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PubMed2005

Two-dimensional waveform analysis in MR elastography of skeletal muscles.

A method for direct determination of anisotropic elastic coefficients using two-dimensional shear wave patterns is introduced. Thereby, the symmetry of the wave patterns is approximated by a squared elliptic equation yielding an explicit relation between waveform and elasticity. The method is used to analyse MR elastography wave images of the biceps acquired by a continuous harmonic excitation at the distal tendon of the muscle. Typically V-shaped wave patterns were observed in this type of tissue, which could be well reproduced by the proposed elliptic approximation of the waveform assuming incompressibility and a transverse isotropic model of elasticity. Without additional experiments, the analysis of straightness, slope and interferences of the wave fronts enabled us to deduce two Young's moduli and one shear modulus, which fully describe the anisotropy of the elasticity of muscles. The results suggest strong anisotropy of the living human biceps causing a shear wave speed parallel to the muscle fibres that is approximately four times faster than the perpendicular shear wave speed.

Algorithms↗
PubMed2003

The use of a Monte Carlo method to calculate the average solid angle subtended by a detector to source in a non-parallel plane.

In a previous scientific note, a short computer program for a personal computer was described that calculated the average solid angle subtended by a circular or rectangular detector window to a circular or rectangular source in a parallel plane by a Monte Carlo method. This note describes the development of the program for conditions where the detector window is not parallel to the plane of the source, and in particular looks at a method of analysing orientations that relates straightforwardly to practical measurement.

Algorithms↗
PubMed2002

Parallel cascade recognition of exon and intron DNA sequences.

Many of the current procedures for detecting coding regions on human DNA sequences combine a number of individual techniques such as discriminant analysis and neural net methods. Recent papers have used techniques from nonlinear systems identification, in particular, parallel cascade identification (PCI), as one means for classifying protein sequences into their structure/function groups. In the present paper, PCI is used in a pilot study to distinguish exon (coding) from intron (noncoding; interspersed within genes) human DNA sequences. Only the first exon and first intron sequences with known boundaries in genomic DNA from the beta T-cell receptor locus were used for training. Then, the parallel cascade classifiers were able to achieve classification rates of about 89% on novel sequences in a test set, and averaged about 82% when results of a blind test were included. In testing over a much wider range of human nucleotide sequences, PCI classifiers averaged 83.6% correct classifications. These results indicate that parallel cascade classifiers may be useful components in future coding region detection programs.

Algorithms↗
PubMed1989

Scattered wave inversion by image projections.

A three-dimensional diffraction tomography algorithm based on image projections is implemented. For each view, the measured scattered field is directly backpropagated onto a single plane in the image space. The backpropagated field evaluated on the plane is defined as the image projection because it closely approximates the straight line projection of the object. The object is then reconstructed by parallel slices using conventional straight ray tomographic techniques. This approach permits practical three-dimensional reconstruction using a limited number of views. The reconstructions made with image projections are of comparable quality to ideal diffraction-limited images. By backpropagating the field prior to filtering, curved or misaligned recording surfaces can be used. The limits on the image projection technique for multiple object systems are explored. A diffuse structure is reconstructed.

Algorithms↗
PubMed2005

Aligning biological sequences on distributed bus networks: a divisible load scheduling approach.

In this paper, we design a multiprocessor strategy that exploits the computational characteristics of the algorithms used for biological sequence comparison proposed in the literature. We employ divisible load theory (DLT) that is suitable for handling large scale processing on network based systems. For the first time in the domain of DLT, the problem of aligning biological sequences is attempted. The objective is to minimize the total processing time of the alignment process. In designing our strategy, DLT facilitates a clever partitioning of the entire computation process involved in such a way that the overall time consumed for aligning the sequences is a minimum. The partitioning takes into account the computation speeds of the nodes and the underlying communication network. Since this is a real-life application, the post-processing phase becomes important, and hence we consider propagating the results back in order to generate an exact alignment. We consider several cases in our analysis such as deriving closed-form solutions for the processing time for heterogeneous, homogeneous, and networks with slow links. Further, we attempt to employ a multiinstallment strategy to distribute the tasks such that a higher degree of parallelism can be achieved. For slow networks, our strategy recommends near-optimal solutions. We derive an important condition to identify such cases and propose two heuristic strategies. Also, our strategy can be extended for multisequence alignment by utilizing a clustering strategy such as the Berger-Munson algorithm proposed in the literature. Finally, we use real-life DNA samples of house mouse mitochondrion (Mus Musculus Mitochondrion, NC_001569) consisting of 16,295 residues and the DNA of human mitochondrion (Homo Sapiens Mitochondrion, NC_001807) consisting of 16,571 residues, obtainable from the GenBank, in our rigorous simulation experiments to illustrate all the theoretical findings.

