzed using computers, are highly useful in diagnostics. This work discusses the effect on the EEG signal due to music and reflexological stimulation. METHODS: In this work, nonlinear parameters like Correlation Dimension (CD), Largest Lyapunov Exponent (LLE), Hurst Exponent (H) and Approximate Entropy (ApEn) are evaluated from the EEG signals under different mental states. RESULTS: The results obtained show that EEG to become less complex relative to the normal state with a confidence level of more than 85% due to stimulation. CONCLUSIONS: It is found that the measures are significantly lower when the subjects are under sound or reflexologic stimulation as compared to the normal state. The dimension increases with the degree of the cognitive activity. This suggests that when the subjects are under sound or reflexologic stimuli, the number of parallel functional processes active in the brain is less and the brain goes to a more relaxed state

Adolescent↗

Impact of antiandrogen treatment on the fatty acid profile of neutral lipids in human meibomian gland secretions.

The purpose of this study was to determine whether the use of antiandrogen medications is associated with significant alterations in the fatty acid (FA) profiles of neutral lipids in human meibomian gland secretions. Meibomian gland secretions were obtained from both eyes of patients receiving antiandrogen therapy and from age-related controls. Samples were processed for high-performance liquid chromatography/mass spectrometry and an evaluation of the mass/charge ratios of neutral lipid FA. Our results demonstrate that antiandrogen therapy is associated with significant and consistent alterations in the mass/charge ratios of neutral lipid fractions of meibomian gland secretions. Patients taking antiandrogen medications had significant changes in the occurrence of numerous diglyceride, triglyceride, and wax/cholesterol ester FA products, compared with age-matched controls. Statistical analyses of data within groups demonstrated very high correlation coefficients, and cross-correlation analyses revealed characteristic shifts in FA patterns between groups. Our findings show that antiandrogen use is paralleled by significant changes in the FA profiles of neutral lipid fractions in meibomian gland secretions.

Aged↗

Novel, adjustable, clinical bymixer measures mixed expired gas concentrations in anesthesia circle circuit.

UNLABELLED: We have introduced a novel, parallel design into a new clinical bymixer (patent pending), named for the bypass of a constant fraction of total flow through a mixing chamber. Over a wide range of tidal volumes (300-1200 mL), frequency (6-20 breaths/min), and PCO(2) (6-50 mm Hg), the bymixer provided accurate measurement of mixed expired gas fractions in the ventilation circuit compared with an expired gas collection in a metabolic lung bench setup (average slope, 1.00; average y intercept, -0.01; average coefficient of determination, R(2) = 0.9988). Simple changes in mixing chamber volume provided adjustable bymixer response times. The fast bymixer response (time constant, 6.4 s) should allow measurements to be updated every 20 s (where 95% response occurs by three time constants). The new clinical bymixer is constructed from standard anesthesia circuit components, attaches easily to the anesthesia machine inspired outlet and expired inlet ports, is simple to clean and sterilize, and has no reservoir to trap condensed water vapor from expired gas. The new clinical bymixer may facilitate indirect calorimetry (CO(2) elimination, VCO(2), and oxygen uptake, VCO(2)) during anesthesia and the noninvasive detection of metabolic upset (e.g., onset of anaerobic metabolism) and critical events (e.g., pulmonary embolism). IMPLICATIONS: A new clinical bymixer (inline mixing chamber) provides a fast response and accurate measurements of mixed expired gas fractions in the anesthesia circle circuit. A novel parallel design facilitates adjustable response, easy cleaning, and construction from standard airway circuit components. The new clinical bymixer may facilitate widespread introduction of indirect calorimetry during anesthesia.

Algorithms↗

Regional variation and function of nucleotide and amino acid sequence.

Two methods of qualitative analysis of sequence distribution in DNA and protein are presented. The first method is based on the finding that the frequency of occurrence of each nucleotide in a defined sequence with functional significance more or less deviates from uniform distribution. The deviation found in this defined sequence seems to parallel the function of this sequence. In the second method, two model compounds (trypsin and its inhibitor) have been used to see the topological fit between their local structures. Acrophilicity parameter for amino acid was used to construct the topological structure. Both methods may find practical application in algorithms to design functional DNA and protein molecules.

