Study of the optimum haplotype length to build genomic relationship matrices.
Ferdosi, Mohammad H; Henshall, John; Tier, Bruce
2016-09-29
As genomic data becomes more abundant, genomic prediction is more routinely used to estimate breeding values. In genomic prediction, the relationship matrix ([Formula: see text]), which is traditionally used in genetic evaluations is replaced by the genomic relationship matrix ([Formula: see text]). This paper considers alternative ways of building relationship matrices either using single markers or haplotypes of different lengths. We compared the prediction accuracies and log-likelihoods when using these alternative relationship matrices and the traditional [Formula: see text] matrix, for real and simulated data. For real data, we built relationship matrices using 50k genotype data for a population of Brahman cattle to analyze three traits: scrotal circumference (SC), age at puberty (AGECL) and weight at first corpus luteum (WTCL). Haplotypes were phased with hsphase and imputed with BEAGLE. The relationship matrices were built using three methods based on haplotypes of different lengths. The log-likelihood was considered to define the optimum haplotype lengths for each trait and each haplotype-based relationship matrix. Based on simulated data, we showed that the inverse of [Formula: see text] matrix and the inverse of the haplotype relationship matrices for methods using one-single nucleotide polymorphism (SNP) phased haplotypes provided coefficients of determination (R(2)) close to 1, although the estimated genetic variances differed across methods. Using real data and multiple SNPs in the haplotype segments to build the relationship matrices provided better results than the [Formula: see text] matrix based on one-SNP haplotypes. However, the optimal haplotype length to achieve the highest log-likelihood depended on the method used and the trait. The optimal haplotype length (7 to 8 SNPs) was similar for SC and AGECL. One of the haplotype-based methods achieved the largest increase in log-likelihood for SC, i.e. from -1330 when using [Formula: see text] to
Directory of Open Access Journals (Sweden)
Northcutt Sally L
2010-04-01
Full Text Available Abstract Background Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Results Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. Conclusions This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.
Loberg, A; Dürr, J W; Fikse, W F; Jorjani, H; Crooks, L
2015-10-01
The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress. © 2015 Blackwell Verlag GmbH.
DEFF Research Database (Denmark)
Gao, Hongding; Christensen, Ole Fredslund; Madsen, Per
2012-01-01
Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to be adjusted because marker-based and pedigree-based relationship matrices may...... not be on the same scale. The same may apply when a GBLUP model includes both genomic breeding values and residual polygenic effects. The objective of this study was to compare single-step blending methods and GBLUP methods with and without adjustment of the genomic relationship matrix for genomic prediction of 16......) a simple GBLUP method, 2) a GBLUP method with a polygenic effect, 3) an adjusted GBLUP method with a polygenic effect, 4) a single-step blending method, and 5) an adjusted single-step blending method. In the adjusted GBLUP and single-step methods, the genomic relationship matrix was adjusted...
DEFF Research Database (Denmark)
Byrne, Stephen; Cericola, Fabio; Janss, Luc;
2015-01-01
, and an average protein Annotation Edit Distance (AED) of 0.14. Genotyping-By-Sequencing (GBS) data was generated after genome complexity reduction with ApeKI for 995 breeding families. Data was aligned against the annotated sequence assembly, and we identified variants at over 1.8 million positions, which were......,273 SNPs), genes with NB-ARC domains (9,056 SNPs), intron (168,023 SNPs), and inter-genic (1,420,866 SNPs). Genomic relationship matrices were created for each annotation class and SNP-explained variances for heading date and disease resistance were calculated...
Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis
Aim of the study was to compare correlation matrices between direct genomic predictions for 31 production, fitness and conformation traits both at genomic and chromosomal level in US Holstein bulls. Multivariate factor analysis was used to quantify basic features of correlation matrices. Factor extr...
HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.
Lekschas, Fritz; Bach, Benjamin; Kerpedjiev, Peter; Gehlenborg, Nils; Pfister, Hanspeter
2017-08-29
This paper presents an interactive visualization interface-HiPiler-for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROIs) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROIs in such large matrices. In HiPiler, ROIs are first-class objects, represented as thumbnail-like "snippets". Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.
Locally epistatic genomic relationship matrices for genomic association
In plant and animal breeding studies a distinction is made between the genetic value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this pa...
SNP effects estimated in genomic selection programs allow for the prediction of direct genomic values (DGV) both at genome-wide and chromosomal level. As a consequence, genome-wide (G_GW) or chromosomal (G_CHR) correlation matrices between genomic predictions for different traits can be calculated. ...
Directory of Open Access Journals (Sweden)
Christensen Ole F
2012-12-01
Full Text Available Abstract Background Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1 adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2 extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. Results The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient γ and an inbreeding coefficient γ / 2. Taken together, this γ parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1 the parameters involved
Christensen, Ole F
2012-12-03
Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1) adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2) extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient γ and an inbreeding coefficient γ / 2. Taken together, this γ parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1) the parameters involved in adjusting marker-based and pedigree
The WISC-III and Raven Coloured Progressive Matrices Test: A Pilot Study of Relationships.
Kluever, Raymond C.; And Others
The relationship between scores on Raven's Coloured Progressive Matrices (CPM) scores and subtest scores and IQs from the Wechsler Intelligence Scale for Children-III (WISC-III) was studied for 28 children aged 6 to 11 years. Subjects had been referred to a university assessment center because they were believed to have exceptional learning…
Flach, Joost; van der Waal, Mark B; van den Nieuwboer, Maurits; Claassen, Eric; Larsen, Olaf F A
2017-06-13
Probiotic microorganisms are increasingly incorporated into food matrices in order to confer proposed health benefits on the consumer. It is important that the health benefits, sensory properties, shelf-life and probiotic gastrointestinal tract (GIT) survival of these products are carefully balanced as they determine functionality and drive consumer acceptance. The strain-specific effects of probiotic species are imperative in this process but carrier matrices may play a pivotal role as well. This study therefore recapitulates the wealth of knowledge on carrier matrices and their interaction with probiotic strains. The most substantiated carrier matrices, factors that influence probiotic functionality and matrix effects on shelf-life, GIT survival and clinical efficacy are reviewed. Results indicate that carrier matrices have a significant impact on the quality of probiotic products. Matrix components, such as proteins, carbohydrates and flavoring agents are shown to alter probiotic efficacy and viability. In vivo studies furthermore revealed strain-dependent matrix effects on the GIT survival of probiotic bacteria. However, only a limited number of studies have specifically addressed the effects of carrier matrices on the aforementioned product-parameters; most studies seem to focus solely on the strain-specific effects of probiotic microorganisms. This hampers the innovation of probiotic products. More human studies, comparing not only different probiotic strains but different carrier matrices as well, are needed to drive the innovation cycle.
Sousa, Angela; Sousa, Fani; Queiroz, João A
2010-09-01
The development of a strategy to plasmid DNA (pDNA) purification has become necessary for the development of gene therapy and DNA vaccine production processes in recent years, since this nucleic acid and most of contaminants, such as RNA, genomic DNA and endotoxins, are negatively charged. An ideal separation methodology may be achieved with the use of affinity interactions between immobilized amino acids and nucleic acids. In this study, the binding behaviour of nucleic acids under the influence of different environmental conditions, such as the composition and ionic strength of elution buffer, and the temperature, is compared with various amino acids immobilized on chromatography resins. Supercoiled (sc) plasmid isoform was isolated with all matrices used, but in some cases preferential interactions with other nucleic acids were found. Particularly, lysine chromatography showed to be an ideal technology mainly on RNA purification using low salt concentration. On the other hand, arginine ligands have shown a greater ability to retain the sc isoform comparatively to the other nucleic acids retention, becoming this support more adequate to sc pDNA purification. The temperature variation, competitive elution and oligonucleotides affinity studies also allowed to recognize the dominant interactions inherent to biorecognition of pDNA molecule and the affinity matrices.
Cardoso, Osmar O; Julião, Fabiana C; Alves, Renato I S; Baena, Antonio R; Díez, Isabel G; Suzuki, Meire N; Celere, Beatriz S; Nadal, Martí; Domingo, José L; Segura-Muñoz, Susana I
2014-07-01
The concentrations of Cd, Cr, Cu, Hg, Mn, Ni, Pb, Sn, and Zn were determined in breast milk of women living in Conceição das Alagoas, Minas Gerais, Brazil. The potential relationships between metal levels in samples of breast milk, drinking water, and soils collected in the study area were also established. Metal levels in breast milk, except Cr, were lower in comparison to WHO reference concentrations. Zinc was the predominant element in breast milk and drinking water samples, with a median level of 46.2 and 82.2 μg · L(-1), respectively. Soils presented a different pattern of metal concentrations with respect to those found in breast milk and drinking water, Chromium showed the highest median levels (148 mg · kg(-1)), while a certain predominance of Zn and Cu was also observed (47.0 and 43.0 mg · kg(-1), respectively). Similar profiles were observed when comparing metal concentrations in drinking water and breast milk (chi-square χ(2) = 14.36; p < 0.05). In contrast, breast milk-soil and drinking water-soil metal concentration profiles showed significant differences (χ(2) = 635.05 and χ(2) = 721.78, respectively; p < 0.05). These results indicate that drinking water is an important exposure pathway for metals to newborns through breast milk. Further studies should be aimed at assessing the body burdens of metals in that population and at evaluating the potential relationships in the concentrations in biological and environmental matrices as well as at estimating the contribution of dietary intake of metals. In addition, the presence of other chemical pollutants in breast milk should be also studied in order to assess the combined newborn exposure to other contaminants.
Localising loci underlying complex trait variation using Regional Genomic Relationship Mapping.
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Yoshitaka Nagamine
Full Text Available The limited proportion of complex trait variance identified in genome-wide association studies may reflect the limited power of single SNP analyses to detect either rare causative alleles or those of small effect. Motivated by studies that demonstrate that loci contributing to trait variation may contain a number of different alleles, we have developed an analytical approach termed Regional Genomic Relationship Mapping that, like linkage-based family methods, integrates variance contributed by founder gametes within a pedigree. This approach takes advantage of very distant (and unrecorded relationships, and this greatly increases the power of the method, compared with traditional pedigree-based linkage analyses. By integrating variance contributed by founder gametes in the population, our approach provides an estimate of the Regional Heritability attributable to a small genomic region (e.g. 100 SNP window covering ca. 1 Mb of DNA in a 300000 SNP GWAS and has the power to detect regions containing multiple alleles that individually contribute too little variance to be detectable by GWAS as well as regions with single common GWAS-detectable SNPs. We use genome-wide SNP array data to obtain both a genome-wide relationship matrix and regional relationship ("identity by state" or IBS matrices for sequential regions across the genome. We then estimate a heritability for each region sequentially in our genome-wide scan. We demonstrate by simulation and with real data that, when compared to traditional ("individual SNP" GWAS, our method uncovers new loci that explain additional trait variation. We analysed data from three Southern European populations and from Orkney for exemplar traits - serum uric acid concentration and height. We show that regional heritability estimates are correlated with results from genome-wide association analysis but can capture more of the genetic variance segregating in the population and identify additional trait loci.
A review of inversion techniques related to the use of relationship matrices in animal breeding
Directory of Open Access Journals (Sweden)
Faux, P.
2014-01-01
Full Text Available Synthèse bibliographique des techniques d'inversion impliquées dans l'utilisation de matrices de parenté en amélioration animale. En amélioration animale, les effets génétiques sont habituellement prédits par l'utilisation de modèles mixtes. Pour n'importe quel effet génétique, les modèles mixtes nécessitent l'inversion de la matrice de covariance associée à cet effet. Cette matrice est égale à la matrice de parenté associée, multipliée par le composant de la variance génétique également associé à cet effet. Etant donné la taille de nombreux systèmes d'évaluations génétiques, établir l'inverse de ces matrices de parenté peut s'avérer couteux d'un point de vue computationnel. Dans cette synthèse bibliographique, notre objectif est de passer en revue les techniques qui facilitent l'inversion de matrices de parenté utilisée en amélioration animale pour la prédiction des types d'effets génétiques suivants : effet additif, effet gamétique, effet dû à la présence de loci marqués de caractères quantitatifs, effet de dominance et différent effet d'épistasie. Les règles de construction de la matrice et les algorithmes d'inversion sont détaillés pour chaque matrice de parenté. Dans la discussion finale, nous esquissons un cadre théorique commun à la plupart des techniques d'inversion passées en revue. Deux contraintes computationnelles ressortent de ce cadre théorique : l'établissement de la matrice de dépendances entre niveaux de l'effet et celui de certaines parties (diagonales ou bloc-diagonales de la matrice de parenté à inverser.
Forneris, N S; Steibel, J P; Legarra, A; Vitezica, Z G; Bates, R O; Ernst, C W; Basso, A L; Cantet, R J C
2016-12-01
Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR-O ) or the base population (GVR-B ) allele frequencies and (ii) identity by descent using linkage analysis (GIBD-L ). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD-L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR-B approximated GIBD-L 's correlation and had lower error than GVR-O . Accuracy of GEBV for selection candidates was significantly higher when GIBD-L was used and identical between GVR-O and GVR-B . In real data, GIBD-L 's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV. © 2016 Blackwell Verlag GmbH.
Paul, Steven M.
1986-01-01
Normative data for the Advanced Raven's Progressive Matrices are presented based on 300 University of California, Berkeley, students. Correlations with the Wechsler Adult Intelligence Scale and the Terman Concept Mastery Test are explored. The relationship between the Advanced Raven's Progressive Matrices and Spearman's g is explored. (Author)
Comparative genomics of the relationship between gene structure and expression
Ren, X.
2006-01-01
The relationship between the structure of genes and their expression is a relatively new aspect of genome organization and regulation. With more genome sequences and expression data becoming available, bioinformatics approaches can help the further elucidation of the relationships between gene struc
Carlson, Jerry S.
1973-01-01
The results of this study support the notion that different parts of Raven's Coloured Progressive Matrices Test tap different processes. Sets A and Ab employ the rationale of the Inhelder-Piaget Test and rely on solution by graphic processes, whereas set B involves solution by opeational means. Total score results may be less appropriate than the…
Quantification of genetic relationships among A genomes of wheats.
Brandolini, A; Vaccino, P; Boggini, G; Ozkan, H; Kilian, B; Salamini, F
2006-04-01
The genetic relationships of A genomes of Triticum urartu (Au) and Triticum monococcum (Am) in polyploid wheats are explored and quantified by AFLP fingerprinting. Forty-one accessions of A-genome diploid wheats, 3 of AG-genome wheats, 19 of AB-genome wheats, 15 of ABD-genome wheats, and 1 of the D-genome donor Ae. tauschii have been analysed. Based on 7 AFLP primer combinations, 423 bands were identified as potentially A genome specific. The bands were reduced to 239 by eliminating those present in autoradiograms of Ae. tauschii, bands interpreted as common to all wheat genomes. Neighbour-joining analysis separates T. urartu from T. monococcum. Triticum urartu has the closest relationship to polyploid wheats. Triticum turgidum subsp. dicoccum and T. turgidum subsp. durum lines are included in tightly linked clusters. The hexaploid spelts occupy positions in the phylogenetic tree intermediate between bread wheats and T. turgidum. The AG-genome accessions cluster in a position quite distant from both diploid and other polyploid wheats. The estimates of similarity between A genomes of diploid and polyploid wheats indicate that, compared with Am, Au has around 20% higher similarity to the genomes of polyploid wheats. Triticum timo pheevii AG genome is molecularly equidistant from those of Au and Am wheats.
Relationship between Genomic Types of Escherichia coli and Clinical Diseases
Institute of Scientific and Technical Information of China (English)
Meiying YI; Ruen LIU; Hanju HUANG
2008-01-01
In this study, by analysis of genome structures of E. coli, the relationships Between the genomic types of E. coli and the associated diseases were investigated. Samples of sputum, urine and other excretions from patients with different infective diseases were collected. And 62 E. coli strains were isolated from these samples. Intact bacterial genomic DNA was cleaved with I-CeuI, separated by pulsed field gel electrophoresis and then typed on the basis of cleavage map. The results showed that 7 I-CeuI sites were found in all the genome structures of the 62 E. coli, indicating that there were 7 rrn operons in the genomes. The size of genome ranged from 4500 kb to 5000 kb. According to thegenome structures, 62 E. coli strains were divided into 30 genome types. It was concluded that genome structures of E. coli isolated from the patients with different infective diseases varied to some extent, suggesting that some genome types of E. coli were closely related to some infective diseases.
Hamilton, Eileen P; Kapusta, Aurélie; Huvos, Piroska E; Bidwell, Shelby L; Zafar, Nikhat; Tang, Haibao; Hadjithomas, Michalis; Krishnakumar, Vivek; Badger, Jonathan H; Caler, Elisabet V; Russ, Carsten; Zeng, Qiandong; Fan, Lin; Levin, Joshua Z; Shea, Terrance; Young, Sarah K; Hegarty, Ryan; Daza, Riza; Gujja, Sharvari; Wortman, Jennifer R; Birren, Bruce W; Nusbaum, Chad; Thomas, Jainy; Carey, Clayton M; Pritham, Ellen J; Feschotte, Cédric; Noto, Tomoko; Mochizuki, Kazufumi; Papazyan, Romeo; Taverna, Sean D; Dear, Paul H; Cassidy-Hanley, Donna M; Xiong, Jie; Miao, Wei; Orias, Eduardo; Coyne, Robert S
2016-11-28
The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymena's germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.
Asymmetric relationships between proteins shape genome evolution.
Notebaart, R.A.; Kensche, P.R.; Huynen, M.A.; Dutilh, B.E.
2009-01-01
BACKGROUND: The relationships between proteins are often asymmetric: one protein (A) depends for its function on another protein (B), but the second protein does not depend on the first. In metabolic networks there are multiple pathways that converge into one central pathway. The enzymes in the conv
DEFF Research Database (Denmark)
Christensen, Ole Fredslund
2012-01-01
Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel......Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker......-based relationship matrix and the pedigree-based relationship matrix. The compatibility issue involves which allele frequencies to use in the marker-based relationship matrix, and also that adjustments of this matrix to the pedigree-based relationship matrix are needed. In addition, it has been overlooked...... in the base population. Here, two ideas are explored. The first idea is to instead adjust the pedigree-based relationship matrix to be compatible to the marker-based relationship matrix, whereas the second idea is to include the likelihood for the observed markers. A single-step method is used where...
Rodríguez, Alicia; Capela, Daniela; Medina, Ángel; Córdoba, Juan J; Magan, Naresh
2015-02-02
Dry-cured sausages are colonised by moulds during the ripening process. The temperature and the salt content (which affects water activity, aw) predispose the surface to colonisation by Penicillium species, including Penicillium nordicum and Penicillium verrucosum which can lead to contamination of the sausages with ochratoxin A (OTA). The objective of this work was to obtain scientific data on the impact that interaction between ionic water stress (aw; 0.97, 0.94, 0.90, 0.87 and 0.84) and temperature (30, 25, 20, 15 and 10°C) may have on lag phases prior to growth, growth and OTA production by some P. verrucosum and P. nordicum strains isolated from dry-cured meat products on a dry-cured sausage-based medium over a period of 12days. Although P. nordicum had shorter lag phases than P. verrucosum, the latter grew faster than P. nordicum in most conditions tested. For both species, there was no growth and OTA production at 0.84 aw at all the temperatures tested. The fungi were more tolerant at moderate ionic aw conditions (0.94 and 0.90) and 20 and 25°C. In contrast, the patterns of production of OTA were very different from those for growth. Different OTA production profiles between the two OTA-producing species were found. While P. nordicum began producing OTA in most of the conditions tested by day 6, P. verrucosum only produced the toxin in these conditions when the temperature and aw were >10°C and >0.90, respectively. However, the P. verrucosum strain produced much higher concentrations of OTA than the P. nordicum strain in all conditions. We developed contour maps of the optimum and marginal aw×temperature conditions for growth/OTA production on dry-cured sausage-based medium for the first time. This suggests that these interacting conditions during the early phases of production must be effectively controlled as these favour growth of the toxigenic Penicillia. Knowledge on the ecophysiology of these two important Penicillium species on these matrices
Jämstorp, Erik; Strømme, Maria; Frenning, Göran
2011-10-01
A unique structure-function relationship investigation of mechanically strong geopolymer drug delivery vehicles for sustained release of potent substances is presented. The effect of in-synthesis water content on geopolymer pore structure and diffusive drug transport is investigated. Scanning electron microscopy, N2 gas adsorption, mercury intrusion porosimetry, compression strength test, drug permeation, and release experiments are performed. Effective diffusion coefficients are measured and compared with corresponding theoretical values as derived from pore size distribution and connectivity via pore-network modeling. By solely varying the in-synthesis water content, mesoporous and mechanically strong geopolymers with porosities of 8%-45% are obtained. Effective diffusion coefficients of the model drugs Saccharin and Zolpidem are observed to span two orders of magnitude (∼1.6-120 × 10(-8) cm(2) /s), comparing very well to theoretical estimations. The ability to predict drug permeation and release from geopolymers, and materials alike, allows future formulations to be tailored on a structural and chemical level for specific applications such as controlled drug delivery of highly potent substances.
Novel Methods for Prioritizing "Close-In" Analogs from Structure-Activity Relationship Matrices.
Zhang, Liying; Johnson, Kjell; Starr, Jeremy; Milbank, Jared; Kuhn, Andrew M; Poss, Christopher; Stanton, Robert V; Shanmugasundaram, Veerabahu
2017-07-24
Here we describe the development of novel methods for compound evaluation and prioritization based on the structure-activity relationship matrix (SARM) framework. The SARM data structure allows automatic and exhaustive extraction of SAR patterns from data sets and their organization into a chemically intuitive scaffold/functional-group format. While SARMs have been used in the retrospective analysis of SAR discontinuity and identifying underexplored regions of chemistry space, there have been only a few attempts to apply SARMs prospectively in the prioritization of "close-in" analogs. In this work, three new ways of prioritizing virtual compounds based on SARMs are described: (1) matrix pattern-based prioritization, (2) similarity weighted, matrix pattern-based prioritization, and (3) analysis of variance based prioritization (ANV). All of these methods yielded high predictive power for six benchmark data sets (prediction accuracy R(2) range from 0.63 to 0.82), yielding confidence in their application to new design ideas. In particular, the ANV method outperformed the previously reported SARM based method for five out of the six data sets tested. The impact of various SARM parameters were investigated and the reasons why SARM-based compound prioritization methods provide higher predictive power are discussed.
The Genomic Diversity and Phylogenetic Relationship in the Family Iridoviridae
Directory of Open Access Journals (Sweden)
Brooke A. Ring
2010-07-01
Full Text Available The Iridoviridae family are large viruses (~120-200 nm that contain a linear double-stranded DNA genome. The genomic size of Iridoviridae family members range from 105,903 bases encoding 97 open reading frames (ORFs for frog virus 3 to 212,482 bases encoding 211 ORFs for Chilo iridescent virus. The family Iridoviridae is currently subdivided into five genera: Chloriridovirus, Iridovirus, Lymphocystivirus, Megalocytivirus, and Ranavirus. Iridoviruses have been found to infect invertebrates and poikilothermic vertebrates, including amphibians, reptiles, and fish. With such a diverse array of hosts, there is great diversity in gene content between different genera. To understand the origin of iridoviruses, we explored the phylogenetic relationship between individual iridoviruses and defined the core-set of genes shared by all members of the family. In order to further explore the evolutionary relationship between the Iridoviridae family repetitive sequences were identified and compared. Each genome was found to contain a set of unique repetitive sequences that could be used in future virus identification. Repeats common to more than one virus were also identified and changes in copy number between these repeats may provide a simple method to differentiate between very closely related virus strains. The results of this paper will be useful in identifying new iridoviruses and determining their relationship to other members of the family.
Mehta, Madan Lal
1990-01-01
Since the publication of Random Matrices (Academic Press, 1967) so many new results have emerged both in theory and in applications, that this edition is almost completely revised to reflect the developments. For example, the theory of matrices with quaternion elements was developed to compute certain multiple integrals, and the inverse scattering theory was used to derive asymptotic results. The discovery of Selberg's 1944 paper on a multiple integral also gave rise to hundreds of recent publications. This book presents a coherent and detailed analytical treatment of random matrices, leading
Bayes linear adjustment for variance matrices
Wilkinson, Darren J
2008-01-01
We examine the problem of covariance belief revision using a geometric approach. We exhibit an inner-product space where covariance matrices live naturally --- a space of random real symmetric matrices. The inner-product on this space captures aspects of our beliefs about the relationship between covariance matrices of interest to us, providing a structure rich enough for us to adjust beliefs about unknown matrices in the light of data such as sample covariance matrices, exploiting second-order exchangeability specifications.
Wang, Chunkao; Da, Yang
2014-01-01
The traditional quantitative genetics model was used as the unifying approach to derive six existing and new definitions of genomic additive and dominance relationships. The theoretical differences of these definitions were in the assumptions of equal SNP effects (equivalent to across-SNP standardization), equal SNP variances (equivalent to within-SNP standardization), and expected or sample SNP additive and dominance variances. The six definitions of genomic additive and dominance relationships on average were consistent with the pedigree relationships, but had individual genomic specificity and large variations not observed from pedigree relationships. These large variations may allow finding least related genomes even within the same family for minimizing genomic relatedness among breeding individuals. The six definitions of genomic relationships generally had similar numerical results in genomic best linear unbiased predictions of additive effects (GBLUP) and similar genomic REML (GREML) estimates of additive heritability. Predicted SNP dominance effects and GREML estimates of dominance heritability were similar within definitions assuming equal SNP effects or within definitions assuming equal SNP variance, but had differences between these two groups of definitions. We proposed a new measure of genomic inbreeding coefficient based on parental genomic co-ancestry coefficient and genomic additive correlation as a genomic approach for predicting offspring inbreeding level. This genomic inbreeding coefficient had the highest correlation with pedigree inbreeding coefficient among the four methods evaluated for calculating genomic inbreeding coefficient in a Holstein sample and a swine sample.
Directory of Open Access Journals (Sweden)
Muslihudeen Abdul-Razaq Abdul-Aziz
2016-10-01
Full Text Available As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, gender, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome-microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms.
Stephanov, M A; Wettig, T
2005-01-01
We review elementary properties of random matrices and discuss widely used mathematical methods for both hermitian and nonhermitian random matrix ensembles. Applications to a wide range of physics problems are summarized. This paper originally appeared as an article in the Wiley Encyclopedia of Electrical and Electronics Engineering.
Krylov, Piotr
2017-01-01
This monograph is a comprehensive account of formal matrices, examining homological properties of modules over formal matrix rings and summarising the interplay between Morita contexts and K theory. While various special types of formal matrix rings have been studied for a long time from several points of view and appear in various textbooks, for instance to examine equivalences of module categories and to illustrate rings with one-sided non-symmetric properties, this particular class of rings has, so far, not been treated systematically. Exploring formal matrix rings of order 2 and introducing the notion of the determinant of a formal matrix over a commutative ring, this monograph further covers the Grothendieck and Whitehead groups of rings. Graduate students and researchers interested in ring theory, module theory and operator algebras will find this book particularly valuable. Containing numerous examples, Formal Matrices is a largely self-contained and accessible introduction to the topic, assuming a sol...
Abdul-Aziz, Muslihudeen A.; Cooper, Alan; Weyrich, Laura S.
2016-01-01
As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, sex, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome–microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms. PMID:27785127
Müller, Dominik; Technow, Frank; Melchinger, Albrecht E
2015-04-01
We evaluated several methods for computing shrinkage estimates of the genomic relationship matrix and demonstrated their potential to enhance the reliability of genomic estimated breeding values of training set individuals. In genomic prediction in plant breeding, the training set constitutes a large fraction of the total number of genotypes assayed and is itself subject to selection. The objective of our study was to investigate whether genomic estimated breeding values (GEBVs) of individuals in the training set can be enhanced by shrinkage estimation of the genomic relationship matrix. We simulated two different population types: a diversity panel of unrelated individuals and a biparental family of doubled haploid lines. For different training set sizes (50, 100, 200), number of markers (50, 100, 200, 500, 2,500) and heritabilities (0.25, 0.5, 0.75), shrinkage coefficients were computed by four different methods. Two of these methods are novel and based on measures of LD, the other two were previously described in the literature, one of which was extended by us. Our results showed that shrinkage estimation of the genomic relationship matrix can significantly improve the reliability of the GEBVs of training set individuals, especially for a low number of markers. We demonstrate that the number of markers is the primary determinant of the optimum shrinkage coefficient maximizing the reliability and we recommend methods eligible for routine usage in practical applications.
DEFF Research Database (Denmark)
van den Berg, Irene; Boichard, Didier; Lund, Mogens Sandø
and HD chips, or two 1 Kb intervals on both sides of each causative mutation, varying the distance between causative mutations and intervals from 1 base to 1 Mb. Subsequently, the regression coefficient of the genomic relationships at prediction markers on the genomic relationships at causal loci...... data is more likely to contain causative mutations and therefore increase the prediction accuracy in such populations. We studied the potential advantage of using real sequence data for prediction of genomic relationships at causative mutations using sequence data of chromosome 1 for 122 Holstein, 27...
Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.)
National Research Council Canada - National Science Library
Laurentin, Hernán; Ratzinger, Astrid; Karlovsky, Petr
2008-01-01
... systematically in diversity surveys. Our objective in this study was to assess metabolic diversity in sesame by nontargeted metabolic profiling and elucidate the relationship between metabolic and genome diversity in this crop...
On the Relationship between Pollen Size and Genome Size
Directory of Open Access Journals (Sweden)
Charles A. Knight
2010-01-01
Full Text Available Here we test whether genome size is a predictor of pollen size. If it were, inferences of ancient genome size would be possible using the abundant paleo-palynolgical record. We performed regression analyses across 464 species of pollen width and genome size. We found a significant positive trend. However, regression analysis using phylogentically independent contrasts did not support the correlated evolution of these traits. Instead, a large split between angiosperms and gymnosperms for both pollen width and genome size was revealed. Sister taxa were not more likely to show a positive contrast when compared to deeper nodes. However, significantly more congeneric species had a positive trend than expected by chance. These results may reflect the strong selection pressure for pollen to be small. Also, because pollen grains are not metabolically active when measured, their biology is different than other cells which have been shown to be strongly related to genome size, such as guard cells. Our findings contrast with previously published research. It was our hope that pollen size could be used as a proxy for inferring the genome size of ancient species. However, our results suggest pollen is not a good candidate for such endeavors.
Jansen, Robert K.; Cai, Zhengqiu; Raubeson, Linda A.; Daniell, Henry; dePamphilis, Claude W.; Leebens-Mack, James; Müller, Kai F.; Guisinger-Bellian, Mary; Haberle, Rosemarie C.; Hansen, Anne K.; Chumley, Timothy W.; Lee, Seung-Bum; Peery, Rhiannon; McNeal, Joel R.; Kuehl, Jennifer V.; Boore, Jeffrey L.
2007-01-01
Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements. PMID:18048330
Directory of Open Access Journals (Sweden)
Yubo Hou
Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.
Pathological rate matrices: from primates to pathogens
Directory of Open Access Journals (Sweden)
Knight Rob
2008-12-01
Full Text Available Abstract Background Continuous-time Markov models allow flexible, parametrically succinct descriptions of sequence divergence. Non-reversible forms of these models are more biologically realistic but are challenging to develop. The instantaneous rate matrices defined for these models are typically transformed into substitution probability matrices using a matrix exponentiation algorithm that employs eigendecomposition, but this algorithm has characteristic vulnerabilities that lead to significant errors when a rate matrix possesses certain 'pathological' properties. Here we tested whether pathological rate matrices exist in nature, and consider the suitability of different algorithms to their computation. Results We used concatenated protein coding gene alignments from microbial genomes, primate genomes and independent intron alignments from primate genomes. The Taylor series expansion and eigendecomposition matrix exponentiation algorithms were compared to the less widely employed, but more robust, Padé with scaling and squaring algorithm for nucleotide, dinucleotide, codon and trinucleotide rate matrices. Pathological dinucleotide and trinucleotide matrices were evident in the microbial data set, affecting the eigendecomposition and Taylor algorithms respectively. Even using a conservative estimate of matrix error (occurrence of an invalid probability, both Taylor and eigendecomposition algorithms exhibited substantial error rates: ~100% of all exonic trinucleotide matrices were pathological to the Taylor algorithm while ~10% of codon positions 1 and 2 dinucleotide matrices and intronic trinucleotide matrices, and ~30% of codon matrices were pathological to eigendecomposition. The majority of Taylor algorithm errors derived from occurrence of multiple unobserved states. A small number of negative probabilities were detected from the Pad�� algorithm on trinucleotide matrices that were attributable to machine precision. Although the Pad
The fiduciary relationship model for managing clinical genomic "incidental" findings.
