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PubMed1993

Algorithm for semi-automatic sorting of objects to specified tissue domains. An aid for co-ordinating morphometric data with identified tissue components.

A personal computer-based technique was developed that reduces the extent of human efforts in obtaining data, like numerical density of profiles on area, describing the distribution of specific features of histological sections, e.g., density of synaptic profiles or of histochemical reaction products in specified tissue compartments. The procedure consists of (i) marking the objects to be counted, (ii) recording the borderlines of (reference) tissue domains of interest, and (iii) allocating the marked objects to the corresponding domains automatically. This automatic sorting of objects into defined tissue domains is achieved by an algorithm operating on two sets of coordinates: (i) coordinates of points that constitute the boundary of tissue domains (perimeter points) and (ii) coordinates of points marking the particular objects to be sorted. The principle of the sorting calculation is to construct 'segments' of the loop by lines parallel to the ordinate which pass through neighbouring perimeter points. The 'items' to be sorted are classified by the sign of marker flags allocated to each point depending on which side of the perimeter segment they are located. Segmentation and classification procedures are sequentially repeated along the entire perimeter of each domain specified by the operator which may result during the procedure in multiple changes of the sign of the flags. The internal or external location of each item finally is represented by the last sign of its flag. Objects, allocated to domains can be counted and processed further for numerical density determination.

Algorithms↗
PubMed2003

Honey characterization and adulteration detection by pattern recognition applied on HPAEC-PAD profiles. 1. Honey floral species characterization.

An improved COFRAC (COmité FRançais d'ACréditation) method for the analysis and evaluation of the quality of honey by high-performance anion-exchange chromatography of sugar profiles is proposed. With this method, both minor and major sugars are simultaneously analyzed and the technique is integrated in a new chemometric approach, which uses the entire chromatographic sugars profile of each analyzed sample to characterize honey floral species. Sixty-eight authentic honey samples (6 varieties) were analyzed by high-performance anion-exchange chromatography-pulsed amperometric detection. A new algorithm was developed to create automatically the corresponding normalized data matrix, ready-to-use in various chemometric procedures. This algorithm transforms the analytical profiles to produce the corresponding calibrated table of the surfaces or intensities according to retention times of peaks. The possibility of taking into account unknown peaks (those for which no standards are available) allows the maximum chemical information provided by the chromatograms to be retained. The parallel application of principal component analysis (PCA)/linear discriminant analysis (LDA) and artificial neural networks (ANN) shows a high capability in the classification of the analyzed samples (LDA, 93%; ANN, 100%) and a very good discrimination of honey groups. This work is the starting point of the elaboration of a new system designed for the automatic pattern recognition of food samples (first application on honey samples) from chromatographic analyses for food characterization and adulteration detection.

Algorithms↗
PubMed1991

Simultaneous multinuclear magnetic resonance imaging and spectroscopy.

A technique has been developed to perform simultaneous multinuclear magnetic resonance imaging and spatially localized spectroscopy. It is inherently superior in terms of time efficiency over current approaches which use sequential or interleaved methods. The pulse sequence uses a parallel excitation and acquisition scheme to acquire multislice proton images concurrently with phosphorus-31 spectroscopic images. Because the phosphorus signal is necessarily collected in the presence of a gradient, an essential element of the technique is an algorithm to extract pure chemical-shift information.

Algorithms↗
PubMed2003

Initial evaluation of commercial optical CT-based 3D gel dosimeter.