Algorithms↗

Singular spectrum analysis applied to backscattered ultrasound signals from in vitro human cancellous bone specimens.

Mean scatterer spacing (MSS) holds particular promise for the detection of changes in quasiperiodic tissue microstructures such as may occur during development of disease in the liver, spleen, or bones. Many techniques that may be applied for MSS estimation (temporal and spectral autocorrelation, power spectrum and cepstrum, higher order statistics, and quadratic transformation) characterize signals that contain a mixture of periodic and nonperiodic contributions. In contrast, singular spectrum analysis (SSA), a method usually applied in nonlinear dynamics, first identifies components of signals corresponding to periodic structures and, second, identifies dominant periodicity. Thus, SSA may better separate periodic structures from nonperiodic structures and noise. Using an ultrasound echo simulation model, we previously demonstrated SSA's potential to identify MSS of structures in quasiperiodic scattering media. The current work aims to observe the behavior of MSS estimation by SSA using ultrasound measurements in phantom materials (two parallel, nylon-line phantoms and four foam phantoms of different densities). The SSA was able to estimate not only the nylon-line distances but also nylon-line thickness. The method also was sensitive to the average pore-size differences of the four sponges. The algorithms then were applied to characterize human cancellous bone microarchitectures. Using 1-MHz center-frequency, radio-frequency ultrasound signals, MSS was measured in 24 in vitro bone samples and ranged from 1.0 to 1.7 mm. The SSA MSS estimates correlate significantly to MSS measured independently from synchrotron microtomography, r2 = 0.68. Thus, application of SSA to backscattered ultrasound signals seems to be useful for providing information linked to tissue microarchitecture that is not evident from clinical images.

Aged↗

Parallelizing a DNA simulation code for the Cray MTA-2.

The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer. Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA. We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.

Algorithms↗

Differences due to collimator blurring in cardiac images with use of circular and elliptic camera orbits.

BACKGROUND: In cardiac imaging systems, an elliptic acquisition orbit about the patient can be used to enhance resolution of single photon emission computed tomography (SPECT) images by minimizing the distance between the object imaged and the rotating detector system. In this study artifacts from images acquired with the standard circular acquisition are compared with those acquired with various elliptic acquisitions. METHODS AND RESULTS: With the use of elliptic camera orbits of different eccentricities, simulated projection data were generated from a slice through the left ventricle (LV). The projection data included a simulation of the degradation due to the depth-dependent response of the collimator. As is common in many clinical systems, SPECT images were reconstructed with the standard filtered backprojection algorithm without correction for the collimator response. When the ratio of the major-to-minor axis of the acquisition arc is changed from 1 (circular) to 1.5 (elliptic), reconstructed SPECT images show an additional loss of counts (about 10%) in the apical region of the LV. The severity of the apical defect is also dependent on the starting angle of the acquisition arc. When the starting angle is changed from 0 degrees (detector parallel to the major axis of the LV) to 60 degrees, the ratio between the minimum count in the apical region and the maximum count in the left ventricular myocardial wall decreases by as much as 20%. CONCLUSIONS: SPECT image artifacts from elliptic acquisitions are significantly more severe than those from circular acquisitions. Because of the significant difference in images reconstructed from circular and elliptic acquisitions, standardized normal files acquired from circular acquisitions should not be used for comparisons with patient data acquired from elliptic acquisitions.

Algorithms↗

Power deposition in the head and neck of an anatomically based human body model for plane wave exposures.