Lázaro-Muñoz, Gabriel
2014-01-01
This paper examines how the application of legal fiduciary principles (e.g., physicians' duty of loyalty and care, duty to inform, and duty act within the scope of authority), can serve as a framework to promote management of clinical genomic "incidental" or secondary target findings that is patient-centered and consistent with recognized patient autonomy rights. The application of fiduciary principles to the clinical genomic testing context gives rise to at least four physician fiduciary duties in conflict with recent recommendations by the American College of Medical Genetics and Genomics (ACMG). These recommendations have generated much debate among lawyers, clinicians, and bioethicists hence I believe this publication will be of value and interest to your readership. © 2014 American Society of Law, Medicine & Ethics, Inc.
Human Genome Project and cystic fibrosis--a symbiotic relationship.
Tolstoi, L G; Smith, C L
1999-11-01
When Watson and Crick determined the structure of DNA in 1953, a biological revolution began. One result of this revolution is the Human Genome Project. The primary goal of this international project is to obtain the complete nucleotide sequence of the human genome by the year 2005. Although molecular biologists and geneticists are most enthusiastic about the Human Genome Project, all areas of clinical medicine and fields of biology will be affected. Cystic fibrosis is the most common, inherited, lethal disease of white persons. In 1989, researchers located the cystic fibrosis gene on the long arm of chromosome 7 by a technique known as positional cloning. The most common mutation (a 3-base pair deletion) of the cystic fibrosis gene occurs in 70% of patients with cystic fibrosis. The knowledge gained from genetic research on cystic fibrosis will help researchers develop new therapies (e.g., gene) and improve standard therapies (e.g., pharmacologic) so that a patient's life span is increased and quality of life is improved. The purpose of this review is twofold. First, the article provides an overview of the Human Genome Project and its clinical significance in advancing interdisciplinary care for patients with cystic fibrosis. Second, the article includes a discussion of the genetic basis, pathophysiology, and management of cystic fibrosis.
Inverse m-matrices and ultrametric matrices
Dellacherie, Claude; San Martin, Jaime
2014-01-01
The study of M-matrices, their inverses and discrete potential theory is now a well-established part of linear algebra and the theory of Markov chains. The main focus of this monograph is the so-called inverse M-matrix problem, which asks for a characterization of nonnegative matrices whose inverses are M-matrices. We present an answer in terms of discrete potential theory based on the Choquet-Deny Theorem. A distinguished subclass of inverse M-matrices is ultrametric matrices, which are important in applications such as taxonomy. Ultrametricity is revealed to be a relevant concept in linear algebra and discrete potential theory because of its relation with trees in graph theory and mean expected value matrices in probability theory. Remarkable properties of Hadamard functions and products for the class of inverse M-matrices are developed and probabilistic insights are provided throughout the monograph.
Goriunova, S V; Kochieva, E Z; Chikida, N N; Pukhal'skiĭ, V A
2004-05-01
RAPD analysis was carried out to study the genetic variation and phylogenetic relationships of polyploid Aegilops species, which contain the D genome as a component of the alloploid genome, and diploid Aegilops tauschii, which is a putative donor of the D genome for common wheat. In total, 74 accessions of six D-genome Aegilops species were examined. The highest intraspecific variation (0.03-0.21) was observed for Ae. tauschii. Intraspecific distances between accessions ranged 0.007-0.067 in Ae. cylindrica, 0.017-0.047 in Ae. vavilovii, and 0.00-0.053 in Ae. juvenalis. Likewise, Ae. ventricosa and Ae. crassa showed low intraspecific polymorphism. The among-accession difference in alloploid Ae. ventricosa (genome DvNv) was similar to that of one parental species, Ae. uniaristata (N), and substantially lower than in the other parent, Ae. tauschii (D). The among-accession difference in Ae. cylindrica (CcDc) was considerably lower than in either parent, Ae. tauschii (D) or Ae. caudata (C). With the exception of Ae. cylindrica, all D-genome species--Ae. tauschii (D), Ae. ventricosa (DvNv), Ae. crassa (XcrDcrl and XcrDcrlDcr2), Ae. juvenalis (XjDjUj), and Ae. vavilovii (XvaDvaSva)--formed a single polymorphic cluster, which was distinct from clusters of other species. The only exception, Ae. cylindrica, did not group with the other D-genome species, but clustered with Ae. caudata (C), a donor of the C genome. The cluster of these two species was clearly distinct from the cluster of the other D-genome species and close to a cluster of Ae. umbellulata (genome U) and Ae. ovata (genome UgMg). Thus, RAPD analysis for the first time was used to estimate and to compare the interpopulation polymorphism and to establish the phylogenetic relationships of all diploid and alloploid D-genome Aegilops species.
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
The St and E are two important basic genomes in the perennial tribe Triticeae (Poaceae). They exist in many perennial species and are very closely related to the A, B and D genomes of bread wheat (Triticum aestivum L.). Genomic Southern hybridization and genomic in situ hybridization (GISH) were used to analyze the genomic relationships between the two genomes (St and E) and the three basic genomes (A, B and D) of T. aestivum. The semi-quantitative analysis of the Southern hybridization suggested that both St and E genomes are most closely related to the D genome, then the A genome, and relatively distant to the B genome. GISH analysis using St and E genomic DNA as probes further confirmed the conclusion.St and E are the two basic genomes of Thinopyrum ponticum (StStEeEbEx) and Th. intermedium (StEeEb), two perennial species successfully used in wheat improvement. Therefore, this paper provides a possible answer as to why most of the spontaneous wheat- Thinopyrum translocations and substitutions usually happen in the D genome, some in the A genome and rarely in the B genome. This would develop further use of alien species for wheat improvement, especially those containing St or E in their genome components.
Taalman, L.; Tongen, A.; Warren, B.; Wyrick-Flax, F.; Yoon, I.
2013-01-01
This paper introduces a new matrix tool for the sowing game Tchoukaillon, which establishes a relationship between board vectors and move vectors that does not depend on actually playing the game. This allows for simpler proofs than currently appear in the literature for two key theorems, as well as a new method for constructing move vectors.We…
Taalman, L.; Tongen, A.; Warren, B.; Wyrick-Flax, F.; Yoon, I.
2013-01-01
This paper introduces a new matrix tool for the sowing game Tchoukaillon, which establishes a relationship between board vectors and move vectors that does not depend on actually playing the game. This allows for simpler proofs than currently appear in the literature for two key theorems, as well as a new method for constructing move vectors.We…
Energy Technology Data Exchange (ETDEWEB)
Zyczkowski, Karol [Centrum Fizyki Teoretycznej, Polska Akademia Nauk, Al. Lotnikow 32/44, 02-668 Warsaw (Poland); Kus, Marek [Centrum Fizyki Teoretycznej, Polska Akademia Nauk, Al. Lotnikow 32/44, 02-668 Warsaw (Poland); Slomczynski, Wojciech [Instytut Matematyki, Uniwersytet Jagiellonski, ul. Reymonta 4, 30-059 Cracow (Poland); Sommers, Hans-Juergen [Fachbereich 7 Physik, Universitaet Essen, 45117 Essen (Germany)
2003-03-28
An ensemble of random unistochastic (orthostochastic) matrices is defined by taking squared moduli of elements of random unitary (orthogonal) matrices distributed according to the Haar measure on U(N) (or O(N)). An ensemble of symmetric unistochastic matrices is obtained with use of unitary symmetric matrices pertaining to the circular orthogonal ensemble. We study the distribution of complex eigenvalues of bistochastic, unistochastic and orthostochastic matrices in the complex plane. We compute averages (entropy, traces) over the ensembles of unistochastic matrices and present inequalities concerning the entropies of products of bistochastic matrices.
Zyczkowski, K.; Slomczynski, W.; Kus, M.; Sommers, H. -J.
2001-01-01
An ensemble of random unistochastic (orthostochastic) matrices is defined by taking squared moduli of elements of random unitary (orthogonal) matrices distributed according to the Haar measure on U(N) (or O(N), respectively). An ensemble of symmetric unistochastic matrices is obtained with use of unitary symmetric matrices pertaining to the circular orthogonal ensemble. We study the distribution of complex eigenvalues of bistochastic, unistochastic and ortostochastic matrices in the complex p...
Skills Underlying Coloured Progressive Matrices
Kirby, J. R.; Das, J. P.
1978-01-01
Raven's Coloured Progressive Matrices and a battery of ability tests were administered to a sample of 104 male fourth graders for purposes of investigating the relationships between 2 previously identified subscales of the Raven and the ability tests. Results indicated use of a spatial strategy and to a lesser extent, use of reasoning, indicating…
The zebrafish reference genome sequence and its relationship to the human genome.
Howe, Kerstin; Clark, Matthew D; Torroja, Carlos F; Torrance, James; Berthelot, Camille; Muffato, Matthieu; Collins, John E; Humphray, Sean; McLaren, Karen; Matthews, Lucy; McLaren, Stuart; Sealy, Ian; Caccamo, Mario; Churcher, Carol; Scott, Carol; Barrett, Jeffrey C; Koch, Romke; Rauch, Gerd-Jörg; White, Simon; Chow, William; Kilian, Britt; Quintais, Leonor T; Guerra-Assunção, José A; Zhou, Yi; Gu, Yong; Yen, Jennifer; Vogel, Jan-Hinnerk; Eyre, Tina; Redmond, Seth; Banerjee, Ruby; Chi, Jianxiang; Fu, Beiyuan; Langley, Elizabeth; Maguire, Sean F; Laird, Gavin K; Lloyd, David; Kenyon, Emma; Donaldson, Sarah; Sehra, Harminder; Almeida-King, Jeff; Loveland, Jane; Trevanion, Stephen; Jones, Matt; Quail, Mike; Willey, Dave; Hunt, Adrienne; Burton, John; Sims, Sarah; McLay, Kirsten; Plumb, Bob; Davis, Joy; Clee, Chris; Oliver, Karen; Clark, Richard; Riddle, Clare; Elliot, David; Eliott, David; Threadgold, Glen; Harden, Glenn; Ware, Darren; Begum, Sharmin; Mortimore, Beverley; Mortimer, Beverly; Kerry, Giselle; Heath, Paul; Phillimore, Benjamin; Tracey, Alan; Corby, Nicole; Dunn, Matthew; Johnson, Christopher; Wood, Jonathan; Clark, Susan; Pelan, Sarah; Griffiths, Guy; Smith, Michelle; Glithero, Rebecca; Howden, Philip; Barker, Nicholas; Lloyd, Christine; Stevens, Christopher; Harley, Joanna; Holt, Karen; Panagiotidis, Georgios; Lovell, Jamieson; Beasley, Helen; Henderson, Carl; Gordon, Daria; Auger, Katherine; Wright, Deborah; Collins, Joanna; Raisen, Claire; Dyer, Lauren; Leung, Kenric; Robertson, Lauren; Ambridge, Kirsty; Leongamornlert, Daniel; McGuire, Sarah; Gilderthorp, Ruth; Griffiths, Coline; Manthravadi, Deepa; Nichol, Sarah; Barker, Gary; Whitehead, Siobhan; Kay, Michael; Brown, Jacqueline; Murnane, Clare; Gray, Emma; Humphries, Matthew; Sycamore, Neil; Barker, Darren; Saunders, David; Wallis, Justene; Babbage, Anne; Hammond, Sian; Mashreghi-Mohammadi, Maryam; Barr, Lucy; Martin, Sancha; Wray, Paul; Ellington, Andrew; Matthews, Nicholas; Ellwood, Matthew; Woodmansey, Rebecca; Clark, Graham; Cooper, James D; Cooper, James; Tromans, Anthony; Grafham, Darren; Skuce, Carl; Pandian, Richard; Andrews, Robert; Harrison, Elliot; Kimberley, Andrew; Garnett, Jane; Fosker, Nigel; Hall, Rebekah; Garner, Patrick; Kelly, Daniel; Bird, Christine; Palmer, Sophie; Gehring, Ines; Berger, Andrea; Dooley, Christopher M; Ersan-Ürün, Zübeyde; Eser, Cigdem; Geiger, Horst; Geisler, Maria; Karotki, Lena; Kirn, Anette; Konantz, Judith; Konantz, Martina; Oberländer, Martina; Rudolph-Geiger, Silke; Teucke, Mathias; Lanz, Christa; Raddatz, Günter; Osoegawa, Kazutoyo; Zhu, Baoli; Rapp, Amanda; Widaa, Sara; Langford, Cordelia; Yang, Fengtang; Schuster, Stephan C; Carter, Nigel P; Harrow, Jennifer; Ning, Zemin; Herrero, Javier; Searle, Steve M J; Enright, Anton; Geisler, Robert; Plasterk, Ronald H A; Lee, Charles; Westerfield, Monte; de Jong, Pieter J; Zon, Leonard I; Postlethwait, John H; Nüsslein-Volhard, Christiane; Hubbard, Tim J P; Roest Crollius, Hugues; Rogers, Jane; Stemple, Derek L
2013-04-25
Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
The zebrafish reference genome sequence and its relationship to the human genome
Howe, Kerstin; Clark, Matthew D.; Torroja, Carlos F.; Torrance, James; Berthelot, Camille; Muffato, Matthieu; Collins, John E.; Humphray, Sean; McLaren, Karen; Matthews, Lucy; McLaren, Stuart; Sealy, Ian; Caccamo, Mario; Churcher, Carol; Scott, Carol; Barrett, Jeffrey C.; Koch, Romke; Rauch, Gerd-Jörg; White, Simon; Chow, William; Kilian, Britt; Quintais, Leonor T.; Guerra-Assunção, José A.; Zhou, Yi; Gu, Yong; Yen, Jennifer; Vogel, Jan-Hinnerk; Eyre, Tina; Redmond, Seth; Banerjee, Ruby; Chi, Jianxiang; Fu, Beiyuan; Langley, Elizabeth; Maguire, Sean F.; Laird, Gavin K.; Lloyd, David; Kenyon, Emma; Donaldson, Sarah; Sehra, Harminder; Almeida-King, Jeff; Loveland, Jane; Trevanion, Stephen; Jones, Matt; Quail, Mike; Willey, Dave; Hunt, Adrienne; Burton, John; Sims, Sarah; McLay, Kirsten; Plumb, Bob; Davis, Joy; Clee, Chris; Oliver, Karen; Clark, Richard; Riddle, Clare; Eliott, David; Threadgold, Glen; Harden, Glenn; Ware, Darren; Mortimer, Beverly; Kerry, Giselle; Heath, Paul; Phillimore, Benjamin; Tracey, Alan; Corby, Nicole; Dunn, Matthew; Johnson, Christopher; Wood, Jonathan; Clark, Susan; Pelan, Sarah; Griffiths, Guy; Smith, Michelle; Glithero, Rebecca; Howden, Philip; Barker, Nicholas; Stevens, Christopher; Harley, Joanna; Holt, Karen; Panagiotidis, Georgios; Lovell, Jamieson; Beasley, Helen; Henderson, Carl; Gordon, Daria; Auger, Katherine; Wright, Deborah; Collins, Joanna; Raisen, Claire; Dyer, Lauren; Leung, Kenric; Robertson, Lauren; Ambridge, Kirsty; Leongamornlert, Daniel; McGuire, Sarah; Gilderthorp, Ruth; Griffiths, Coline; Manthravadi, Deepa; Nichol, Sarah; Barker, Gary; Whitehead, Siobhan; Kay, Michael; Brown, Jacqueline; Murnane, Clare; Gray, Emma; Humphries, Matthew; Sycamore, Neil; Barker, Darren; Saunders, David; Wallis, Justene; Babbage, Anne; Hammond, Sian; Mashreghi-Mohammadi, Maryam; Barr, Lucy; Martin, Sancha; Wray, Paul; Ellington, Andrew; Matthews, Nicholas; Ellwood, Matthew; Woodmansey, Rebecca; Clark, Graham; Cooper, James; Tromans, Anthony; Grafham, Darren; Skuce, Carl; Pandian, Richard; Andrews, Robert; Harrison, Elliot; Kimberley, Andrew; Garnett, Jane; Fosker, Nigel; Hall, Rebekah; Garner, Patrick; Kelly, Daniel; Bird, Christine; Palmer, Sophie; Gehring, Ines; Berger, Andrea; Dooley, Christopher M.; Ersan-Ürün, Zübeyde; Eser, Cigdem; Geiger, Horst; Geisler, Maria; Karotki, Lena; Kirn, Anette; Konantz, Judith; Konantz, Martina; Oberländer, Martina; Rudolph-Geiger, Silke; Teucke, Mathias; Osoegawa, Kazutoyo; Zhu, Baoli; Rapp, Amanda; Widaa, Sara; Langford, Cordelia; Yang, Fengtang; Carter, Nigel P.; Harrow, Jennifer; Ning, Zemin; Herrero, Javier; Searle, Steve M. J.; Enright, Anton; Geisler, Robert; Plasterk, Ronald H. A.; Lee, Charles; Westerfield, Monte; de Jong, Pieter J.; Zon, Leonard I.; Postlethwait, John H.; Nüsslein-Volhard, Christiane; Hubbard, Tim J. P.; Crollius, Hugues Roest; Rogers, Jane; Stemple, Derek L.
2013-01-01
Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3–5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination. PMID:23594743
GENERALIZED NEKRASOV MATRICES AND APPLICATIONS
Institute of Scientific and Technical Information of China (English)
Mingxian Pang; Zhuxiang Li
2003-01-01
In this paper, the concept of generalized Nekrasov matrices is introduced, some properties of these matrices are discussed, obtained equivalent representation of generalized diagonally dominant matrices.
Introduction into Hierarchical Matrices
Litvinenko, Alexander
2013-12-05
Hierarchical matrices allow us to reduce computational storage and cost from cubic to almost linear. This technique can be applied for solving PDEs, integral equations, matrix equations and approximation of large covariance and precision matrices.
Goriunova, S V; Chikida, N N; Kochieva, E Z
2010-07-01
RAPD analysis was used to study the genetic variation and phylogenetic relationships of polyploid Aegilops species with the U genome. In total, 115 DNA samples of eight polyploid species containing the U genome and the diploid species Ae. umbellulata (U) were examined. Substantial interspecific polymorphism was observed for the majority of the polyploid species with the U genome (interspecific differences, 0.01-0,2; proportion of polymorphic loci, 56.6-88.2%). Aegilops triuncialis was identified as the only alloploid species with low interspecific polymorphism (interspecific differences, 0-0.01, P = 50%) in the U-genome group. The U-genome Aegilops species proved to be separated from other species of the genus. The phylogenetic relationships were established for the U-genome species. The greatest separation within the U-genome group was observed for the US-genome species Ae. kotschyi and Ae. variabilis. The tetraploid species Ae. triaristata and Ae. columnaris, which had the UX genome, and the hexaploid species Ae. recta (UXN) were found to be related to each other and separate from the UM-genome species. A similarity was observed between the U M-genome species Ae. ovata and Ae. biuncialis, which had the UM genome, and the ancestral diploid U-genome species Ae. umbellulata. The UC-genome species Ae. triuncialis was rather separate and slightly similar to the UX-genome species.
BLOCK H-MATRICES AND SPECTRUM OF BLOCK MATRICES
Institute of Scientific and Technical Information of China (English)
黄廷祝; 黎稳
2002-01-01
The block H-matrices are studied by the concept of G-functions, several concepts of block matrices are introduced. Equivalent characters of block H-matrices are obtained. Spectrum localizations claracterized by Gfunctions for block matrices are got.
Arisue, Nobuko; Hashimoto, Tetsuo; Mitsui, Hideya; Palacpac, Nirianne M Q; Kaneko, Akira; Kawai, Satoru; Hasegawa, Masami; Tanabe, Kazuyuki; Horii, Toshihiro
2012-09-01
Apicoplast, a nonphotosynthetic plastid derived from secondary symbiotic origin, is essential for the survival of malaria parasites of the genus Plasmodium. Elucidation of the evolution of the apicoplast genome in Plasmodium species is important to better understand the functions of the organelle. However, the complete apicoplast genome is available for only the most virulent human malaria parasite, Plasmodium falciparum. Here, we obtained the near-complete apicoplast genome sequences from eight Plasmodium species that infect a wide variety of vertebrate hosts and performed structural and phylogenetic analyses. We found that gene repertoire, gene arrangement, and other structural attributes were highly conserved. Phylogenetic reconstruction using 30 protein-coding genes of the apicoplast genome inferred, for the first time, a close relationship between P. ovale and rodent parasites. This close relatedness was robustly supported using multiple evolutionary assumptions and models. The finding suggests that an ancestral host switch occurred between rodent and human Plasmodium parasites.
Circulant conference matrices for new complex Hadamard matrices
Dita, Petre
2011-01-01
The circulant real and complex matrices are used to find new real and complex conference matrices. With them we construct Sylvester inverse orthogonal matrices by doubling the size of inverse complex conference matrices. When the free parameters take values on the unit circle the inverse orthogonal matrices transform into complex Hadamard matrices. The method is used for $n=6$ conference matrices and in this way we find new parametrisations of Hadamard matrices for dimension $ n=12$.
Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan
2016-07-05
Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN.
Directory of Open Access Journals (Sweden)
Yael eKotton
2015-01-01
Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and
Energy Technology Data Exchange (ETDEWEB)
Cappellini, Valerio [' Mark Kac' Complex Systems Research Centre, Uniwersytet Jagiellonski, ul. Reymonta 4, 30-059 Krakow (Poland); Sommers, Hans-Juergen [Fachbereich Physik, Universitaet Duisburg-Essen, Campus Duisburg, 47048 Duisburg (Germany); Bruzda, Wojciech; Zyczkowski, Karol [Instytut Fizyki im. Smoluchowskiego, Uniwersytet Jagiellonski, ul. Reymonta 4, 30-059 Krakow (Poland)], E-mail: valerio@ictp.it, E-mail: h.j.sommers@uni-due.de, E-mail: w.bruzda@uj.edu.pl, E-mail: karol@cft.edu.pl
2009-09-11
Ensembles of random stochastic and bistochastic matrices are investigated. While all columns of a random stochastic matrix can be chosen independently, the rows and columns of a bistochastic matrix have to be correlated. We evaluate the probability measure induced into the Birkhoff polytope of bistochastic matrices by applying the Sinkhorn algorithm to a given ensemble of random stochastic matrices. For matrices of order N = 2 we derive explicit formulae for the probability distributions induced by random stochastic matrices with columns distributed according to the Dirichlet distribution. For arbitrary N we construct an initial ensemble of stochastic matrices which allows one to generate random bistochastic matrices according to a distribution locally flat at the center of the Birkhoff polytope. The value of the probability density at this point enables us to obtain an estimation of the volume of the Birkhoff polytope, consistent with recent asymptotic results.
Cappellini, V; Bruzda, W; Zyczkowski, K
2009-01-01
Ensembles of random stochastic and bistochastic matrices are investigated. While all columns of a random stochastic matrix can be chosen independently, the rows and columns of a bistochastic matrix have to be correlated. We evaluate the probability measure induced into the Birkhoff polytope of bistochastic matrices by applying the Sinkhorn algorithm to a given ensemble of random stochastic matrices. For matrices of order N=2 we derive explicit formulae for the probability distributions induced by random stochastic matrices with columns distributed according to the Dirichlet distribution. For arbitrary $N$ we construct an initial ensemble of stochastic matrices which allows one to generate random bistochastic matrices according to a distribution locally flat at the center of the Birkhoff polytope. The value of the probability density at this point enables us to obtain an estimation of the volume of the Birkhoff polytope, consistent with recent asymptotic results.
Comparison of assembled Clostridium botulinum A1 genomes revealed their evolutionary relationship.
Ng, Virginia; Lin, Wei-Jen
2014-01-01
Clostridium botulinum encompasses bacteria that produce at least one of the seven serotypes of botulinum neurotoxin (BoNT/A-G). The availability of genome sequences of four closely related Type A1 or A1(B) strains, as well as the A1-specific microarray, allowed the analysis of their genomic organizations and evolutionary relationship. The four genomes share >90% core genes and >96% functional groups. Phylogenetic analysis based on COG shows closer relations of the A1(B) strain, NCTC 2916, to B1 and F1 than A1 strains. Alignment of the genomes of the three A1 strains revealed a highly similar chromosomal structure with three small gaps in the genome of ATCC 19397 and one additional gap in the genome of Hall A, suggesting ATCC 19379 as an evolutionary intermediate between Hall A and ATCC 3502. Analyses of the four gap regions indicated potential horizontal gene transfer and recombination events important for the evolution of A1 strains.
Merrill, Bryan D; Grose, Julianne H; Breakwell, Donald P; Burnett, Sandra H
2014-08-30
Paenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages. P. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium
Complex Hadamard matrices from Sylvester inverse orthogonal matrices
Dita, Petre
2009-01-01
A novel method to obtain parametrizations of complex inverse orthogonal matrices is provided. These matrices are natural generalizations of complex Hadamard matrices which depend on non zero complex parameters. The method we use is via doubling the size of inverse complex conference matrices. When the free parameters take values on the unit circle the inverse orthogonal matrices transform into complex Hadamard matrices, and in this way we find new parametrizations of Hadamard matrices for dim...
Compatibility of pedigree-based and marker-based relationships for single-step genomic prediction
DEFF Research Database (Denmark)
Christensen, Ole Fredslund
2012-01-01
Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel......Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker......-based relationship matrix and the pedigree-based relationship matrix. The compatibility issue involves which allele frequencies to use in the marker-based relationship matrix, and also that adjustments of this matrix to the pedigree-based relationship matrix are needed. In addition, it has been overlooked...... in the base population. Here, two ideas are explored. The first idea is to instead adjust the pedigree-based relationship matrix to be compatible to the marker-based relationship matrix, whereas the second idea is to include the likelihood for the observed markers. A single-step method is used where...
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes
Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann
2013-01-01
Summary: At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. Availability and Implementation: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required. Contact: leeann.mccue@pnnl.gov PMID:23956303
SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes
Energy Technology Data Exchange (ETDEWEB)
Curtis, Darren S.; Phillips, Aaron R.; Callister, Stephen J.; Conlan, Sean; McCue, Lee Ann
2013-10-15
At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.
Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.).
Laurentin, Hernán; Ratzinger, Astrid; Karlovsky, Petr
2008-05-29
Diversity estimates in cultivated plants provide a rationale for conservation strategies and support the selection of starting material for breeding programs. Diversity measures applied to crops usually have been limited to the assessment of genome polymorphism at the DNA level. Occasionally, selected morphological features are recorded and the content of key chemical constituents determined, but unbiased and comprehensive chemical phenotypes have not been included systematically in diversity surveys. Our objective in this study was to assess metabolic diversity in sesame by nontargeted metabolic profiling and elucidate the relationship between metabolic and genome diversity in this crop. Ten sesame accessions were selected that represent most of the genome diversity of sesame grown in India, Western Asia, Sudan and Venezuela based on previous AFLP studies. Ethanolic seed extracts were separated by HPLC, metabolites were ionized by positive and negative electrospray and ions were detected with an ion trap mass spectrometer in full-scan mode for m/z from 50 to 1000. Genome diversity was determined by Amplified Fragment Length Polymorphism (AFLP) using eight primer pair combinations. The relationship between biodiversity at the genome and at the metabolome levels was assessed by correlation analysis and multivariate statistics. Patterns of diversity at the genomic and metabolic levels differed, indicating that selection played a significant role in the evolution of metabolic diversity in sesame. This result implies that when used for the selection of genotypes in breeding and conservation, diversity assessment based on neutral DNA markers should be complemented with metabolic profiles. We hypothesize that this applies to all crops with a long history of domestication that possess commercially relevant traits affected by chemical phenotypes.
Evolution of the mitochondrial genome in snakes: Gene rearrangements and phylogenetic relationships
Directory of Open Access Journals (Sweden)
Zhou Kaiya
2008-11-01
Full Text Available Abstract Background Snakes as a major reptile group display a variety of morphological characteristics pertaining to their diverse behaviours. Despite abundant analyses of morphological characters, molecular studies using mitochondrial and nuclear genes are limited. As a result, the phylogeny of snakes remains controversial. Previous studies on mitochondrial genomes of snakes have demonstrated duplication of the control region and translocation of trnL to be two notable features of the alethinophidian (all serpents except blindsnakes and threadsnakes mtDNAs. Our purpose is to further investigate the gene organizations, evolution of the snake mitochondrial genome, and phylogenetic relationships among several major snake families. Results The mitochondrial genomes were sequenced for four taxa representing four different families, and each had a different gene arrangement. Comparative analyses with other snake mitochondrial genomes allowed us to summarize six types of mitochondrial gene arrangement in snakes. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (BI, ML, MP, NJ arrived at a similar topology, which was used to reconstruct the evolution of mitochondrial gene arrangements in snakes. Conclusion The phylogenetic relationships among the major families of snakes are in accordance with the mitochondrial genomes in terms of gene arrangements. The gene arrangement in Ramphotyphlops braminus mtDNA is inferred to be ancestral for snakes. After the divergence of the early Ramphotyphlops lineage, three types of rearrangements occurred. These changes involve translocations within the IQM tRNA gene cluster and the duplication of the CR. All phylogenetic methods support the placement of Enhydris plumbea outside of the (Colubridae + Elapidae cluster, providing mitochondrial genomic evidence for the familial rank of Homalopsidae.
Directory of Open Access Journals (Sweden)
Michael S Brewer
Full Text Available BACKGROUND: Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda. RESULTS: The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly. As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic. CONCLUSIONS: The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic
Matrices and linear transformations
Cullen, Charles G
1990-01-01
""Comprehensive . . . an excellent introduction to the subject."" - Electronic Engineer's Design Magazine.This introductory textbook, aimed at sophomore- and junior-level undergraduates in mathematics, engineering, and the physical sciences, offers a smooth, in-depth treatment of linear algebra and matrix theory. The major objects of study are matrices over an arbitrary field. Contents include Matrices and Linear Systems; Vector Spaces; Determinants; Linear Transformations; Similarity: Part I and Part II; Polynomials and Polynomial Matrices; Matrix Analysis; and Numerical Methods. The first
A Simple Cocyclic Jacket Matrices
Directory of Open Access Journals (Sweden)
Moon Ho Lee
2008-01-01
Full Text Available We present a new class of cocyclic Jacket matrices over complex number field with any size. We also construct cocyclic Jacket matrices over the finite field. Such kind of matrices has close relation with unitary matrices which are a first hand tool in solving many problems in mathematical and theoretical physics. Based on the analysis of the relation between cocyclic Jacket matrices and unitary matrices, the common method for factorizing these two kinds of matrices is presented.
Directory of Open Access Journals (Sweden)
Xiao Zhang
2017-09-01
Full Text Available Gynostemma BL., belonging to the family Cucurbitaceae, is a genus containing 17 creeping herbaceous species mainly distributed in East Asia. It can be divided into two subgenera based on different fruit morphology. Herein, we report eight complete chloroplast genome sequences of the genus Gynostemma, which were obtained by Illumina paired-end sequencing, assembly, and annotation. The length of the eight complete cp genomes ranged from 157,576 bp (G. pentaphyllum to 158,273 bp (G. laxiflorum. Each encoded 133 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The four types of repeated sequences had been discovered and indicated that the repeated structure for species in the Subgen. Triostellum was greater than that for species in the Subgen. Gynostemma. The percentage of variation of the eight cp genomes in different regions were calculated, which demonstrated that the coding and inverted repeats regions were highly conserved. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Gynostemma as a member of family Cucurbitaceae. The phylogenetic relationships among the eight species were clearly resolved using the complete cp genome sequences in this study. It will also provide potential molecular markers and candidate DNA barcodes for future studies and enrich the valuable complete cp genome resources of Cucurbitaceae.
Genome data from a sixteenth century pig illuminate modern breed relationships.
Ramírez, O; Burgos-Paz, W; Casas, E; Ballester, M; Bianco, E; Olalde, I; Santpere, G; Novella, V; Gut, M; Lalueza-Fox, C; Saña, M; Pérez-Enciso, M
2015-02-01
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.
DEFF Research Database (Denmark)
Wu, Xiaoping; Lund, Mogens Sandø; Sun, Dongxiao
This study investigated reliability of genomic prediction in various scenarios with regard to relationship between test and reference animals and between animals within the reference population. Different reference populations were generated from EuroGenomics data and 1288 Nordic Holstein bulls...... as a common test population. A GBLUP model and a Bayesian mixture model were applied to predict Genomic breeding values for bulls in the test data. Result showed that a closer relationship between test and reference animals led to a higher reliability, while a closer relationship between reference animal...
