Search results for "Matrix"
showing 10 items of 3205 documents
CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA
2011
Pyrosequencing technologies are frequently used for sequencing the 16S rRNA marker gene for metagenomic studies of microbial communities. Computing a pairwise genetic distance matrix from the produced reads is an important but highly time consuming task. In this paper, we present a parallelized tool (called CRiSPy) for scalable pairwise genetic distance matrix computation and clustering that is based on the processing pipeline of the popular ESPRIT software package. To achieve high computational efficiency, we have designed massively parallel CUDA algorithms for pairwise k-mer distance and pairwise genetic distance computation. We have also implemented a memory-efficient sparse matrix clust…
From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Car…
2017
Premise of the study The Caryophyllales contain ~12,500 species and are known for their cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear, and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods We generated 84 transcriptomes and combined these with 224 publicly available transcriptomes to perform a phylogenomic analysis of Caryophyllales. To overcome the computational challenge of ortholog detection in s…
Molluscan Shell Proteins: Primary Structure, Origin, and Evolution
2007
In the last few years, the field of molluscan biomineralization has known a tremendous mutation, regarding fundamental concepts on biomineralization regulation as well as regarding the methods of investigation. The most recent advances deal more particularly with the structure of shell biominerals at nanoscale and the identification of an increasing number of shell matrix protein components. Although the matrix is quantitatively a minor constituent in the shell of mollusks (less than 5% w/w), it is, however, the major component that controls different aspects of the shell formation processes: synthesis of transient amorphous minerals and evolution to crystalline phases, choice of the calciu…
Molluscan shell proteins
2004
Abstract The shell secreted by molluscs is one of the most remarkable examples of a matrix-mediated mineralisation performed outside living tissues. The calcifying matrix is a mixture of proteins, glycoproteins, and polysaccharides that precisely self-assemble and control the CaCO 3 polymorph (calcite, aragonite), the size, the shapes of the crystallites, and finally, the texture of the shell. In spite of several biochemical studies, the molecular aspects of the shell building are far from being understood. The present article makes an overview of the most recent molecular data on the proteinaceous components of the shell matrix. These data put into question the classical models of mollusca…
Influence of different biomaterials on the viability of Aggregatibacter actinomycetemcomitans
2011
Abstract Objectives The aim of the present in vitro study was to evaluate the effects of different biomaterials used for regenerative periodontal surgery on the growth of the periodontopathogen Aggregatibacter actinomycetemcomitans . Methods Three commercially available biomaterials of synthetic origin (hydroxyapatite/beta-tricalcium phosphate, nanostructured hydroxyapatite paste, oily calcium hydroxide suspension), a bovine-derived xenograft as well as an enamel matrix derivative (EMD) were added in different concentrations to calibrated suspensions of A. actinomycetemcomitans ATCC 43718/33384 (serotype b/c). Equal aliquots (0.1 ml) for the viability assay were taken after 5 min, 1 h, 3 h,…
Amplified morphogenetic and bone forming activity of amorphous versus crystalline calcium phosphate/polyphosphate.
2020
Amorphous Ca-phosphate (ACP) particles stabilized by inorganic polyphosphate (polyP) were prepared by co-precipitation of calcium and phosphate in the presence of polyP (15% [w/w]). These hybrid nanoparticles showed no signs of crystallinity according to X-ray diffraction analysis, in contrast to the particles obtained at a lower (5% [w/w]) polyP concentration or to hydroxyapatite. The ACP/15% polyP particles proved to be a suitable matrix for cell growth and attachment and showed pronounced osteoblastic and vasculogenic activity in vitro. They strongly stimulated mineralization of the human osteosarcoma cell line SaOS-2, as well as cell migration/microvascularization, as demonstrated in th…
Microstructure, mechanical characteristics and cell compatibility of β-tricalcium phosphate reinforced with biodegradable Fe–Mg metal phase
2015
The use of beta-tricalcium phosphate (β-TCP) ceramic as a bioresorbable bone substitute is limited to non-load-bearing sites by the material׳s brittleness and low bending strength. In the present work, new biocompatible β-TCP-based composites with improved mechanical properties were developed via reinforcing the ceramic matrix with 30 vol% of a biodegradable iron-magnesium metallic phase. β-TCP-15Fe15Mg and β-TCP-24Fe6Mg (vol%) composites were fabricated using a combination of high energy attrition milling, cold sintering/high pressure consolidation of powders at room temperature and annealing at 400 °C. The materials synthesized had a hierarchical nanocomposite structure with a nanocrystal…
Short time guided bone regeneration using beta-tricalcium phosphate with and without fibronectin. An experimental study in rats
2020
Background The aim of this histomorphometric study was to assess the bone regeneration potential of beta-tricalcium phosphate with fibronectin (β-TCP-Fn) in critical-sized defects (CSDs) in rats calvarial, to know whether Fn improves the new bone formation in a short time scope. Material and Methods CSDs were created in 30 Sprague Dawley rats, and divided into four groups (2 or 6 weeks of healing) and type of filling (β-TCP-Fn, β-TCP, empty control). Variables studied were augmented area (AA), gained tissue (GT), mineralized/non mineralized bone matrix (MBM/NMT) and bone substitute (BS). Results 60 samples at 2 and six weeks were evaluated. AA was higher for treatment groups comparing to …
In-situ suspended aggregate microextraction: A sample preparation approach for the enrichment of organic compounds in aqueous solutions.
2015
Abstract This work presents in-situ suspended aggregate microextraction (iSAME) as a new and expedient sample preparation method. This new concept capitalizes on the general principles of in-situ solvent formation microextraction, in the sense that extraction is carried out in a supramolecular aggregate phase, which is formed in-situ in the sample through one-step process involving ion-association between a cationic surfactant and a benzene sulfonic acid derivative. The suspended aggregate containing the analytes is then collected in the form of a thin-film on the surface of a common filter paper by suction filtration. The entrapped analytes are released by completely dissolving the thin-fi…
Plant sterol oxides in functional beverages: Influence of matrix and storage
2014
Three plant sterol (PS)-enriched beverages, milk based fruit juice (MFJPS), fruit juice (FJPS) and milk beverage (MPS), were stored at 4, 24, or 37 °C and analysed at regular time intervals of 2 months until 6 months. PS stability was analysed from the production of phytosterol oxidation products (POPs). The β-sitosterol oxides (7α/7β-hydroxy, β/α-epoxy, triol, and 7-keto) and campesterol oxides (β/α-epoxy, and 7-keto) were detected in all beverages and at all storage times and temperatures. Total POP contents followed the order MPS≫FJPSMFJPS. In general, the beverages showed low PS oxidation levels (0.17%). Predictive models of POP content versus storage time were established. These models…