We evaluated the OCTOPUS-ONE research laser CT scanner developed and manufactured by MGS Research, Inc. (Madison, CT). The scanner is designed for imaging 3D optical density distributions in BANG gels. The scanner operates in a translate-rotate configuration with a single scanning laser beam. The rotating cylindrical gel phantom is immersed in a refractive index matching solution and positioned at the center of a square tank made of plastic and glass. A stationary polarized He-Ne laser beam (633 nm) is reflected from a mirror moving parallel to the tank wall and scans the gel. Another mirror moves synchronously along the opposite side of the tank and collects the transmitted light and sends it to a single stationary silicon photodetector. A filtered backprojection algorithm is used to reconstruct projection data in a plane. The laser-mirrors-detector assembly is mounted on a horizontal platform that moves vertically for slice selection. We have tested the mechanical and optical setup, projection centering on the axis of rotation, linearity, and spatial resolution. We found the optical detector to respond linearly to transmitted light from control samples. The spatial resolution of the scanner was determined by employing a split field resolution technique. We obtained the horizontal and vertical full widths at half maxima of the laser beam intensity profiles as 0.6 and 0.8 mm, respectively. Dose calibration tests of the gel were performed using a nine-field (2 x 2 cm2 each) dose pattern irradiated at different dose levels. Finally, we compared gel-derived 2D planar dose distribution against radiochromic film measured dose distribution for both the nine-field and a uniform 5 x 5 cm2 field of 6 MV x rays. Very similar dose distributions were observed in gel and radiochromic film except in regions of steep dose gradient and highest dose. A dose normalization of 15.6% was required between the two dosimeters due to differences in overall radiation response. After normalization, analysis using the gamma evaluation showed that the radiochromic film and gel-measured dose distributions differed by a maximum gamma of 1.3 using 5% and 1.5 mm dose difference and distance-to-agreement criteria. The optical CT scanner has great potential as a 3D dosimeter, but a few refinements and further testing are necessary before its routine clinical use.

Algorithms↗
PubMed1998

Beginning insulin treatment of obese patients with evening 70/30 insulin plus glimepiride versus insulin alone. Glimepiride Combination Group.

OBJECTIVE: This study tested a simple algorithm for beginning insulin for obese patients with type 2 diabetes after sulfonylurea failure, comparing suppertime 70/30 insulin plus continued glimepiride with insulin alone. RESEARCH DESIGN AND METHODS: This was a multicenter ambulatory randomized double-masked parallel comparison. There were 208 subjects with secondary failure to sulfonylureas who took glimepiride titrated to 8 mg b.i.d. for 8 weeks; 145 subjects with fasting plasma glucose (FPG) 180-300 mg/dl (10-16.7 mmol/l) on this treatment were randomized to placebo plus insulin (PI) or glimepiride plus insulin (GI) for 24 weeks. A dosage of 70/30 insulin before supper was titrated, seeking fasting capillary blood glucose (FBG) 120 mg/dl (6.7 mmol/l), equivalent to FPG 140 mg/dl (7.8 mmol/l). Outcome measures included FPG, HbA1c, insulin dosage, weight, serum insulin and lipids, and adverse events. RESULTS: FPG and HbA1c were equivalent at baseline: 261 vs. 250 mg/dl (14.5 vs. 13.9 mmol/l), and 9.9 vs. 9.7%. At 24 weeks, the FPG target was achieved in both groups (136 vs. 138 mg/dl, 7.6 vs. 7.6 mmol/l), and HbA1c values were equal (7.7 vs. 7.6%). However, with GI, control improved faster and fewer subjects dropped out (3 vs. 15%, P < 0.01), and less insulin was needed (49 vs. 78 U/d, P < 0.001). The outcomes were alike in other respects. No subject had severe hypoglycemia. CONCLUSIONS: Injection of 70/30 insulin before supper safely restored glycemic control of type 2 diabetes not controlled by glimepiride alone. Control was restored more rapidly and with less injected insulin when glimepiride was continued.

Aged↗
PubMed1995

Transmission maximum-likelihood reconstruction with ordered subsets for cone beam CT.

An iterative algorithm is presented for accelerated reconstruction of cone beam transmission CT data (CBCT). CBCT supplies an attenuation map for SPECT attenuation compensation and anatomical correlation. Iterative algorithms are necessary to reduce truncation artifacts and 3D reconstruction artifacts. An existing transmission maximum-likelihood algorithm (TRML) is accurate but the reconstruction time is too long. The new algorithm is a modified EM algorithm, based on ordered subsets (OSEM). OSEM was evaluated in comparison to TRML using a thorax phantom and a 3D Defrise phantom. A wide range of image measures were evaluated, including spatial resolution, noise, log likelihood, region quantification, truncation artifact removal, and 3D artifact removal. For appropriate subset size, OSEM produced essentially the same image as TRML, but required only one-tenth as many iterations. Thus, adequate images were available in two to four iterations (20-30 min on a SPARC 2 workstation). Further, OSEM still approximately maximizes likelihood: divergence occurs only for very high (and clinically irrelevant) iterations. Ordered subsets are likely to be useful in other geometries (fan and parallel) and for emission CT as well. Therefore, with ordered subsets, high-quality iterative reconstruction is now available in clinically practical reconstructions times.