DEFF Research Database (Denmark)
Wu, Xiaoping; Lund, Mogens Sandø; Sun, Dongxiao
as a common test population. A GBLUP model and a Bayesian mixture model were applied to predict Genomic breeding values for bulls in the test data. Result showed that a closer relationship between test and reference animals led to a higher reliability, while a closer relationship between reference animal......This study investigated reliability of genomic prediction in various scenarios with regard to relationship between test and reference animals and between animals within the reference population. Different reference populations were generated from EuroGenomics data and 1288 Nordic Holstein bulls...... resulted in a lower reliability. Therefore, the design of reference population is important for improving the reliability of genomic prediction. With regard to model, the Bayesian mixture model in general led to slightly a higher reliability of genomic prediction than the GBLUP model....
On greedy and submodular matrices
Faigle, U.; Kern, Walter; Peis, Britta; Marchetti-Spaccamela, Alberto; Segal, Michael
2011-01-01
We characterize non-negative greedy matrices, i.e., 0-1 matrices $A$ such that max $\\{c^Tx|Ax \\le b,\\,x \\ge 0\\}$ can be solved greedily. We identify submodular matrices as a special subclass of greedy matrices. Finally, we extend the notion of greediness to $\\{-1,0,+1\\}$-matrices. We present
Gaussian Fibonacci Circulant Type Matrices
Directory of Open Access Journals (Sweden)
Zhaolin Jiang
2014-01-01
Full Text Available Circulant matrices have become important tools in solving integrable system, Hamiltonian structure, and integral equations. In this paper, we prove that Gaussian Fibonacci circulant type matrices are invertible matrices for n>2 and give the explicit determinants and the inverse matrices. Furthermore, the upper bounds for the spread on Gaussian Fibonacci circulant and left circulant matrices are presented, respectively.
Karlsson, Fredrik H; Ussery, David,; Nielsen, Jens; Nookaew, Intawat
2011-01-01
The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chloro...
Reyes-Prieto, Mariana; Vargas-Chávez, Carlos; Latorre, Amparo; Moya, Andrés
2015-01-01
Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic-host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major
Raman, Gurusamy; Choi, Kyoung Su; Park, SeonJoo
2016-12-02
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS) value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago) and might have moved from Eurasia to Dokdo Island.
Justino, Júlia
2017-06-01
Matrices with coefficients having uncertainties of type o (.) or O (.), called flexible matrices, are studied from the point of view of nonstandard analysis. The uncertainties of the afore-mentioned kind will be given in the form of the so-called neutrices, for instance the set of all infinitesimals. Since flexible matrices have uncertainties in their coefficients, it is not possible to define the identity matrix in an unique way and so the notion of spectral identity matrix arises. Not all nonsingular flexible matrices can be turned into a spectral identity matrix using Gauss-Jordan elimination method, implying that that not all nonsingular flexible matrices have the inverse matrix. Under certain conditions upon the size of the uncertainties appearing in a nonsingular flexible matrix, a general theorem concerning the boundaries of its minors is presented which guarantees the existence of the inverse matrix of a nonsingular flexible matrix.
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Kleinhofs Andris
2004-06-01
Full Text Available Abstract Background Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported. Results Based on an informatics method (SCUO we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC32 + 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC32 + 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation. Conclusions The synonymous codon usage bias could be simply expressed as 1+ (p/2log2(p/2 + ((1-p/2log2((l-p/2, where p = GC3. The software we developed for measuring SCUO (codonO is available at http://digbio.missouri.edu/~wanx/cu/codonO.
On the tensor Permutation Matrices
Rakotonirina, Christian
2011-01-01
A property that tensor permutation matrices permutate tensor product of rectangle matrices is shown. Some examples, in the particular case of tensor commutation matrices, for studying some linear matricial equations are given.
Matrices with restricted entries and q-analogues of permutations
Lewis, Joel Brewster; Morales, Alejandro H; Panova, Greta; Sam, Steven V; Zhang, Yan
2010-01-01
We study the functions that count matrices of given rank over a finite field with specified positions equal to zero. We show that these matrices are $q$-analogues of permutations with certain restricted values. We obtain a simple closed formula for the number of invertible matrices with zero diagonal, a $q$-analogue of derangements, and a curious relationship between invertible skew-symmetric matrices and invertible symmetric matrices with zero diagonal. In addition, we provide recursions to enumerate matrices and symmetric matrices with zero diagonal by rank, and we frame some of our results in the context of Lie theory. Finally, we provide a brief exposition of polynomiality results for enumeration questions related to those mentioned, and give several open questions.
DEFF Research Database (Denmark)
Britz, Thomas
Bipartite graphs and digraphs are used to describe algebraic operations on a free matrix, including Moore-Penrose inversion, finding Schur complements, and normalized LU factorization. A description of the structural properties of a free matrix and its Moore-Penrose inverse is proved, and necessa...... and sufficient conditions are given for the Moore-Penrose inverse of a free matrix to be free. Several of these results are generalized with respect to a family of matrices that contains both the free matrices and the nearly reducible matrices....
DEFF Research Database (Denmark)
Britz, Thomas
Bipartite graphs and digraphs are used to describe algebraic operations on a free matrix, including Moore-Penrose inversion, finding Schur complements, and normalized LU factorization. A description of the structural properties of a free matrix and its Moore-Penrose inverse is proved, and necessa...... and sufficient conditions are given for the Moore-Penrose inverse of a free matrix to be free. Several of these results are generalized with respect to a family of matrices that contains both the free matrices and the nearly reducible matrices....
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Charmet Gilles
2008-11-01
Full Text Available Abstract Background Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14 as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA locus region of the S genome of Ae. speltoides (2n = 14 to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42. Results Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35 268, 22 739, 43 397 and 53 919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE insertions, all of which inserted after the progenitors of the four genomes divergence. Conclusion On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, Ae speltoides appears to be more evolutionary related to the B genome of T. aestivum than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of Ae. speltoides has diverged very early from the progenitor of the B genome which remains to be identified.
Indian Academy of Sciences (India)
Narendra Singh
2003-01-01
Assuming a relation between the quark mass matrices of the two sectors a unique solution can be obtained for the CKM ﬂavor mixing matrix. A numerical example is worked out which is in excellent agreement with experimental data.
Schierenbeck, S; Pimentel, E C G; Tietze, M; Körte, J; Reents, R; Reinhardt, F; Simianer, H; König, S
2011-12-01
Because of the relatively high levels of genetic relationships among potential bull sires and bull dams, innovative selection tools should consider both genetic gain and genetic relationships in a long-term perspective. Optimum genetic contribution theory using official estimated breeding values for a moderately heritable trait (production index, Index-PROD), and a lowly heritable functional trait (index for somatic cell score, Index-SCS) was applied to find optimal allocations of bull dams and bull sires. In contrast to previous practical applications using optimizations based on Lagrange multipliers, we focused on semi-definite programming (SDP). The SDP methodology was combined with either pedigree (a(ij)) or genomic relationships (f(ij)) among selection candidates. Selection candidates were 484 genotyped bulls, and 499 preselected genotyped bull dams completing a central test on station. In different scenarios separately for PROD and SCS, constraints on the average pedigree relationships among future progeny were varied from a(ij)=0.08 to a(ij)=0.20 in increments of 0.01. Corresponding constraints for single nucleotide polymorphism-based kinship coefficients were derived from regression analysis. Applying the coefficient of 0.52 with an intercept of 0.14 estimated for the regression pedigree relationship on genomic relationship, the corresponding range to alter genomic relationships varied from f(ij) = 0.18 to f(ij) = 0.24. Despite differences for some bulls in genomic and pedigree relationships, the same trends were observed for constraints on pedigree and corresponding genomic relationships regarding results in genetic gain and achieved coefficients of relationships. Generally, allowing higher values for relationships resulted in an increase of genetic gain for Index-PROD and Index-SCS and in a reduction in the number of selected sires. Interestingly, more sires were selected for all scenarios when restricting genomic relationships compared with restricting
Galla, Stephanie J; Buckley, Thomas R; Elshire, Rob; Hale, Marie L; Knapp, Michael; McCallum, John; Moraga, Roger; Santure, Anna W; Wilcox, Phillip; Steeves, Tammy E
2016-11-01
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
Relationships among the A Genomes of Triticum L. Species as Evidenced by SSR Markers, in Iran
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Simon G. Krattinger
2010-11-01
Full Text Available The relationships among 55 wheat accessions (47 accessions collected from Iran and eight accessions provided by the Institute of Plant Biology of the University of Zurich, Switzerland belonging to eight species carrying A genome (Triticum monococcum L., T. boeoticum Boiss., T. urartu Tumanian ex Gandilyan, T. durum Desf., T. turgidum L., T. dicoccum Schrank ex Schübler, T. dicoccoides (Körn. ex Asch. & Graebner Schweinf. and T. aestivum L. were evaluated using 31 A genome specific microsatellite markers. A high level of polymorphism was observed among the accessions studied (PIC = 0.77. The highest gene diversity was revealed among T. durum genotypes, while the lowest genetic variation was found in T. dicoccoides accessions. The analysis of molecular variance (AMOVA showed a significant genetic variance (75.56% among these accessions, representing a high intra-specific genetic diversity within Triticum taxa in Iran. However, such a variance was not observed among their ploidy levels. Based on the genetic similarity analysis, the accessions collected from Iran were divided into two main groups: diploids and polyploids. The genetic similarity among the diploid and polyploid species was 0.85 and 0.89 respectively. There were no significant differences in A genome diversity from different geographic regions. Based on the genetic diversity analyses, we consider there is value in a greater sampling of each species in Iran to discover useful genes for breeding purposes.
Dreher, Theo W; Brown, Nathan; Bozarth, Connie S; Schwartz, Andrew D; Riscoe, Erin; Thrash, Cameron; Bennett, Samuel E; Tzeng, Shin-Cheng; Maier, Claudia S
2011-07-01
Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to be present in the upper Klamath River valley in northern California and Oregon. The genome of this lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes and 33 tRNA genes that represent all 20-amino-acid specificities. Analyses based on gene sequence and gene content indicate a close phylogenetic relationship to the 'photosynthetic' marine cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that freshwater and marine phages can draw on a common gene pool. The genome can be considered as being comprised of three regions. Region 1 is populated predominantly with structural genes, recognized as such by homology to other T4-like phages and by identification in a proteomic analysis of purified virions. Region 2 contains most of the genes with roles in replication, recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6 signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS is present in Region 3). Much of Regions 1 and 2 are syntenic with marine cyanomyophage genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions 1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA core sequences. Two predicted genes that are unusual in phage genomes are homologues of cellular spoT and nusG.
Matrices in Engineering Problems
Tobias, Marvin
2011-01-01
This book is intended as an undergraduate text introducing matrix methods as they relate to engineering problems. It begins with the fundamentals of mathematics of matrices and determinants. Matrix inversion is discussed, with an introduction of the well known reduction methods. Equation sets are viewed as vector transformations, and the conditions of their solvability are explored. Orthogonal matrices are introduced with examples showing application to many problems requiring three dimensional thinking. The angular velocity matrix is shown to emerge from the differentiation of the 3-D orthogo
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Regeard Christophe
2010-07-01
Full Text Available Abstract Background Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification. Results Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate. Conclusions We can thus condense, in relatively simple figures, this phage information dispersed over many publications.
Institute of Scientific and Technical Information of China (English)
FENG Xiao-rong; ZHU Jian-zhong; DENG Feng-jiao; Jacob Douek; Baruch Rinkevich
2004-01-01
Objective: The self-cross colonial prochordate, Botryllus schlosseri ( B. schlosseri) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B.schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods:AFLP markersare extremely sensitive to even smell sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% poiymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2,F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation-new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southem hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion:The se results suggest that there are high frequency of polymorphic loci and mutation in genome of B.schlosseri. Gene deletion or iow diversity may be the reason for high rate of death of the offspring of inbred laboratory-reared strains.
Zhang, W Q; Zhang, M H
2013-09-03
Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.
Harris, Simon R.; Clarke, Ian N.; Seth-Smith, Helena M. B.; Solomon, Anthony W.; Cutcliffe, Lesley T.; Marsh, Peter; Skilton, Rachel J.; Holland, Martin J.; Mabey, David; Peeling, Rosanna W.; Lewis, David A.; Spratt, Brian G.; Unemo, Magnus; Persson, Kenneth; Bjartling, Carina; Brunham, Robert; de Vries, Henry J.C.; Morré, Servaas A.; Speksnijder, Arjen; Bébéar, Cécile M.; Clerc, Maïté; de Barbeyrac, Bertille; Parkhill, Julian; Thomson, Nicholas R.
2012-01-01
Chlamydia trachomatis is responsible for both trachoma and sexually transmitted infections causing substantial morbidity and economic cost globally. Despite this, our knowledge of its population and evolutionary genetics is limited. Here we present a detailed whole genome phylogeny from representative strains of both trachoma and lymphogranuloma venereum (LGV) biovars from temporally and geographically diverse sources. Our analysis demonstrates that predicting phylogenetic structure using the ompA gene, traditionally used to classify Chlamydia, is misleading because extensive recombination in this region masks true relationships. We show that in many instances ompA is a chimera that can be exchanged in part or whole, both within and between biovars. We also provide evidence for exchange of, and recombination within, the cryptic plasmid, another important diagnostic target. We have used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b. PMID:22406642
Stiller, John W
2004-05-01
Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.
Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms
Institute of Scientific and Technical Information of China (English)
John W. Stiller
2004-01-01
Sequence-based molecular phylogenies have provided new models of early eukaryotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alternative tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomorphic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution.
Infinite matrices and sequence spaces
Cooke, Richard G
2014-01-01
This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi
Karlsson, Fredrik H; Ussery, David W; Nielsen, Jens; Nookaew, Intawat
2011-04-01
The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number of extracytoplasmic function σ factors (ECF σ factors) and two component systems for extracellular signal transduction compared to other Bacteroidetes/Chlorobi species. A whole-genome phylogenetic analysis shows a very little difference between the Parabacteroides and Bacteroides genera. Further analysis shows that Bacteroides and Parabacteroides species share a large common core of 1,085 protein families. Genome atlases illustrate that there are few and only small unique areas on the chromosomes of four Bacteroides/Parabacteroides genomes. Functional classification to clusters of othologus groups show that Bacteroides species are enriched in carbohydrate transport and metabolism proteins. Classification of proteins in KEGG metabolic pathways gives a detailed view of the genome's metabolic capabilities that can be linked to its habitat. Bacteroides pectinophilus and Bacteroides capillosus do not cluster together with other Bacteroides species, based on analysis of 16S rRNA sequence, whole-genome protein families and functional content, 16S rRNA sequences of the two species suggest that they belong to the Firmicutes phylum. We have presented a more detailed and precise description of the phylogenetic relationships of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for
Octonion generalization of Pauli and Dirac matrices
Chanyal, B. C.
2015-10-01
Starting with octonion algebra and its 4 × 4 matrix representation, we have made an attempt to write the extension of Pauli's matrices in terms of division algebra (octonion). The octonion generalization of Pauli's matrices shows the counterpart of Pauli's spin and isospin matrices. In this paper, we also have obtained the relationship between Clifford algebras and the division algebras, i.e. a relation between octonion basis elements with Dirac (gamma), Weyl and Majorana representations. The division algebra structure leads to nice representations of the corresponding Clifford algebras. We have made an attempt to investigate the octonion formulation of Dirac wave equations, conserved current and weak isospin in simple, compact, consistent and manifestly covariant manner.
Infinite matrices and their recent applications
Shivakumar, P N; Zhang, Yang
2016-01-01
This monograph covers the theory of finite and infinite matrices over the fields of real numbers, complex numbers and over quaternions. Emphasizing topics such as sections or truncations and their relationship to the linear operator theory on certain specific separable and sequence spaces, the authors explore techniques like conformal mapping, iterations and truncations that are used to derive precise estimates in some cases and explicit lower and upper bounds for solutions in the other cases. Most of the matrices considered in this monograph have typically special structures like being diagonally dominated or tridiagonal, possess certain sign distributions and are frequently nonsingular. Such matrices arise, for instance, from solution methods for elliptic partial differential equations. The authors focus on both theoretical and computational aspects concerning infinite linear algebraic equations, differential systems and infinite linear programming, among others. Additionally, the authors cover topics such ...
Machado, Lilian de Oliveira; Vieira, Leila do Nascimento; Stefenon, Valdir Marcos; Oliveira Pedrosa, Fábio de; Souza, Emanuel Maltempi de; Guerra, Miguel Pedro; Nodari, Rubens Onofre
2017-04-01
Given their distribution, importance, and richness, Myrtaceae species comprise a model system for studying the evolution of tropical plant diversity. In addition, chloroplast (cp) genome sequencing is an efficient tool for phylogenetic relationship studies. Feijoa [Acca sellowiana (O. Berg) Burret; CN: pineapple-guava] is a Myrtaceae species that occurs naturally in southern Brazil and northern Uruguay. Feijoa is known for its exquisite perfume and flavorful fruits, pharmacological properties, ornamental value and increasing economic relevance. In the present work, we reported the complete cp genome of feijoa. The feijoa cp genome is a circular molecule of 159,370 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC 88,028 bp) and a Small Single Copy region (SSC 18,598 bp) separated by Inverted Repeat regions (IRs 26,372 bp). The genome structure, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. When compared to other cp genome sequences of Myrtaceae, feijoa showed closest relationship with pitanga (Eugenia uniflora L.). Furthermore, a comparison of pitanga synonymous (Ks) and nonsynonymous (Ka) substitution rates revealed extremely low values. Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of three Myrtoideae clades.
Mirror-Symmetric Matrices and Their Application
Institute of Scientific and Technical Information of China (English)
李国林; 冯正和
2002-01-01
The well-known centrosymmetric matrices correctly reflect mirror-symmetry with no component or only one component on the mirror plane. Mirror-symmetric matrices defined in this paper can represent mirror-symmetric structures with various components on the mirror plane. Some basic properties of mirror-symmetric matrices were studied and applied to interconnection analysis. A generalized odd/even-mode decomposition scheme was developed based on the mirror reflection relationship for mirror-symmetric multiconductor transmission lines (MTLs). The per-unit-length (PUL) impedance matrix Z and admittance matrix Y can be divided into odd-mode and even-mode PUL matrices. Thus the order of the MTL system is reduced from n to k and k+p, where p(≥0)is the conductor number on the mirror plane. The analysis of mirror-symmetric matrices is related to the theory of symmetric group, which is the most effective tool for the study of symmetry.
Directory of Open Access Journals (Sweden)
Zhaolin Jiang
2014-01-01
Full Text Available Circulant matrices play an important role in solving delay differential equations. In this paper, circulant type matrices including the circulant and left circulant and g-circulant matrices with any continuous Fibonacci and Lucas numbers are considered. Firstly, the invertibility of the circulant matrix is discussed and the explicit determinant and the inverse matrices by constructing the transformation matrices are presented. Furthermore, the invertibility of the left circulant and g-circulant matrices is also studied. We obtain the explicit determinants and the inverse matrices of the left circulant and g-circulant matrices by utilizing the relationship between left circulant, g-circulant matrices and circulant matrix, respectively.
Introduction to matrices and vectors
Schwartz, Jacob T
2001-01-01
In this concise undergraduate text, the first three chapters present the basics of matrices - in later chapters the author shows how to use vectors and matrices to solve systems of linear equations. 1961 edition.
Paraunitary matrices and group rings
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Barry Hurley
2014-03-01
Full Text Available Design methods for paraunitary matrices from complete orthogonal sets of idempotents and related matrix structuresare presented. These include techniques for designing non-separable multidimensional paraunitary matrices. Properties of the structures are obtained and proofs given. Paraunitary matrices play a central role in signal processing, inparticular in the areas of filterbanks and wavelets.
Domcke, Valerie
2016-01-01
We study natural lepton mass matrices, obtained assuming the stability of physical flavour observables with respect to the variations of individual matrix elements. We identify all four possible stable neutrino textures from algebraic conditions on their entries. Two of them turn out to be uniquely associated to specific neutrino mass patterns. We then concentrate on the semi-degenerate pattern, corresponding to an overall neutrino mass scale within the reach of future experiments. In this context we show that i) the neutrino and charged lepton mixings and mass matrices are largely constrained by the requirement of stability, ii) naturalness considerations give a mild preference for the Majorana phase most relevant for neutrinoless double-beta decay, $\\alpha \\sim \\pi/2$, and iii) SU(5) unification allows to extend the implications of stability to the down quark sector. The above considerations would benefit from an experimental determination of the PMNS ratio $|U_{32}/U_{31}|$, i.e. of the Dirac phase $\\delta...
Bapat, Ravindra B
2014-01-01
This new edition illustrates the power of linear algebra in the study of graphs. The emphasis on matrix techniques is greater than in other texts on algebraic graph theory. Important matrices associated with graphs (for example, incidence, adjacency and Laplacian matrices) are treated in detail. Presenting a useful overview of selected topics in algebraic graph theory, early chapters of the text focus on regular graphs, algebraic connectivity, the distance matrix of a tree, and its generalized version for arbitrary graphs, known as the resistance matrix. Coverage of later topics include Laplacian eigenvalues of threshold graphs, the positive definite completion problem and matrix games based on a graph. Such an extensive coverage of the subject area provides a welcome prompt for further exploration. The inclusion of exercises enables practical learning throughout the book. In the new edition, a new chapter is added on the line graph of a tree, while some results in Chapter 6 on Perron-Frobenius theory are reo...
Gil, José J; José, Ignacio San
2015-01-01
Singular Mueller matrices play an important role in polarization algebra and have peculiar properties that stem from the fact that either the medium exhibits maximum diattenuation and/or polarizance, or because its associated canonical depolarizer has the property of fully randomizing, the circular component (at least) of the states of polarization of light incident on it. The formal reasons for which the Mueller matrix M of a given medium is singular are systematically investigated, analyzed and interpreted in the framework of the serial decompositions and the characteristic ellipsoids of M. The analysis allows for a general classification and geometric representation of singular Mueller matrices, of potential usefulness to experimentalists dealing with such media.
Nanoceramic Matrices: Biomedical Applications
Directory of Open Access Journals (Sweden)
Willi Paul
2006-01-01
Full Text Available Natural bone consisted of calcium phosphate with nanometer-sized needle-like crystals of approximately 5-20 nm width by 60 nm length. Synthetic calcium phosphates and Bioglass are biocompatible and bioactive as they bond to bone and enhance bone tissue formation. This property is attributed to their similarity with the mineral phase of natural bone except its constituent particle size. Calcium phosphate ceramics have been used in dentistry and orthopedics for over 30 years because of these properties. Several studies indicated that incorporation of growth hormones into these ceramic matrices facilitated increased tissue regeneration. Nanophase calcium phosphates can mimic the dimensions of constituent components of natural tissues; can modulate enhanced osteoblast adhesion and resorption with long-term functionality of tissue engineered implants. This mini review discusses some of the recent developments in nanophase ceramic matrices utilized for bone tissue engineering.
On Random Correlation Matrices
1988-10-28
the spectral features of the resulting matrices are unknown. Method 2: Perturbation about a Mean This method is discussed by Marsaglia and Okin,10...complete regressor set. Finally, Marsaglia and Olkin (1984, Reference 10) give a rigorous mathematical description of Methods 2 through 4 described in the...short paper by Marsaglia 46 has a review of these early contributions, along with an improved method. More recent references are the pragmatic paper
Concentration for noncommutative polynomials in random matrices
2011-01-01
We present a concentration inequality for linear functionals of noncommutative polynomials in random matrices. Our hypotheses cover most standard ensembles, including Gaussian matrices, matrices with independent uniformly bounded entries and unitary or orthogonal matrices.
Figueroa, Diego F.; Baco, Amy R.
2014-01-01
In the past decade, molecular phylogenetic analyses of octocorals have shown that the current morphological taxonomic classification of these organisms needs to be revised. The latest phylogenetic analyses show that most octocorals can be divided into three main clades. One of these clades contains the families Coralliidae and Paragorgiidae. These families share several taxonomically important characters and it has been suggested that they may not be monophyletic; with the possibility of the Coralliidae being a derived branch of the Paragorgiidae. Uncertainty exists not only in the relationship of these two families, but also in the classification of the two genera that make up the Coralliidae, Corallium and Paracorallium. Molecular analyses suggest that the genus Corallium is paraphyletic, and it can be divided into two main clades, with the Paracorallium as members of one of these clades. In this study we sequenced the whole mitochondrial genome of five species of Paragorgia and of five species of Corallium to use in a phylogenetic analysis to achieve two main objectives; the first to elucidate the phylogenetic relationship between the Paragorgiidae and Coralliidae and the second to determine whether the genera Corallium and Paracorallium are monophyletic. Our results show that other members of the Coralliidae share the two novel mitochondrial gene arrangements found in a previous study in Corallium konojoi and Paracorallium japonicum; and that the Corallium konojoi arrangement is also found in the Paragorgiidae. Our phylogenetic reconstruction based on all the protein coding genes and ribosomal RNAs of the mitochondrial genome suggest that the Coralliidae are not a derived branch of the Paragorgiidae, but rather a monophyletic sister branch to the Paragorgiidae. While our manuscript was in review a study was published using morphological data and several fragments from mitochondrial genes to redefine the taxonomy of the Coralliidae. Paracorallium was subsumed
Directory of Open Access Journals (Sweden)
Soumya Raychaudhuri
2009-06-01
Full Text Available Translating a set of disease regions into insight about pathogenic mechanisms requires not only the ability to identify the key disease genes within them, but also the biological relationships among those key genes. Here we describe a statistical method, Gene Relationships Among Implicated Loci (GRAIL, that takes a list of disease regions and automatically assesses the degree of relatedness of implicated genes using 250,000 PubMed abstracts. We first evaluated GRAIL by assessing its ability to identify subsets of highly related genes in common pathways from validated lipid and height SNP associations from recent genome-wide studies. We then tested GRAIL, by assessing its ability to separate true disease regions from many false positive disease regions in two separate practical applications in human genetics. First, we took 74 nominally associated Crohn's disease SNPs and applied GRAIL to identify a subset of 13 SNPs with highly related genes. Of these, ten convincingly validated in follow-up genotyping; genotyping results for the remaining three were inconclusive. Next, we applied GRAIL to 165 rare deletion events seen in schizophrenia cases (less than one-third of which are contributing to disease risk. We demonstrate that GRAIL is able to identify a subset of 16 deletions containing highly related genes; many of these genes are expressed in the central nervous system and play a role in neuronal synapses. GRAIL offers a statistically robust approach to identifying functionally related genes from across multiple disease regions--that likely represent key disease pathways. An online version of this method is available for public use (http://www.broad.mit.edu/mpg/grail/.
DEFF Research Database (Denmark)
Karlsson, Fredrik H.; Ussery, David; Nielsen, Jens;
2011-01-01
The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105 Bacte...... of members of the Bacteroidetes/Chlorobi phylum by whole genome comparison. Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for diet digestion.......The human gut is extremely densely inhabited by bacteria mainly from two phyla, Bacteroidetes and Firmicutes, and there is a great interest in analyzing whole-genome sequences for these species because of their relation to human health and disease. Here, we do whole-genome comparison of 105...... Bacteroidetes/Chlorobi genomes to elucidate their phylogenetic relationship and to gain insight into what is separating the gut living Bacteroides and Parabacteroides genera from other Bacteroidetes/Chlorobi species. A comprehensive analysis shows that Bacteroides species have a higher number...
Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B
2015-11-01
Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.
Degli Esposti, Mauro
2015-11-27
Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure-function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.
Nolte, Tom M; Ragas, Ad M J
2017-03-22
Many organic chemicals are ionizable by nature. After use and release into the environment, various fate processes determine their concentrations, and hence exposure to aquatic organisms. In the absence of suitable data, such fate processes can be estimated using Quantitative Structure-Property Relationships (QSPRs). In this review we compiled available QSPRs from the open literature and assessed their applicability towards ionizable organic chemicals. Using quantitative and qualitative criteria we selected the 'best' QSPRs for sorption, (a)biotic degradation, and bioconcentration. The results indicate that many suitable QSPRs exist, but some critical knowledge gaps remain. Specifically, future focus should be directed towards the development of QSPR models for biodegradation in wastewater and sediment systems, direct photolysis and reaction with singlet oxygen, as well as additional reactive intermediates. Adequate QSPRs for bioconcentration in fish exist, but more accurate assessments can be achieved using pharmacologically based toxicokinetic (PBTK) models. No adequate QSPRs exist for bioconcentration in non-fish species. Due to the high variability of chemical and biological species as well as environmental conditions in QSPR datasets, accurate predictions for specific systems and inter-dataset conversions are problematic, for which standardization is needed. For all QSPR endpoints, additional data requirements involve supplementing the current chemical space covered and accurately characterizing the test systems used.
Schneider, Hans
1989-01-01
Linear algebra is one of the central disciplines in mathematics. A student of pure mathematics must know linear algebra if he is to continue with modern algebra or functional analysis. Much of the mathematics now taught to engineers and physicists requires it.This well-known and highly regarded text makes the subject accessible to undergraduates with little mathematical experience. Written mainly for students in physics, engineering, economics, and other fields outside mathematics, the book gives the theory of matrices and applications to systems of linear equations, as well as many related t
Universality of Covariance Matrices
Pillai, Natesh S
2011-01-01
We prove the universality of covariance matrices of the form $H_{N \\times N} = {1 \\over N} \\tp{X}X$ where $[X]_{M \\times N}$ is a rectangular matrix with independent real valued entries $[x_{ij}]$ satisfying $\\E \\,x_{ij} = 0$ and $\\E \\,x^2_{ij} = {1 \\over M}$, $N, M\\to \\infty$. Furthermore it is assumed that these entries have sub-exponential tails. We will study the asymptotics in the regime $N/M = d_N \\in (0,\\infty), \\lim_{N\\to \\infty}d_N \
M Wedderburn, J H
1934-01-01
It is the organization and presentation of the material, however, which make the peculiar appeal of the book. This is no mere compendium of results-the subject has been completely reworked and the proofs recast with the skill and elegance which come only from years of devotion. -Bulletin of the American Mathematical Society The very clear and simple presentation gives the reader easy access to the more difficult parts of the theory. -Jahrbuch über die Fortschritte der Mathematik In 1937, the theory of matrices was seventy-five years old. However, many results had only recently evolved from sp
Xiang, Zuoshuang; Qin, Tingting; Qin, Zhaohui S; He, Yongqun
2013-10-16
The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining
Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.
Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J
2016-11-27
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
Directory of Open Access Journals (Sweden)
Ren Jianfeng
2009-03-01
Full Text Available Abstract Background There are many advantages to the application of complete mitochondrial (mt genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248. It contains thirteen protein-coding genes (PCGs with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%. All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid
Constructing random matrices to represent real ecosystems.
James, Alex; Plank, Michael J; Rossberg, Axel G; Beecham, Jonathan; Emmerson, Mark; Pitchford, Jonathan W
2015-05-01
Models of complex systems with n components typically have order n(2) parameters because each component can potentially interact with every other. When it is impractical to measure these parameters, one may choose random parameter values and study the emergent statistical properties at the system level. Many influential results in theoretical ecology have been derived from two key assumptions: that species interact with random partners at random intensities and that intraspecific competition is comparable between species. Under these assumptions, community dynamics can be described by a community matrix that is often amenable to mathematical analysis. We combine empirical data with mathematical theory to show that both of these assumptions lead to results that must be interpreted with caution. We examine 21 empirically derived community matrices constructed using three established, independent methods. The empirically derived systems are more stable by orders of magnitude than results from random matrices. This consistent disparity is not explained by existing results on predator-prey interactions. We investigate the key properties of empirical community matrices that distinguish them from random matrices. We show that network topology is less important than the relationship between a species' trophic position within the food web and its interaction strengths. We identify key features of empirical networks that must be preserved if random matrix models are to capture the features of real ecosystems.
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Gurusamy eRaman
2016-03-01
Full Text Available Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of
REFINING GENETICALLY INFERRED RELATIONSHIPS USING TREELET COVARIANCE SMOOTHING1
Crossett, Andrew; Lee, Ann B.; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn
2013-01-01
Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic investigations is familial relationships. Close relatives can be identified from family records, and more distant relatives can be inferred from large panels of genetic markers. Unfortunately these empirical estimates can be noisy, especially regarding distant relatives. We propose a new method for denoising genetically—inferred relationship matrices by exploiting the underlying structure due to hierarchical groupings of correlated individuals. The approach, which we call Treelet Covariance Smoothing, employs a multiscale decomposition of covariance matrices to improve estimates of pairwise relationships. On both simulated and real data, we show that smoothing leads to better estimates of the relatedness amongst distantly related individuals. We illustrate our method with a large genome-wide association study and estimate the “heritability” of body mass index quite accurately. Traditionally heritability, defined as the fraction of the total trait variance attributable to additive genetic effects, is estimated from samples of closely related individuals using random effects models. We show that by using smoothed relationship matrices we can estimate heritability using population-based samples. Finally, while our methods have been developed for refining genetic relationship matrices and improving estimates of heritability, they have much broader potential application in statistics. Most notably, for error-in-variables random effects models and settings that require regularization of matrices with block or hierarchical structure. PMID:24587841
REFINING GENETICALLY INFERRED RELATIONSHIPS USING TREELET COVARIANCE SMOOTHING.
