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Results for “parameter optimization”

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At least 883 records · Page 49Linked to original sources

PubMed2003

A two-stage interval-stochastic programming model for waste management under uncertainty.

This study introduces a two-stage interval-stochastic programming (TISP) model for the planning of solid-waste management systems under uncertainty. The model is derived by incorporating the concept of two-stage stochastic programming within an interval-parameter optimization framework. The approach has the advantage that policy determined by the authorities, and uncertain information expressed as intervals and probability distributions, can be effectively communicated into the optimization processes and resulting solutions. In the modeling formulation, penalties are imposed when policies expressed as allowable waste-loading levels are violated. In its solution algorithm, the TISP model is converted into two deterministic submodels, which correspond to the lower and upper bounds for the desired objective-function value. Interval solutions, which are stable in the given decision space with associated levels of system-failure risk, can then be obtained by solving the two submodels sequentially. Two special characteristics of the proposed approach make it unique compared with other optimization techniques that deal with uncertainties. First, the TISP model provides a linkage to predefined policies determined by authorities that have to be respected when a modeling effort is undertaken; second, it furnishes the reflection of uncertainties presented as both probabilities and intervals. The developed model is applied to a hypothetical case study of regional solid-waste management. The results indicate that reasonable solutions have been generated. They provide desired waste-flow patterns with minimized system costs and maximized system feasibility. The solutions present as stable interval solutions with different risk levels in violating the waste-loading criterion and can be used for generating decision alternatives.

Environment↗

PubMed2006

A practical extension of hydrodynamic theory of porous transport for hydrophilic solutes.

OBJECTIVE: The equations for transport of hydrophilic solutes through aqueous pores provide a fundamental basis for examining capillary-tissue exchange and water and solute flux through transmembrane channels, but the theory remains incomplete for ratios, alpha, of sphere diameters to pore diameters greater than 0.4. Values for permeabilities, P, and reflection coefficients, sigma, from Lewellen, working with Lightfoot et al., at alpha = 0.5 and 0.95, were combined with earlier values for alpha < 0.4, and the physically required values at alpha = 1.0, to provide accurate expressions over the whole range of 0 < alpha < 1. METHODS: The "data" were the long-accepted theory for alpha < 0.2 and the computational results from Lewellen and Lightfoot et al. on hard spheres (of 5 different alpha's) moving by convection and diffusion through a tight cylindrical pore, accounting for molecular exclusion, viscous forces, pressure drop, torque and rotation of spheres off the center line (averaging across all accessible radial positions), and the asymptotic values at alpha = 1.0. Coefficients for frictional hindrance to diffusion, F(alpha), and drag, G(alpha), and functions for sigma(alpha) and P(alpha), were represented by power law functions and the parameters optimized to give best fits to the combined "data." RESULTS: The reflection coefficient sigma = {1 - [1 - (1 - phi)2]G'(alpha)} + 2alpha2 phi F'(alpha), and the relative permeability P/Pmax = phi F '(alpha)[1 + 9alpha5.5 x (1.0 - alpha5)0.02], where phi is the partition coefficient or volume fraction of the pore available to solute. The new expression for the diffusive hindrance is F'(alpha) = (1 - alpha2)(3/2) phi/[1 + 0.2 x alpha2 x (1 - alpha2)16], and for the drag factor is G'(alpha) = (1 - 2alpha(2)/3 - 0.20217 alpha5)/(1 - 0.75851 alpha5) - 0.0431[1 - (1 - alpha10)]. All of these converge monotonically to the correct limits at alpha = 1. CONCLUSIONS: These are the first expressions providing hydrodynamically based estimates of sigma(alpha) and P(alpha) over 0 < alpha < 1 They should be accurate to within 1-2%.

Animals↗

PubMed2001

Hair removal with a combined light/heat based photo-epilation system.