Algorithms↗
PubMed2000

Computational design of D-peptide inhibitors of hepatitis delta antigen dimerization.

Hepatitis delta virus (HDV) encodes a single polypeptide called hepatitis delta antigen (DAg). Dimerization of DAg is required for viral replication. The structure of the dimerization region, residues 12 to 60, consists of an anti-parallel coiled coil [Zuccola et al., Structure, 6(1998)821]. Multiple Copy Simultaneous Searches (MCSS) of the hydrophobic core region formed by the bend in the helix of one monomer of this structure were carried out for many diverse functional groups. Six critical interaction sites were identified. The Protein Data Bank was searched for backbone templates to use in the subsequent design process by matching to these sites. A 14 residue helix expected to bind to the D-isomer of the target structure was selected as the template. Over 200,000 mutant sequences of this peptide were generated based on the MCSS results. A secondary structure prediction algorithm was used to screen all sequences. and in general only those that were predicted to be highly helical were retained. Approximately 100 of these 14-mers were model built as D-peptides and docked with the L-isomer of the target monomer. Based on calculated interaction energies, predicted helicity, and intrahelical salt bridge patterns, a small number of peptides were selected as the most promising candidates. The ligand design approach presented here is the computational analogue of mirror image phage display. The results have been used to characterize the interactions responsible for formation of this model anti-parallel coiled coil and to suggest potential ligands to disrupt it.

Algorithms↗
PubMed1997

Convergence Suppression and Divergence Facilitation: Minimum and Joint Use of Hidden Units by Multiple Outputs.

Pruning of multi-layer neural network structure is not a simple problem if two or more output units are present; unlike the single-output case, removing a hidden-output synaptic link does not necessarily mean elimination of a hidden unit. A new pruning algorithm called CSDF is presented. Its aim is to minimize the total number of active hidden units, thereby making some hidden units utilized jointly by more than one output unit. In addition to the backpropagation (BP) term, two antagonistic actions are introduced for controlling the synaptic development of hidden-output links; the incoming pathways to each output unit try to prevent each other from growing, whereas those outgoing from each hidden unit help each other for growing. CSDF works by dynamically balancing these two lateral interaction effects in the presence of the BP action, and hidden units not indispensable for any output unit will disappear. The process has some parallel with recent findings in developmental neurobiology. The CSDF pruning is applied to some multi-task problems, including one that exemplifies the importance of "structural compatibility" and demonstrates easy discovery of the optimum modular architecture which is difficult to deduce from separate structural optimization for each task alone. In most cases examined here, CSDF outperformed other pruning algorithms such as "weight decay" and "optimum brain damage." In particular, no existing algorithm other than CSDF can deal with pruning of auto-encoders. Some examples are also given for such paradigm of input-output identy mapping. Copyright 1997 Elsevier Science Ltd. All Rights Reserved.

Journal Article↗
PubMed2000

DARWIN: a program for docking flexible molecules.

A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM to make the energy calculations. A second important feature is its parallel interface, which allows simultaneous use of multiple stand-alone copies of CHARMM to rapidly evaluate large numbers of potential solutions. This permits an "accuracy first" approach to docking, which avoids many of the common assumptions and shortcuts often made to reduce computation time. The method was applied to three protein-carbohydrate complexes: the crystallographically determined structures of Concanavalin A and Fab Se155-4; and a model structure for Fab ME36.1. Conformations close to the crystal structures were obtained with this approach, but some "false positive" solutions were also selected. Many of these could be eliminated by introducing different methods for simulating solvent effects. An effective screening method for docking a database of compounds to a single target enzyme using DARWIN is also presented.