Crossett, Andrew; Lee, Ann B; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn
2013-06-27
Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic investigations is familial relationships. Close relatives can be identified from family records, and more distant relatives can be inferred from large panels of genetic markers. Unfortunately these empirical estimates can be noisy, especially regarding distant relatives. We propose a new method for denoising genetically-inferred relationship matrices by exploiting the underlying structure due to hierarchical groupings of correlated individuals. The approach, which we call Treelet Covariance Smoothing, employs a multiscale decomposition of covariance matrices to improve estimates of pairwise relationships. On both simulated and real data, we show that smoothing leads to better estimates of the relatedness amongst distantly related individuals. We illustrate our method with a large genome-wide association study and estimate the "heritability" of body mass index quite accurately. Traditionally heritability, defined as the fraction of the total trait variance attributable to additive genetic effects, is estimated from samples of closely related individuals using random effects models. We show that by using smoothed relationship matrices we can estimate heritability using population-based samples. Finally, while our methods have been developed for refining genetic relationship matrices and improving estimates of heritability, they have much broader potential application in statistics. Most notably, for error-in-variables random effects models and settings that require regularization of matrices with block or hierarchical structure.
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Píndaro Díaz-Jaimes
2016-02-01
Full Text Available Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992 that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop. The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.
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Zhe Zhang
Full Text Available BACKGROUND: With the availability of high density whole-genome single nucleotide polymorphism chips, genomic selection has become a promising method to estimate genetic merit with potentially high accuracy for animal, plant and aquaculture species of economic importance. With markers covering the entire genome, genetic merit of genotyped individuals can be predicted directly within the framework of mixed model equations, by using a matrix of relationships among individuals that is derived from the markers. Here we extend that approach by deriving a marker-based relationship matrix specifically for the trait of interest. METHODOLOGY/PRINCIPAL FINDINGS: In the framework of mixed model equations, a new best linear unbiased prediction (BLUP method including a trait-specific relationship matrix (TA was presented and termed TABLUP. The TA matrix was constructed on the basis of marker genotypes and their weights in relation to the trait of interest. A simulation study with 1,000 individuals as the training population and five successive generations as candidate population was carried out to validate the proposed method. The proposed TABLUP method outperformed the ridge regression BLUP (RRBLUP and BLUP with realized relationship matrix (GBLUP. It performed slightly worse than BayesB with an accuracy of 0.79 in the standard scenario. CONCLUSIONS/SIGNIFICANCE: The proposed TABLUP method is an improvement of the RRBLUP and GBLUP method. It might be equivalent to the BayesB method but it has additional benefits like the calculation of accuracies for individual breeding values. The results also showed that the TA-matrix performs better in predicting ability than the classical numerator relationship matrix and the realized relationship matrix which are derived solely from pedigree or markers without regard to the trait. This is because the TA-matrix not only accounts for the Mendelian sampling term, but also puts the greater emphasis on those markers that
Institute of Scientific and Technical Information of China (English)
侯素梅
2002-01-01
实矩阵A称为是almostP-矩阵,如果A的行列式是正的,而所有真主子式是负的.本文给出了almostP-矩阵的一些性质以及almostP-矩阵与弱almostP-矩阵之间的关系.%An almost P-matrix A is one with real entries whose determinant is negative and all proper minors are positive. Obtain some properties for almost P-matrices, and the relationship between almost P-matrices and weak almost P-matrices.
Truncations of random unitary matrices
Zyczkowski, K; Zyczkowski, Karol; Sommers, Hans-Juergen
1999-01-01
We analyze properties of non-hermitian matrices of size M constructed as square submatrices of unitary (orthogonal) random matrices of size N>M, distributed according to the Haar measure. In this way we define ensembles of random matrices and study the statistical properties of the spectrum located inside the unit circle. In the limit of large matrices, this ensemble is characterized by the ratio M/N. For the truncated CUE we derive analytically the joint density of eigenvalues from which easily all correlation functions are obtained. For N-M fixed and N--> infinity the universal resonance-width distribution with N-M open channels is recovered.
Criteria of the Nonsingular H-Matrices
Institute of Scientific and Technical Information of China (English)
GAO jian; LIU Futi; HUANG Tingzhu
2004-01-01
The nonsingular H-matrices play an important role in the study of the matrix theory and the iterative method of systems of linear equations,etc.It has always been searched how to verify nonsingular H-matrices.In this paper,nonsingular H-matrices is studies by applying diagonally dominant matrices,irreducible diagonally dominant matrices and comparison matrices and several practical criteria for identifying nonsingular H-matrices are obtained.
Du, Hongli; Hu, Haofu; Meng, Yuhuan; Zheng, Weihao; Ling, Fei; Wang, Jufang; Zhang, Xiquan; Nie, Qinghua; Wang, Xiaoning
2010-09-24
In this study, we present a new method for evaluating animal evolutionary relationships. We used the GC% levels of genome-wide genes to determine the correlation between the GC% content and evolutionary relationship. The correlation coefficients of the GC% content of the orthologous genes of the paired animal species were calculated for a total of 21 species, and the evolutionary branching dates of these 21 species were derived from fossil records. The correlation coefficient of the GC% content of the orthologous genes of the species pair under study served as an indicator of their evolutionary relationship. Moreover, there was a decreasing linear relationship between the correlation coefficient and evolutionary branching date (R(2)=0.930).
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
Lee, S. Hong; Ripke, Stephan; Neale, Benjamin M.; Faraone, Stephen V.; Purcell, Shaun M.; Perlis, Roy H.; Mowry, Bryan J.; Thapar, Anita; Goddard, Michael E.; Witte, John S.; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A.; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E.; Asherson, Philip; Azevedo, Maria H.; Backlund, Lena; Badner, Judith A.; Bailey, Anthony J.; Banaschewski, Tobias; Barchas, Jack D.; Barnes, Michael R.; Barrett, Thomas B.; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayes, Monica; Bellivier, Frank; Bergen, Sarah E.; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B.; Black, Donald W.; Blackwood, Douglas H. R.; Bloss, Cinnamon S.; Boehnke, Michael; Boomsma, Dorret I.; Breen, Gerome; Breuer, Rene; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G.; Buitelaar, Jan K.; Bunney, William E.; Buxbaum, Joseph D.; Byerley, William F.; Byrne, Enda M.; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M.; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C. Robert; Collier, David A.; Cook, Edwin H.; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H.; Craig, David W.; Craig, Ian W.; Crosbie, Jennifer; Cuccaro, Michael L.; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J.; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J.; Doyle, Alysa E.; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P.; Edenberg, Howard J.; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E.; Ferrier, I. Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B.; Freitag, Christine M.; Friedl, Marion; Frisen, Louise; Gallagher, Louise; Gejman, Pablo V.; Georgieva, Lyudmila; Gershon, Elliot S.; Geschwind, Daniel H.; Giegling, Ina; Gill, Michael; Gordon, Scott D.; Gordon-Smith, Katherine; Green, Elaine K.; Greenwood, Tiffany A.; Grice, Dorothy E.; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L.; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P.; Hamshere, Marian L.; Hansen, Thomas F.; Hartmann, Annette M.; Hautzinger, Martin; Heath, Andrew C.; Henders, Anjali K.; Herms, Stefan; Hickie, Ian B.; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A.; Holsboer, Florian; Hoogendijk, Witte J.; Hottenga, Jouke-Jan; Hultman, Christina M.; Hus, Vanessa; Ingason, Andres; Ising, Marcus; Jamain, Stephane; Jones, Edward G.; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kaehler, Anna K.; Kahn, Rene S.; Kandaswamy, Radhika; Keller, Matthew C.; Kennedy, James L.; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K.; Klauck, Sabine M.; Klei, Lambertus; Knowles, James A.; Kohli, Martin A.; Koller, Daniel L.; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landen, Mikael; Langstrom, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B.; Leboyer, Marion; Ledbetter, David H.; Lee, Phil H.; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F.; Lewis, Cathryn M.; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A.; Lin, Dan-Yu; Linszen, Don H.; Liu, Chunyu; Lohoff, Falk W.; Loo, Sandra K.; Lord, Catherine; Lowe, Jennifer K.; Lucae, Susanne; MacIntyre, Donald J.; Madden, Pamela A. F.; Maestrini, Elena; Magnusson, Patrik K. E.; Mahon, Pamela B.; Maier, Wolfgang; Malhotra, Anil K.; Mane, Shrikant M.; Martin, Christa L.; Martin, Nicholas G.; Mattheisen, Manuel; Matthews, Keith; Mattingsdal, Morten; McCarroll, Steven A.; McGhee, Kevin A.; McGough, James J.; McGrath, Patrick J.; McGuffin, Peter; McInnis, Melvin G.; McIntosh, Andrew; McKinney, Rebecca; McLean, Alan W.; McMahon, Francis J.; McMahon, William M.; McQuillin, Andrew; Medeiros, Helena; Medland, Sarah E.; Meier, Sandra; Melle, Ingrid; Meng, Fan; Meyer, Jobst; Middeldorp, Christel M.; Middleton, Lefkos; Milanova, Vihra; Miranda, Ana; Monaco, Anthony P.; Montgomery, Grant W.; Moran, Jennifer L.; Moreno-De-Luca, Daniel; Morken, Gunnar; Morris, Derek W.; Morrow, Eric M.; Moskvina, Valentina; Muglia, Pierandrea; Muehleisen, Thomas W.; Muir, Walter J.; Mueller-Myhsok, Bertram; Murtha, Michael; Myers, Richard M.; Myin-Germeys, Inez; Neale, Michael C.; Nelson, Stan F.; Nievergelt, Caroline M.; Nikolov, Ivan; Nimgaonkar, Vishwajit; Nolen, Willem A.; Noethen, Markus M.; Nurnberger, John I.; Nwulia, Evaristus A.; Nyholt, Dale R.; O'Dushlaine, Colm; Oades, Robert D.; Olincy, Ann; Oliveira, Guiomar; Olsen, Line; Ophoff, Roel A.; Osby, Urban; Owen, Michael J.; Palotie, Aarno; Parr, Jeremy R.; Paterson, Andrew D.; Pato, Carlos N.; Pato, Michele T.; Penninx, Brenda W.; Pergadia, Michele L.; Pericak-Vance, Margaret A.; Pickard, Benjamin S.; Pimm, Jonathan; Piven, Joseph; Posthuma, Danielle; Potash, James B.; Poustka, Fritz; Propping, Peter; Puri, Vinay; Quested, Digby J.; Quinn, Emma M.; Antoni Ramos-Quiroga, Josep; Rasmussen, Henrik B.; Raychaudhuri, Soumya; Rehnstroem, Karola; Reif, Andreas; Ribases, Marta; Rice, John P.; Rietschel, Marcella; Roeder, Kathryn; Roeyers, Herbert; Rossin, Lizzy; Rothenberger, Aribert; Rouleau, Guy; Ruderfer, Douglas; Rujescu, Dan; Sanders, Alan R.; Sanders, Stephan J.; Santangelo, Susan L.; Sergeant, Joseph A.; Schachar, Russell; Schalling, Martin; Schatzberg, Alan F.; Scheftner, William A.; Schellenberg, Gerard D.; Scherer, Stephen W.; Schork, Nicholas J.; Schulze, Thomas G.; Schumacher, Johannes; Schwarz, Markus; Scolnick, Edward; Scott, Laura J.; Shi, Jianxin; Shilling, Paul D.; Shyn, Stanley I.; Silverman, Jeremy M.; Slager, Susan L.; Smalley, Susan L.; Smit, Johannes H.; Smith, Erin N.; Sonuga-Barke, Edmund J. S.; St Clair, David; State, Matthew; Steffens, Michael; Steinhausen, Hans-Christoph; Strauss, John S.; Strohmaier, Jana; Stroup, T. Scott; Sutcliffe, James S.; Szatmari, Peter; Szelinger, Szabocls; Thirumalai, Srinivasa; Thompson, Robert C.; Todorov, Alexandre A.; Tozzi, Federica; Treutlein, Jens; Uhr, Manfred; van den Oord, Edwin J. C. G.; Van Grootheest, Gerard; Van Os, Jim; Vicente, Astrid M.; Vieland, Veronica J.; Vincent, John B.; Visscher, Peter M.; Walsh, Christopher A.; Wassink, Thomas H.; Watson, Stanley J.; Weissman, Myrna M.; Werge, Thomas; Wienker, Thomas F.; Wijsman, Ellen M.; Willemsen, Gonneke; Williams, Nigel; Willsey, A. Jeremy; Witt, Stephanie H.; Xu, Wei; Young, Allan H.; Yu, Timothy W.; Zammit, Stanley; Zandi, Peter P.; Zhang, Peng; Zitman, Frans G.; Zoellner, Sebastian; Devlin, Bernie; Kelsoe, John R.; Sklar, Pamela; Daly, Mark J.; O'Donovan, Michael C.; Craddock, Nicholas; Sullivan, Patrick F.; Smoller, Jordan W.; Kendler, Kenneth S.; Wray, Naomi R.
2013-01-01
Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases
Genomic relationships computed from either next- generation sequence or array SNP data
Perez Enciso, M.
2014-01-01
The use of sequence data in genomic prediction models is a topic of high interest, given the decreasing prices of current next'-generation sequencing technologies (NGS) and the theoretical possibility of directly interrogating the genomes for all causal mutations. Here, we compare by simulation how
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
Lee, S. Hong; Ripke, Stephan; Neale, Benjamin M.; Faraone, Stephen V.; Purcell, Shaun M.; Perlis, Roy H.; Mowry, Bryan J.; Thapar, Anita; Goddard, Michael E.; Witte, John S.; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A.; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E.; Asherson, Philip; Azevedo, Maria H.; Backlund, Lena; Badner, Judith A.; Bailey, Anthony J.; Banaschewski, Tobias; Barchas, Jack D.; Barnes, Michael R.; Barrett, Thomas B.; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayes, Monica; Bellivier, Frank; Bergen, Sarah E.; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B.; Black, Donald W.; Blackwood, Douglas H. R.; Bloss, Cinnamon S.; Boehnke, Michael; Boomsma, Dorret I.; Breen, Gerome; Breuer, Rene; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G.; Buitelaar, Jan K.; Bunney, William E.; Buxbaum, Joseph D.; Byerley, William F.; Byrne, Enda M.; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M.; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C. Robert; Collier, David A.; Cook, Edwin H.; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H.; Craig, David W.; Craig, Ian W.; Crosbie, Jennifer; Cuccaro, Michael L.; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J.; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J.; Doyle, Alysa E.; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P.; Edenberg, Howard J.; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E.; Ferrier, I. Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B.; Freitag, Christine M.; Friedl, Marion; Frisen, Louise; Gallagher, Louise; Gejman, Pablo V.; Georgieva, Lyudmila; Gershon, Elliot S.; Geschwind, Daniel H.; Giegling, Ina; Gill, Michael; Gordon, Scott D.; Gordon-Smith, Katherine; Green, Elaine K.; Greenwood, Tiffany A.; Grice, Dorothy E.; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L.; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P.; Hamshere, Marian L.; Hansen, Thomas F.; Hartmann, Annette M.; Hautzinger, Martin; Heath, Andrew C.; Henders, Anjali K.; Herms, Stefan; Hickie, Ian B.; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A.; Holsboer, Florian; Hoogendijk, Witte J.; Hottenga, Jouke-Jan; Hultman, Christina M.; Hus, Vanessa; Ingason, Andres; Ising, Marcus; Jamain, Stephane; Jones, Edward G.; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kaehler, Anna K.; Kahn, Rene S.; Kandaswamy, Radhika; Keller, Matthew C.; Kennedy, James L.; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K.; Klauck, Sabine M.; Klei, Lambertus; Knowles, James A.; Kohli, Martin A.; Koller, Daniel L.; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landen, Mikael; Langstrom, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B.; Leboyer, Marion; Ledbetter, David H.; Lee, Phil H.; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F.; Lewis, Cathryn M.; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A.; Lin, Dan-Yu; Linszen, Don H.; Liu, Chunyu; Lohoff, Falk W.; Loo, Sandra K.; Lord, Catherine; Lowe, Jennifer K.; Lucae, Susanne; MacIntyre, Donald J.; Madden, Pamela A. F.; Maestrini, Elena; Magnusson, Patrik K. E.; Mahon, Pamela B.; Maier, Wolfgang; Malhotra, Anil K.; Mane, Shrikant M.; Martin, Christa L.; Martin, Nicholas G.; Mattheisen, Manuel; Matthews, Keith; Mattingsdal, Morten; McCarroll, Steven A.; McGhee, Kevin A.; McGough, James J.; McGrath, Patrick J.; McGuffin, Peter; McInnis, Melvin G.; McIntosh, Andrew; McKinney, Rebecca; McLean, Alan W.; McMahon, Francis J.; McMahon, William M.; McQuillin, Andrew; Medeiros, Helena; Medland, Sarah E.; Meier, Sandra; Melle, Ingrid; Meng, Fan; Meyer, Jobst; Middeldorp, Christel M.; Middleton, Lefkos; Milanova, Vihra; Miranda, Ana; Monaco, Anthony P.; Montgomery, Grant W.; Moran, Jennifer L.; Moreno-De-Luca, Daniel; Morken, Gunnar; Morris, Derek W.; Morrow, Eric M.; Moskvina, Valentina; Muglia, Pierandrea; Muehleisen, Thomas W.; Muir, Walter J.; Mueller-Myhsok, Bertram; Murtha, Michael; Myers, Richard M.; Myin-Germeys, Inez; Neale, Michael C.; Nelson, Stan F.; Nievergelt, Caroline M.; Nikolov, Ivan; Nimgaonkar, Vishwajit; Nolen, Willem A.; Noethen, Markus M.; Nurnberger, John I.; Nwulia, Evaristus A.; Nyholt, Dale R.; O'Dushlaine, Colm; Oades, Robert D.
Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs
DEFF Research Database (Denmark)
Lee, S Hong; Ripke, Stephan; Neale, Benjamin M
2013-01-01
Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cas...
DEFF Research Database (Denmark)
Orlando, Ludovic Antoine Alexandre
2014-01-01
of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene...
The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships.
Elmerot, Christian; Arnason, Ulfur; Gojobori, Takashi; Janke, Axel
2002-08-07
The small nuclear genome of the pufferfish, Fugu rubripes (order Tetraodontiformes), makes this species highly interesting for genome research. In order to establish the phylogenetic position of the Tetraodontiformes relative to other teleostean orders that might also have a reduced nuclear genome size, we have sequenced the mitochondrial (mt) genome of the pufferfish. The gene order, nucleotide composition and evolutionary rate of the mt genome of the fugu correspond to those of other teleosts. This suggests that the evolution of this genome has not been affected by the processes that led to the dramatic reduction of the size of the nuclear genome of the fugu. The phylogenetic analyses, which were based on the concatenated amino acid sequences of twelve protein-coding mt genes, placed the fugu among the percomorphs. The affinities between the Tetraodontiformes and either the Perciformes or the Zeiformes were limited, however. The common notion of a separate euteleostean clade remained unsupported. The analyses did not support the traditional systematic understanding that the Clupeiformes constitute a basal teleostean lineage. In addition the findings strongly suggest that three teleostean orders, the Perciformes, Zeiformes and Scorpaeniformes, are paraphyletic.
Generalisations of Fisher Matrices
Directory of Open Access Journals (Sweden)
Alan Heavens
2016-06-01
Full Text Available Fisher matrices play an important role in experimental design and in data analysis. Their primary role is to make predictions for the inference of model parameters—both their errors and covariances. In this short review, I outline a number of extensions to the simple Fisher matrix formalism, covering a number of recent developments in the field. These are: (a situations where the data (in the form of ( x , y pairs have errors in both x and y; (b modifications to parameter inference in the presence of systematic errors, or through fixing the values of some model parameters; (c Derivative Approximation for LIkelihoods (DALI - higher-order expansions of the likelihood surface, going beyond the Gaussian shape approximation; (d extensions of the Fisher-like formalism, to treat model selection problems with Bayesian evidence.
Generalisations of Fisher Matrices
Heavens, Alan
2016-01-01
Fisher matrices play an important role in experimental design and in data analysis. Their primary role is to make predictions for the inference of model parameters - both their errors and covariances. In this short review, I outline a number of extensions to the simple Fisher matrix formalism, covering a number of recent developments in the field. These are: (a) situations where the data (in the form of (x,y) pairs) have errors in both x and y; (b) modifications to parameter inference in the presence of systematic errors, or through fixing the values of some model parameters; (c) Derivative Approximation for LIkelihoods (DALI) - higher-order expansions of the likelihood surface, going beyond the Gaussian shape approximation; (d) extensions of the Fisher-like formalism, to treat model selection problems with Bayesian evidence.
VanderLaan Circulant Type Matrices
Directory of Open Access Journals (Sweden)
Hongyan Pan
2015-01-01
Full Text Available Circulant matrices have become a satisfactory tools in control methods for modern complex systems. In the paper, VanderLaan circulant type matrices are presented, which include VanderLaan circulant, left circulant, and g-circulant matrices. The nonsingularity of these special matrices is discussed by the surprising properties of VanderLaan numbers. The exact determinants of VanderLaan circulant type matrices are given by structuring transformation matrices, determinants of well-known tridiagonal matrices, and tridiagonal-like matrices. The explicit inverse matrices of these special matrices are obtained by structuring transformation matrices, inverses of known tridiagonal matrices, and quasi-tridiagonal matrices. Three kinds of norms and lower bound for the spread of VanderLaan circulant and left circulant matrix are given separately. And we gain the spectral norm of VanderLaan g-circulant matrix.
Insights into the Bamboo Genome: Syntenic Relationships to Rice and Sorghum
Institute of Scientific and Technical Information of China (English)
Yi-Jie Gui; Nai-Xun Ma; Tian-Zhen Zhang; Long-Jiang Fan; Yan Zhou; Yu Wang; Sheng Wang; Sheng-Yue Wang; Yan Hu; Shi-Ping Bo; Huan Chen; Chang-Ping Zhou
2010-01-01
Bamboo occupies an important phylogenetic node in the grass family and plays a significant role in the forest industry.We produced 1.2 Mb of tetraploid moso bamboo(Phyllostachys pubescens E.Mazel ex H.de Leh.)sequences from 13 bacterial artificial chromosome(BAC)clones,and these are the largest genomic sequences available so far from the subfamily Bambusoideae.The content of repetitive elements(36.2%)in bamboo is similar to that in rice.Both rice and sorghum exhibit high genomic synteny with bamboo,which suggests that rice and sorghum may be useful as models for decoding Bambusoideae genomes.
Masta, Susan E; McCall, Andrew; Longhorn, Stuart J
2010-10-01
Pycnogonids, or sea spiders, are an enigmatic group of arthropods. Their unique anatomical features have made them difficult to place within the broader group Arthropoda. Most attempts to classify members of Pycnogonida have focused on utilizing these anatomical features to infer relatedness. Using data from mitochondrial genomes, we show that pycnogonids are placed as derived chelicerates, challenging the hypothesis that they diverged early in arthropod history. Our increased taxon sampling of three new mitochondrial genomes also allows us to infer phylogenetic relatedness among major pycnogonid lineages. Phylogenetic analyses based on all 13 mitochondrial protein-coding genes yield well-resolved relationships among the sea spider lineages. Gene order and tRNA secondary structure characters provide independent lines of evidence for these inferred phylogenetic relationships among pycnogonids, and show a minimal amount of homoplasy. Additionally, rare changes in three tRNA genes unite pycnogonids as a clade; these include changes in anticodon identity in tRNA(Lys) and tRNA(Ser(AGN)) and the shared loss of D-arm sequence in the tRNA(Ala) gene. Using mitochondrial genome changes and tRNA structural changes is especially useful for resolving relationships among the major lineages of sea spiders in light of the fact that there have been multiple independent evolutionary changes in nucleotide strand bias among sea spiders. Such reversed nucleotide biases can mislead phylogeny reconstruction based on sequences, although the use of appropriate methods can overcome these effects. With pycnogonids, we find that applying methods to compensate for strand bias and that using genome-level characters yield congruent phylogenetic signals.
Raman, Gurusamy; Choi, Kyoung Su; Park, SeonJoo
2016-12-02
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS) value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago) and might have moved from Eurasia to Dokdo Island.
Polynomial Fibonacci-Hessenberg matrices
Energy Technology Data Exchange (ETDEWEB)
Esmaeili, Morteza [Dept. of Mathematical Sciences, Isfahan University of Technology, 84156-83111 Isfahan (Iran, Islamic Republic of)], E-mail: emorteza@cc.iut.ac.ir; Esmaeili, Mostafa [Dept. of Electrical and Computer Engineering, Isfahan University of Technology, 84156-83111 Isfahan (Iran, Islamic Republic of)
2009-09-15
A Fibonacci-Hessenberg matrix with Fibonacci polynomial determinant is referred to as a polynomial Fibonacci-Hessenberg matrix. Several classes of polynomial Fibonacci-Hessenberg matrices are introduced. The notion of two-dimensional Fibonacci polynomial array is introduced and three classes of polynomial Fibonacci-Hessenberg matrices satisfying this property are given.
Enhancing Understanding of Transformation Matrices
Dick, Jonathan; Childrey, Maria
2012-01-01
With the Common Core State Standards' emphasis on transformations, teachers need a variety of approaches to increase student understanding. Teaching matrix transformations by focusing on row vectors gives students tools to create matrices to perform transformations. This empowerment opens many doors: Students are able to create the matrices for…
Enhancing Understanding of Transformation Matrices
Dick, Jonathan; Childrey, Maria
2012-01-01
With the Common Core State Standards' emphasis on transformations, teachers need a variety of approaches to increase student understanding. Teaching matrix transformations by focusing on row vectors gives students tools to create matrices to perform transformations. This empowerment opens many doors: Students are able to create the matrices for…
Hierarchical matrices algorithms and analysis
Hackbusch, Wolfgang
2015-01-01
This self-contained monograph presents matrix algorithms and their analysis. The new technique enables not only the solution of linear systems but also the approximation of matrix functions, e.g., the matrix exponential. Other applications include the solution of matrix equations, e.g., the Lyapunov or Riccati equation. The required mathematical background can be found in the appendix. The numerical treatment of fully populated large-scale matrices is usually rather costly. However, the technique of hierarchical matrices makes it possible to store matrices and to perform matrix operations approximately with almost linear cost and a controllable degree of approximation error. For important classes of matrices, the computational cost increases only logarithmically with the approximation error. The operations provided include the matrix inversion and LU decomposition. Since large-scale linear algebra problems are standard in scientific computing, the subject of hierarchical matrices is of interest to scientists ...
Genome data from a sixteenth century pig illuminate modern breed relationships
Ramírez, Óscar; Burgos-Paz, W; Ballester, Maria; Bianco, E; Olalde, Iñigo; Santpere, Gabriel; Lalueza-Fox, Carles; Pérez-Enciso, Miguel
2014-01-01
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage...
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Lee, Hong; Ripke, Stephan; Neale, Benjamin; Faraone, Stephen,; Purcell, Shaun; Perlis, Roy,; Mowry, Bryan; Thapar, Anita; Goddard, Michael; Witte, John,; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole,
2013-01-01
International audience; Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply uni...
Chen, Miao-Miao; Li, Yan; Chen, Mo; Wang, Huan; Li, Qun; Xia, Run-Xi; Zeng, Cai-Yun; Li, Yu-Ping; Liu, Yan-Qun; Qin, Li
2014-07-15
Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect with the largest wing surface area of all moths. The mitogenome of A. atlas is a circular molecule of 15,282 bp long, and its nucleotide composition shows heavily biased towards As and Ts, accounting for 79.30%. This genome comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A+T-rich region. It is of note that this genome exhibits a slightly positive AT skew, which is different from the other known Saturniidae species. All PCGs are initiated by ATN codons, except for COI with CGA instead. Only six PCGs use a common stop codon of TAA or TAG, whereas the remaining seven use an incomplete termination codon T or TA. All tRNAs have the typical clover-leaf structure, with an exception for tRNA(Ser)(AGN). The A. atlas A+T-rich region contains non-repetitive sequences, but harbors several features common to the Bombycoidea insects. The phylogenetic relationships based on Maximum Likelihood method provide a well-supported outline of Saturniidae, which is in accordance with the traditional morphological classification and recent molecular works.
Inference for High-dimensional Differential Correlation Matrices.
Cai, T Tony; Zhang, Anru
2016-01-01
Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical guarantees are given. Minimax rate of convergence is established and the proposed estimator is shown to be adaptively rate-optimal over collections of paired correlation matrices with approximately sparse differences. Simulation results show that the procedure significantly outperforms two other natural methods that are based on separate estimation of the individual correlation matrices. The procedure is also illustrated through an analysis of a breast cancer dataset, which provides evidence at the gene co-expression level that several genes, of which a subset has been previously verified, are associated with the breast cancer. Hypothesis testing on the differential correlation matrices is also considered. A test, which is particularly well suited for testing against sparse alternatives, is introduced. In addition, other related problems, including estimation of a single sparse correlation matrix, estimation of the differential covariance matrices, and estimation of the differential cross-correlation matrices, are also discussed.
Directory of Open Access Journals (Sweden)
Janke Axel
2008-05-01
Full Text Available Abstract Background A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew, probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. Results The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95–100 million years ago. Many of the following divergences occurred only a few (2–4 million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. Conclusion The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in
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Thomas M Carmen
2008-06-01
Full Text Available Abstract Background Protozoan parasites of the genus Leishmania are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryotic lineage possess a number of unusual genomic, molecular and biochemical features. The completion of the genome projects for three Leishmania species has generated invaluable information enabling a direct analysis of genome structure and organization. Results By using DNA macroarrays, made with Leishmania infantum genomic clones and hybridized with total DNA from the parasite, we identified a clone containing a repeated sequence. An analysis of the recently completed genome sequence of L. infantum, using this repeated sequence as bait, led to the identification of a new class of repeated elements that are interspersed along the different L. infantum chromosomes. These elements turned out to be homologues of SIDER2 sequences, which were recently identified in the Leishmania major genome; thus, we adopted this nomenclature for the Leishmania elements described herein. Since SIDER2 elements are very heterogeneous in sequence, their precise identification is rather laborious. We have characterized 54 LiSIDER2 elements in chromosome 32 and 27 ones in chromosome 20. The mean size for these elements is 550 bp and their sequence is G+C rich (mean value of 66.5%. On the basis of sequence similarity, these elements can be grouped in subfamilies that show a remarkable relationship of proximity, i.e. SIDER2s of a given subfamily locate close in a chromosomal region without intercalating elements. For comparative purposes, we have identified the SIDER2 elements existing in L. major and Leishmania braziliensis chromosomes 32. While SIDER2 elements are highly conserved both in number and location between L. infantum and L. major, no such conservation exists when comparing with SIDER2s in L. braziliensis chromosome 32. Conclusion
Indian Academy of Sciences (India)
A. PAVAN-KUMAR; SUDHANSHU RAMAN; PRAKASH G. KORINGA; NAMRATA PATEL; TEJAS SHAH; RAJEEV K. SINGH; GOPAL KRISHNA; C. G. JOSHI; P. GIREESH-BABU; APARNA CHAUDHARI
2016-12-01
The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000×. Comparative mitogenome analysis shows higher divergence value at ND1 gene than COI gene. Further, occurrence of a distinct genetic lineage of T. tor is revealed. The phylogenetic relationship among mahseer group has been defined as Neolissochilus hexagonolepis ((T. sinensis (T. putitora, T. tor), (T. khudree, T. tambroides)).
Rapakoulia, Trisevgeni
2017-08-09
Motivation: Drug combination therapy for treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect, while reducing the likelihood of drug resistance. In order to reduce time and cost spent in comprehensive screens, methods are needed which can model additive effects of possible drug combinations. Results: We here show that the transcriptional response to combinatorial drug treatment at promoters, as measured by single molecule CAGE technology, is accurately described by a linear combination of the responses of the individual drugs at a genome wide scale. We also find that the same linear relationship holds for transcription at enhancer elements. We conclude that the described approach is promising for eliciting the transcriptional response to multidrug treatment at promoters and enhancers in an unbiased genome wide way, which may minimize the need for exhaustive combinatorial screens.