BACKGROUND: A variety of lasers and light sources have been used for removal of unwanted hair. A novel, new, flashlamp-based device, with a mechanism of action based on a combination of both emitted light and heat, has been developed for safe and reliable hair removal. OBJECTIVE: To assess the efficacy and safety of hair removal by a combined light/heat based photoepilation system. METHODS: A pilot trial was undertaken. Twenty one anatomic sites received one to three treatments with the SpaTouch light/heat based photoepilation system. Fluences ranging from 6.25 to 6.45 J/cm(2) and pulse duration of 35 ms were used. Evaluations of hair regrowth was performed at 4 months after the last treatment by comparing the terminal hair count to the baseline values. Patient satisfaction and potential complications were evaluated. RESULTS: Average hair reduction after photoepilation was 27% for one to three treatments at 4 months following the final treatment. 46% and 15% of subjects reported being 'mildly pleased' and 'very pleased' with the results of treatment. No hyperpigmentation, hypopigmentation or scarring was observed at 4 months after treatment. CONCLUSION: The SpaTouch light/heat based photoepilation system represents the newest efficient and safe method in hair removal. Further study of optimal parameters is required.

Adult↗

PubMed2000

Combining two excitation wavelengths for pulsed photothermal profiling of hypervascular lesions in human skin.

When pulsed photothermal radiometry (PPTR) is used for depth profiling of hypervascular lesions in human skin, melanin absorption also heats the most superficial skin layer (epidermis). Determination of lesion depth may be difficult when it lies close to the epidermal dermal junction, due to PPTR's limited spatial resolution. To overcome this problem, we have developed an approximation technique, which uses two excitation wavelengths (585 and 600 nm) to separate the vascular and epidermal components of the PPTR signal. This technique permits a noninvasive determination of lesion depth and epidermal thickness in vivo, even when the two layers are in close physical proximity to each other. Such information provides the physician with guidance in selecting the optimal parameters for laser therapy on an individual patient basis.

Blood↗

PubMed2002

Preliminary evaluation of second harmonic direct detection scheme for low-dose range in alanine/EPR dosimetry.

The usefulness of a direct detection scheme of the second harmonic (2h) overmodulated signal from irradiated alanine in EPR dosimetry was studied. For this purpose, a group of DL-alanine/paraffin cylindrical pellets was produced. The dosimeters were irradiated with a 60Co radiotherapy gamma source with doses of 0.05, 0.1, 0.5, 1 and 5 Gy. The EPR measurements were carried out in a VARIAN-E4 spectrometer operating in X-band with optimized parameters to obtain highest amplitude signals of both harmonics. The 2h signal was detected directly at twice the modulation frequency. In preliminary results, the 2h showed some advantages over the 1 h such as better resolution for doses below 1 Gy, better repeatability results and better linear behaviour in the dose range indicated.

Alanine↗

PubMed2000

Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data.

Although two-color fluorescent DNA microarrays are now standard equipment in many molecular biology laboratories, methods for identifying differentially expressed genes in microarray data are still evolving. Here, we report a refined test for differentially expressed genes which does not rely on gene expression ratios but directly compares a series of repeated measurements of the two dye intensities for each gene. This test uses a statistical model to describe multiplicative and additive errors influencing an array experiment, where model parameters are estimated from observed intensities for all genes using the method of maximum likelihood. A generalized likelihood ratio test is performed for each gene to determine whether, under the model, these intensities are significantly different. We use this method to identify significant differences in gene expression among yeast cells growing in galactose-stimulating versus non-stimulating conditions and compare our results with current approaches for identifying differentially-expressed genes. The effect of sample size on parameter optimization is also explored, as is the use of the error model to compare the within- and between-slide intensity variation intrinsic to an array experiment.

Galactose↗

PubMed2001

Detection of recombination in DNA multiple alignments with hidden Markov models.

Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected.

Algorithms↗

PubMed2003

Production of nuclear transfer llama (lama glama) embryos from in vitro matured llama oocytes.