Algorithms↗
PubMed1999

Use of a quantitative structure-property relationship to design larger model proteins that fold rapidly.

A quantitative structure-property relationship (QSPR) was used to design model protein sequences that fold repeatedly and relatively rapidly to stable target structures. The specific model was a 125-residue heteropolymer chain subject to Monte Carlo dynamics on a simple cubic lattice. The QSPR was derived from an analysis of a database of 200 sequences by a statistical method that uses a genetic algorithm to select the sequence attributes that are most important for folding and a neural network to determine the corresponding functional dependence of folding ability on the chosen attributes. The QSPR depends on the number of anti-parallel sheet contacts, the energy gap between the native state and quasi-continuous part of the spectrum and the total energy of the contacts between surface residues. Two Monte Carlo procedures were used in series to optimize both the target structures and the sequences. We generated 20 fully optimized sequences and 60 partially optimized control sequences and tested each for its ability to fold in dynamic MC simulations. Although sequences in which either the number of anti-parallel sheet contacts or the energy of the surface residues is non-optimal are capable of folding almost as well as fully optimized ones, sequences in which only the energy gap is optimized fold markedly more slowly. Implications of the results for the design of proteins are discussed.

Databases, Factual↗
PubMed2026

Integrating NECTIN4 Amplification With Membranous Nectin-4 Expression to Develop a Scoring System for Predicting Enfortumab Vedotin Response in Urothelial Carcinoma.

PURPOSE: Enfortumab vedotin (EV) is standard therapy for metastatic urothelial carcinoma (mUC), yet the predictive relevance of NECTIN4 expression-especially membranous versus cytoplasmic-remains unclear. Here, we sought to extend previous findings on NECTIN4 gene amplification in parallel with a systematic subcellular evaluation of NECTIN4 expression. EXPERIMENTAL DESIGN: We retrospectively analyzed 179 EV-treated mUC patients. NECTIN4 amplification was assessed by FISH and NECTIN4 protein levels by IHC. A four-tier membranous scoring algorithm (0,1+,2+,3+) adapted from CAP HER2 gastric guidelines was benchmarked against H-score. We integrated amplification status with membranous staining to refine predictive stratification and compared associations with objective response rate (ORR) to EV-301 data. RESULTS: Combining membranous and cytoplasmic compartments resulted in a median composite H-score of 260 (78.2% &#x2265;150), closely matching NECTIN4 expression prevalence reported in EV-301 (median 250; 82.6% &#x2265; 150). A &#x2265;150 cut-off enriched for EV responders in both cohorts; in EV-301 with ORR of 45.8% vs. 20% (P = 0.001). High membranous expression based on the scoring (2+/3+) predicted response (ORR 55.1% vs. 25.5%; P < 0.001), with longer PFS (7.1 vs. 2.9 months; HR 0.45) and OS (12.3 vs. 6.9 months; HR 0.57), whereas cytoplasmic expression lacked predictive value. NECTIN4-amplified tumors showed particularly favorable outcomes (PFS 12.2 months; OS 30.1 months). An integrated three-tier model-amplified, non-amplified/high-membranous, and non-amplified/low-membranous-yielded ORRs of 77.2%, 42.9%, and 26.1% and separated survival outcomes. CONCLUSIONS: Our NECTIN4 scoring system integrating NECTIN4 amplification with membranous NECTIN4 expression accurately predicts outcomes, supporting combined genomic and membranous assessment as complementary biomarkers for optimizing EV selection.

Journal Article↗
PubMed2006

Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions.

BACKGROUND/AIMS: The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure. METHODS: We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals. RESULTS AND CONCLUSION: The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.

Alu Elements↗
PubMed2006

Fast computation of a gated dipole field.

