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PubMedDate not supplied

The relationship between traumatic tympanic membrane perforations and pneumatization of the mastoid.

We evaluated the possible relationship between tympanic membrane perforations resulting from blast trauma or slap and pneumatization of the mastoid cells. A total of 25 male patients with tympanic membrane perforations resulting from blast injury (n = 7), slap (n = 17), and football hit (n = 1) and 20 healthy male volunteers without any ear problem had temporal bone computed tomographic scans in the axial plane, parallel to the infraorbitomeatal line, with 2 mm slice thickness and 2-mm intervals using bone algorithm with a ProSpeed Spiral tomography machine. The area of air cells in each slice was measured using trace and area measurement functions of the tomography machine, and by multiplying the resulting area by slice thickness, the volume of each slice was calculated. For each ear, the total of volumes of air cells was calculated by adding the volumes of each slice containing air cells. The calculated volumes of mastoid cells were evaluated by comparing microscopic findings. Both patient and control groups consisted of males, and their ages ranged from 17 to 32 (mean 24.5) years. Microscopic examinations revealed that perforations were frequently located in the lower quadrants and that most of them were less than 3 mm. There were no pars flaccida and marginal perforations. Ossicular chain destruction was noted neither in temporal bone tomographic nor during intraoperative examinations. The mean (+/- SD) volumes of right and left ear mastoid air cells in patient and control groups were 6.92 +/- 2.45 vs. 7.00 +/- 2.59 cm(3) and 9.04 +/- 4.55 vs. 8.95 +/- 4.53 cm(3), respectively, and the differences were not statistically significant. It was found that the level of mastoid pneumatization has no statistically significant effect on tympanic membrane pathologies due to blast or other injuries.

Adolescent↗

PubMed2005

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes.

BACKGROUND: Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. Such procedures require the design of large sets of probes using application-specific design constraints. RESULTS: ProbeMaker is a software framework for computer-assisted design and analysis of sets of oligonucleotide probe sequences. The tool assists in the design of probes for sets of target sequences, incorporating sequence motifs for purposes such as amplification, visualization, or identification. An extension system allows the framework to be equipped with application-specific components for evaluation of probe sequences, and provides the possibility to include support for importing sequence data from a variety of file formats. CONCLUSION: ProbeMaker is a suitable tool for many different oligonucleotide design and analysis tasks, including the design of probe sets for various types of parallel genetic analyses, experimental validation of design parameters, and in silico testing of probe sequence evaluation algorithms.

Algorithms↗

PubMed1996

Parallel hardware for sequence comparison and alignment.

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures is also noted.

Algorithms↗

PubMed2003

[Algorithm for diagnosis and therapy of pain].

Certain basic principles are applicable to all forms of pain treatment when the aims are pain relief and the avoidance of chronicety. Such algorithms, as guidelines are even more important when pain is becoming chronic. The use of the described algorithms is necessary in the diagnosis and therapy of acute pain and also to avoid the establishment of chronic pain due to the changes of neuroplasticity in the central nervous system. The most important basic principles in the form of algorithms are first of all that therapies should be simultaneously applied and not sequentially. Secondly, the challenge should be met to create a concept where by various therapies can be preformed in a parallel fashion, without compete one another and being effective on different aspects and causes of the pain.

Administration, Oral↗

PubMed2006

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

UNLABELLED: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. AVAILABILITY: icwww.epfl.ch/~stamatak

Algorithms↗

PubMed1997

Comparison of non parallel immunoassay curves resulting from mixtures of competing antigens.

Relative potency is a measure that has been used for many years to summarize the comparison of dose-response curves in parallel line bioassays. When response curves for two preparations are not parallel the traditional definition of relative potency no longer applies. We review the concept of relative potency and show that, in some situations, it can be given meaning for non-parallel curves as the ratio of biological activity in full strength assay preparations. Under an assumption that non-parallel curves result from the competition of mixtures of antigens for receptor binding sites, estimation of relative potency for non-parallel curves can be accomplished. We show that estimation of models for both parallel curve and response attenuation situations may be accomplished within the framework of generalized linear models. This estimation depends on the ability to deal with non-linear parameters appearing in the link function, and an iterative algorithm depending on direct parameter updates is outlined. The topics discussed are illustrated with the analysis of data from two immunoassays conducted with veterinary vaccines. The models developed here depend in an essential way on the assumption of response attenuation by competing antigens. Our methods may not be appropriate for non-parallel curves caused by other phenomena.