To date, there have been no reports of somatic cell nuclear transfer in llamas. The application of this methodology to the camelid industry could be helpful in the propagation of genetically valuable animals. The objective of this study was to produce nuclear transfer llama embryos comparing the development of these llama embryos cultured in either CR1aa medium (treatment A) or G1.2 medium (treatment B) medium. Llamas were superstimulated by double dominant follicle reduction 12 days apart, followed by pFSH administered in daily descending doses over a 3-day interval (total dose of 200 mg). Animals were ovariectomized by flank laparotomy, follicles were aspirated from excised ovaries and oocytes were in vitro matured for a 30-h period. Adult female llama fibroblasts were used as donor karyoplasts and injected into enucleated llama oocytes. Embryo development was assessed after 2 days of culture. A total of 307 follicles were aspirated from nine treated females, resulting in 298 (97%) oocytes recovered. Of a total of 229 evaluated oocytes, 120 (52%) achieved nuclear maturation. Of a total of 80 reconstructed couplets, 50 (62.5%) were successfully fused. Subsequent cleavage rates were 32 and 40% for treatments A and B, respectively, with no significant difference (p < 0.05) detected between treatment groups. A total of 11 embryos (8-cell to morula stages) were transferred to synchronized recipient llamas. Ultrasonography at 14 days post-transfer indicated that no pregnancies were established. This study shows that nuclear transfer can be successfully applied to the production of llama embryos. Further research is needed to identify optimal parameters to improve efficiency of nuclear transfer in this species.

Animals↗

PubMed1991

Low-intensive lasers in the treatment of peptic gastric and duodenal ulcers.

Pharmacochemical achievements have brought about considerable improvement in treating peptic ulcers. But possible side effects demand a very cautious approach to the administration of every new drug, and stimulate the search for nontraditional treatment. In 638 patients who were treated by semiconductor laser transcutaneously (external irradiation), an average term of ulcer healing was 11.5 days, that is, half the time required for controls. The healing process under laser therapy depends on the disease gravity as well as the diameter and depth of the ulcer. Morphologically, we noted a quick restoration of microvessels in the ulcer area. The most optimal parameters of laser irradiation are chosen with the help of biophotometry.

Adolescent↗

PubMed1991

Denervation of the gastric acid-producing zone by a gastric wall laser seromyotomy.

The application of various surgical laser devices offers the possibility for significant simplification of the technique of the selective denervation of a gastric acid-producing zone proposed by Tylor as the gastric wall seromyotomy. The application of laser technique results in decreased operative time, a wide range of surgical practice, less operative bleeding, and more reliable denervation. Operations performed in 38 patients provide a basis for recommending optimal parameters of laser energy for the gastric wall incision and reveal the advantages and disadvantages of different irradiation sources. Early results of of the operation are not worse than after the proximal selective vagotomy.

Duodenal Ulcer↗

PubMed2006

Maximum likelihood molecular clock comb: analytic solutions.

Maximum likelihood (ML) is increasingly used as an optimality criterion for selecting evolutionary trees, but finding the global optimum is a hard computational task. Because no general analytic solution is known, numeric techniques such as hill climbing or expectation maximization (EM), are used in order to find optimal parameters for a given tree. So far, analytic solutions were derived only for the simplest model--three taxa, two state characters, under a molecular clock. Four taxa rooted trees have two topologies--the fork (two subtrees with two leaves each) and the comb (one subtree with three leaves, the other with a single leaf). In a previous work, we devised a closed form analytic solution for the ML molecular clock fork. In this work, we extend the state of the art in the area of analytic solutions ML trees to the family of all four taxa trees under the molecular clock assumption. The change from the fork topology to the comb incurs a major increase in the complexity of the underlying algebraic system and requires novel techniques and approaches. We combine the ultrametric properties of molecular clock trees with the Hadamard conjugation to derive a number of topology dependent identities. Employing these identities, we substantially simplify the system of polynomial equations. We finally use tools from algebraic geometry (e.g., Gröbner bases, ideal saturation, resultants) and employ symbolic algebra software to obtain analytic solutions for the comb. We show that in contrast to the fork, the comb has no closed form solutions (expressed by radicals in the input data). In general, four taxa trees can have multiple ML points. In contrast, we can now prove that under the molecular clock assumption, the comb has a unique (local and global) ML point. (Such uniqueness was previously shown for the fork.).