We address the need to develop efficient algorithms for numerical simulation of models, based in part or entirely on adaptive resonance theory. We introduce modifications that speed up the computation of the gated dipole field (GDF) in the Exact ART neural network. The speed increase of our solution amounts to at least an order of magnitude for fields with more than 100 gated dipoles. We adopt a 'divide and rule' approach towards the original GDF differential equations by grouping them into three categories, and modify each category in a separate way. We decouple the slow-dynamics part - the neurotransmitters from the rest of system, solve their equations analytically, and adapt the solution to the remaining fast-dynamics processes. Part of the node activations are integrated by an unsophisticated numerical procedure switched on and off according to rules. The remaining activations are calculated at equilibrium. We implement this logic in a Generalized Net (GN) - a tool for parallel processes simulation which enables a fresh look at developing efficient models. Our software implementation of generalized nets appears to add little computational overhead.

Algorithms↗
PubMed2005

Gene identification in novel eukaryotic genomes by self-training algorithm.

Finding new protein-coding genes is one of the most important goals of eukaryotic genome sequencing projects. However, genomic organization of novel eukaryotic genomes is diverse and ab initio gene finding tools tuned up for previously studied species are rarely suitable for efficacious gene hunting in DNA sequences of a new genome. Gene identification methods based on cDNA and expressed sequence tag (EST) mapping to genomic DNA or those using alignments to closely related genomes rely either on existence of abundant cDNA and EST data and/or availability on reference genomes. Conventional statistical ab initio methods require large training sets of validated genes for estimating gene model parameters. In practice, neither one of these types of data may be available in sufficient amount until rather late stages of the novel genome sequencing. Nevertheless, we have shown that gene finding in eukaryotic genomes could be carried out in parallel with statistical models estimation directly from yet anonymous genomic DNA. The suggested method of parallelization of gene prediction with the model parameters estimation follows the path of the iterative Viterbi training. Rounds of genomic sequence labeling into coding and non-coding regions are followed by the rounds of model parameters estimation. Several dynamically changing restrictions on the possible range of model parameters are added to filter out fluctuations in the initial steps of the algorithm that could redirect the iteration process away from the biologically relevant point in parameter space. Tests on well-studied eukaryotic genomes have shown that the new method performs comparably or better than conventional methods where the supervised model training precedes the gene prediction step. Several novel genomes have been analyzed and biologically interesting findings are discussed. Thus, a self-training algorithm that had been assumed feasible only for prokaryotic genomes has now been developed for ab initio eukaryotic gene identification.

Algorithms↗
PubMed1995

Flexible protocols improve parallel experimentation throughput.

Advanced chemical workstations offer the potential to substantially improve the productivity of experimental research. To fully exploit such technologies, effective scheduling of experiments is crucial. Chemists tend to define experimental protocols with rigid time constraints, although often the scientific objectives can be achieved without adhering to such constraints. Investigation of a scheduling algorithm that allows flexible time constraints shows that improvements in workstation throughput as great as 50% can be reached by modest flexibility in the timing of operations in the experiments. Several heuristics that might be used with the scheduling algorithm were tested; a heuristic that schedules long experiments while first keeping the workstation busy was shown to be a good general choice.

Algorithms↗
PubMed1999

[Calculating the localization and dimension of the real pupil in keratoconus with ray tracing of corneal topography data].

BACKGROUND: It is crucial to center surgical procedures for optical indications on the pupil or the optical axis of the eye. In keratoconus the pupil appears to be dislocated due to optical aberrations of corneal topography. The purpose of this study was to evaluate the real pupil structure from the virtual image using exact raytracing techniques. PATIENTS AND METHODS: Eighty-eight patients with keratoconus (46 with mild and 42 with severe clinical signs) and a control group of 40 normal subjects were included in this study. Topographic height data were calculated from refraction data of a commercially available topographer (TMS-1) using a local approximation algorithm and a convex surface was modelled using a subdivision scheme. For the posterior corneal surface we postulated an aspherical surface with a central radius of curvature of 6.5 mm using Navarro's model eye. At the virtual pupil outline a bundle of parallel rays were intersected with the anterior and posterior corneal surface and refracted into the anterior chamber. The intersections of these rays with the pupil plane was defined as the real pupil outline. We assessed the amount and direction of pupil dislocation, the ratio between the virtual and real pupil size for each group and correlated these parameters with the central corneal power. RESULTS: The size of the virtual pupil exceeded the reference value of the real pupil in the normal group by 11%, in the group with mild keratoconus by 19% and in the group with severe keratoconus by 35%. The center of the virtual pupil was decentered 0.06 mm in the normal group, 0.49 in the group with mild keratoconus and 1.24 mm in the group with severe keratoconus. Whereas the direction of decentration was randomly in the normal group, we measured a preferred decentration to the inferior quadrants in mild keratoconus and a systematic decentration to the temporal inferior quadrant in severe keratoconus. Correlation of the optical dislocation did not correlate with central corneal power in any group. CONCLUSIONS: In keratoconic eyes the pupil outline is distorted and dislocated due to optical aberrations of the cornea. Exact raytracing technique allows the calculation of the real pupil outline from the virtual image and the topographic height of both corneal surfaces. Knowledge about the real pupil position may have an impact on adequate centration of keratorefractive surgery and penetrating keratoplasty.