Zhang, Yucheng; Qiu, Sai
2015-11-01
The genera Erwinia and Pantoea contain species that are devastating plant pathogens, non-pathogen epiphytes, and opportunistic human pathogens. However, some controversies persist in the taxonomic classification of these two closely related genera. The phylogenomic analysis of these two genera was investigated via a comprehensive analysis of 25 Erwinia genomes and 23 Pantoea genomes. Single-copy orthologs could be extracted from the Erwinia/Pantoea core-genome to reconstruct the Erwinia/Pantoea phylogeny. This tree has strong bootstrap support for almost all branches. We also estimated the in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) values between each genome; strains from the same species showed ANI values ≥96% and isDDH values >70%. These data confirm that whole genome sequence data provides a powerful tool to resolve the complex taxonomic questions of Erwinia/Pantoea, e.g. Pantoea agglomerans 299R was not clustered into a single group with other P. agglomerans strains, and the ANI values and isDDH values between them were Erwinia/Pantoea phylogeny.
Guo, Aijiang
2016-08-31
Tapeworms Cladotaenia spp. are among the most important wildlife pathogens in birds of prey. The genus Cladotaenia is placed in the family Paruterinidae based on morphological characteristics and hosts. However, limited molecular information is available for studying the phylogenetic position of this genus in relation to other cestodes. In this study, the complete mitochondrial (mt) genome of Cladotaenia vulturi was amplified using "Long-PCR" and then sequenced by primer walking. Sequence annotation and gene identification were performed by comparison with published flatworm mt genomes. The phylogenetic relationships of C. vulturi with other cestode species were established using the concatenated amino acid sequences of 12 protein-coding genes with Bayesian Inference and Maximum Likelihood methods. The complete mitochondrial genome of the Cladotaenia vulturi is 13,411 kb in size and contains 36 genes. The gene arrangement of C. vulturi is identical to those in Anoplocephala spp. (Anoplocephalidae), Hymenolepis spp. (Hymenolepididae) and Dipylidium caninum (Dipylidiidae), but different from that in taeniids owing to the order shift between the tRNA (L1) and tRNA (S2) genes. Phylogenetic analyses based on the amino acid sequences of the concatenated 12 protein-coding genes showed that the species in the Taeniidae form a group and C. vulturi is a sister taxon to the species of the family Taeniidae. To our knowledge, the present study provides the first molecular data to support the early proposal from morphological evidence that the Taeniidae is a sister group to the family Paruterinidae. This novel mt genome sequence will be useful for further investigations into the population genetics, phylogenetics and systematics of the family Paruterinidae and inferring phylogenetic relationships among several lineages within the order Cyclophyllidea.
Estimating sparse precision matrices
Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross
2016-08-01
We apply a method recently introduced to the statistical literature to directly estimate the precision matrix from an ensemble of samples drawn from a corresponding Gaussian distribution. Motivated by the observation that cosmological precision matrices are often approximately sparse, the method allows one to exploit this sparsity of the precision matrix to more quickly converge to an asymptotic 1/sqrt{N_sim} rate while simultaneously providing an error model for all of the terms. Such an estimate can be used as the starting point for further regularization efforts which can improve upon the 1/sqrt{N_sim} limit above, and incorporating such additional steps is straightforward within this framework. We demonstrate the technique with toy models and with an example motivated by large-scale structure two-point analysis, showing significant improvements in the rate of convergence. For the large-scale structure example, we find errors on the precision matrix which are factors of 5 smaller than for the sample precision matrix for thousands of simulations or, alternatively, convergence to the same error level with more than an order of magnitude fewer simulations.
Generating random density matrices
Zyczkowski, Karol; Nechita, Ion; Collins, Benoit
2010-01-01
We study various methods to generate ensembles of quantum density matrices of a fixed size N and analyze the corresponding probability distributions P(x), where x denotes the rescaled eigenvalue, x=N\\lambda. Taking a random pure state of a two-partite system and performing the partial trace over one subsystem one obtains a mixed state represented by a Wishart--like matrix W=GG^{\\dagger}, distributed according to the induced measure and characterized asymptotically, as N -> \\infty, by the Marchenko-Pastur distribution. Superposition of k random maximally entangled states leads to another family of explicitly derived distributions, describing singular values of the sum of k independent random unitaries. Taking a larger system composed of 2s particles, constructing $s$ random bi-partite states, performing the measurement into a product of s-1 maximally entangled states and performing the partial trace over the remaining subsystem we arrive at a random state characterized by the Fuss-Catalan distribution of order...
Graph-theoretical matrices in chemistry
Janezic, Dusanka; Nikolic, Sonja; Trinajstic, Nenad
2015-01-01
Graph-Theoretical Matrices in Chemistry presents a systematic survey of graph-theoretical matrices and highlights their potential uses. This comprehensive volume is an updated, extended version of a former bestseller featuring a series of mathematical chemistry monographs. In this edition, nearly 200 graph-theoretical matrices are included.This second edition is organized like the previous one-after an introduction, graph-theoretical matrices are presented in five chapters: The Adjacency Matrix and Related Matrices, Incidence Matrices, The Distance Matrix and Related Matrices, Special Matrices
Hadamard Matrices and Their Applications
Horadam, K J
2011-01-01
In Hadamard Matrices and Their Applications, K. J. Horadam provides the first unified account of cocyclic Hadamard matrices and their applications in signal and data processing. This original work is based on the development of an algebraic link between Hadamard matrices and the cohomology of finite groups that was discovered fifteen years ago. The book translates physical applications into terms a pure mathematician will appreciate, and theoretical structures into ones an applied mathematician, computer scientist, or communications engineer can adapt and use. The first half of the book expl
Qiao, X; Casini, G.; Qiao, J; Mindich, L
1995-01-01
Bacteriophage phi 6 has a genome of three segments of double-stranded RNA enclosed in a procapsid composed of four different proteins. The preformed procapsid is capable of packaging plus-strand transcripts of the genomic segments in an in vitro reaction. The packaging of the three segments shows a strong order of dependence in that segment S packages alone, but segment M requires S and and segment L requires S and M for efficient packaging. Packaging of individual segments is dependent on un...
Tiley, George P; Burleigh, J Gordon; Burleigh, Gordon
2015-09-16
Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. Recombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. After correcting recombination rates for euchromatin content, we also found an association between global recombination rate and average gene family size. This suggests a role for recombination in the preservation of duplicate genes or expansion of gene families. An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates (dN/dS) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. We also identified shifts in dN/dS for recombination proteins that are associated with shifts in global recombination rate across our sample of angiosperms. Although our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective
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Laurel S Burall
Full Text Available In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra analysis plots standardized (z-score tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2. This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as
Burall, Laurel S; Grim, Christopher J; Mammel, Mark K; Datta, Atin R
2016-01-01
In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as links between two
Insights into the Musa genome: Syntenic relationships to rice and between Musa species
Piffanelli, P.; Ciampi, A.Y.; Silva, F.R.; Santos, C.R.; Dhont, A.; Vilarinhos, A.; Pappas, G.; Souza, M.T.; Milller, R.N.G.
2008-01-01
Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no la
Application of Graph Theory to the elaboration of personal genomic data for genealogical research
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Vincenzo Palleschi
2015-10-01
Full Text Available In this communication a representation of the links between DNA-relatives based on Graph Theory is applied to the analysis of personal genomic data to obtain genealogical information. The method is tested on both simulated and real data and its applicability to the field of genealogical research is discussed. We envisage the proposed approach as a valid tool for a streamlined application to the publicly available data generated by many online personal genomic companies. In this way, anonymized matrices of pairwise genome sharing counts can help to improve the retrieval of genetic relationships between customers who provide explicit consent to the treatment of their data.
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Jung Sung Kim
Full Text Available Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae and 155,510bp in Alstroemeria aurea (Alstroemeriaceae. Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.
Kim, Jung Sung; Kim, Joo-Hwan
2013-01-01
Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.
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Ana Paula S Peruca
2008-08-01
Full Text Available The bacterial strain Bacillus cereus is closely related to Bacillus thuringiensis, although any genetic relationship between the two strains is still in debate. Using rep-PCR genomic fingerprinting, we established the genetic relationships between Brazilian sympatric populations of B. cereus and B. thuringiensis simultaneously collected from two geographically separate sites. We observed the formation of both B. thuringiensis and B. cereus clusters, as well as strains of B. cereus that are more closely related to B. thuringiensis than to other B. cereus strains. In addition, lower genetic variability was observed among B. thuringiensis clusters compared to B. cereus clusters, indicating that either the two species should be categorized as separate or that B. thuringiensis may represent a clone from a B. cereus background.
Carbonell-Caballero, Jose; Alonso, Roberto; Ibañez, Victoria; Terol, Javier; Talon, Manuel; Dopazo, Joaquin
2015-08-01
Citrus genus includes some of the most important cultivated fruit trees worldwide. Despite being extensively studied because of its commercial relevance, the origin of cultivated citrus species and the history of its domestication still remain an open question. Here, we present a phylogenetic analysis of the chloroplast genomes of 34 citrus genotypes which constitutes the most comprehensive and detailed study to date on the evolution and variability of the genus Citrus. A statistical model was used to estimate divergence times between the major citrus groups. Additionally, a complete map of the variability across the genome of different citrus species was produced, including single nucleotide variants, heteroplasmic positions, indels (insertions and deletions), and large structural variants. The distribution of all these variants provided further independent support to the phylogeny obtained. An unexpected finding was the high level of heteroplasmy found in several of the analyzed genomes. The use of the complete chloroplast DNA not only paves the way for a better understanding of the phylogenetic relationships within the Citrus genus but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance, heteroplasmy, and gene selection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Jansen Robert K
2006-09-01
Full Text Available Abstract Background The production of Citrus, the largest fruit crop of international economic value, has recently been imperiled due to the introduction of the bacterial disease Citrus canker. No significant improvements have been made to combat this disease by plant breeding and nuclear transgenic approaches. Chloroplast genetic engineering has a number of advantages over nuclear transformation; it not only increases transgene expression but also facilitates transgene containment, which is one of the major impediments for development of transgenic trees. We have sequenced the Citrus chloroplast genome to facilitate genetic improvement of this crop and to assess phylogenetic relationships among major lineages of angiosperms. Results The complete chloroplast genome sequence of Citrus sinensis is 160,129 bp in length, and contains 133 genes (89 protein-coding, 4 rRNAs and 30 distinct tRNAs. Genome organization is very similar to the inferred ancestral angiosperm chloroplast genome. However, in Citrus the infA gene is absent. The inverted repeat region has expanded to duplicate rps19 and the first 84 amino acids of rpl22. The rpl22 gene in the IRb region has a nonsense mutation resulting in 9 stop codons. This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries. Repeat analysis identified 29 direct and inverted repeats 30 bp or longer with a sequence identity ≥ 90%. Comparison of protein-coding sequences with expressed sequence tags revealed six putative RNA edits, five of which resulted in non-synonymous modifications in petL, psbH, ycf2 and ndhA. Phylogenetic analyses using maximum parsimony (MP and maximum likelihood (ML methods of a dataset composed of 61 protein-coding genes for 30 taxa provide strong support for the monophyly of several major clades of angiosperms, including monocots, eudicots, rosids and asterids. The MP and ML trees are incongruent in three areas: the position of Amborella and
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Gasser Robin B
2012-10-01
Full Text Available Abstract Background Dictyocaulus species are strongylid nematodes of major veterinary significance in ruminants, such as cattle and cervids, and cause serious bronchitis or pneumonia (dictyocaulosis or “husk”. There has been ongoing controversy surrounding the validity of some Dictyocaulus species and their host specificity. Here, we sequenced and characterized the mitochondrial (mt genomes of Dictyocaulus viviparus (from Bos taurus with Dictyocaulus sp. cf. eckerti from red deer (Cervus elaphus, used mt datasets to assess the genetic relationship between these and related parasites, and predicted markers for future population genetic or molecular epidemiological studies. Methods The mt genomes were amplified from single adult males of D. viviparus and Dictyocaulus sp. cf. eckerti (from red deer by long-PCR, sequenced using 454-technology and annotated using bioinformatic tools. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI, also employing data for other strongylids for comparative purposes. Results The circular mt genomes were 13,310 bp (D. viviparus and 13,296 bp (Dictyocaulus sp. cf. eckerti in size, and each contained 12 protein-encoding, 22 transfer RNA and 2 ribosomal RNA genes, consistent with other strongylid nematodes sequenced to date. Sliding window analysis identified genes with high or low levels of nucleotide diversity between the mt genomes. At the predicted mt proteomic level, there was an overall sequence difference of 34.5% between D. viviparus and Dictyocaulus sp. cf. eckerti, and amino acid sequence variation within each species was usually much lower than differences between species. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 mt proteins showed that both D. viviparus and Dictyocaulus sp. cf. eckerti were closely related, and grouped to the exclusion of
Chen, Peng; Han, Yuqing; Zhu, Chaoying; Gao, Bin; Ruan, Luzhang
2017-09-23
The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNA(Ser (AGY)), which lost its "DHU" arm. Based on the concatenated nucleotide sequences of the complete mitochondrial DNA genes of 16 Rallidae species, reconstruction of phylogenetic trees and analysis of the molecular clock of P. fusca and P. pusilla indicated that these species from a sister group, which in turn are sister group to Rallina eurizonoides. The genus Gallirallus is a sister group to genus Lewinia, and these groups in turn are sister groups to genus Porphyrio. Moreover, molecular clock analyses suggested that the basal divergence of Rallidae could be traced back to 40.47 (41.46‒39.45) million years ago (Mya), and the divergence of Porzana occurred approximately 5.80 (15.16‒0.79) Mya.
Energy Technology Data Exchange (ETDEWEB)
Macey, J. Robert; Papenfuss, Theodore J.; Kuehl, Jennifer V.; Fourcade, H. Matthew; Boore, Jeffrey L.
2004-05-19
Complete mitochondrial genomic sequences are reported from 12 members in the four families of the reptile group Amphisbaenia. Analysis of 11,946 aligned nucleotide positions (5,797 informative) produces a robust phylogenetic hypothesis. The family Rhineuridae is basal and Bipedidae is the sister taxon to the Amphisbaenidae plus Trogonophidae. Amphisbaenian reptiles are surprisingly old, predating the breakup of Pangaea 200 million years before present, because successive basal taxa (Rhineuridae and Bipedidae) are situated in tectonic regions of Laurasia and nested taxa (Amphisbaenidae and Trogonophidae) are found in Gondwanan regions. Thorough sampling within the Bipedidae shows that it is not tectonic movement of Baja California away from the Mexican mainland that is primary in isolating Bipes species, but rather that primary vicariance occurred between northern and southern groups. Amphisbaenian families show parallel reduction in number of limbs and Bipes species exhibit parallel reduction in number of digits. A measure is developed for comparing the phylogenetic information content of various genes. A synapomorphic trait defining the Bipedidae is a shift from the typical vertebrate mitochondrial gene arrangement to the derived state of trnE and nad6. In addition, a tandem duplication of trnT and trnP is observed in B. biporus with a pattern of pseudogene formation that varies among populations. The first case of convergent rearrangement of the mitochondrial genome among animals demonstrated by complete genomic sequences is reported. Relative to most vertebrates, the Rhineuridae has the block nad6, trnE switched in order with cob, trnT, trnP, as they are in birds.
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Gupta Vibha
2008-03-01
Full Text Available Abstract Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome and A. thaliana and analyzed the arrangement of 24 (previously described genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study with the A and B genomes of B. napus and B. nigra respectively (described earlier, revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements
Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Lee, S Hong; Ripke, Stephan; Neale, Benjamin M; Faraone, Stephen V; Purcell, Shaun M; Perlis, Roy H; Mowry, Bryan J; Thapar, Anita; Goddard, Michael E; Witte, John S; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E; Asherson, Philip; Azevedo, Maria H; Backlund, Lena; Badner, Judith A; Bailey, Anthony J; Banaschewski, Tobias; Barchas, Jack D; Barnes, Michael R; Barrett, Thomas B; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayés, Mònica; Bellivier, Frank; Bergen, Sarah E; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B; Black, Donald W; Blackwood, Douglas H R; Bloss, Cinnamon S; Boehnke, Michael; Boomsma, Dorret I; Breen, Gerome; Breuer, René; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G; Buitelaar, Jan K; Bunney, William E; Buxbaum, Joseph D; Byerley, William F; Byrne, Enda M; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C Robert; Collier, David A; Cook, Edwin H; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H; Craig, David W; Craig, Ian W; Crosbie, Jennifer; Cuccaro, Michael L; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J; Doyle, Alysa E; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P; Edenberg, Howard J; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E; Ferrier, I Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B; Freitag, Christine M; Friedl, Marion; Frisén, Louise; Gallagher, Louise; Gejman, Pablo V; Georgieva, Lyudmila; Gershon, Elliot S; Geschwind, Daniel H; Giegling, Ina; Gill, Michael; Gordon, Scott D; Gordon-Smith, Katherine; Green, Elaine K; Greenwood, Tiffany A; Grice, Dorothy E; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P; Hamshere, Marian L; Hansen, Thomas F; Hartmann, Annette M; Hautzinger, Martin; Heath, Andrew C; Henders, Anjali K; Herms, Stefan; Hickie, Ian B; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A; Holsboer, Florian; Hoogendijk, Witte J; Hottenga, Jouke-Jan; Hultman, Christina M; Hus, Vanessa; Ingason, Andrés; Ising, Marcus; Jamain, Stéphane; Jones, Edward G; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kähler, Anna K; Kahn, René S; Kandaswamy, Radhika; Keller, Matthew C; Kennedy, James L; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K; Klauck, Sabine M; Klei, Lambertus; Knowles, James A; Kohli, Martin A; Koller, Daniel L; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landén, Mikael; Långström, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B; Leboyer, Marion; Ledbetter, David H; Lee, Phil H; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F; Lewis, Cathryn M; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A; Lin, Dan-Yu; Linszen, Don H; Liu, Chunyu; Lohoff, Falk W; Loo, Sandra K; Lord, Catherine; Lowe, Jennifer K; Lucae, Susanne; MacIntyre, Donald J; Madden, Pamela A F; Maestrini, Elena; Magnusson, Patrik K E; Mahon, Pamela B; Maier, Wolfgang; Malhotra, Anil K; Mane, Shrikant M; Martin, Christa L; Martin, Nicholas G; Mattheisen, Manuel; Matthews, Keith; Mattingsdal, Morten; McCarroll, Steven A; McGhee, Kevin A; McGough, James J; McGrath, Patrick J; McGuffin, Peter; McInnis, Melvin G; McIntosh, Andrew; McKinney, Rebecca; McLean, Alan W; McMahon, Francis J; McMahon, William M; McQuillin, Andrew; Medeiros, Helena; Medland, Sarah E; Meier, Sandra; Melle, Ingrid; Meng, Fan; Meyer, Jobst; Middeldorp, Christel M; Middleton, Lefkos; Milanova, Vihra; Miranda, Ana; Monaco, Anthony P; Montgomery, Grant W; Moran, Jennifer L; Moreno-De-Luca, Daniel; Morken, Gunnar; Morris, Derek W; Morrow, Eric M; Moskvina, Valentina; Muglia, Pierandrea; Mühleisen, Thomas W; Muir, Walter J; Müller-Myhsok, Bertram; Murtha, Michael; Myers, Richard M; Myin-Germeys, Inez; Neale, Michael C; Nelson, Stan F; Nievergelt, Caroline M; Nikolov, Ivan; Nimgaonkar, Vishwajit; Nolen, Willem A; Nöthen, Markus M; Nurnberger, John I; Nwulia, Evaristus A; Nyholt, Dale R; O'Dushlaine, Colm; Oades, Robert D; Olincy, Ann; Oliveira, Guiomar; Olsen, Line; Ophoff, Roel A; Osby, Urban; Owen, Michael J; Palotie, Aarno; Parr, Jeremy R; Paterson, Andrew D; Pato, Carlos N; Pato, Michele T; Penninx, Brenda W; Pergadia, Michele L; Pericak-Vance, Margaret A; Pickard, Benjamin S; Pimm, Jonathan; Piven, Joseph; Posthuma, Danielle; Potash, James B; Poustka, Fritz; Propping, Peter; Puri, Vinay; Quested, Digby J; Quinn, Emma M; Ramos-Quiroga, Josep Antoni; Rasmussen, Henrik B; Raychaudhuri, Soumya; Rehnström, Karola; Reif, Andreas; Ribasés, Marta; Rice, John P; Rietschel, Marcella; Roeder, Kathryn; Roeyers, Herbert; Rossin, Lizzy; Rothenberger, Aribert; Rouleau, Guy; Ruderfer, Douglas; Rujescu, Dan; Sanders, Alan R; Sanders, Stephan J; Santangelo, Susan L; Sergeant, Joseph A; Schachar, Russell; Schalling, Martin; Schatzberg, Alan F; Scheftner, William A; Schellenberg, Gerard D; Scherer, Stephen W; Schork, Nicholas J; Schulze, Thomas G; Schumacher, Johannes; Schwarz, Markus; Scolnick, Edward; Scott, Laura J; Shi, Jianxin; Shilling, Paul D; Shyn, Stanley I; Silverman, Jeremy M; Slager, Susan L; Smalley, Susan L; Smit, Johannes H; Smith, Erin N; Sonuga-Barke, Edmund J S; St Clair, David; State, Matthew; Steffens, Michael; Steinhausen, Hans-Christoph; Strauss, John S; Strohmaier, Jana; Stroup, T Scott; Sutcliffe, James S; Szatmari, Peter; Szelinger, Szabocls; Thirumalai, Srinivasa; Thompson, Robert C; Todorov, Alexandre A; Tozzi, Federica; Treutlein, Jens; Uhr, Manfred; van den Oord, Edwin J C G; Van Grootheest, Gerard; Van Os, Jim; Vicente, Astrid M; Vieland, Veronica J; Vincent, John B; Visscher, Peter M; Walsh, Christopher A; Wassink, Thomas H; Watson, Stanley J; Weissman, Myrna M; Werge, Thomas; Wienker, Thomas F; Wijsman, Ellen M; Willemsen, Gonneke; Williams, Nigel; Willsey, A Jeremy; Witt, Stephanie H; Xu, Wei; Young, Allan H; Yu, Timothy W; Zammit, Stanley; Zandi, Peter P; Zhang, Peng; Zitman, Frans G; Zöllner, Sebastian; Devlin, Bernie; Kelsoe, John R; Sklar, Pamela; Daly, Mark J; O'Donovan, Michael C; Craddock, Nicholas; Sullivan, Patrick F; Smoller, Jordan W; Kendler, Kenneth S; Wray, Naomi R
2013-09-01
Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.
Multiplicative equations over commuting matrices
Energy Technology Data Exchange (ETDEWEB)
Babai, L. [Univ. of Chicago, IL (United States)]|[Eotvos Univ., Budapest (Hungary); Beals, R. [Rutgers Univ., Piscataway, NJ (United States); Cai, Jin-Yi [SUNY, Buffalo, NY (United States)] [and others
1996-12-31
We consider the solvability of the equation and generalizations, where the A{sub i} and B are given commuting matrices over an algebraic number field F. In the semigroup membership problem, the variables x{sub i} are constrained to be nonnegative integers. While this problem is NP-complete for variable k, we give a polynomial time algorithm if k is fixed. In the group membership problem, the matrices are assumed to be invertible, and the variables x{sub i} may take on negative values. In this case we give a polynomial time algorithm for variable k and give an explicit description of the set of all solutions (as an affine lattice). The special case of 1 x 1 matrices was recently solved by Guoqiang Ge; we heavily rely on his results.
Free probability and random matrices
Mingo, James A
2017-01-01
This volume opens the world of free probability to a wide variety of readers. From its roots in the theory of operator algebras, free probability has intertwined with non-crossing partitions, random matrices, applications in wireless communications, representation theory of large groups, quantum groups, the invariant subspace problem, large deviations, subfactors, and beyond. This book puts a special emphasis on the relation of free probability to random matrices, but also touches upon the operator algebraic, combinatorial, and analytic aspects of the theory. The book serves as a combination textbook/research monograph, with self-contained chapters, exercises scattered throughout the text, and coverage of important ongoing progress of the theory. It will appeal to graduate students and all mathematicians interested in random matrices and free probability from the point of view of operator algebras, combinatorics, analytic functions, or applications in engineering and statistical physics.
Cross-talk in phase encoded volume holographic memories employing unitary matrices
Zhang, X.; Berger, G.; Dietz, M.; Denz, C.
2006-12-01
The cross-talk noise in phase encoded holographic memories employing unitary matrices is theoretically investigated. After reviewing some earlier work in this area, we derive a relationship for the noise-to-signal ratio for phase-code multiplexing with unitary matrices. The noise-to-signal ratio rises in a zigzag way on increasing the storage capacity. Cross-talk is mainly caused by high-frequency phase codes. Unitary matrices of even orders have only one bad code, while unitary matrices of odd orders have four bad codes. The signal-to-noise ratios of all other codes can in each case be drastically improved by omission of these bad codes. We summarize the optimal orders of Hadamard and unitary matrices for recording a given number of holograms. The unitary matrices can enable us to adjust the available spatial light modulators to achieve the maximum possible storage capacity in both circumstances with and without bad codes.
Immanant Conversion on Symmetric Matrices
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Purificação Coelho M.
2014-01-01
Full Text Available Letr Σn(C denote the space of all n χ n symmetric matrices over the complex field C. The main objective of this paper is to prove that the maps Φ : Σn(C -> Σn (C satisfying for any fixed irre- ducible characters X, X' -SC the condition dx(A +aB = dχ·(Φ(Α + αΦ(Β for all matrices A,В ε Σ„(С and all scalars a ε C are automatically linear and bijective. As a corollary of the above result we characterize all such maps Φ acting on ΣИ(С.
Iterative methods for Toeplitz-like matrices
Energy Technology Data Exchange (ETDEWEB)
Huckle, T. [Universitaet Wurzburg (Germany)
1994-12-31
In this paper the author will give a survey on iterative methods for solving linear equations with Toeplitz matrices, Block Toeplitz matrices, Toeplitz plus Hankel matrices, and matrices with low displacement rank. He will treat the following subjects: (1) optimal (w)-circulant preconditioners is a generalization of circulant preconditioners; (2) Optimal implementation of circulant-like preconditioners in the complex and real case; (3) preconditioning of near-singular matrices; what kind of preconditioners can be used in this case; (4) circulant preconditioning for more general classes of Toeplitz matrices; what can be said about matrices with coefficients that are not l{sub 1}-sequences; (5) preconditioners for Toeplitz least squares problems, for block Toeplitz matrices, and for Toeplitz plus Hankel matrices.
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Matthew N. Ezewudo
2015-03-01
Full Text Available Neisseria gonorrhoeae is the causative agent of gonorrhea, a sexually transmitted infection (STI of major importance. As a result of antibiotic resistance, there are now limited options for treating patients. We collected draft genome sequence data and associated metadata data on 76 N. gonorrhoeae strains from around the globe and searched for known determinants of antibiotics resistance within the strains. The population structure and evolutionary forces within the pathogen population were analyzed. Our results indicated a cosmopolitan gonoccocal population mainly made up of five subgroups. The estimated ratio of recombination to mutation (r/m = 2.2 from our data set indicates an appreciable level of recombination occurring in the population. Strains with resistance phenotypes to more recent antibiotics (azithromycin and cefixime were mostly found in two of the five population subgroups.
Directory of Open Access Journals (Sweden)
Asger Hobolth
2007-02-01
Full Text Available The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 +/- 0.4 million years, and fairly large ancestral effective population sizes (65,000 +/- 30,000 for the human-chimp ancestor and 45,000 +/- 10,000 for the human-chimp-gorilla ancestor. Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.
Sign pattern matrices that admit M-, N-, P- or inverse M-matrices
Araújo, C. Mendes; Torregrosa, Juan R.
2009-01-01
In this paper we identify the sign pattern matrices that occur among the N–matrices, the P–matrices and the M–matrices. We also address to the class of inverse M–matrices and the related admissibility of sign pattern matrices problem. Fundação para a Ciência e a Tecnologia (FCT) Spanish DGI grant number MTM2007-64477
Directory of Open Access Journals (Sweden)
Eric eGamazon
2013-05-01
Full Text Available Given recent advances in the generation of high-throughput data such as whole genome genetic variation and transcriptome expression, it is critical to come up with novel methods to integrate these heterogeneous datasets and to assess the significance of identified phenotype-genotype relationships. Recent studies show that genome-wide association findings are likely to fall in loci with gene regulatory effects such as expression quantitative trait loci (eQTLs, demonstrating the utility of such integrative approaches. When genotype and gene expression data are available on the same individuals, we developed methods wherein top phenotype-associated genetic variants are prioritized if they are associated, as eQTLs, with gene expression traits that are themselves associated with the phenotype. Yet there has been no method to determine an overall p-value for the findings that arise specifically from the integrative nature of the approach. We propose a computationally feasible permutation method that accounts for the assimilative nature of the method and the correlation structure among gene expression traits and among genotypes. We apply the method to data from a study of cellular sensitivity to etoposide, one of the most widely used chemotherapeutic drugs. To our knowledge, this study is the first statistically sound quantification of the significance of the genotype-phenotype relationships resulting from applying an integrative approach. This method can be easily extended to cases in which gene expression data are replaced by other molecular phenotypes of interest, e.g., microRNA or proteomic data. This study has important implications for studies seeking to expand on genetic association studies by the use of omics data. Finally, we provide an R code to compute the empirical FDR when p-values for the observed and simulated phenotypes are available.
Hamiltonian formalism and symplectic matrices; Formalisme Hamiltonien et Matrices symplectiques
Energy Technology Data Exchange (ETDEWEB)
Bertrand, P. [Project SPIRAL, Grand Accelerateur National d`Ions Lourds, BP 5027, Bd. H. Becquerel, 14076 Caen cedex 5 (France)
1997-12-31
This work consists of five sections. The first one introduces the Lagrangian formalism starting from the fundamental equation of the dynamics. The sections 2 to 4 are devoted to the Hamiltonian formalism and to symplectic matrices. Lie algebra and groups were avoided, although these notions are very useful if higher order effects have to be investigated. The paper is dealing with the properties of the transfer matrices describing different electromagnetic objects like, for instance: dipoles, quadrupoles, cyclotrons, electrostatic deflectors, spiral inflectors, etc. A remarkable property of the first order exact transfer matrices, is the symplecticity which in case of a 3-D object, described in 6-D phase space, provides 15 non-linear equations relating the matrix coefficients. The symplectic matrix ensemble forms an multiplication non-commuting group, consequently the product of n symplectic matrices is still a symplectic matrix. This permits the global description of a system of n objects. Thus, the notion symplecticity is fundamental for the selection of a given electromagnetic object, for its optimization and insertion in a line of beam transfer. The symplectic relations indicate actually that if a given beam characteristic is modified, then another characteristic will be affected and as a result the spurious effects can be limited when a line is to be adjusted. The last section is devoted to the application of the elaborated procedure to describe the drift of non-relativistic and relativistic particles, the dipole and the Muller inflector. Hopefully, this elementary Hamiltonian formalism will help in the familiarization with the symplectic matrices extensively utilized at GANIL 10 refs.
Molnár, István; Šimková, Hana; Leverington-Waite, Michelle; Goram, Richard; Cseh, András; Vrána, Jan; Farkas, András; Doležel, Jaroslav; Molnár-Láng, Márta; Griffiths, Simon
2013-01-01
Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.
Directory of Open Access Journals (Sweden)
István Molnár
Full Text Available Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.
A Bayesian Approach to Genome/Linguistic Relationships in Native South Americans
Carlos Eduardo Guerra Amorim; Rafael Bisso-Machado; Virginia Ramallo; Maria Cátira Bortolini; Sandro Luis Bonatto; Francisco Mauro Salzano; Tábita Hünemeier
2013-01-01
The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native ...
Phillips, Naomi; Calhoun, Samantha; Moustafa, Ahmed; Bhattacharya, Debashish; Braun, Edward L
2008-02-01
Heterokonts comprise a large and diverse group of organisms unified by the heterokont biflagellate condition. Monophyly of many of these lineages is well established, but evolutionary relationships among the various lineages remain elusive. Among these lineages, the brown algae (Phaeophyceae) are a monophyletic, taxonomically diverse, and ecologically critical group common to marine environments. Despite their biological and scientific importance, consensus regarding brown algal phylogeny and taxonomic relationships is missing. Our long-term research goal is to produce a well-resolved taxon-rich phylogeny of the class to assess evolutionary patterns and taxonomic relationships among brown algal lineages and their relationship to other closely related heterokont groups. To accomplish this goal and augment existing loci for phaeophycean-wide systematic studies, we generated expressed sequence tags (ESTs) from several major brown algal lineages and from the heterokont lineage representing the closest sister group to brown algae. To date, we have successfully constructed cDNA libraries for two lineages (Choristocarpus tenellus Zanardini and Schizocladia ischiensis E. C. Henry, Okuda et H. Kawai) and in the library test phase obtained up to 1,600 ESTs per organism. Annotation results showed a gene discovery rate of 45%-50% for each library revealing 500-700 unique genes from each organism. We have identified several potential genes for phylogenetic inference and used these loci for preliminary molecular clock analyses. Our molecular clock analysis suggests that the basal divergence in brown algae occurred around the time of the pennate-centric diatom divergence. Here we report this analysis and other uses of ESTs in brown algal phylogenomics and the utility of these data for resolving the phylogeny of this group. © 2008 Phycological Society of America.