Evolution, Molecular↗

PubMed1993

Iontophoresis of reactive black 5 for pulsed dye laser sclerostomy.

Ab interno pulsed dye laser sclerostomy uses a gonioscopic approach to form a limbal fistula for the treatment of glaucoma. This procedure requires a full thickness penetration of stain in sclera for adequate absorption of the visible light energy. Iontophoresis is a technique using an electrical current to noninvasively deliver Reactive Black 5 (RB5) stain into sclera. This project determined the stability of RB5 stain as well as the optimal parameters for iontophoresis (probe tip surface area, current, and duration) in a rabbit model. RB5 stain was stable over time (72 hr) as well as after exposure to extreme heat (120 degrees C), scleral constituents (namely collagen), high concentrations of oxidants (1.5% H2O2), and laser light energy. Ideal parameters for iontophoresis included a probe tip surface area between 0.1 and 0.7 mm2, a current of 0.5 mA, and a duration of 5 min. The maximum concentration of RB5 stain achieved in sclera was 0.15%. The threshold of ablation for RB5 using an energy of 250 mJ was 0.001%. Iontophoresis can effectively deliver RB5 stain into sclera and may be a viable adjunct to ab interno pulsed dye laser sclerostomy procedures in the eye.

Animals↗

PubMed2001

Amino acid similarity matrices based on force fields.

MOTIVATION: We propose a general method for deriving amino acid substitution matrices from low resolution force fields. Unlike current popular methods, the approach does not rely on evolutionary arguments or alignment of sequences or structures. Instead, residues are computationally mutated and their contribution to the total energy/score is collected. The average of these values over each position within a set of proteins results in a substitution matrix. RESULTS: Example substitution matrices have been calculated from force fields based on different philosophies and their performance compared with conventional substitution matrices. Although this can produce useful substitution matrices, the methodology highlights the virtues, deficiencies and biases of the source force fields. It also allows a rather direct comparison of sequence alignment methods with the score functions underlying protein sequence to structure threading. AVAILABILITY: Example substitution matrices are available from http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html. SUPPLEMENTARY INFORMATION: The list of proteins used for data collection and the optimized parameters for the alignment are given as supplementary material at http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices.html.

Amino Acid Substitution↗

PubMed2025

qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics.

SUMMARY: Clonal hematopoiesis (CH) is a molecular biomarker associated with various adverse outcomes in both healthy individuals and those with underlying conditions, including cancer. Detecting CH usually involves genomic sequencing of individual blood samples followed by robust bioinformatics data filtering. We report an R package, qcCHIP, a bioinformatics pipeline that implements permutation-based parameter optimization to guide quality control filtering and cohort-specific CH identification. We benchmark qcCHIP under various data settings, including different sequencing depths, ranges of cohort sizes, with and without normal-tumor paired samples, and across different cancer types. We show that qcCHIP allows users to customize analysis needs to generate CH calls based on cohort-specific data characteristics. AVAILABILITY AND IMPLEMENTATION: qcCHIP R package is freely accessible at GitHub https://github.com/tenglab/qcCHIP and DOI: 10.5281/zenodo.16421861.

Humans↗

PubMed2004

A comparison of scoring functions for protein sequence profile alignment.