At certain frequencies, when the human head becomes a resonant structure, the power absorbed by the head and neck, when the body is exposed to a vertically polarized plane wave propagating from front to back, becomes significantly larger than would ordinarily be expected from its shadow cross section. This has possible implications in the study of the biological effects of electromagnetic fields. Additionally the frequencies at which these resonances occur are not readily predicted by simple approximations of the head in isolation. In order to determine these resonant conditions an anatomically based model of the whole human body has been used, with the finite-difference time-domain (FDTD) algorithm to accurately determine field propagation, specific absorption rate (SAR) distributions and power absorption in both the whole body and the head region (head and neck). This paper shows that resonant frequencies can be determined using two methods. The first is by use of the accurate anatomically based model (with heterogeneous tissue properties) and secondly using a model built from parallelepiped sections (for the torso and legs), an ellipsoid for the head and a cylinder for the neck. This approximation to the human body is built from homogeneous tissue the equivalent of two-thirds the conductivity and dielectric constant of that of muscle. An IBM SP-2 supercomputer together with a parallel FDTD code has been used to accommodate the large problem size. We find resonant frequencies for the head and neck at 207 MHz and 193 MHz for the isolated and grounded conditions, with absorption cross sections that are respectively 3.27 and 2.62 times the shadow cross section.

Adult↗

Solution structure of bovine heart fatty acid-binding protein (H-FABPc).

Fatty acid-binding protein (FABP) from bovine heart, a 15 kDa cytoplasmic protein has been investigated by multi-dimensional homonuclear and heteronuclear NMR-spectroscopy. Perdeuterated palmitic acid has been used as fatty acid ligand. The tertiary structure has been determined from distance geometry calculations with the variable target functions algorithm (DIANA) utilizing 1027 interproton distance constraints, which were obtained from 1H-homonuclear NOESY spectra. Overlapping NOE crosspeaks were assigned by heteronuclear multidimensional NMR-experiments with a 15N-labelled sample. The tertiary structure resembles a beta-barrel (beta-clam) consisting of ten anti-parallel beta-strands and a short helix-turn-helix motif. The beta-strands are arranged in two nearly orthogonal beta-sheets composed of 5 strands each. The solution structure is compared with the x-ray crystal structure of bovine heart and rat intestinal FABPs.

Animals↗

Enhancing TOF/TOF-based de novo sequencing capability for high throughput protein identification with amino acid-coded mass tagging.

Because of the intrinsic physical properties of single- or double-charged ions, MALDI-based CID on these peptide precursor ions tends to be incomplete, resulting in a large number of MS/MS spectra unassigned or ambiguously identified. Consequently, the TOF/TOF high throughput capability may not be fully explored and utilized. Here, we describe a novel method for de novo sequence assignment of those MALDI TOF/TOF MS/MS spectra with incomplete or weak fragment ion series. In this approach, the deuterium-labeled lysine and leucine precursors were used in parallel to mass-tag the proteome of a metastatic human hepatocellular carcinoma (HCC) cell line during in vivo cell culturing. These stable isotope precursor markers not only position at terminal but at internal MS/MS fragment ions with the characteristic isotope pattern induced by multiple mass tagging in parallel. This enhanced signal specificity evidently resolved ambiguities in those sparse poor-quality TOF/TOF spectra by providing critical sequential links among MS/MS fragment ions. Our data-dependent approach was able to reduce many false-positives in current genome sequence-based peptide sequencing. With developing new algorithms accordingly, our approach is amenable for automation that will lead to more comprehensive and reliable identification for proteomes.

Carcinoma, Hepatocellular↗

Phase transition in multiprocessor scheduling.

An "easy-hard" phase transition is shown to characterize the multiprocessor scheduling problem in which one has to distribute the workload on a parallel computer such as to minimize the overall run time. The transition can be analyzed in detail by mapping it on a mean-field antiferromagnetic Potts model. The static phase transition, characterized by a vanishing ground state entropy, corresponds to a transition in the performance of practical scheduling algorithms.

Journal Article↗

Rapid 3D-T1rho mapping of the knee joint at 3.0T with parallel imaging.