Algorithms↗

PubMedDate not supplied

Efficient split synthesis for targeted libraries.

We propose a new approach for fabricating more sophisticated combinatorial chemistry libraries via split synthesis and evaluate its potential through extensive simulation. Our algorithmically intensive method promises to reduce the time and materials costs of synthesizing libraries which are (1) too large to synthesize economically by sequential or parallel synthesis, (2) too long or irregular for conventional split synthesis generation techniques, and (3) not used in sufficient quantity to justify the setup costs of array makers. It also encourages the design of more focused and interesting libraries than are typically constructed using split synthesis. Our algorithms automate the design of efficient synthesis procedures for motif-based libraries which are too complex to design by hand. Our software allows the user to select the most desirable tradeoff between minimizing the number of steps in the synthesis process and containing the combinatorial explosion of the number of compounds synthesized.

Algorithms↗

PubMed2004

Tone-dependent error diffusion.

We present an enhanced error diffusion halftoning algorithm for which the filter weights and the quantizer thresholds vary depending on input pixel value. The weights and thresholds are optimized based on a human visual system model. Based on an analysis of the edge behavior, a tone dependent threshold is designed to reduce edge effects and start-up delay. We also propose an error diffusion system with parallel scan that uses variable weight locations to reduce worms.

Algorithms↗

PubMed1991

Sample size estimation for comparing two or more treatment groups in clinical trials.

Methods for estimating required sample size for comparing two population means have been published. Most involve the use of complicated formulae and tables. These methods are limited to comparing two groups. Although techniques exist to determine sample sizes for comparing more than two groups, they are intrinsically far more complicated. A simple linear nomogram is proposed as a solution to these problems, and its use is illustrated with examples of parallel group, ordered parallel group and factorial designs.

Algorithms↗

PubMed2006

Application of clinical trial simulation to compare proof-of-concept study designs for drugs with a slow onset of effect; an example in Alzheimer's disease.

OBJECTIVE: Clinical trial simulation (CTS) was used to select a robust design to test the hypothesis that a new treatment was effective for Alzheimer's disease (AD). Typically, a parallel group, placebo controlled, 12-week trial in 200-400 AD patients would be used to establish drug effect relative to placebo (i.e., Ho: Drug Effect = 0). We evaluated if a crossover design would allow smaller and shorter duration trials. MATERIALS AND METHODS: A family of plausible drug and disease models describing the time course of the AD assessment scale (ADAS-Cog) was developed based on Phase I data and literature reports of other treatments for AD. The models included pharmacokinetic, pharmacodynamic, disease progression, and placebo components. Eight alternative trial designs were explored via simulation. One hundred replicates of each combination of drug and disease model and trial design were simulated. A 'positive trial' reflecting drug activity was declared considering both a dose trend test (p < 0.05) and pair-wise comparisons to placebo (p < 0.025). RESULTS: A 4 x 4 Latin Square design was predicted to have at least 80% power to detect activity across a range of drug and disease models. The trial design was subsequently implemented and the trial was completed. Based on the results of the actual trial, a conclusive decision about further development was taken. The crossover design provided enhanced power over a parallel group design due to the lower residual variability. CONCLUSION: CTS aided the decision to use a more efficient proof of concept trial design, leading to savings of up to US 4 M dollars in direct costs and a firm decision 8-12 months earlier than a 12-week parallel group trial.

Algorithms↗

PubMed2003

Brownian dynamics simulations of the interaction of Chlamydomonas cytochrome f with plastocyanin and cytochrome c6.

