Search results for "A* algorithm"
showing 10 items of 2538 documents
Fast dendrogram-based OTU clustering using sequence embedding
2014
Biodiversity assessment is an important step in a metagenomic processing pipeline. The biodiversity of a microbial metagenome is often estimated by grouping its 16S rRNA reads into operational taxonomic units or OTUs. These metagenomic datasets are typically large and hence require effective yet accurate computational methods for processing.In this paper, we introduce a new hierarchical clustering method called CRiSPy-Embed which aims to produce high-quality clustering results at a low computational cost. We tackle two computational issues of the current OTU hierarchical clustering approach: (1) the compute-intensive sequence alignment operation for building the distance matrix and (2) the …
Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
2020
Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…
Influence of ANN parameters on the performance of a refined procedure to solve the load-flow problem
1999
In recent years, interest in the application of Artificial Neural Networks (ANN) to electrical power systems has grown rapidly. In particular the use of ANN in the solution of the load-flow problem in wide electrical networks is an interesting research topic, because it constitutes a good alternative to the classical numerical algorithms. In this paper a refined solution strategy based on statistical methods, on a particular Grouping Genetic Algorithm (GGA) and on Progressive Learning Network (PLN) is presented. Tests on the solution of load-flow equations of the standard IEEE 118 bus network confirm the good potential of this approach; in particular the search for optimal values of the PLN…
Flow cytometry and spectral imaging multiphoton microscopy analysis of CD36 expression with quantum dots 605 of untreated and 7-ketocholesterol-treat…
2006
To evaluate CD36 expression with quantum dots 605 (QDs 605) on untreated and 7-ketocholesterol (7KC)-treated monocytic U937 cells by flow cytometry (FCM) and confocal and multiphoton laser scanning microscopy (CLSM).Cells were analyzed by CLSM, following flow cytometric quantification of CD36 expression and 7KC uptake. Image sequences were obtained by spectral analysis in monophoton and multiphoton CLSM and analyzed by the factor analysis of medical image sequences (FAMIS) algorithm to differentiate emission spectra. In CLSM analysis, cell deposits were screened in ultraviolet excitation modes to optimize the possibilities of QDs 605 and have the benefit of nuclei counterstaining by DAPI.FC…
Comparative analysis of variation and selection in the HCV genome
2016
AbstractGenotype 1 of the hepatitis C virus (HCV) is the most prevalent of the variants of this virus. Its two main subtypes, HCV-1a and HCV-1b, are associated to differences in epidemic features and risk groups, despite sharing similar features in most biological properties. We have analyzed the impact of positive selection on the evolution of these variants using complete genome coding regions, and compared the levels of genetic variability and the distribution of positively selected sites. We have also compared the distributions of positively selected and conserved sites considering different factors such as RNA secondary structure, the presence of different epitopes (antibody, CD4 and C…
Attitude measurement by artificial vision
2005
The recent development of light and low-cost airborne platforms (microlight, drones, kites, balloons,...) has led to the need for simple and low-cost devices allowing attitude measurement with respect to a reference horizon of the platform itself or of an embedded setting. A theoretical study of the conditions for measuring attitude angles from artificial vision is proposed and an original practical algorithm allowing these measurements to be performed in real time is described. An implementation in a CMOS retina circuit is also presented. These points are illustrated by experiments confirming the feasibility of the device.
Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs
2014
Estimation of the pose in which two given molecules might bind together to form a potential complex is a crucial task in structural biology. To solve this so-called "docking problem", most algorithms initially generate large numbers of candidate poses (or decoys) which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates ranges from thousands to millions, performing the clustering on standard CPUs is highly time consuming. In this paper we analyze and evaluate different approaches to parallelize the nearest neighbor chain algorithm to perform hierarchical Ward clustering of protein structures usin…
Coordinate mutation and transformation of mouse fibroblasts: induction by nitroquinoline oxide and modulation by caffeine
1981
Mutation and malignant transformation were followed in the same cells. Mouse fibroblasts (C3H 10T 1/2) were mutated and transformed by 4-nitroquinoline-1-oxide with similar, approximately linear dose-responses. The presence of caffeine immediately after exposure to 4-nitroquinoline-1-oxide potently inhibited mutation and transformation at high but not at low doses of 4-nitroquinoline-1-oxide. Whilst the coordinate induction of mutation and transformation could be explained by both a common target (DNA) or a common reactive species hitting several targets, the identical modulation by a DNA repair inhibitor of both end points suggests fundamental similarities in the nature of the lesions lead…
XPO1E571K Mutation Modifies Exportin 1 Localisation and Interactome in B-cell Lymphoma
2020
The XPO1 gene encodes exportin 1 (XPO1) that controls the nuclear export of cargo proteins and RNAs. Almost 25% of primary mediastinal B-cell lymphoma (PMBL) and classical Hodgkin lymphoma (cHL) cases harboured a recurrent XPO1 point mutation (NM_003400, chr2:g61718472C>
Clinical use of RNA sequencing and oncobox analytics to predict personalized targeted therapeutic efficacy.
2020
e13676 Background: Analysis of mutation profiles in cancer patients does not provide clinical benefits in 80-90% of cases in the US (Marquart et al., 2018). Gene expression analysis potentially complements standard detection of clinically relevant mutations. Methods: 239 adult late-stage cancer patients. RNA gene expression sequencing completed on solid tumor samples using FFPE blocks. Patient mRNA profiles were analyzed using Oncobox bioinformatics, prioritizing target drugs according to their personalized predicted efficacy. Summary reports were provided to oncologists and resulting treatment selection and outcomes were assessed. Results: As of February 2020, feedback was received from p…