Search results for "Computational Theory and Mathematic"
showing 10 items of 567 documents
AFS: identification and quantification of species composition by metagenomic sequencing
2017
Abstract Summary DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-sav…
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …
REGGAE : a novel approach for the identification of key transcriptional regulators
2019
Abstract Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines assoc…
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
2018
Abstract Motivation Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy. Therefore, an important issue is to understand if, and to what extent, the structural differences in the chromatin organization between in vit…
Modeling mass transfer in fracture flows with the time domain-random walk method
2019
The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous ma…
Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study
2018
[EN] Anatomically based procedures to ablate atrial fibrillation (AF) are often successful in terminating paroxysmal AF. However, the ability to terminate persistent AF remains disappointing. New mechanistic approaches use multiple-electrode basket catheter mapping to localize and target AF drivers in the form of rotors but significant concerns remain about their accuracy. We aimed to evaluate how electrode-endocardium distance, far-field sources and inter-electrode distance affect the accuracy of localizing rotors. Sustained rotor activation of the atria was simulated numerically and mapped using a virtual basket catheter with varying electrode densities placed at different positions withi…
ON THE CALCULATION OF THE HEAT CAPACITY IN PATH INTEGRAL MONTE CARLO SIMULATIONS
1992
In Path Integral Monte Carlo simulations the systems partition function is mapped to an equivalent classical one at the expense of a temperature-dependent Hamiltonian with an additional imaginary time dimension. As a consequence the standard relation linking the heat capacity Cv to the energy fluctuations, <E2>−<E>2, which is useful in standard classical problems with temperature-independent Hamiltonian, becomes invalid. Instead, it gets replaced by the general relation [Formula: see text] for the intensive heat capacity estimator; β being the inverse temperature and the subscript P indicates the P-fold discretization in the imaginary time direction. This heatcapacity estimator…
Interactions of amino acids with aluminum octacarboxyphthalocyanine hydroxide. Experimental and DFT studies
2017
The influence of albumin and amino acids (l-serine, glycine, l-histidine, l-tryptophan, l-cysteine) on the properties of aluminum octacarboxyphthalocyanine hydroxide (Al(OH)PcOC) was investigated in a phosphate buffer (pH 8.0). Particular attention was paid to the spectroscopic properties and photostability of Al(OH)PcOC. The effect of albumin or amino acids on the photodegradation of Al(OH)PcOC was examined in water using red light: 685 nm and daylight irradiation. Analysis of kinetic curves indicated that interaction with those molecules increases the photostability of Al(OH)PcOC. The molecular structure of Al(OH)PcOC complexes (in vacuum and in water) with axially or equatorially coordin…
A computational model of postprandial adipose tissue lipid metabolism derived using human arteriovenous stable isotope tracer data
2019
Given the association of disturbances in non-esterified fatty acid (NEFA) metabolism with the development of Type 2 Diabetes and Non-Alcoholic Fatty Liver Disease, computational models of glucose-insulin dynamics have been extended to account for the interplay with NEFA. In this study, we use arteriovenous measurement across the subcutaneous adipose tissue during a mixed meal challenge test to evaluate the performance and underlying assumptions of three existing models of adipose tissue metabolism and construct a new, refined model of adipose tissue metabolism. Our model introduces new terms, explicitly accounting for the conversion of glucose to glyceraldehye-3-phosphate, the postprandial …