Correlation exploration of metabolic and genomic diversity in rice
Directory of Open Access Journals (Sweden)
Shinozaki Kazuo
2009-12-01
Full Text Available Abstract Background It is essential to elucidate the relationship between metabolic and genomic diversity to understand the genetic regulatory networks associated with the changing metabolo-phenotype among natural variation and/or populations. Recent innovations in metabolomics technologies allow us to grasp the comprehensive features of the metabolome. Metabolite quantitative trait analysis is a key approach for the identification of genetic loci involved in metabolite variation using segregated populations. Although several attempts have been made to find correlative relationships between genetic and metabolic diversity among natural populations in various organisms, it is still unclear whether it is possible to discover such correlations between each metabolite and the polymorphisms found at each chromosomal location. To assess the correlative relationship between the metabolic and genomic diversity found in rice accessions, we compared the distance matrices for these two "omics" patterns in the rice accessions. Results We selected 18 accessions from the world rice collection based on their population structure. To determine the genomic diversity of the rice genome, we genotyped 128 restriction fragment length polymorphism (RFLP markers to calculate the genetic distance among the accessions. To identify the variations in the metabolic fingerprint, a soluble extract from the seed grain of each accession was analyzed with one dimensional 1H-nuclear magnetic resonance (NMR. We found no correlation between global metabolic diversity and the phylogenetic relationships among the rice accessions (rs = 0.14 by analyzing the distance matrices (calculated from the pattern of the metabolic fingerprint in the 4.29- to 0.71-ppm 1H chemical shift and the genetic distance on the basis of the RFLP markers. However, local correlation analysis between the distance matrices (derived from each 0.04-ppm integral region of the 1H chemical shift against genetic
Fractal Structure of Random Matrices
Hussein, M S
2000-01-01
A multifractal analysis is performed on the universality classes of random matrices and the transition ones.Our results indicate that the eigenvector probability distribution is a linear sum of two chi-squared distribution throughout the transition between the universality ensembles of random matrix theory and Poisson .
Open string fields as matrices
Kishimoto, Isao; Masuda, Toru; Takahashi, Tomohiko; Takemoto, Shoko
2015-03-01
We show that the action expanded around Erler-Maccaferri's N D-brane solution describes the N+1 D-brane system where one D-brane disappears due to tachyon condensation. String fields on multi-branes can be regarded as block matrices of a string field on a single D-brane in the same way as matrix theories.
Open String Fields as Matrices
Kishimoto, Isao; Takahashi, Tomohiko; Takemoto, Shoko
2014-01-01
We show that the action expanded around Erler-Maccaferri's N D-branes solution describes the N+1 D-branes system where one D-brane disappears due to tachyon condensation. String fields on the multi-branes can be regarded as block matrices of a string field on a single D-brane in the same way as matrix theories.
Arnold's Projective Plane and -Matrices
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K. Uchino
2010-01-01
Full Text Available We will explain Arnold's 2-dimensional (shortly, 2D projective geometry (Arnold, 2005 by means of lattice theory. It will be shown that the projection of the set of nontrivial triangular -matrices is the pencil of tangent lines of a quadratic curve on Arnold's projective plane.
Fibonacci Identities, Matrices, and Graphs
Huang, Danrun
2005-01-01
General strategies used to help discover, prove, and generalize identities for Fibonacci numbers are described along with some properties about the determinants of square matrices. A matrix proof for identity (2) that has received immense attention from many branches of mathematics, like linear algebra, dynamical systems, graph theory and others…
Scattering matrices with block symmetries
Życzkowski, Karol
1997-01-01
Scattering matrices with block symmetry, which corresponds to scattering process on cavities with geometrical symmetry, are analyzed. The distribution of transmission coefficient is computed for different number of channels in the case of a system with or without the time reversal invariance. An interpolating formula for the case of gradual time reversal symmetry breaking is proposed.
Making almost commuting matrices commute
Energy Technology Data Exchange (ETDEWEB)
Hastings, Matthew B [Los Alamos National Laboratory
2008-01-01
Suppose two Hermitian matrices A, B almost commute ({parallel}[A,B]{parallel} {<=} {delta}). Are they close to a commuting pair of Hermitian matrices, A', B', with {parallel}A-A'{parallel},{parallel}B-B'{parallel} {<=} {epsilon}? A theorem of H. Lin shows that this is uniformly true, in that for every {epsilon} > 0 there exists a {delta} > 0, independent of the size N of the matrices, for which almost commuting implies being close to a commuting pair. However, this theorem does not specifiy how {delta} depends on {epsilon}. We give uniform bounds relating {delta} and {epsilon}. The proof is constructive, giving an explicit algorithm to construct A' and B'. We provide tighter bounds in the case of block tridiagonal and tridiagnonal matrices. Within the context of quantum measurement, this implies an algorithm to construct a basis in which we can make a projective measurement that approximately measures two approximately commuting operators simultaneously. Finally, we comment briefly on the case of approximately measuring three or more approximately commuting operators using POVMs (positive operator-valued measures) instead of projective measurements.
The diagonalization of cubic matrices
Cocolicchio, D.; Viggiano, M.
2000-08-01
This paper is devoted to analysing the problem of the diagonalization of cubic matrices. We extend the familiar algebraic approach which is based on the Cardano formulae. We rewrite the complex roots of the associated resolvent secular equation in terms of transcendental functions and we derive the diagonalizing matrix.
Spectral problems for operator matrices
Bátkai, A.; Binding, P.; Dijksma, A.; Hryniv, R.; Langer, H.
2005-01-01
We study spectral properties of 2 × 2 block operator matrices whose entries are unbounded operators between Banach spaces and with domains consisting of vectors satisfying certain relations between their components. We investigate closability in the product space, essential spectra and generation of
Bai, Lina; Xie, Ting; Hu, Qingqing; Deng, Changyan; Zheng, Rong; Chen, Wanping
2015-10-01
Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.
Bai, Lina; Xie, Ting; Hu, Qingqing; Deng, Changyan; Zheng, Rong; Chen, Wanping
2015-10-01
Ferritins are highly conserved proteins that are widely distributed in various species from archaea to humans. The ubiquitous characteristic of these proteins reflects the pivotal contribution of ferritins to the safe storage and timely delivery of iron to achieve iron homeostasis. This study investigated the ferritin genes in 248 genomes from various species, including viruses, archaea, bacteria, and eukarya. The distribution comparison suggests that mammals and eudicots possess abundant ferritin genes, whereas fungi contain very few ferritin genes. Archaea and bacteria show considerable numbers of ferritin genes. Generally, prokaryotes possess three types of ferritin (the typical ferritin, bacterioferritin, and DNA-binding protein from starved cell), whereas eukaryotes have various subunit types of ferritin, thereby indicating the individuation of the ferritin family during evolution. The characteristic motif analysis of ferritins suggested that all key residues specifying the unique structural motifs of ferritin are highly conserved across three domains of life. Meanwhile, the characteristic motifs were also distinguishable between ferritin groups, especially phytoferritins, which show a plant-specific motif. The phylogenetic analyses show that ferritins within the same subfamily or subunits are generally clustered together. The phylogenetic relationships among ferritin members suggest that both gene duplication and horizontal transfer contribute to the wide variety of ferritins, and their possible evolutionary scenario was also proposed. The results contribute to a better understanding of the distribution, characteristic motif, and evolutionary relationship of the ferritin family.
The MATRICS Consensus Cognitive Battery (MCCB): performance and functional correlates.
Lystad, June Ullevoldsæter; Falkum, Erik; Mohn, Christine; Haaland, Vegard Øksendal; Bull, Helen; Evensen, Stig; Rund, Bjørn Rishovd; Ueland, Torill
2014-12-30
Neurocognitive impairment is a core feature in psychotic disorders and the MATRICS Consensus Cognitive Battery (MCCB) is now widely used to assess neurocognition in this group. The MATRICS has been translated into several languages, including Norwegian; although this version has yet to be investigated in an adult clinical population. Further, the relationship between the MATRICS and different measures of functioning needs examination. The purpose of this study was to describe neurocognition assessed with the Norwegian version of the MATRICS battery in a sample of patients with psychotic disorders compared to age and gender matched healthy controls and to examine the association with educational-, occupational- and social-functioning in the patient group. One hundred and thirty one patients and 137 healthy controls completed the battery. The Norwegian version of the MATRICS was sensitive to the magnitude of neurocognitive impairments in patients with psychotic disorders, with patients displaying significant impairments on all domains relative to healthy controls. Neurocognition was also related to both self-rated and objective functional measures such as social functioning, educational- and employment-history.
DEFF Research Database (Denmark)
Fussing, V.
1998-01-01
The aim of the present study was to examine the genomic relationship among 112 Actinobacillus pleuropneumoniae serotype 2 strains obtained throughout Europe and North America. HindIII ribotyping of the strains resulted in five ribotypes of high similarity (87-98%). Sequence analysis of the riboso...
Institute of Scientific and Technical Information of China (English)
张晓东; 杨尚骏
2001-01-01
本文探讨矩阵的一个重要子类（F-矩阵）的性质.F-矩阵包含以下在理论及应用中都很重要的三个矩阵类：对称正半定矩阵，M-矩阵和完全非负矩阵.我们首先证明F-矩阵的一些有趣性，特别是给出n-阶F-矩阵A满足detA=an…ann的充分必要条件.接着研究逆F-矩阵的性质，特别是证明逆M-矩阵和逆完全非负矩阵都是F-矩阵，从而满足Fischer不等式.最后我们引入F-矩阵一个子类:W-矩阵并证明逆W-矩阵也是F-矩阵.%We investigate a class of P0-matrices, called F-matrices, whichcontains well known three important classes of matrices satisfying Hadamard's inequality and Fischer's inequality-positive semidefinite symmetric matrices, M-matrices and totally nonnegative matrices. Firstly we prove some interesting properties of F-matrices and give the necessary and sufficient condition for an n×n F-matrix to satisfy det A=a11…ann. Then we investigate inverse F-matrices and prove both inverse M-matrices and inverse totally nonnegative matrices are F-matrices. Finally we introduce a new class of F-matrices, i.e. W-matrices and prove both W-matrices and inverse W-matrices are also F-matrices.
STABILITY FOR SEVERAL TYPES OF INTERVAL MATRICES
Institute of Scientific and Technical Information of China (English)
NianXiaohong; GaoJintai
1999-01-01
The robust stability for some types of tlme-varying interval raatrices and nonlineartime-varying interval matrices is considered and some sufficient conditions for robust stability of such interval matrices are given, The main results of this paper are only related to the verticesset of a interval matrices, and therefore, can be easily applied to test robust stability of interval matrices. Finally, some examples are given to illustrate the results.
Eigenvalue variance bounds for covariance matrices
Dallaporta, Sandrine
2013-01-01
This work is concerned with finite range bounds on the variance of individual eigenvalues of random covariance matrices, both in the bulk and at the edge of the spectrum. In a preceding paper, the author established analogous results for Wigner matrices and stated the results for covariance matrices. They are proved in the present paper. Relying on the LUE example, which needs to be investigated first, the main bounds are extended to complex covariance matrices by means of the Tao, Vu and Wan...
The Bessel Numbers and Bessel Matrices
Institute of Scientific and Technical Information of China (English)
Sheng Liang YANG; Zhan Ke QIAO
2011-01-01
In this paper,using exponential Riordan arrays,we investigate the Bessel numbers and Bessel matrices.By exploring links between the Bessel matrices,the Stirling matrices and the degenerate Stirling matrices,we show that the Bessel numbers are special case of the degenerate Stirling numbers,and derive explicit formulas for the Bessel numbers in terms of the Stirling numbers and binomial coefficients.
Li, Peirong; Zhang, Shujiang; Li, Fei; Zhang, Shifan; Zhang, Hui; Wang, Xiaowu; Sun, Rifei; Bonnema, Guusje; Borm, Theo J. A.
2017-01-01
The Brassica genus comprises many economically important worldwide cultivated crops. The well-established model of the Brassica genus, U’s triangle, consists of three basic diploid plant species (Brassica rapa, Brassica oleracea, and Brassica nigra) and three amphidiploid species (Brassica napus, Brassica juncea, and Brassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of the Brassica species and the relationships within and among these six species still remain open questions. Here, we successfully de novo assembled 60 complete chloroplast genomes of Brassica genotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of different Brassica species was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated the Brassica genus into four clades. B. carinata and B. juncea share their chloroplast genome with one of their hybridization donors B. nigra and B. rapa, respectively, which fits the U model. B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions. B. napus clearly has evidence for two independent hybridization events, as it contains either B. rapa chloroplast genomes. The divergence estimation suggests that B. nigra and B. carinata diverged from the main Brassica clade 13.7 million years ago (Mya), while B. rapa and B. oleracea diverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic
Acharya, Laxmikanta; Mukherjee, Arup Kumar; Panda, Pratap Chandra
2004-01-01
Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.
DEFF Research Database (Denmark)
Kadri, Naveen; Guldbrandtsen, Bernt; Sørensen, Peter;
2014-01-01
) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic......Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K...... corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree...
Institute of Scientific and Technical Information of China (English)
马君; 王雎; 杨灿
2012-01-01
This study utilizes referent cognitions theory to probe into the impact of perceived fairness of performance appraisal on job performance under difference matrices. Considerting the differences in personal perception and difference matrices, using multiple data from 39 work groups comprising 274 employees and applying the hierarchical linear model, we examine the cross-level interactions between individuals' perceived fairness of performance appraisal and difference matrices on job performance and test the effort of strengthening fairness of performance appraisal in order to reduce favoritism. The result shows that pereeption of performance appraisal fairness is positively related to task performance only under the atmosphere of low different matrices, which is different from the classic western theories. Thus, reducing the impact of different matrices and lessening director's dominant rights are two ways to improve the predictive power of perceived fairness on task performance. The interactive effect on job performance between formalization and procedural fairness perception, as well as distributive fairness perception, is negative, which shows a fairness paradox in practices which means that if we don't use rigidity appraisal system, it is difficult to eliminate the black box operation; otherwise it would be easy to fall into the trap of on the folly for rewarding A, while hoping for B. However, the interactive effects on job performance between formalization and interaction fairness perception is positive, which indicates that integrating emotional and contextual awareness with rational analysis, and enhancing the tension of rules will improve the effectiveness of performance appraisal.%运用参照认知理论,探讨差序格局下员工绩效评价公平感知对工作绩效的特殊作用机理.以本土企业39个工作组274名员工为研究对象,结合个体感知差异和组织差序氛围两个层面的影响因素,运用线性阶层模型检验二者
Quantum Hilbert matrices and orthogonal polynomials
DEFF Research Database (Denmark)
Andersen, Jørgen Ellegaard; Berg, Christian
2009-01-01
Using the notion of quantum integers associated with a complex number q≠0 , we define the quantum Hilbert matrix and various extensions. They are Hankel matrices corresponding to certain little q -Jacobi polynomials when |q|matrices...... of reciprocal Fibonacci numbers called Filbert matrices. We find a formula for the entries of the inverse quantum Hilbert matrix....
Simultaneous diagonalization of two quaternion matrices
Institute of Scientific and Technical Information of China (English)
ZhouJianhua
2003-01-01
The simultaneous diagonalization by congruence of pairs of Hermitian quatemion matrices is discussed. The problem is reduced to a parallel one on complex matrices by using the complex adjoint matrix related to each quatemion matrix. It is proved that any two semi-positive definite Hermitian quatemion matrices can be simultaneously diagonalized by congruence.
Wolc, Anna; Stricker, Chris; Arango, Jesus; Settar, Petek; Fulton, Janet E; O'Sullivan, Neil P; Preisinger, Rudolf; Habier, David; Fernando, Rohan; Garrick, Dorian J; Lamont, Susan J; Dekkers, Jack C M
2011-01-21
Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line. The following traits were analyzed: egg production, egg weight, egg color, shell strength, age at sexual maturity, body weight, albumen height, and yolk weight. Predictions appropriate for early or late selection were compared. A total of 2,708 birds were genotyped for 23,356 segregating SNP, including 1,563 females with records. Phenotypes on relatives without genotypes were incorporated in the analysis (in total 13,049 production records).The data were analyzed with a Reduced Animal Model using a relationship matrix based on pedigree data or on marker genotypes and with a Bayesian method using model averaging. Using a validation set that consisted of individuals from the generation following training, these methods were compared by correlating EBV with phenotypes corrected for fixed effects, selecting the top 30 individuals based on EBV and evaluating their mean phenotype, and by regressing phenotypes on EBV. Using high-density SNP genotypes increased accuracies of EBV up to two-fold for selection at an early age and by up to 88% for selection at a later age. Accuracy increases at an early age can be mostly attributed to improved estimates of parental EBV for shell quality and egg production, while for other egg quality traits it is mostly due to improved estimates of Mendelian sampling effects. A relatively small number of markers was sufficient to explain most of the genetic variation for egg weight and body weight.
Allele coding in genomic evaluation
Directory of Open Access Journals (Sweden)
Christensen Ole F
2011-06-01
Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being
Bombardelli, Diego
2016-08-01
In these notes we review the S-matrix theory in (1+1)-dimensional integrable models, focusing mainly on the relativistic case. Once the main definitions and physical properties are introduced, we discuss the factorization of scattering processes due to integrability. We then focus on the analytic properties of the two-particle scattering amplitude and illustrate the derivation of the S-matrices for all the possible bound states using the so-called bootstrap principle. General algebraic structures underlying the S-matrix theory and its relation with the form factors axioms are briefly mentioned. Finally, we discuss the S-matrices of sine-Gordon and SU(2), SU(3) chiral Gross-Neveu models. In loving memory of Lilia Grandi.
Directory of Open Access Journals (Sweden)
Martinetz Thomas
2011-06-01
Full Text Available Abstract Background Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome. Results Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed. Conclusions The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at http://www.biochem.uni-luebeck.de/public/software/phylomap.html
Fu, Songzhe; Octavia, Sophie; Wang, Qinning; Tanaka, Mark M.; Tay, Chin Yen; Sintchenko, Vitali; Lan, Ruiting
2016-01-01
Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing human infections in Australia and many other countries. A total of 12,112 S. Typhimurium isolates from New South Wales were analyzed by multi-locus variable number of tandem repeat (VNTR) analysis (MLVA) using five VNTRs from 2007 to 2014. We found that mid ranges of repeat units of 8–14 in VNTR locus STTR5, 6–13 in STTR6, and 9–12 in STTR10 were always predominant in the population (>50%). In vitro passaging experiments using MLVA type carrying extreme length alleles found that the majority of long length alleles mutated to short ones and short length alleles mutated to longer ones. Both data suggest directional mutability of VNTRs toward mid-range repeats. Sequencing of 28 isolates from a newly emerged MLVA type and its five single locus variants revealed that single nucleotide variation between isolates with up to two MLVA differences ranged from 0 to 12 single nucleotide polymorphisms (SNPs). However, there was no relationship between SNP and VNTR differences. A population genetic model of the joint distribution of VNTRs and SNPs variations was used to estimate the mutation rates of the two markers, yielding a ratio of 1 VNTR change to 6.9 SNP changes. When only one VNTR repeat difference was considered, the majority of pairwise SNP difference between isolates were 4 SNPs or fewer. Based on this observation and our previous findings of SNP differences of outbreak isolates, we suggest that investigation of S. Typhimurium community outbreaks should include cases of 1 repeat difference to increase sensitivity. This study offers new insights into the short-term VNTR evolution of S. Typhimurium and its application for epidemiological typing. PMID:28082952
Rotationally invariant ensembles of integrable matrices.
Yuzbashyan, Emil A; Shastry, B Sriram; Scaramazza, Jasen A
2016-05-01
We construct ensembles of random integrable matrices with any prescribed number of nontrivial integrals and formulate integrable matrix theory (IMT)-a counterpart of random matrix theory (RMT) for quantum integrable models. A type-M family of integrable matrices consists of exactly N-M independent commuting N×N matrices linear in a real parameter. We first develop a rotationally invariant parametrization of such matrices, previously only constructed in a preferred basis. For example, an arbitrary choice of a vector and two commuting Hermitian matrices defines a type-1 family and vice versa. Higher types similarly involve a random vector and two matrices. The basis-independent formulation allows us to derive the joint probability density for integrable matrices, similar to the construction of Gaussian ensembles in the RMT.
Rotationally invariant ensembles of integrable matrices
Yuzbashyan, Emil A.; Shastry, B. Sriram; Scaramazza, Jasen A.
2016-05-01
We construct ensembles of random integrable matrices with any prescribed number of nontrivial integrals and formulate integrable matrix theory (IMT)—a counterpart of random matrix theory (RMT) for quantum integrable models. A type-M family of integrable matrices consists of exactly N -M independent commuting N ×N matrices linear in a real parameter. We first develop a rotationally invariant parametrization of such matrices, previously only constructed in a preferred basis. For example, an arbitrary choice of a vector and two commuting Hermitian matrices defines a type-1 family and vice versa. Higher types similarly involve a random vector and two matrices. The basis-independent formulation allows us to derive the joint probability density for integrable matrices, similar to the construction of Gaussian ensembles in the RMT.
Directory of Open Access Journals (Sweden)
Mohan Babu
2014-02-01
Full Text Available Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI screens can provide insights into the biological role(s of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.
Projection Matrices, Generalized Inverse Matrices, and Singular Value Decomposition
Yanai, Haruo; Takane, Yoshio
2011-01-01
Aside from distribution theory, projections and the singular value decomposition (SVD) are the two most important concepts for understanding the basic mechanism of multivariate analysis. The former underlies the least squares estimation in regression analysis, which is essentially a projection of one subspace onto another, and the latter underlies principal component analysis, which seeks to find a subspace that captures the largest variability in the original space. This book is about projections and SVD. A thorough discussion of generalized inverse (g-inverse) matrices is also given because
Vlaminckx, Bart J M; Schuren, Frank H J; Montijn, Roy C; Caspers, Martien P M; Fluit, Ad C; Wannet, Wim J B; Schouls, Leo M; Verhoef, Jan; Jansen, Wouter T M
2007-05-01
Group A streptococci (GAS), or Streptococcus pyogenes, are associated with a remarkable variety of diseases, ranging from superficial infections to life-threatening diseases such as toxic-shock-like syndrome (TSS). GAS strains belonging to M types M1 and M3 are associated with TSS. This study aims to obtain insight into the gene profiles underlying different M types and disease manifestations. Genomic differences between 76 clinically well characterized GAS strains collected in The Netherlands were examined using a mixed-genome microarray. Inter-M-type genomic differences clearly outweighed intra-M-type genome variation. Phages were major contributors to observed genome diversification. We identified four novel genes, including two genes encoding fibronectin-binding-like proteins, which are highly specific to a subset of M types and thus may contribute to M-type-associated disease manifestations. All M12 strains were characterized by the unique absence of the citrate lyase complex and reduced growth under hypoxic, nutrient-deprived conditions. Furthermore, six virulence factors, including genes encoding a complement-inhibiting protein (sic), an exotoxin (speA), iron(III) binding factor, collagen binding factor (cpa), and fibrinogen binding factor (prt2-like), were unique to M1 and/or M3 strains. These virulence factors may contribute to the potential of these strains to cause TSS. Finally, in contrast to M-type-specific virulence profiles, we did not identify a common virulence profile among strains associated with TSS irrespective of their M type.
Dow, M M; Cheverud, J M
1985-11-01
Questions concerning the relative effects of various evolutionary forces in molding the genetic variability exhibited by groups of human populations have typically been investigated by comparing a variety of genetic and cultural/historical "distance" matrices. A major methodological difficulty has been the lack of formal testing procedures with which to assess the degree of confirmation or disconfirmation of an estimated measure of relationship between such matrices. In this paper, we examine a very flexible matrix combinatorial procedure which generates statistical significance levels for correlational measures of pattern similarity between distance matrices. A recent generalization of the basic procedure to the three-matrix case allows questions concerning which of two matrices best fits a third matrix to be formally tested. Applications of these hypothesis testing and inference procedures to two separate sets of genetic, geographic, and cultural distance matrices illustrates their potential for finally solving a long-standing problem in anthropological genetics.
Random matrices and Riemann hypothesis
Pierre, Christian
2011-01-01
The curious connection between the spacings of the eigenvalues of random matrices and the corresponding spacings of the non trivial zeros of the Riemann zeta function is analyzed on the basis of the geometric dynamical global program of Langlands whose fundamental structures are shifted quantized conjugacy class representatives of bilinear algebraic semigroups.The considered symmetry behind this phenomenology is the differential bilinear Galois semigroup shifting the product,right by left,of automorphism semigroups of cofunctions and functions on compact transcendental quanta.
Sparse Matrices in Frame Theory
DEFF Research Database (Denmark)
Lemvig, Jakob; Krahmer, Felix; Kutyniok, Gitta
2014-01-01
Frame theory is closely intertwined with signal processing through a canon of methodologies for the analysis of signals using (redundant) linear measurements. The canonical dual frame associated with a frame provides a means for reconstruction by a least squares approach, but other dual frames...... yield alternative reconstruction procedures. The novel paradigm of sparsity has recently entered the area of frame theory in various ways. Of those different sparsity perspectives, we will focus on the situations where frames and (not necessarily canonical) dual frames can be written as sparse matrices...
Cosmetic crossings and Seifert matrices
Balm, Cheryl; Kalfagianni, Efstratia; Powell, Mark
2011-01-01
We study cosmetic crossings in knots of genus one and obtain obstructions to such crossings in terms of knot invariants determined by Seifert matrices. In particular, we prove that for genus one knots the Alexander polynomial and the homology of the double cover branching over the knot provide obstructions to cosmetic crossings. As an application we prove the nugatory crossing conjecture for twisted Whitehead doubles of non-cable knots. We also verify the conjecture for several families of pretzel knots and all genus one knots with up to 12 crossings.
Superalgebraic representation of Dirac matrices
Monakhov, V. V.
2016-01-01
We consider a Clifford extension of the Grassmann algebra in which operators are constructed from products of Grassmann variables and derivatives with respect to them. We show that this algebra contains a subalgebra isomorphic to a matrix algebra and that it additionally contains operators of a generalized matrix algebra that mix states with different numbers of Grassmann variables. We show that these operators are extensions of spin-tensors to the case of superspace. We construct a representation of Dirac matrices in the form of operators of a generalized matrix algebra.
Orthogonal polynomials and random matrices
Deift, Percy
2000-01-01
This volume expands on a set of lectures held at the Courant Institute on Riemann-Hilbert problems, orthogonal polynomials, and random matrix theory. The goal of the course was to prove universality for a variety of statistical quantities arising in the theory of random matrix models. The central question was the following: Why do very general ensembles of random n {\\times} n matrices exhibit universal behavior as n {\\rightarrow} {\\infty}? The main ingredient in the proof is the steepest descent method for oscillatory Riemann-Hilbert problems.
Robust Generalized Low Rank Approximations of Matrices.
Directory of Open Access Journals (Sweden)
Jiarong Shi
Full Text Available In recent years, the intrinsic low rank structure of some datasets has been extensively exploited to reduce dimensionality, remove noise and complete the missing entries. As a well-known technique for dimensionality reduction and data compression, Generalized Low Rank Approximations of Matrices (GLRAM claims its superiority on computation time and compression ratio over the SVD. However, GLRAM is very sensitive to sparse large noise or outliers and its robust version does not have been explored or solved yet. To address this problem, this paper proposes a robust method for GLRAM, named Robust GLRAM (RGLRAM. We first formulate RGLRAM as an l1-norm optimization problem which minimizes the l1-norm of the approximation errors. Secondly, we apply the technique of Augmented Lagrange Multipliers (ALM to solve this l1-norm minimization problem and derive a corresponding iterative scheme. Then the weak convergence of the proposed algorithm is discussed under mild conditions. Next, we investigate a special case of RGLRAM and extend RGLRAM to a general tensor case. Finally, the extensive experiments on synthetic data show that it is possible for RGLRAM to exactly recover both the low rank and the sparse components while it may be difficult for previous state-of-the-art algorithms. We also discuss three issues on RGLRAM: the sensitivity to initialization, the generalization ability and the relationship between the running time and the size/number of matrices. Moreover, the experimental results on images of faces with large corruptions illustrate that RGLRAM obtains the best denoising and compression performance than other methods.
Robust Generalized Low Rank Approximations of Matrices.
Shi, Jiarong; Yang, Wei; Zheng, Xiuyun
2015-01-01
In recent years, the intrinsic low rank structure of some datasets has been extensively exploited to reduce dimensionality, remove noise and complete the missing entries. As a well-known technique for dimensionality reduction and data compression, Generalized Low Rank Approximations of Matrices (GLRAM) claims its superiority on computation time and compression ratio over the SVD. However, GLRAM is very sensitive to sparse large noise or outliers and its robust version does not have been explored or solved yet. To address this problem, this paper proposes a robust method for GLRAM, named Robust GLRAM (RGLRAM). We first formulate RGLRAM as an l1-norm optimization problem which minimizes the l1-norm of the approximation errors. Secondly, we apply the technique of Augmented Lagrange Multipliers (ALM) to solve this l1-norm minimization problem and derive a corresponding iterative scheme. Then the weak convergence of the proposed algorithm is discussed under mild conditions. Next, we investigate a special case of RGLRAM and extend RGLRAM to a general tensor case. Finally, the extensive experiments on synthetic data show that it is possible for RGLRAM to exactly recover both the low rank and the sparse components while it may be difficult for previous state-of-the-art algorithms. We also discuss three issues on RGLRAM: the sensitivity to initialization, the generalization ability and the relationship between the running time and the size/number of matrices. Moreover, the experimental results on images of faces with large corruptions illustrate that RGLRAM obtains the best denoising and compression performance than other methods.
Searching for partial Hadamard matrices
Álvarez, Víctor; Frau, María-Dolores; Gudiel, Félix; Güemes, María-Belén; Martín, Elena; Osuna, Amparo
2012-01-01
Three algorithms looking for pretty large partial Hadamard matrices are described. Here "large" means that hopefully about a third of a Hadamard matrix (which is the best asymptotic result known so far, [dLa00]) is achieved. The first one performs some kind of local exhaustive search, and consequently is expensive from the time consuming point of view. The second one comes from the adaptation of the best genetic algorithm known so far searching for cliques in a graph, due to Singh and Gupta [SG06]. The last one consists in another heuristic search, which prioritizes the required processing time better than the final size of the partial Hadamard matrix to be obtained. In all cases, the key idea is characterizing the adjacency properties of vertices in a particular subgraph G_t of Ito's Hadamard Graph Delta (4t) [Ito85], since cliques of order m in G_t can be seen as (m+3)*4t partial Hadamard matrices.
Directory of Open Access Journals (Sweden)
Vining Kelly J
2012-01-01
Full Text Available Abstract Background DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem in the reference tree species black cottonwood (Populus trichocarpa. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq, we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation" had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation. Conclusions We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.
Directory of Open Access Journals (Sweden)
Kim Min-Ju
2012-11-01
Full Text Available Abstract Background Elevated blood pressure (BP is a major risk factor for the progression of chronic kidney disease (CKD. However, little is known about the influence of prehypertension on CKD. In this study, we investigated the relationship between prehypertension and CKD in a middle-aged Korean population. Furthermore, we prospectively evaluated the effect of active BP control on deterioration of kidney function during the two-year follow-up. Methods The Korean Genome and Epidemiology Study is a community-based prospective cohort study started in 2001, with a follow-up survey conducted every two years. A total of 9509 participants aged 40–69 years were included in a baseline study. BP was classified according to the Seventh Report of the Joint National Committee on High BP (JNC-7 categories and CKD was defined as the presence of proteinuria or eGFR2. A multivariable logistic regression model was used to identify associations between BP and CKD. Results The overall prevalence of CKD was 13.2%, and significantly increased with BP level. The multivariable-adjusted odds ratio of CKD was 1.59 for prehypertension and 2.27 for hypertension, compared with a normal BP. At the two-year follow-up, among the participants with prehypertension, subjects whose BP was poorly controlled had a significantly higher risk of eGFR drop (OR, 1.37; 95% CI, 1.13-1.67, as compared to controls. The prevalence of eGFR drop was 57.8% in the controlled BP group and 66.0% in the poorly-controlled BP group. Conclusions Prehypertension, as well as hypertension, is significantly associated with CKD among middle-aged Koreans. Our results indicate that active control of the blood-pressure of prehypertensive individuals is needed to prevent deterioration of kidney function.