Three-dimensional spin-lattice relaxation time in the rotating frame (3D-T1rho) with parallel imaging at 3.0T was implemented on a whole-body clinical scanner. A 3D gradient-echo sequence with a self-compensating spin-lock pulse cluster was combined with generalized autocalibrating partially parallel acquisitions (GRAPPA) to acquire T1rho-weighted images. 3D-T1rho maps of an agarose phantom and three healthy subjects were constructed using an eight-channel phased-array coil without parallel imaging and with parallel imaging acceleration factors of 2 and 3, in order to assess the reproducibility of the method. The coefficient of variation (CV) of the median T1rho of the agarose phantom was 0.44%, which shows excellent reproducibility. The reproducibility of in vivo 3D-T1rho maps was also investigated in three healthy subjects. The CV of the median T1rho of the patellar cartilage varied between approximately 1.1% and 4.3%. Similarly, the CV varied between approximately 2.1-5.8%, approximately 1.4-8.7%, and approximately 1.5-4.1% for the biceps femoris and lateral and medial gastrocnemius muscles, respectively. The preliminary results demonstrate that 3D-T1rho maps can be constructed with good reproducibility using parallel imaging. 3D-T1rho with parallel imaging capability is an important clinical tool for reducing both the total acquisition time and RF energy deposition at 3T.

Adult↗

DNA computation model to solve 0-1 programming problem.

0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.

Algorithms↗

The electrochemistry of ubiquinone-10 in a phospholipid model membrane.

The electrochemistry of ubiquinone-10, UQ, incorporated over a phospholipid layer adsorbed on a mercury drop electrode has been investigated over a wide pH range. It is shown that the position of the quinone headgroup in relation to the lipid determines the reversibility of the redox chemistry. For pH <7, the reaction follows a disproportionation route involving the ubiquione radical. There is evidence for the presence of a parallel reaction sequence. The bifurcation point appears to occur for the UQ molecule, which disproportionates after protonation and reduction, in parallel with direct electron transfer to yield the UQ--radical anion. The incorporation of UQ in a lipid monolayer makes its reduction very irreversible for pH > 7.

Algorithms↗

Assembly of fingerprint contigs: parallelized FPC.

SUMMARY: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest 'fingerprints' of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of 'parallelized FPC' has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints. AVAILABILITY: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.

Algorithms↗

The concentration-effect relationship of the respiratory depressant effects of alfentanil and fentanyl.

UNLABELLED: The relative potencies of fentanyl and alfentanil for respiratory depression were determined in eight healthy male volunteers in a double-blinded, randomized study with a cross-over design. The drugs were delivered by computer-driven infusion with logarithmically ascending plasma concentrations until the respiratory rate reached 2/min and/or oxygen saturation decreased below 85% with subjects breathing room air. Ventilation was measured with respiratory inductive plethysmography, indirect calorimetry, and arterial blood gas analysis, and plasma drug concentrations were determined. Pharmacodynamic modeling was performed using a fractional E(max) model for minute volume and respiratory rate and the concentrations producing 50% depression (i.e., apparent 50% effective concentration [EC(50)] values) were determined. Both drugs decreased ventilation in a similar manner, and drug infusions were terminated at mean +/- SD measured plasma concentrations of 254 +/- 88 ng/mL and 5.1 +/- 1.7 ng/mL for alfentanil and fentanyl, respectively. Alfentanil decreased minute volume from baseline by 54% +/- 19% and respiratory rate by 40% +/- 11% with EC(50) values of 234 +/- 57 ng/mL and 195 +/- 101 ng/mL. The respective decreases for fentanyl were 50% +/- 11%, 41% +/- 15%, and the estimated EC(50) values were 6.1 +/- 1.4 ng/mL and 3.5 +/- 1.4 ng/mL, respectively. Using the apparent EC(50) values, the calculated potency ratio for alfentanil:fentanyl was (mean and 95% confidence interval) 1:39 (1:31-1:46) for minute volume and 1:51 (1:34-1:68) for respiratory rate. This is analogous to the analgesic effect studied earlier. The findings support the notion of parallel analgesic and respiratory depressant effects of alfentanil and fentanyl. Therefore equianalgesic concentrations of both drugs will lead to equally pronounced respiratory depression. IMPLICATIONS: This double-blinded, randomized study evaluated the potency ratio of alfentanil and fentanyl-induced respiratory depression. The findings support the notion of parallel analgesic and respiratory depressant effects of alfentanil and fentanyl. Therefore equianalgesic concentrations of both drugs will lead to equally pronounced respiratory depression.

Adult↗