The interaction of Chlamydomonas cytochrome f (cyt f) with either Chlamydomonas plastocyanin (PC) or Chlamydomonas cytochrome c(6) (cyt c(6)) was studied using Brownian dynamics simulations. The two electron acceptors (PC and cyt c(6)) were found to be essentially interchangeable despite a lack of sequence homology and different secondary structures (beta-sheet for PC and alpha-helix for cyt c(6)). Simulations using PC and cyt c(6) interacting with cyt f showed approximately equal numbers of successful complexes and calculated rates of electron transfer. Cyt f-PC and cyt f-cyt c(6) showed the same types of interactions. Hydrophobic residues surrounding the Y1 ligand to the heme on cyt f interacted with hydrophobic residues on PC (surrounding the H87 ligand to the Cu) or cyt c(6) (surrounding the heme). Both types of complexes were stabilized by electrostatic interactions between K65, K188, and K189 on cyt f and conserved anionic residues on PC (E43, D44, D53, and E85) or cyt c(6) (E2, E70, and E71). Mutations on cyt f had identical effects on its interaction with either PC or cyt c(6). K65A, K188A, and K189A showed the largest effects whereas residues such as K217A, R88A, and K110A, which are located far from the positive patch on cyt f, showed very little inhibition. The effect of mutations observed in Brownian dynamics simulations paralleled those observed in experiments.

Algorithms↗

PubMedDate not supplied

Pharmacokinetics of D,L-3-hydroxy-3-ethyl-3-phenylpropionamide (HEPP) in pregnant rats at different stages of gestation and maternal-fetal disposition during late pregnancy.

The pharmacokinetics of D,L-3-hydroxy-3-ethyl-3-phenylpropionamide (HEPP), an investigational anticonvulsant drug, was evaluated in nonpregnant and in pregnant rats on gestation day (GD) 7, 12, and 21 after an intraperitoneal (i.p.) dose of 50mg/kg. Maternal-fetal disposition in the GD21 group was also evaluated. In all groups, HEPP was rapidly absorbed and the disposition was well described by an open two-compartment kinetic model. The most pronounced effects of pregnancy on the kinetics of HEPP were observed at GD21 in which significant increases in the first-order hybrid disposition rate constants alpha and beta, with corresponding decreases in half-lives were observed. Gestation also affected the intercompartmental transfer rate constants k(12) and k(21), specially at GD12 and at GD21. These changes could be associated with the physiologic increases in blood flow and cardiac output of pregnancy. There was also a slight decrease in the apparent volume of distribution at GD21, and a progressive decrease in the clearance values normalized by the body weight. No other significant differences in kinetic parameters were observed. On GD21, HEPP rapidly transfers from maternal blood to fetuses, to reach concentrations in the placenta and fetuses slightly higher than those of the maternal plasma (fetal:maternal ratio ranging from 1.07 to 1.45). After equilibrium, the concentrations in maternal, placental, and fetal tissues decreased in parallel.

Algorithms↗

PubMed2003

Comparison of correlation vector methods for ligand-based similarity searching.

Correlation vector methods were tested for their usefulness in ligand-based virtual screening. Three molecular descriptors--two based on potential pharmacophore points and one on partial atom charges--and three similarity measures--the Manhattan distance, the Euclidian distance and the Tanimoto coefficient--were compared. The alignment-free descriptors seem to be particularly applicable when a course-grain filtering of data sets is required in combination with a high execution speed. Significant enrichment of actives was obtained by retrospective analysis. The cumulative percentages for all three descriptors allow for the retrieval of up to 78% of the active molecules in the first five percent of the reference database. Different descriptors retrieved only weakly overlapping sets of active molecules among the top-ranking compounds. If a single similarity index is to be used, the Manhattan distance seems to be particularly applicable. Generally, none of the three different descriptors tested in this study clearly outperformed the others. The suitability of a descriptor critically depends on the ligand-receptor interaction under investigation. For ligand-based similarity searching it is recommended to exploit several descriptors in parallel.

Algorithms↗

PubMed2004

Modality independent elastography (MIE): a new approach to elasticity imaging.