A concise guide to complex Hadamard matrices
Tadej, W; Tadej, Wojciech; Zyczkowski, Karol
2005-01-01
Complex Hadamard matrices, consisting of unimodular entries with arbitrary phases, play an important role in the theory of quantum information. We review basic properties of complex Hadamard matrices and present a catalogue of inequivalent cases known for dimension N=2,...,16. In particular, we explicitly write down some families of complex Hadamard matrices for N=12,14 and 16, which we could not find in the existing literature.
Tung tree (Vernicia fordii) is an economically important plant widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized the complete chloroplast genome. The chloroplast genome was 161,524 bp in length...
Veerkamp, R F; Mulder, H A; Thompson, R; Calus, M P L
2011-08-01
Genetic parameters were estimated using relationships between animals that were based either on pedigree, 43,011 single nucleotide polymorphisms, or a combination of these, considering genotyped and non-genotyped animals. The standard error of the estimates and a parametric bootstrapping procedure was used to investigate sampling properties of the estimated variance components. The data set contained milk yield, dry matter intake and body weight for 517 first-lactation heifers with genotypes and phenotypes, and another 112 heifers with phenotypes only. Multivariate models were fitted using the different relationships in ASReml software. Estimates of genetic variance were lower based on genomic relationships than using pedigree relationships. Genetic variances from genomic and pedigree relationships were, however, not directly comparable because they apply to different base populations. Standard errors indicated that using the genomic relationships gave more accurate estimates of heritability but equally accurate estimates of genetic correlation. However, the estimates of standard errors were affected by the differences in scale between the 2 relationship matrices, causing differences in values of the genetic parameters. The bootstrapping results (with genetic parameters at the same level), confirmed that both heritability and genetic correlations were estimated more accurately with genomic relationships in comparison with using the pedigree relationships. Animals without genotype were included in the analysis by merging genomic and pedigree relationships. This allowed all phenotypes to be used, including those from non-genotyped animals. This combination of genomic and pedigree relationships gave the most accurate estimates of genetic variance. When a small data set is available it might be more advantageous for the estimation of genetic parameters to genotype existing animals, rather than collecting more phenotypes. Copyright © 2011 American Dairy Science
Design of Damping and Control Matrices by Modification of Eigenvalues and Eigenvectors
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Vernon H. Neubert
1994-01-01
. Advantage is taken of the special state-space form of the structural plant and eigenvector matrices to develop efficient numerical procedures. Essential relationships are derived between the upper and lower portions of the left and right eigenvector matrices for systems with simple eigenvalues. We distinguish between displacement mode shapes and eigenvectors in state space. A unique method is presented by which the [C+G] matrices are designed to achieve specified real parts of the eigenvalues, with no change in mode shapes or eigenvectors. In addition, two general methods are discussed. suitable for systems with nonproportional damping, where the eigenvalues are specified with or without change in mode shapes.
Lambda-matrices and vibrating systems
Lancaster, Peter; Stark, M; Kahane, J P
1966-01-01
Lambda-Matrices and Vibrating Systems presents aspects and solutions to problems concerned with linear vibrating systems with a finite degrees of freedom and the theory of matrices. The book discusses some parts of the theory of matrices that will account for the solutions of the problems. The text starts with an outline of matrix theory, and some theorems are proved. The Jordan canonical form is also applied to understand the structure of square matrices. Classical theorems are discussed further by applying the Jordan canonical form, the Rayleigh quotient, and simple matrix pencils with late
Matrices with totally positive powers and their generalizations
Kushel, Olga Y.
2013-01-01
In this paper, eventually totally positive matrices (i.e. matrices all whose powers starting with some point are totally positive) are studied. We present a new approach to eventual total positivity which is based on the theory of eventually positive matrices. We mainly focus on the spectral properties of such matrices. We also study eventually J-sign-symmetric matrices and matrices, whose powers are P-matrices.
A NOTE ON THE STOCHASTIC ROOTS OF STOCHASTIC MATRICES
Institute of Scientific and Technical Information of China (English)
Qi-Ming HE; Eldon GUNN
2003-01-01
In this paper, we study the stochastic root matrices of stochastic matrices. All stochastic roots of 2×2 stochastic matrices are found explicitly. A method based on characteristic polynomial of matrix is developed to find all real root matrices that are functions of the original 3×3 matrix, including all possible (function) stochastic root matrices. In addition, we comment on some numerical methods for computing stochastic root matrices of stochastic matrices.
Institute of Scientific and Technical Information of China (English)
YANG Lizhen; CHEN Kefei
2004-01-01
In this paper, we analyze the structure of the orders of matrices (mod n), and present the relation between the orders of matrices over finite fields and their Jordan normal forms. Then we generalize 2-dimensional Arnold transformation matrix to two types of n-dimensional Arnold transformation matrices: A-type Arnold transformation matrix and B-type transformation matrix, and analyze their orders and other properties based on our earlier results about the orders of matrices.
The lower bounds for the rank of matrices and some sufficient conditions for nonsingular matrices.
Wang, Dafei; Zhang, Xumei
2017-01-01
The paper mainly discusses the lower bounds for the rank of matrices and sufficient conditions for nonsingular matrices. We first present a new estimation for [Formula: see text] ([Formula: see text] is an eigenvalue of a matrix) by using the partitioned matrices. By using this estimation and inequality theory, the new and more accurate estimations for the lower bounds for the rank are deduced. Furthermore, based on the estimation for the rank, some sufficient conditions for nonsingular matrices are obtained.
Angular distortive matrices of phase transitions in the fcc-bcc-hcp system
Cayron, Cyril
2016-01-01
This work generalizes the one-step model previously developed on fcc-bcc martensitic transformations to the larger family of phase transitions in the fcc-bcc-hcp system. The angular distortive matrices are calculated for the bcc-fcc, bcc-hcp and fcc-hcp transitions, and for fcc-fcc mechanical twinning. The analytical expressions of the continuous atomic displacements, lattice distortion and lattice correspondence matrices result directly from the orientation relationships; the unique assumpti...
The importance of identity-by-state information for the accuracy of genomic selection
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Luan Tu
2012-08-01
Full Text Available Abstract Background It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information. Methods The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci. The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data. Results We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree. Conclusions Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require
A note on "Block H-matrices and spectrum of block matrices"
Institute of Scientific and Technical Information of China (English)
LIU Jian-zhou; HUANG Ze-jun
2008-01-01
In this paper, we make further discussions and improvements on the results presented in the previously published work "Block H-matrices and spectrum of block matrices". Furthermore, a new bound for eigenvalues of block matrices is given with examples to show advantages of the new result.
A partial classification of primes in the positive matrices and in the doubly stochastic matrices
G. Picci; J.M. van den Hof; J.H. van Schuppen (Jan)
1995-01-01
textabstractThe algebraic structure of the set of square positive matrices is that of a semi-ring. The concept of a prime in the positive matrices has been introduced. A few examples of primes in the positive matrices are known but there is no general classification. In this paper a partial
Dynamical invariance for random matrices
Unterberger, Jeremie
2016-01-01
We consider a general Langevin dynamics for the one-dimensional N-particle Coulomb gas with confining potential $V$ at temperature $\\beta$. These dynamics describe for $\\beta=2$ the time evolution of the eigenvalues of $N\\times N$ random Hermitian matrices. The equilibrium partition function -- equal to the normalization constant of the Laughlin wave function in fractional quantum Hall effect -- is known to satisfy an infinite number of constraints called Virasoro or loop constraints. We introduce here a dynamical generating function on the space of random trajectories which satisfies a large class of constraints of geometric origin. We focus in this article on a subclass induced by the invariance under the Schr\\"odinger-Virasoro algebra.
Tensor Products of Random Unitary Matrices
Tkocz, Tomasz; Kus, Marek; Zeitouni, Ofer; Zyczkowski, Karol
2012-01-01
Tensor products of M random unitary matrices of size N from the circular unitary ensemble are investigated. We show that the spectral statistics of the tensor product of random matrices becomes Poissonian if M=2, N become large or M become large and N=2.
Products of Generalized Stochastic Sarymsakov Matrices
Xia, Weiguo; Liu, Ji; Cao, Ming; Johansson, Karl; Basar, Tamer
2015-01-01
In the set of stochastic, indecomposable, aperiodic (SIA) matrices, the class of stochastic Sarymsakov matrices is the largest known subset (i) that is closed under matrix multiplication and (ii) the inﬁnitely long left-product of the elements from a compact subset converges to a rank-one matrix. In
Abel-Grassmann's Groupoids of Modulo Matrices
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Muhammad Rashad
2016-01-01
Full Text Available The binary operation of usual addition is associative in all matrices over R. However, a binary operation of addition in matrices over Z n of a nonassociative structures of AG-groupoids and AG-groups are defined and investigated here. It is shown that both these structures exist for every integer n > 3. Various properties of these structures are explored like: (i Every AG-groupoid of matrices over Z n is transitively commutative AG-groupoid and is a cancellative AG-groupoid ifn is prime. (ii Every AG-groupoid of matrices over Z n of Type-II is a T3-AG-groupoid. (iii An AG-groupoid of matrices over Z n ; G nAG(t,u, is an AG-band, ift+ u=1(mod n.
Indian Academy of Sciences (India)
Qiongqiong Ren; Jian Yuan; Liqian Ren; Liqin Zhang; Lei Zhang; Lan Jiang; Dongsheng Chen; Xianzhao Kan; Baowei Zhang
2014-12-01
Mitochondrial genomes have proved to be powerful tools in resolving phylogenetic relationships. Emberiza chrysophrys (least concern species: IUCN 2013) is a passerine bird in the bunting family, Emberizidae. The complete mitochondrial genome of E. chrysophrys was sequenced. This circular mitochondrial genome was 16,803 bp in length, with an A+T content of 52.26%, containing 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a putative control region (CR). The CR of E. chrysophrys was divided into three conserved domains. Six conserved sequence boxes in the central conserved domain II were identified as F, E, D, C, b and B. An obvious positive AT-skew and negative GC-skew bias were found for all 28 genes encoded by the H strand, whereas it was the reverse in the remaining nine genes encoded by the L strand. Remarkable rate heterogeneity was present in the mitochondrial genome of E. chrysophrys. Notably, unusual slow rate of evolution in the mitochondrial CR of E. chrysophrys was detected, which is rarely seen in other birds. Phylogenetic analyses were carried out based on 13 PCGs that showed E. pusilla was the sister group of E. rustica, and the monophyly of Emberiza was established.
Humphreys-Pereira, Danny A; Elling, Axel A
2014-01-01
Root-knot nematodes (Meloidogyne spp.) are among the most important plant pathogens. In this study, the mitochondrial (mt) genomes of the root-knot nematodes, M. chitwoodi and M. incognita were sequenced. PCR analyses suggest that both mt genomes are circular, with an estimated size of 19.7 and 18.6-19.1kb, respectively. The mt genomes each contain a large non-coding region with tandem repeats and the control region. The mt gene arrangement of M. chitwoodi and M. incognita is unlike that of other nematodes. Sequence alignments of the two Meloidogyne mt genomes showed three translocations; two in transfer RNAs and one in cox2. Compared with other nematode mt genomes, the gene arrangement of M. chitwoodi and M. incognita was most similar to Pratylenchus vulnus. Phylogenetic analyses (Maximum Likelihood and Bayesian inference) were conducted using 78 complete mt genomes of diverse nematode species. Analyses based on nucleotides and amino acids of the 12 protein-coding mt genes showed strong support for the monophyly of class Chromadorea, but only amino acid-based analyses supported the monophyly of class Enoplea. The suborder Spirurina was not monophyletic in any of the phylogenetic analyses, contradicting the Clade III model, which groups Ascaridomorpha, Spiruromorpha and Oxyuridomorpha based on the small subunit ribosomal RNA gene. Importantly, comparisons of mt gene arrangement and tree-based methods placed Meloidogyne as sister taxa of Pratylenchus, a migratory plant endoparasitic nematode, and not with the sedentary endoparasitic Heterodera. Thus, comparative analyses of mt genomes suggest that sedentary endoparasitism in Meloidogyne and Heterodera is based on convergent evolution.
Oppenheim, Sara J; Rosenfeld, Jeffrey A; DeSalle, Rob
2017-02-27
The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they
DEFF Research Database (Denmark)
Cericola, Fabio; Janss, Luc; Byrne, Stephen
2015-01-01
the diagonal elements by estimating the amount of genetic variance caused by the reduction of the coverage depth. Secondly we developed a method to scale the relationship matrix by taking into account the overall amount of pairwise non-missing loci between all families. Rust resistance and heading date were...... investigated how this reduction of the coverage depth affects the genomic relationship matrices used to estimated breeding value of F2 family pools in perennial ryegrass. A total of 995 families were genotyped via GBS providing more than 1.8M allele frequency estimates for each family with an average coverage...... depth of 12.6 per marker. Simulated datasets with a progressively reduced depth showed an increasing level of missing values together with an overestimated genetic variance caused by inflated diagonals in the genomic relationship matrix. In order to address these drawbacks we first showed how to correct...
DEFF Research Database (Denmark)
Cericola, Fabio; Janss, Luc; Byrne, Stephen
the diagonal elements by estimating the amount of genetic variance caused by the reduction of the coverage depth. Secondly we developed a method to scale the relationship matrix by taking into account the overall amount of pairwise non-missing loci between all families. Rust resistance and heading date were...... investigated how this reduction of the coverage depth affects the genomic relationship matrices used to estimated breeding value of F2 family pools in perennial ryegrass. A total of 995 families were genotyped via GBS providing more than 1.8M allele frequency estimates for each family with an average coverage...... depth of 12.6 per marker. Simulated datasets with a progressively reduced depth showed an increasing level of missing values together with an overestimated genetic variance caused by inflated diagonals in the genomic relationship matrix. In order to address these drawbacks we first showed how to correct...
Generalized graph states based on Hadamard matrices
Energy Technology Data Exchange (ETDEWEB)
Cui, Shawn X. [Department of Mathematics, University of California, Santa Barbara, California 93106 (United States); Yu, Nengkun [Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1 (Canada); UTS-AMSS Joint Research Laboratory for Quantum Computation and Quantum Information Processing, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190 (China); Zeng, Bei [Institute for Quantum Computing, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada); Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1 (Canada); Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8 (Canada)
2015-07-15
Graph states are widely used in quantum information theory, including entanglement theory, quantum error correction, and one-way quantum computing. Graph states have a nice structure related to a certain graph, which is given by either a stabilizer group or an encoding circuit, both can be directly given by the graph. To generalize graph states, whose stabilizer groups are abelian subgroups of the Pauli group, one approach taken is to study non-abelian stabilizers. In this work, we propose to generalize graph states based on the encoding circuit, which is completely determined by the graph and a Hadamard matrix. We study the entanglement structures of these generalized graph states and show that they are all maximally mixed locally. We also explore the relationship between the equivalence of Hadamard matrices and local equivalence of the corresponding generalized graph states. This leads to a natural generalization of the Pauli (X, Z) pairs, which characterizes the local symmetries of these generalized graph states. Our approach is also naturally generalized to construct graph quantum codes which are beyond stabilizer codes.
Directory of Open Access Journals (Sweden)
Barbara J. MacGregor
2016-11-01
Full Text Available For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis. Recognition (REC domains are short (~125 amino acids and well conserved, simplifying sequence alignments and phylogenetic calculations. Over 100 of these were identified in the BOGUAY genome and found to have a wide range of inferred phylogenetic relationships. Two sets were chosen here for detailed study. One set of four BOGUAY ORFs has closest relatives among other Beggiatoaceae and Cyanobacteria. A second set of four has REC domains with more mixed affiliations, including other Beggiatoaceae, several sulfate-reducing Deltaproteobacteria and Firmicutes, magnetotactic Nitrospirae, one Shewanella and one Ferrimonas strain (both Gammaproteobacteria, and numerous Vibrio vulnificus and V. navarrensis strains (also Gammaproteobacteria. For an overview of the possible origins of the whole proteins and the surrounding genomic regions, color-coded BLASTP results were produced and displayed against cartoons showing protein domain structure of predicted genes. This is suggested as a visualization method for investigation of possible horizontally transferred regions, giving more detail than scans of DNA composition and codon usage but much faster than carrying out full phylogenetic analyses for multiple proteins. As expected, most of the predicted sensor histidine kinases investigated have two or more segments with distinct
Directory of Open Access Journals (Sweden)
Cai Lei
2011-11-01
Full Text Available Abstract Background Halophilic bacteria have shown their significance in industrial production of polyhydroxyalkanoates (PHA and are gaining more attention for genetic engineering modification. Yet, little information on the genomics and PHA related genes from halophilic bacteria have been disclosed so far. Results The draft genome of moderately halophilic bacterium, Halomonas sp. TD01, a strain of great potential for industrial production of short-chain-length polyhydroxyalkanoates (PHA, was analyzed through computational methods to reveal the osmoregulation mechanism and the evolutionary relationship of the enzymes relevant to PHA and ectoine syntheses. Genes involved in the metabolism of PHA and osmolytes were annotated and studied in silico. Although PHA synthase, depolymerase, regulator/repressor and phasin were all involved in PHA metabolic pathways, they demonstrated different horizontal gene transfer (HGT events between the genomes of different strains. In contrast, co-occurrence of ectoine genes in the same genome was more frequently observed, and ectoine genes were more likely under coincidental horizontal gene transfer than PHA related genes. In addition, the adjacent organization of the homologues of PHA synthase phaC1 and PHA granule binding protein phaP was conserved in the strain TD01, which was also observed in some halophiles and non-halophiles exclusively from γ-proteobacteria. In contrast to haloarchaea, the proteome of Halomonas sp. TD01 did not show obvious inclination towards acidity relative to non-halophilic Escherichia coli MG1655, which signified that Halomonas sp. TD01 preferred the accumulation of organic osmolytes to ions in order to balance the intracellular osmotic pressure with the environment. Conclusions The accessibility of genome information would facilitate research on the genetic engineering of halophilic bacteria including Halomonas sp. TD01.
On Decompositions of Matrices over Distributive Lattices
Directory of Open Access Journals (Sweden)
Yizhi Chen
2014-01-01
Full Text Available Let L be a distributive lattice and Mn,q (L(Mn(L, resp. the semigroup (semiring, resp. of n × q (n × n, resp. matrices over L. In this paper, we show that if there is a subdirect embedding from distributive lattice L to the direct product ∏i=1mLi of distributive lattices L1,L2, …,Lm, then there will be a corresponding subdirect embedding from the matrix semigroup Mn,q(L (semiring Mn(L, resp. to semigroup ∏i=1mMn,q(Li (semiring ∏i=1mMn(Li, resp.. Further, it is proved that a matrix over a distributive lattice can be decomposed into the sum of matrices over some of its special subchains. This generalizes and extends the decomposition theorems of matrices over finite distributive lattices, chain semirings, fuzzy semirings, and so forth. Finally, as some applications, we present a method to calculate the indices and periods of the matrices over a distributive lattice and characterize the structures of idempotent and nilpotent matrices over it. We translate the characterizations of idempotent and nilpotent matrices over a distributive lattice into the corresponding ones of the binary Boolean cases, which also generalize the corresponding structures of idempotent and nilpotent matrices over general Boolean algebras, chain semirings, fuzzy semirings, and so forth.
Compressed Adjacency Matrices: Untangling Gene Regulatory Networks.
Dinkla, K; Westenberg, M A; van Wijk, J J
2012-12-01
We present a novel technique-Compressed Adjacency Matrices-for visualizing gene regulatory networks. These directed networks have strong structural characteristics: out-degrees with a scale-free distribution, in-degrees bound by a low maximum, and few and small cycles. Standard visualization techniques, such as node-link diagrams and adjacency matrices, are impeded by these network characteristics. The scale-free distribution of out-degrees causes a high number of intersecting edges in node-link diagrams. Adjacency matrices become space-inefficient due to the low in-degrees and the resulting sparse network. Compressed adjacency matrices, however, exploit these structural characteristics. By cutting open and rearranging an adjacency matrix, we achieve a compact and neatly-arranged visualization. Compressed adjacency matrices allow for easy detection of subnetworks with a specific structure, so-called motifs, which provide important knowledge about gene regulatory networks to domain experts. We summarize motifs commonly referred to in the literature, and relate them to network analysis tasks common to the visualization domain. We show that a user can easily find the important motifs in compressed adjacency matrices, and that this is hard in standard adjacency matrix and node-link diagrams. We also demonstrate that interaction techniques for standard adjacency matrices can be used for our compressed variant. These techniques include rearrangement clustering, highlighting, and filtering.
Directory of Open Access Journals (Sweden)
Marina Arav
2009-01-01
Full Text Available Let H be an m×n real matrix and let Zi be the set of column indices of the zero entries of row i of H. Then the conditions |Zk∩(∪i=1k−1Zi|≤1 for all k (2≤k≤m are called the (row Zero Position Conditions (ZPCs. If H satisfies the ZPC, then H is said to be a (row ZPC matrix. If HT satisfies the ZPC, then H is said to be a column ZPC matrix. The real matrix H is said to have a zero cycle if H has a sequence of at least four zero entries of the form hi1j1,hi1j2,hi2j2,hi2j3,…,hikjk,hikj1 in which the consecutive entries alternatively share the same row or column index (but not both, and the last entry has one common index with the first entry. Several connections between the ZPC and the nonexistence of zero cycles are established. In particular, it is proved that a matrix H has no zero cycle if and only if there are permutation matrices P and Q such that PHQ is a row ZPC matrix and a column ZPC matrix.
Random Matrices and Lyapunov Coefficients Regularity
Gallavotti, Giovanni
2017-02-01
Analyticity and other properties of the largest or smallest Lyapunov exponent of a product of real matrices with a "cone property" are studied as functions of the matrices entries, as long as they vary without destroying the cone property. The result is applied to stability directions, Lyapunov coefficients and Lyapunov exponents of a class of products of random matrices and to dynamical systems. The results are not new and the method is the main point of this work: it is is based on the classical theory of the Mayer series in Statistical Mechanics of rarefied gases.
Statistical properties of random density matrices
Sommers, H J; Sommers, Hans-Juergen; Zyczkowski, Karol
2004-01-01
Statistical properties of ensembles of random density matrices are investigated. We compute traces and von Neumann entropies averaged over ensembles of random density matrices distributed according to the Bures measure. The eigenvalues of the random density matrices are analyzed: we derive the eigenvalue distribution for the Bures ensemble which is shown to be broader then the quarter--circle distribution characteristic of the Hilbert--Schmidt ensemble. For measures induced by partial tracing over the environment we compute exactly the two-point eigenvalue correlation function.
Statistical properties of random density matrices
Energy Technology Data Exchange (ETDEWEB)
Sommers, Hans-Juergen [Fachbereich Physik, Universitaet Duisburg-Essen, Campus Essen, 45117 Essen (Germany); Zyczkowski, Karol [Instytut Fizyki im. Smoluchowskiego, Uniwersytet Jagiellonski, ul. Reymonta 4, 30-059 Cracow (Poland)
2004-09-03
Statistical properties of ensembles of random density matrices are investigated. We compute traces and von Neumann entropies averaged over ensembles of random density matrices distributed according to the Bures measure. The eigenvalues of the random density matrices are analysed: we derive the eigenvalue distribution for the Bures ensemble which is shown to be broader then the quarter-circle distribution characteristic of the Hilbert-Schmidt ensemble. For measures induced by partial tracing over the environment we compute exactly the two-point eigenvalue correlation function.
Direct dialling of Haar random unitary matrices
Russell, Nicholas J.; Chakhmakhchyan, Levon; O’Brien, Jeremy L.; Laing, Anthony
2017-03-01
Random unitary matrices find a number of applications in quantum information science, and are central to the recently defined boson sampling algorithm for photons in linear optics. We describe an operationally simple method to directly implement Haar random unitary matrices in optical circuits, with no requirement for prior or explicit matrix calculations. Our physically motivated and compact representation directly maps independent probability density functions for parameters in Haar random unitary matrices, to optical circuit components. We go on to extend the results to the case of random unitaries for qubits.
A method for generating realistic correlation matrices
Garcia, Stephan Ramon
2011-01-01
Simulating sample correlation matrices is important in many areas of statistics. Approaches such as generating normal data and finding their sample correlation matrix or generating random uniform $[-1,1]$ deviates as pairwise correlations both have drawbacks. We develop an algorithm for adding noise, in a highly controlled manner, to general correlation matrices. In many instances, our method yields results which are superior to those obtained by simply simulating normal data. Moreover, we demonstrate how our general algorithm can be tailored to a number of different correlation models. Finally, using our results with an existing clustering algorithm, we show that simulating correlation matrices can help assess statistical methodology.
The Antitriangular Factorization of Saddle Point Matrices
Pestana, J.
2014-01-01
Mastronardi and Van Dooren [SIAM J. Matrix Anal. Appl., 34 (2013), pp. 173-196] recently introduced the block antitriangular ("Batman") decomposition for symmetric indefinite matrices. Here we show the simplification of this factorization for saddle point matrices and demonstrate how it represents the common nullspace method. We show that rank-1 updates to the saddle point matrix can be easily incorporated into the factorization and give bounds on the eigenvalues of matrices important in saddle point theory. We show the relation of this factorization to constraint preconditioning and how it transforms but preserves the structure of block diagonal and block triangular preconditioners. © 2014 Society for Industrial and Applied Mathematics.
Sae-Lim, Panya; Kause, Antti; Lillehammer, Marie; Mulder, Han A
2017-03-07
In farmed Atlantic salmon, heritability for uniformity of body weight is low, indicating that the accuracy of estimated breeding values (EBV) may be low. The use of genomic information could be one way to increase accuracy and, hence, obtain greater response to selection. Genomic information can be merged with pedigree information to construct a combined relationship matrix ([Formula: see text] matrix) for a single-step genomic evaluation (ssGBLUP), allowing realized relationships of the genotyped animals to be exploited, in addition to numerator pedigree relationships ([Formula: see text] matrix). We compared the predictive ability of EBV for uniformity of body weight in Atlantic salmon, when implementing either the [Formula: see text] or [Formula: see text] matrix in the genetic evaluation. We used double hierarchical generalized linear models (DHGLM) based either on a sire-dam (sire-dam DHGLM) or an animal model (animal DHGLM) for both body weight and its uniformity. With the animal DHGLM, the use of [Formula: see text] instead of [Formula: see text] significantly increased the correlation between the predicted EBV and adjusted phenotypes, which is a measure of predictive ability, for both body weight and its uniformity (41.1 to 78.1%). When log-transformed body weights were used to account for a scale effect, the use of [Formula: see text] instead of [Formula: see text] produced a small and non-significant increase (1.3 to 13.9%) in predictive ability. The sire-dam DHGLM had lower predictive ability for uniformity compared to the animal DHGLM. Use of the combined numerator and genomic relationship matrix ([Formula: see text]) significantly increased the predictive ability of EBV for uniformity when using the animal DHGLM for untransformed body weight. The increase was only minor when using log-transformed body weights, which may be due to the lower heritability of scaled uniformity, the lower genetic correlation of transformed body weight with its
Katyal, Isha; Chaban, Bonnie; Hill, Janet E
2016-11-01
Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.
Wang, H; Misztal, I; Legarra, A
2014-12-01
This work studied differences between expected (calculated from pedigree) and realized (genomic, from markers) relationships in a real population, the influence of quality control on these differences, and their fit to current theory. Data included 4940 pure line chickens across five generations genotyped for 57,636 SNP. Pedigrees (5762 animals) were available for the five generations, pedigree starting on the first one. Three levels of quality control were used. With no quality control, mean difference between realized and expected relationships for different type of relationships was ≤ 0.04 with standard deviation ≤ 0.10. With strong quality control (call rate ≥ 0.9, parent-progeny conflicts, minor allele frequency and use of only autosomal chromosomes), these numbers reduced to ≤ 0.02 and ≤ 0.04, respectively. While the maximum difference was 1.02 with the complete data, it was only 0.18 with the latest three generations of genotypes (but including all pedigrees). Variation of expected minus realized relationships agreed with theoretical developments and suggests an effective number of loci of 70 for this population. When the pedigree is complete and as deep as the genotypes, the standard deviation of difference between the expected and realized relationships is around 0.04, all categories confounded. Standard deviation of differences larger than 0.10 suggests bad quality control, mistakes in pedigree recording or genotype labelling, or insufficient depth of pedigree. © 2014 Blackwell Verlag GmbH.
Synchronous correlation matrices and Connes’ embedding conjecture
Energy Technology Data Exchange (ETDEWEB)
Dykema, Kenneth J., E-mail: kdykema@math.tamu.edu [Department of Mathematics, Texas A& M University, College Station, Texas 77843-3368 (United States); Paulsen, Vern, E-mail: vern@math.uh.edu [Department of Mathematics, University of Houston, Houston, Texas 77204 (United States)
2016-01-15
In the work of Paulsen et al. [J. Funct. Anal. (in press); preprint arXiv:1407.6918], the concept of synchronous quantum correlation matrices was introduced and these were shown to correspond to traces on certain C*-algebras. In particular, synchronous correlation matrices arose in their study of various versions of quantum chromatic numbers of graphs and other quantum versions of graph theoretic parameters. In this paper, we develop these ideas further, focusing on the relations between synchronous correlation matrices and microstates. We prove that Connes’ embedding conjecture is equivalent to the equality of two families of synchronous quantum correlation matrices. We prove that if Connes’ embedding conjecture has a positive answer, then the tracial rank and projective rank are equal for every graph. We then apply these results to more general non-local games.
THE EIGENVALUE PERTURBATION BOUND FOR ARBITRARY MATRICES
Institute of Scientific and Technical Information of China (English)
Wen Li; Jian-xin Chen
2006-01-01
In this paper we present some new absolute and relative perturbation bounds for the eigenvalue for arbitrary matrices, which improves some recent results. The eigenvalue inclusion region is also discussed.
Sufficient Conditions of Nonsingular H-matrices
Institute of Scientific and Technical Information of China (English)
王广彬; 洪振杰; 高中喜
2004-01-01
From the concept of a diagonally dominant matrix, two sufficient conditions of nonsingular H-matrices were obtained in this paper. An example was given to show that these results improve the known results.
Optimizing the Evaluation of Finite Element Matrices
Kirby, Robert C; Logg, Anders; Scott, L Ridgway; 10.1137/040607824
2012-01-01
Assembling stiffness matrices represents a significant cost in many finite element computations. We address the question of optimizing the evaluation of these matrices. By finding redundant computations, we are able to significantly reduce the cost of building local stiffness matrices for the Laplace operator and for the trilinear form for Navier-Stokes. For the Laplace operator in two space dimensions, we have developed a heuristic graph algorithm that searches for such redundancies and generates code for computing the local stiffness matrices. Up to cubics, we are able to build the stiffness matrix on any triangle in less than one multiply-add pair per entry. Up to sixth degree, we can do it in less than about two. Preliminary low-degree results for Poisson and Navier-Stokes operators in three dimensions are also promising.
Orthogonal Polynomials from Hermitian Matrices II
Odake, Satoru
2016-01-01
This is the second part of the project `unified theory of classical orthogonal polynomials of a discrete variable derived from the eigenvalue problems of hermitian matrices.' In a previous paper, orthogonal polynomials having Jackson integral measures were not included, since such measures cannot be obtained from single infinite dimensional hermitian matrices. Here we show that Jackson integral measures for the polynomials of the big $q$-Jacobi family are the consequence of the recovery of self-adjointness of the unbounded Jacobi matrices governing the difference equations of these polynomials. The recovery of self-adjointness is achieved in an extended $\\ell^2$ Hilbert space on which a direct sum of two unbounded Jacobi matrices acts as a Hamiltonian or a difference Schr\\"odinger operator for an infinite dimensional eigenvalue problem. The polynomial appearing in the upper/lower end of Jackson integral constitutes the eigenvector of each of the two unbounded Jacobi matrix of the direct sum. We also point out...
A Few Applications of Imprecise Matrices
Directory of Open Access Journals (Sweden)
Sahalad Borgoyary
2015-07-01
Full Text Available This article introduces generalized form of extension definition of the Fuzzy set and its complement in the sense of reference function namely in imprecise set and its complement. Discuss Partial presence of element, Membership value of an imprecise number in the normal and subnormal imprecise numbers. Further on the basis of reference function define usual matrix into imprecise form with new notation. And with the help of maximum and minimum operators, obtain some new matrices like reducing imprecise matrices, complement of reducing imprecise matrix etc. Along with discuss some of the classical matrix properties which are hold good in the imprecise matrix also. Further bring out examples of application of the addition of imprecise matrices, subtraction of imprecise matrices etc. in the field of transportation problems.