Adult↗
PubMed2000

Interior-point methodology for 3-D PET reconstruction.

Interior-point methods have been successfully applied to a wide variety of linear and nonlinear programming applications. This paper presents a class of algorithms, based on path-following interior-point methodology, for performing regularized maximum-likelihood (ML) reconstructions on three-dimensional (3-D) emission tomography data. The algorithms solve a sequence of subproblems that converge to the regularized maximum likelihood solution from the interior of the feasible region (the nonnegative orthant). We propose two methods, a primal method which updates only the primal image variables and a primal-dual method which simultaneously updates the primal variables and the Lagrange multipliers. A parallel implementation permits the interior-point methods to scale to very large reconstruction problems. Termination is based on well-defined convergence measures, namely, the Karush-Kuhn-Tucker first-order necessary conditions for optimality. We demonstrate the rapid convergence of the path-following interior-point methods using both data from a small animal scanner and Monte Carlo simulated data. The proposed methods can readily be applied to solve the regularized, weighted least squares reconstruction problem.

Algorithms↗
PubMed2006

32-element receiver-coil array for cardiac imaging.

A lightweight 32-element MRI receiver-coil array was designed and built for cardiac imaging. It comprises an anterior array of 21 copper rings (75 mm diameter) and a posterior array of 11 rings (107 mm diameter) that are arranged in hexagonal lattices so as to decouple nearest neighbors, and curved around the left side of the torso. Imaging experiments on phantoms and human volunteers show that it yields superior performance relative to an eight-element cardiac array as well as a 32-element whole-torso array for both traditional nonaccelerated cardiac imaging and 3D parallel imaging with acceleration factors as high as 16.

Algorithms↗
PubMed2002

Investigating cervical spinal cord structure using axial diffusion tensor imaging.

This study describes a new technique for Diffusion Tensor Imaging (DTI) that acquires axial (transverse) images of the cervical spinal cord. The DTI images depict axonal fiber orientation, enable quantification of diffusion characteristics along the spinal cord, and have the potential to demonstrate the connectivity of cord white matter tracts. Because of the high sensitivity to motion of diffusion-weighted magnetic resonance imaging and the small size of the spinal cord, a fast imaging method with high in-plane resolution was developed. Images were acquired with a single-shot EPI technique, named ZOOM-EPI (zonally magnified oblique multislice echo planar imaging), which selects localized areas and reduces artefacts caused by susceptibility changes between soft tissue and the adjacent vertebrae. Cardiac gating was used to reduce pulsatile flow artefacts from the surrounding cerebrospinal fluid. Voxel resolution was 1.25 x 1.25 mm(2) in-plane with 5-mm slice thickness. Both the mean diffusivity (MD) and the fractional anisotropy (FA) indices of the cervical spinal cord were measured. The FA index demonstrated high anisotropy of the spinal cord with an average value of 0.61 +/- 0.05 (highest value of 0.66 +/- 0.03 at C3), comparable to white matter tracts in the brain. The diffusivity components parallel and orthogonal to the longitudinal axes of the cord were lambda( parallel) = (1648 +/- 123) x 10(-6) mm(2)s(-1) and lambda( perpendicular) = (570 +/- 47) x 10(-6) mm(2) s(-1), respectively. The high axial resolution allowed preliminary evaluation of fiber connectivity using the fast-marching tractography algorithm, which generated traces of fiber paths consistent with the well-known cord anatomy.

Algorithms↗