Algorithms↗
PubMed1991

Mathematical resolution of mixed in vivo voltammetry signals. Models, equipment, assessment by simultaneous microdialysis sampling.

A microcomputer-assisted curve-fitting procedure was developed for the quantitative estimation of the components of the mixed "catechol peak" recorded with differential normal pulse voltammetry (DNPV) at electrochemically pretreated carbon fiber microelectrodes in the living brain. The contribution of each of the relevant electroactive species is fitted by a normal probability function, the parameters of which are previously determined in vitro for each electrode and substance. The voltammogram is thus modeled as a mixture of normal curves corresponding to the individual oxidizable substances plus a low order polynomial approximating the baseline. In a former approach the function was solved by linear least squares techniques. As a further improvement, we now propose a non-linear model of the voltammogram and a Gauss-Newton iterative algorithm with stepwise regression for parameter estimation. This report shows the application of the method for the resolution of the dopamine (DA) and dihydroxyphenylacetic acid (DOPAC) components of the DNPV signal recorded from the striatum of freely moving animals in response to amphetamine and pargyline. The method was validated by the chemical assay of contralateral microdialysates collected simultaneously. The changes detected by both methodologies were closely parallel, with highly significant correlation coefficients (0.87 and 0.99 for DA and DOPAC, respectively, P less than 0.001). This study further illustrates that the in vivo voltammetry methodology can be improved substantially by incorporating a suitable mathematical treatment of the electrochemical signals.

3,4-Dihydroxyphenylacetic Acid↗
PubMed1993

Thermal stability and conformational transitions of scrapie amyloid (prion) protein correlate with infectivity.

The scrapie amyloid (prion) protein (PrP27-30) is the protease-resistant core of a larger precursor (PrPSc) and a component of the infectious scrapie agent; the potential to form amyloid is a result of posttranslational event or conformational abnormality. The conformation, heat stability, and solvent-induced conformational transitions of PrP27-30 were studied in the solid state in films by CD spectroscopy and correlated with the infectivity of rehydrated and equilibrated films. The exposure of PrP27-30 in films to 60 degrees C, 100 degrees C, and 132 degrees C for 30 min did not change the beta-sheet secondary structure; the infectivity slightly diminished at 132 degrees C and correlated with a decreased solubility of PrP27-30 in sodium dodecyl sulfate (SDS), probably due to cross-linking. Exposing PrP27-30 films to formic acid (FA), trifluoroacetic acid (TFA), trifluoroethanol (TFE), hexafluoro-2-propanol (HFIP), and SDS transformed the amide CD band, diminished the mean residue ellipticity of aromatic bands, and inactivated scrapie infectivity. The convex constraint algorithm (CAA) deconvolution of the CD spectra of the solvent-exposed and rehydrated solid state PrP27-30 identified five common spectral components. The loss of infectivity quantitatively correlated with a decreasing proportion of native, beta-pleated sheet-like secondary structure component, an increasing amount of alpha-helical component, and an increasingly disordered tertiary structure. The results demonstrate the unusual thermal stability of the beta-sheet secondary structure of PrP27-30 protein in the solid state. The conformational perturbations of PrP27-30 parallel the changes in infectivity and suggest that the beta-sheet structure plays a key role in the physical stability of scrapie amyloid and in the ability to propagate and replicate scrapie.

Algorithms↗
PubMed1998

Optimal design of planar-concave collimators for SPECT--an analytical approach.

In this paper we present an analytical tool for the design and optimization of planar-concave collimators for SPECT. We conclude that a single general planar-concave collimator that eliminates the non-isotropic blurring for all SPECT applications does not exist. On the other hand, it is possible to achieve pseudo-optimal collimators for different clinical applications by a careful choice of the design parameters. By classifying the clinical applications into two groups, for instance body and brain studies, the non-isotropic blurring for most SPECT situations may be dramatically reduced by means of planar-concave collimators. The results based on Monte Carlo simulations show that the shape of the point source response function of the reconstructed image obtained from the planar-concave collimator is more isotropic than that obtained from a conventional parallel-hole collimator. Specifically, the ratio of the FWHM of the reconstructed point response function in the radial and tangential direction is increased from 0.5 for the parallel-hole to 0.85 for the planar-concave collimator for sources 200 mm away from the centre of rotation.

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↗
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↗
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↗