The correlation between tissue stiffness and health is an accepted form of organ disease assessment. As a result, there has been a significant amount of interest in developing methods to image elasticity parameters (i.e., elastography). The modality independent elastography (MIE) method combines a nonlinear optimization framework, computer models of soft-tissue deformation, and standard measures of image similarity to reconstruct elastic property distributions within soft tissue. In this paper, simulation results demonstrate successful elasticity image reconstructions in breast cross-sectional images acquired from magnetic resonance (MR) imaging. Results from phantom experiments illustrate its modality independence by reconstructing elasticity images of the same phantom in both MR and computed tomographic imaging units. Additional results regarding the performance of a new multigrid strategy to MIE and the implementation of a parallel architecture are also presented.

Algorithms↗

PubMedDate not supplied

Toward an optimal procedure for variable selection and QSAR model building.

In this work, we report the development of a novel QSAR technique combining genetic algorithms and neural networks for selecting a subset of relevant descriptors and building the optimal neural network architecture for QSAR studies. This technique uses a neural network to map the dependent property of interest with the descriptors preselected by the genetic algorithm. This technique differs from other variable selection techniques combining genetic algorithms to neural networks by two main features: (1) The variable selection search performed by the genetic algorithm is not constrained to a defined number of descriptors. (2) The optimal neural network architecture is explored in parallel with the variable selection by dynamically modifying the size of the hidden layer. By using both artificial data and real biological data, we show that this technique can be used to build both classification and regression models and outperforms simpler variable selection techniques mainly for nonlinear data sets. The results obtained on real data are compared to previous work using other modeling techniques. We also discuss some important issues in building QSAR models and good practices for QSAR studies.

Algorithms↗

PubMed1991

Asymmetric Boltzmann machines.

We study asymmetric stochastic networks from two points of view: combinatorial optimization and learning algorithms based on relative entropy minimization. We show that there are non trivial classes of asymmetric networks which admit a Lyapunov function L under deterministic parallel evolution and prove that the stochastic augmentation of such networks amounts to a stochastic search for global minima of L. The problem of minimizing L for a totally antisymmetric parallel network is shown to be associated to an NP-complete decision problem. The study of entropic learning for general asymmetric networks, performed in the non equilibrium, time dependent formalism, leads to a Hebbian rule based on time averages over the past history of the system. The general algorithm for asymmetric networks is tested on a feed-forward architecture.

Algorithms↗

PubMed2001

On the parallelisation of bioinformatics applications.

This paper surveys the computational strategies followed to parallelise the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database-searching applications, to very irregularly structured patterns (phylogenetic trees). Fine- and coarse-grained parallel strategies are discussed for these very diverse sets of applications. This overview outlines computational issues related to parallelism, physical machine models, parallel programming approaches and scheduling strategies for a broad range of computer architectures. In particular, it deals with shared, distributed and shared/distributed memory architectures.

Algorithms↗

PubMed2005

Optimized interstitial PDT prostate treatment planning with the Cimmino feasibility algorithm.

The primary aim of this study was to determine whether optimized photodynamic therapy (PDT) treatment planning (seeking optimized positions, lengths, and strengths of the light sources to satisfy a given dose prescription) can improve dose coverage to the prostate and the sparing of critical organs relative to what can be achieved by the standard PDT plan. The Cimmino algorithm and search procedures based on that algorithm were tested for this purpose. A phase I motexafin lutetium (MLu)-mediated photodynamic therapy protocol is ongoing at the University of Pennsylvania. PDT for the prostate is performed with cylindrical diffusing fibers of various lengths inserted perpendicular to a base plate to obtain longitudinal coverage by a matrix of parallel catheters. The standard plan for the protocol uses sources of equal strength with equal spaced (1-cm) loading. Uniform optical properties were assumed. Our algorithms produce plans that cover the prostate and spare the urethra and rectum with less discrepancy from the dose prescription than the standard plan. The Cimmino feasibility algorithm is fast enough that changes to the treatment plan may be made in the operating room before and during PDT to optimize light delivery.

Algorithms↗