MOTIVATION: In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSI-BLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTALW. However, little is known about the relative performance of different profile-profile scoring functions. In this work, we evaluate the alignment accuracy of 23 different profile-profile scoring functions by comparing alignments of 488 pairs of sequences with identity < or =30% against structural alignments. We optimize parameters for all scoring functions on the same training set and use profiles of alignments from both PSI-BLAST and SAM-T99. Structural alignments are constructed from a consensus between the FSSP database and CE structural aligner. We compare the results with sequence-sequence and sequence-profile methods, including BLAST and PSI-BLAST. RESULTS: We find that profile-profile alignment gives an average improvement over our test set of typically 2-3% over profile-sequence alignment and approximately 40% over sequence-sequence alignment. No statistically significant difference is seen in the relative performance of most of the scoring functions tested. Significantly better results are obtained with profiles constructed from SAM-T99 alignments than from PSI-BLAST alignments. AVAILABILITY: Source code, reference alignments and more detailed results are freely available at http://phylogenomics.berkeley.edu/profilealignment/

Algorithms↗

PubMed2005

Density guided importance sampling: application to a reduced model of protein folding.

MOTIVATION: Monte Carlo methods are the most effective means of exploring the energy landscapes of protein folding. The rugged topography of folding energy landscapes causes sampling inefficiencies however, particularly at low, physiological temperatures. RESULTS: A hybrid Monte Carlo method, termed density guided importance sampling (DGIS), is presented that overcomes these sampling inefficiencies. The method is shown to be highly accurate and efficient in determining Boltzmann weighted structural metrics of a discrete off-lattice protein model. In comparison to the Metropolis Monte Carlo method, and the hybrid Monte Carlo methods, jump-walking, smart-walking and replica-exchange, the DGIS method is shown to be more efficient, requiring no parameter optimization. The method guides the simulation towards under-sampled regions of the energy spectrum and recognizes when equilibrium has been reached, avoiding arbitrary and excessively long simulation times. AVAILABILITY: Fortran code available from authors upon request. CONTACT: m.j.parker@leeds.ac.uk.

Algorithms↗

PubMed2005

Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs.

MOTIVATION: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We evaluate our capability to discriminate phosphate- and methionine-responding genes on the basis of putative regulatory elements, despite the similarity between Met4p/Met28p/Cbf1p and Pho4p consensus. RESULTS: We scanned upstream regions of methionine, phosphate and control genes with position-specific weight matrices for Pho4p, Met4p/Met28p/Cbf1p and Met31p/Met32p, and applied discriminant analysis to classify genes according to matrix matching scores. This analysis showed that matrix scores provided a good discrimination between phosphate, methionine and control genes. The optimal parameters have then been used to predict phosphate and methionine regulation at a genome scale. The genome-scale analysis predicts 37 genes as methionine-regulated and 40 as phosphate-regulated. We compare the predictive results with high throughput data and discuss the difference. AVAILABILITY: The programs for sequence retrieval and analysis, as well as the complete data and results, are available on the website on regulatory sequence analysis tools (http://rsat.scmbb.ulb.ac.be/rsat/). CONTACT: jvanheld@scmbb.ulb.ac.be SUPPLEMENTARY INFORMATION: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/

Algorithms↗

PubMed2006

LSAT: learning about alternative transcripts in MEDLINE.

MOTIVATION: Generation of alternative transcripts from the same gene is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose the task of extracting information around this complex topic using a two-step procedure involving machine learning and information extraction. RESULTS: In the first step, we trained a classifier that inductively learns to identify sentences about physiological transcript diversity from the MEDLINE abstracts. Using a large hand-built corpus, we compared the sentence classification performance of various text categorization methods. Support vector machines (SVMs) followed by the maximum entropy classifier outperformed other methods for the sentence classification task. The SVM with the radial basis function kernel and optimized parameters achieved Fbeta-measure of 91% during the 4-fold cross validation and of 74% when applied to all sentences in more than 12 million abstracts of MEDLINE. In the second step, we identified eight frequently present semantic categories in the sentences and performed a limited amount of semantic role labeling. The role labeling step also achieved very high Fbeta-measure for all eight categories. AVAILABILITY: The results of our two-step procedure are summarized in the LSAT database of alternative transcripts. LSAT is available at http://www.bork.embl.de/LSAT CONTACT: shah@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Benchmarking↗