Balanced random Toeplitz and Hankel Matrices
Basak, Anirban
2010-01-01
Except the Toeplitz and Hankel matrices, the common patterned matrices for which the limiting spectral distribution (LSD) are known to exist, share a common property--the number of times each random variable appears in the matrix is (more or less) same across the variables. Thus it seems natural to ask what happens to the spectrum of the Toeplitz and Hankel matrices when each entry is scaled by the square root of the number of times that entry appears in the matrix instead of the uniform scaling by $n^{-1/2}$. We show that the LSD of these balanced matrices exist and derive integral formulae for the moments of the limit distribution. Curiously, it is not clear if these moments define a unique distribution.
KAMG: A Tool for Converting Blood Ties and Affinity Ties into Adjacency Matrices
Directory of Open Access Journals (Sweden)
Hang Xiong
2016-07-01
Full Text Available Kinship Adjacency Matrix Generator (KAMG is a browser-based software for creating adjacency matrices using the information of kinship ties. Specifically, it is capable of converting the family trees in the format of GEDCOM files into adjacency matrices of blood relationship. With the data of intermarriages between different families, it can further create the adjacency matrix of affinity relationship for the families. The outcomes can be directly used to create networks. KAMG is written in JavaScript and implemented on web browsers. It is completely open source and the source code is publicly available on GitHub.
Jin, Xiaoxiao; Wang, Rixin; Wei, Tao; Tang, Da; Xu, Tianjun
2015-01-01
The fishes of suborder Gobioidei is the largest group of those in present living Perciformes, which contains about 2,200 species belonging to 270 genera of 9 families in the world. The monophyly and phylogenetic relationships of gobies have been controversial and disputable for a long time. In the present study, the complete mitochondrial genome of the shimofuri goby Tridentiger bifasciatus (T. bifasciatus) and shokihaze goby Tridentiger barbatus (T. barbatus) were firstly determined. The two mitochondrial genomes were both consisted of 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one major control region (CR). They shared similar features with those of other gobies in terms of gene arrangement, base composition, and tRNA structures. The CR was absence of typical conserved blocks (CSB-E, and CSB-F) respectively for the T. bifasciatus and T. barbatus. Phylogenomic analyses, which based on 12 concatenated protein-coding genes and complete mitochondrial genome sequences, revealed that there were two groups within the Gobiidae. A large group consisted of the Amblyopinae, Gobionellinae, Oxudercinae and Sicydiinae, and Amblyopinae was nested in Oxudercinae and they were both paraphyletic to Sicydiinae. The other group was the Gobiinae. As a whole, our phylogenetic data was different from the traditionally classification of Gobiidae, but supported the new phylogenetic taxonomy view of Thacker (Copeia 2009:93-104, 2009).
Boolean Inner product Spaces and Boolean Matrices
Gudder, Stan; Latremoliere, Frederic
2009-01-01
This article discusses the concept of Boolean spaces endowed with a Boolean valued inner product and their matrices. A natural inner product structure for the space of Boolean n-tuples is introduced. Stochastic boolean vectors and stochastic and unitary Boolean matrices are studied. A dimension theorem for orthonormal bases of a Boolean space is proven. We characterize the invariant stochastic Boolean vectors for a Boolean stochastic matrix and show that they can be used to reduce a unitary m...
Generalized Inverses of Matrices over Rings
Institute of Scientific and Technical Information of China (English)
韩瑞珠; 陈建龙
1992-01-01
Let R be a ring,*be an involutory function of the set of all finite matrices over R. In this pa-per,necessary and sufficient conditions are given for a matrix to have a (1,3)-inverse,(1,4)-inverse,or Morre-Penrose inverse,relative to *.Some results about generalized inverses of matrices over division rings are generalized and improved.
A Euclidean algorithm for integer matrices
DEFF Research Database (Denmark)
Lauritzen, Niels; Thomsen, Jesper Funch
2015-01-01
We present a Euclidean algorithm for computing a greatest common right divisor of two integer matrices. The algorithm is derived from elementary properties of finitely generated modules over the ring of integers.......We present a Euclidean algorithm for computing a greatest common right divisor of two integer matrices. The algorithm is derived from elementary properties of finitely generated modules over the ring of integers....
Infinite Products of Random Isotropically Distributed Matrices
Il'yn, A S; Zybin, K P
2016-01-01
Statistical properties of infinite products of random isotropically distributed matrices are investigated. Both for continuous processes with finite correlation time and discrete sequences of independent matrices, a formalism that allows to calculate easily the Lyapunov spectrum and generalized Lyapunov exponents is developed. This problem is of interest to probability theory, statistical characteristics of matrix T-exponentials are also needed for turbulent transport problems, dynamical chaos and other parts of statistical physics.
A Wegner estimate for Wigner matrices
Maltsev, Anna
2011-01-01
In the first part of these notes, we review some of the recent developments in the study of the spectral properties of Wigner matrices. In the second part, we present a new proof of a Wegner estimate for the eigenvalues of a large class of Wigner matrices. The Wegner estimate gives an upper bound for the probability to find an eigenvalue in an interval $I$, proportional to the size $|I|$ of the interval.
Matrices related to some Fock space operators
Directory of Open Access Journals (Sweden)
Krzysztof Rudol
2011-01-01
Full Text Available Matrices of operators with respect to frames are sometimes more natural and easier to compute than the ones related to bases. The present work investigates such operators on the Segal-Bargmann space, known also as the Fock space. We consider in particular some properties of matrices related to Toeplitz and Hankel operators. The underlying frame is provided by normalised reproducing kernel functions at some lattice points.
Linear algebra for skew-polynomial matrices
Abramov, Sergei; Bronstein, Manuel
2002-01-01
We describe an algorithm for transforming skew-polynomial matrices over an Ore domain in row-reduced form, and show that this algorithm can be used to perform the standard calculations of linear algebra on such matrices (ranks, kernels, linear dependences, inhomogeneous solving). The main application of our algorithm is to desingularize recurrences and to compute the rational solutions of a large class of linear functional systems. It also turns out to be efficient when applied to ordinary co...
Moment matrices, border bases and radical computation
Mourrain, B.; J. B. Lasserre; Laurent, Monique; Rostalski, P.; Trebuchet, Philippe
2013-01-01
In this paper, we describe new methods to compute the radical (resp. real radical) of an ideal, assuming it complex (resp. real) variety is nte. The aim is to combine approaches for solving a system of polynomial equations with dual methods which involve moment matrices and semi-denite programming. While the border basis algorithms of [17] are ecient and numerically stable for computing complex roots, algorithms based on moment matrices [12] allow the incorporation of additional polynomials, ...
Infinite Products of Random Isotropically Distributed Matrices
Il'yn, A. S.; Sirota, V. A.; Zybin, K. P.
2017-01-01
Statistical properties of infinite products of random isotropically distributed matrices are investigated. Both for continuous processes with finite correlation time and discrete sequences of independent matrices, a formalism that allows to calculate easily the Lyapunov spectrum and generalized Lyapunov exponents is developed. This problem is of interest to probability theory, statistical characteristics of matrix T-exponentials are also needed for turbulent transport problems, dynamical chaos and other parts of statistical physics.
Transplantation of rat hepatic stem-like (HSL) cells with collagen matrices.
Ueno, Yasuharu; Nagai, Hirokazu; Watanabe, Go; Ishikawa, Kiyoshi; Yoshikawa, Kiwamu; Koizumi, Yukio; Kameda, Takashi; Sugiyama, Toshihiro
2005-12-01
Organ restitution using somatic stem cells is of great clinical interest. Recent advances in the field of tissue engineering have demonstrated that the use of collagen matrices as scaffolds facilitates tissue reconstruction. Here, we examine the efficacy of transplantation of HSL cells, a previously established liver epithelial cell line with a potential for differentiation, using collagen scaffolds. To this end, HSL cells were transplanted into Nagase's analbuminemic rat with spongy or gelatinous type I collagen matrices. Consequently, immunohistochemical analyses and genomic PCR experiments revealed engraftment of the transplanted cells. Furthermore, the levels of serum albumin in recipient rats were found to increase up to 2.5-fold relative to controls after transplantation. These findings suggest that HSL cells are able to differentiate into functional hepatocytes in vivo, and that biodegradable collagen matrices enhance this phenomenon by providing an appropriate microenvironment for hepatocytic repopulation.
Directory of Open Access Journals (Sweden)
Singh Nagendra
2009-03-01
Full Text Available Abstract Background Completely sequenced plant genomes provide scope for designing a large number of microsatellite markers, which are useful in various aspects of crop breeding and genetic analysis. With the objective of developing genic but non-coding microsatellite (GNMS markers for the rice (Oryza sativa L. genome, we characterized the frequency and relative distribution of microsatellite repeat-motifs in 18,935 predicted protein coding genes including 14,308 putative promoter sequences. Results We identified 19,555 perfect GNMS repeats with densities ranging from 306.7/Mb in chromosome 1 to 450/Mb in chromosome 12 with an average of 357.5 GNMS per Mb. The average microsatellite density was maximum in the 5' untranslated regions (UTRs followed by those in introns, promoters, 3'UTRs and minimum in the coding sequences (CDS. Primers were designed for 17,966 (92% GNMS repeats, including 4,288 (94% hypervariable class I types, which were bin-mapped on the rice genome. The GNMS markers were most polymorphic in the intronic region (73.3% followed by markers in the promoter region (53.3% and least in the CDS (26.6%. The robust polymerase chain reaction (PCR amplification efficiency and high polymorphic potential of GNMS markers over genic coding and random genomic microsatellite markers suggest their immediate use in efficient genotyping applications in rice. A set of these markers could assess genetic diversity and establish phylogenetic relationships among domesticated rice cultivar groups. We also demonstrated the usefulness of orthologous and paralogous conserved non-coding microsatellite (CNMS markers, identified in the putative rice promoter sequences, for comparative physical mapping and understanding of evolutionary and gene regulatory complexities among rice and other members of the grass family. The divergence between long-grained aromatics and subspecies japonica was estimated to be more recent (0.004 Mya compared to short
Directory of Open Access Journals (Sweden)
Omnia Gamal El-Dien
2016-03-01
Full Text Available The open-pollinated (OP family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A
2016-01-22
The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates' offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of "half-sibling" in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
Hind, Katharine R; Saunders, Gary W
2013-05-01
The use of molecular markers in taxonomic studies has become a standard practice in biology. However, consensus on which markers to use at the species level is lacking because evolutionary lineages show differences in divergence rates between organellar genomes. Ideally, researchers use multiple lines of evidence when first describing a species, such as the incorporation of several molecular markers from varied genomes (mitochondrion, plastid and nucleus). This study examined species boundaries in the red algal genus Chiharaea. We used five molecular markers, with at least one marker from each genome, coupled with thorough morphological analyses. We recognized three species in Chiharaea (C.americana, C. rhododactyla sp. nov., C. silvae) and two forms (C. americana f. americana and C. americana f. bodegensis (H.W. Johansen) stat. nov.). For C. americana f. americana and C. americana f. bodegensis differentiation based on morphological data was reflected in the plastid-encoded large subunit of RuBisCO (rbcL), but was not concordant with either the mitochondrial cytochrome c oxidase subunit 1 (COI-5P) or nuclear internal transcribed spacer (ITS) sequence data. We suggest that this discordance is indicative of ongoing hybridization and introgression between populations of C. americana f. americana and C. americana f. bodegensis. In addition, we used a PCR assay with ITS specific primers to amplify multiple ITS variants for collections assignable to C. americana indicating that there is genetic variability within ITS copies most likely due to introgression, crossing over and/or the retention of ancestral variants.
DEFF Research Database (Denmark)
Ashraf, Bilal; Fé, Dario; Jensen, Just
2014-01-01
at each SNP in family pools or polyploids. There are, however, several statistical challenges associated with this method, including low sequencing depth and missing values. Low sequencing depth results in inaccuracies in estimates of allele frequencies for each SNP. In this work we have focused...... on optimizing methods and models utilizing F2 family phenotype records and NGS information from F2 family pools in perennial ryegrass. Genomic variance was estimated using genomic relationship matrices based on different coverage depths to verify effects of coverage depth. Example traits were seed yield, rust...... score and heading date. A total of 995 F2 families were genotyped via GBS, resulting in allele frequency estimates at 1 million SNPs in each family, the coverage within family ranging from 0 to 60. Results from both real and simulated data show that genomic variance is overestimated at lower coverage...
MERSENNE AND HADAMARD MATRICES CALCULATION BY SCARPIS METHOD
Directory of Open Access Journals (Sweden)
N. A. Balonin
2014-05-01
Full Text Available Purpose. The paper deals with the problem of basic generalizations of Hadamard matrices associated with maximum determinant matrices or not optimal by determinant matrices with orthogonal columns (weighing matrices, Mersenne and Euler matrices, ets.; calculation methods for the quasi-orthogonal local maximum determinant Mersenne matrices are not studied enough sufficiently. The goal of this paper is to develop the theory of Mersenne and Hadamard matrices on the base of generalized Scarpis method research. Methods. Extreme solutions are found in general by minimization of maximum for absolute values of the elements of studied matrices followed by their subsequent classification according to the quantity of levels and their values depending on orders. Less universal but more effective methods are based on structural invariants of quasi-orthogonal matrices (Silvester, Paley, Scarpis methods, ets.. Results. Generalizations of Hadamard and Belevitch matrices as a family of quasi-orthogonal matrices of odd orders are observed; they include, in particular, two-level Mersenne matrices. Definitions of section and layer on the set of generalized matrices are proposed. Calculation algorithms for matrices of adjacent layers and sections by matrices of lower orders are described. Approximation examples of the Belevitch matrix structures up to 22-nd critical order by Mersenne matrix of the third order are given. New formulation of the modified Scarpis method to approximate Hadamard matrices of high orders by lower order Mersenne matrices is proposed. Williamson method is described by example of one modular level matrices approximation by matrices with a small number of levels. Practical relevance. The efficiency of developing direction for the band-pass filters creation is justified. Algorithms for Mersenne matrices design by Scarpis method are used in developing software of the research program complex. Mersenne filters are based on the suboptimal by
A Brief Historical Introduction to Matrices and Their Applications
Debnath, L.
2014-01-01
This paper deals with the ancient origin of matrices, and the system of linear equations. Included are algebraic properties of matrices, determinants, linear transformations, and Cramer's Rule for solving the system of algebraic equations. Special attention is given to some special matrices, including matrices in graph theory and electrical…
A Brief Historical Introduction to Matrices and Their Applications
Debnath, L.
2014-01-01
This paper deals with the ancient origin of matrices, and the system of linear equations. Included are algebraic properties of matrices, determinants, linear transformations, and Cramer's Rule for solving the system of algebraic equations. Special attention is given to some special matrices, including matrices in graph theory and electrical…
Representation-independent manipulations with Dirac matrices and spinors
2007-01-01
Dirac matrices, also known as gamma matrices, are defined only up to a similarity transformation. Usually, some explicit representation of these matrices is assumed in order to deal with them. In this article, we show how it is possible to proceed without any such assumption. Various important identities involving Dirac matrices and spinors have been derived without assuming any representation at any stage.
Condition number estimation of preconditioned matrices.
Kushida, Noriyuki
2015-01-01
The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager's method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei's matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei's matrix, and matrices generated with the finite element method.
Condition number estimation of preconditioned matrices.
Directory of Open Access Journals (Sweden)
Noriyuki Kushida
Full Text Available The present paper introduces a condition number estimation method for preconditioned matrices. The newly developed method provides reasonable results, while the conventional method which is based on the Lanczos connection gives meaningless results. The Lanczos connection based method provides the condition numbers of coefficient matrices of systems of linear equations with information obtained through the preconditioned conjugate gradient method. Estimating the condition number of preconditioned matrices is sometimes important when describing the effectiveness of new preconditionerers or selecting adequate preconditioners. Operating a preconditioner on a coefficient matrix is the simplest method of estimation. However, this is not possible for large-scale computing, especially if computation is performed on distributed memory parallel computers. This is because, the preconditioned matrices become dense, even if the original matrices are sparse. Although the Lanczos connection method can be used to calculate the condition number of preconditioned matrices, it is not considered to be applicable to large-scale problems because of its weakness with respect to numerical errors. Therefore, we have developed a robust and parallelizable method based on Hager's method. The feasibility studies are curried out for the diagonal scaling preconditioner and the SSOR preconditioner with a diagonal matrix, a tri-daigonal matrix and Pei's matrix. As a result, the Lanczos connection method contains around 10% error in the results even with a simple problem. On the other hand, the new method contains negligible errors. In addition, the newly developed method returns reasonable solutions when the Lanczos connection method fails with Pei's matrix, and matrices generated with the finite element method.
Institute of Scientific and Technical Information of China (English)
Serge N. Vinogradov; Iván Fernández; David Hoogewijs; Raúl Arredondo-Peter
2011-01-01
Land plants and algae form a supergroup, the Archaeplastida, believed to be monophyletic. We report the results of an analysis of the phylogeny of putative globins in the currently available genomes to bacterial and other eu-karyote hemoglobins (Hbs). Archaeplastida genomes have 3/3 and 2/2 Hbs, with the land plant genomes having group 2 2/2 Hbs, except for the unexpected occurrence of two group 1 2/2 Hbs in Ricinus communis. Bayesian analysis shows that plant 3/3 Hbs are related to vertebrate neuroglobins and bacterial flavohemoglobins (FHbs). We sought to define the bacterial groups, whose ancestors shared the precursors of Archaeplastida Hbs, via Bayesian and neighbor-joining anal-yses based on COBALTalignment of representative sets of bacterial 3/3 FHb-like globins and group 1 and 2 2/2 Hbs with the corresponding Archaeplastida Hbs. The results suggest that the Archaeplastida 3/3 and group 1 2/2 Hbs could have orig-inated from the horizontal gene transfers (HGTs) that accompanied the two generally accepted endosymbioses of a pro-teobacterium and a cyanobacterium with a eukaryote ancestor. In contrast, the origin of the group 2 2/2 Hbs unexpectedly appears to involve HGT from a bacterium ancestral to Chloroflexi, Deinococcales, Bacilli, and Actinomycetes. Furthermore,although intron positions and phases are mostly conserved among the land plant 3/3 and 2/2 globin genes, introns are absent in the algal 3/3 genes and intron positions and phases are highly variable in their 2/2 genes. Thus, introns are irrelevant to globin evolution in Archaeplastida.
Biomimetic matrices self-initiating the induction of bone formation.
Ripamonti, Ugo; Roden, Laura C; Ferretti, Carlo; Klar, Roland M
2011-09-01
The new strategy of tissue engineering, and regenerative medicine at large, is to construct biomimetic matrices to mimic nature's hierarchical structural assemblages and mechanisms of simplicity and elegance that are conserved throughout genera and species. There is a direct spatial and temporal relationship of morphologic and molecular events that emphasize the biomimetism of the remodeling cycles of the osteonic corticocancellous bone versus the "geometric induction of bone formation," that is, the induction of bone by "smart" concavities assembled in biomimetic matrices of macroporous calcium phosphate-based constructs. The basic multicellular unit of the corticocancellous bone excavates a trench across the bone surface, leaving in its wake a hemiosteon rather than an osteon, that is, a trench with cross-sectional geometric cues of concavities after cyclic episodes of osteoclastogenesis, eventually leading to osteogenesis. The concavities per se are geometric regulators of growth-inducing angiogenesis and osteogenesis as in the remodeling processes of the corticocancellous bone. The concavities act as a powerful geometric attractant for myoblastic/myoendothelial and/or endothelial/pericytic stem cells, which differentiate into bone-forming cells. The lacunae, pits, and concavities cut by osteoclastogenesis within the biomimetic matrices are the driving morphogenetic cues that induce bone formation in a continuum of sequential phases of resorption/dissolution and formation. To induce the cascade of bone differentiation, the soluble osteogenic molecular signals of the transforming growth factor β supergene family must be reconstituted with an insoluble signal or substratum that triggers the bone differentiation cascade. By carving a series of repetitive concavities into solid and/or macroporous biomimetic matrices of highly crystalline hydroxyapatite or biphasic hydroxyapatite/β-tricalcium phosphate, we were able to embed smart biologic functions within
Bayesian Nonparametric Clustering for Positive Definite Matrices.
Cherian, Anoop; Morellas, Vassilios; Papanikolopoulos, Nikolaos
2016-05-01
Symmetric Positive Definite (SPD) matrices emerge as data descriptors in several applications of computer vision such as object tracking, texture recognition, and diffusion tensor imaging. Clustering these data matrices forms an integral part of these applications, for which soft-clustering algorithms (K-Means, expectation maximization, etc.) are generally used. As is well-known, these algorithms need the number of clusters to be specified, which is difficult when the dataset scales. To address this issue, we resort to the classical nonparametric Bayesian framework by modeling the data as a mixture model using the Dirichlet process (DP) prior. Since these matrices do not conform to the Euclidean geometry, rather belongs to a curved Riemannian manifold,existing DP models cannot be directly applied. Thus, in this paper, we propose a novel DP mixture model framework for SPD matrices. Using the log-determinant divergence as the underlying dissimilarity measure to compare these matrices, and further using the connection between this measure and the Wishart distribution, we derive a novel DPM model based on the Wishart-Inverse-Wishart conjugate pair. We apply this model to several applications in computer vision. Our experiments demonstrate that our model is scalable to the dataset size and at the same time achieves superior accuracy compared to several state-of-the-art parametric and nonparametric clustering algorithms.
Using Elimination Theory to construct Rigid Matrices
Kumar, Abhinav; Patankar, Vijay M; N, Jayalal Sarma M
2009-01-01
The rigidity of a matrix A for target rank r is the minimum number of entries of A that must be changed to ensure that the rank of the altered matrix is at most r. Since its introduction by Valiant (1977), rigidity and similar rank-robustness functions of matrices have found numerous applications in circuit complexity, communication complexity, and learning complexity. Almost all nxn matrices over an infinite field have a rigidity of (n-r)^2. It is a long-standing open question to construct infinite families of explicit matrices even with superlinear rigidity when r=Omega(n). In this paper, we construct an infinite family of complex matrices with the largest possible, i.e., (n-r)^2, rigidity. The entries of an nxn matrix in this family are distinct primitive roots of unity of orders roughly exp(n^4 log n). To the best of our knowledge, this is the first family of concrete (but not entirely explicit) matrices having maximal rigidity and a succinct algebraic description. Our construction is based on elimination...
Griffith, Jacqulyn L; Coleman, Laura E; Raymond, Adam S; Goodson, Summer G; Pittard, William S; Tsui, Circe; Devine, Scott E
2003-07-01
Retroviruses and their relatives, the long terminal repeat (LTR) retrotransposons, carry out complex life cycles within the cells of their hosts. We have exploited a collection of gene deletion mutants developed by the Saccharomyces Genome Deletion Project to perform a functional genomics screen for host factors that influence the retrovirus-like Ty1 element in yeast. A total of 101 genes that presumably influence many different aspects of the Ty1 retrotransposition cycle were identified from our analysis of 4483 homozygous diploid deletion strains. Of the 101 identified mutants, 46 had significantly altered levels of Ty1 cDNA, whereas the remaining 55 mutants had normal levels of Ty1 cDNA. Thus, approximately half of the mutants apparently affected the early stages of retrotransposition leading up to the assembly of virus-like particles and cDNA replication, whereas the remaining half affected steps that occur after cDNA replication. Although most of the mutants retained the ability to target Ty1 integration to tRNA genes, 2 mutants had reduced levels of tRNA gene targeting. Over 25% of the gene products identified in this study were conserved in other organisms, suggesting that this collection of host factors can serve as a starting point for identifying host factors that influence LTR retroelements and retroviruses in other organisms. Overall, our data indicate that Ty1 requires a large number of cellular host factors to complete its retrotransposition cycle efficiently.
Directory of Open Access Journals (Sweden)
Ehsan Kayal
2015-11-01
Full Text Available Hydrozoans display the most morphological diversity within the phylum Cnidaria. While recent molecular studies have provided some insights into their evolutionary history, sister group relationships remain mostly unresolved, particularly at mid-taxonomic levels. Specifically, within Hydroidolina, the most speciose hydrozoan subclass, the relationships and sometimes integrity of orders are highly unsettled. Here we obtained the near complete mitochondrial sequence of twenty-six hydroidolinan hydrozoan species from a range of sources (DNA and RNA-seq data, long-range PCR. Our analyses confirm previous inference of the evolution of mtDNA in Hydrozoa while introducing a novel genome organization. Using RNA-seq data, we propose a mechanism for the expression of mitochondrial mRNA in Hydroidolina that can be extrapolated to the other medusozoan taxa. Phylogenetic analyses using the full set of mitochondrial gene sequences provide some insights into the order-level relationships within Hydroidolina, including siphonophores as the first diverging clade, a well-supported clade comprised of Leptothecata-Filifera III–IV, and a second clade comprised of Aplanulata-Capitata s.s.-Filifera I–II. Finally, we describe our relatively inexpensive and accessible multiplexing strategy to sequence long-range PCR amplicons that can be adapted to most high-throughput sequencing platforms.
Kayal, Ehsan; Bentlage, Bastian; Cartwright, Paulyn; Yanagihara, Angel A; Lindsay, Dhugal J; Hopcroft, Russell R; Collins, Allen G
2015-01-01
Hydrozoans display the most morphological diversity within the phylum Cnidaria. While recent molecular studies have provided some insights into their evolutionary history, sister group relationships remain mostly unresolved, particularly at mid-taxonomic levels. Specifically, within Hydroidolina, the most speciose hydrozoan subclass, the relationships and sometimes integrity of orders are highly unsettled. Here we obtained the near complete mitochondrial sequence of twenty-six hydroidolinan hydrozoan species from a range of sources (DNA and RNA-seq data, long-range PCR). Our analyses confirm previous inference of the evolution of mtDNA in Hydrozoa while introducing a novel genome organization. Using RNA-seq data, we propose a mechanism for the expression of mitochondrial mRNA in Hydroidolina that can be extrapolated to the other medusozoan taxa. Phylogenetic analyses using the full set of mitochondrial gene sequences provide some insights into the order-level relationships within Hydroidolina, including siphonophores as the first diverging clade, a well-supported clade comprised of Leptothecata-Filifera III-IV, and a second clade comprised of Aplanulata-Capitata s.s.-Filifera I-II. Finally, we describe our relatively inexpensive and accessible multiplexing strategy to sequence long-range PCR amplicons that can be adapted to most high-throughput sequencing platforms.
Polymer tensiometers with ceramic cones: direct observations of matric pressures in drying soils
Ploeg, van der M.J.; Gooren, H.P.A.; Bakker, G.; Hoogendam, C.W.; Huiskes, C.; Koopal, L.K.; Kruidhof, H.; Rooij, de G.H.
2010-01-01
Measuring soil water potentials is crucial to characterize vadose zone processes. Conventional tensiometers only measure until approximately -0.09 MPa, and indirect methods may suffer from the non-uniqueness in the relationship between matric potential and measured properties. Recently developed pol
Geometry of 2×2 hermitian matrices
Institute of Scientific and Technical Information of China (English)
HUANG; Liping(黄礼平); WAN; Zhexian(万哲先)
2002-01-01
Let D be a division ring which possesses an involution a→ā. Assume that F = {a∈D|a=ā} is a proper subfield of D and is contained in the center of D. It is pointed out that if D is of characteristic not two, D is either a separable quadratic extension of F or a division ring of generalized quaternions over F and that if D is of characteristic two, D is a separable quadratic extension of F. Thus the trace map Tr: D→F,hermitian matrices over D when n≥3 and now can be deleted. When D is a field, the fundamental theorem of 2×2 hermitian matrices over D has already been proved. This paper proves the fundamental theorem of 2×2 hermitian matrices over any division ring of generalized quaternions of characteristic not two.
INERTIA SETS OF SYMMETRIC SIGN PATTERN MATRICES
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
A sign pattern matrix is a matrixwhose entries are from the set {+ ,- ,0}. The symmetric sign pattern matrices that require unique inertia have recently been characterized. The purpose of this paper is to more generally investigate the inertia sets of symmetric sign pattern matrices. In particular, nonnegative fri-diagonal sign patterns and the square sign pattern with all + entries are examined. An algorithm is given for generating nonnegative real symmetric Toeplitz matrices with zero diagonal of orders n≥3 which have exactly two negative eigenvalues. The inertia set of the square pattern with all + off-diagonal entries and zero diagonal entries is then analyzed. The types of inertias which can be in the inertia set of any sign pattern are also obtained in the paper. Specifically, certain compatibility and consecutiveness properties are established.
Generalized Inverse Eigenvalue Problem for Centrohermitian Matrices
Institute of Scientific and Technical Information of China (English)
刘仲云; 谭艳祥; 田兆录
2004-01-01
In this paper we first consider the existence and the general form of solution to the following generalized inverse eigenvalue problem(GIEP) : given a set of n-dimension complex vectors { xj }jm = 1 and a set of complex numbers { λj} jm = 1, find two n × n centrohermitian matrices A, B such that { xj }jm = 1 and { λj }jm= 1 are the generalized eigenvectors and generalized eigenvalues of Ax = λBx, respectively. We then discuss the optimal approximation problem for the GIEP. More concretely, given two arbitrary matrices, A-, B- ∈Cn×n , we find two matrices A* and B* such that the matrix (A* ,B* ) is closest to (A- ,B-) in the Frobenius norm, where the matrix (A*, B* ) is the solution to the GIEP. We show that the expression of the solution of the optimal approximation is unique and derive the expression for it.
PRM: A database of planetary reflection matrices
Stam, D. M.; Batista, S. F. A.
2014-04-01
We present the PRM database with reflection matrices of various types of planets. With the matrices, users can calculate the total, and the linearly and circularly polarized fluxes of incident unpolarized light that is reflected by a planet for arbitrary illumination and viewing geometries. To allow for flexibility in these geometries, the database does not contain the elements of reflection matrices, but the coefficients of their Fourier series expansion. We describe how to sum these coefficients for given illumination and viewing geometries to obtain the local reflection matrix. The coefficients in the database can also be used to calculate flux and polarization signals of exoplanets, by integrating, for a given planetary phase angle, locally reflected fluxes across the visible part of the planetary disk. Algorithms for evaluating the summation for locally reflected fluxes, as applicable to spatially resolved observations of planets, and the subsequent integration for the disk-integrated fluxes, as applicable to spatially unresolved exoplanets are also in the database
On classification of dynamical r-matrices
Schiffmann, O
1997-01-01
Using recent results of P. Etingof and A. Varchenko on the Classical Dynamical Yang-Baxter equation, we reduce the classification of dynamical r-matrices on a commutative subalgebra l of a Lie algebra g to a purely algebraic problem when l admits a g^l-invariant complement, where g^l is the centralizer of l in g. Using this, we then classify all non skew-symmetric dynamical r-matrices when g is a simple Lie algebra and l a commutative subalgebra containing a regular semisimple element. This partially answers an open problem in [EV] q-alg/9703040, and generalizes the Belavin-Drinfled classification of constant r-matrices. This classification is similar and in some sense simpler than the Belavin-Drinfled classification.
A Multipath Connection Model for Traffic Matrices
Directory of Open Access Journals (Sweden)
Mr. M. V. Prabhakaran
2015-02-01
Full Text Available Peer-to-Peer (P2P applications have witnessed an increasing popularity in recent years, which brings new challenges to network management and traffic engineering (TE. As basic input information, P2P traffic matrices are of significant importance for TE. Because of the excessively high cost of direct measurement. In this paper,A multipath connection model for traffic matrices in operational networks. Media files can share the peer to peer, the localization ratio of peer to peer traffic. This evaluates its performance using traffic traces collected from both the real peer to peer video-on-demand and file-sharing applications. The estimation of the general traffic matrices (TM then used for sending the media file without traffic. Share the media file, source to destination traffic is not occur. So it give high performance and short time process.
Block TERM factorization of block matrices
Institute of Scientific and Technical Information of China (English)
SHE Yiyuan; HAO Pengwei
2004-01-01
Reversible integer mapping (or integer transform) is a useful way to realize Iossless coding, and this technique has been used for multi-component image compression in the new international image compression standard JPEG 2000. For any nonsingular linear transform of finite dimension, its integer transform can be implemented by factorizing the transform matrix into 3 triangular elementary reversible matrices (TERMs) or a series of single-row elementary reversible matrices (SERMs). To speed up and parallelize integer transforms, we study block TERM and SERM factorizations in this paper. First, to guarantee flexible scaling manners, the classical determinant (det) is generalized to a matrix function, DET, which is shown to have many important properties analogous to those of det. Then based on DET, a generic block TERM factorization,BLUS, is presented for any nonsingular block matrix. Our conclusions can cover the early optimal point factorizations and provide an efficient way to implement integer transforms for large matrices.
Advanced incomplete factorization algorithms for Stiltijes matrices
Energy Technology Data Exchange (ETDEWEB)
Il`in, V.P. [Siberian Division RAS, Novosibirsk (Russian Federation)
1996-12-31
The modern numerical methods for solving the linear algebraic systems Au = f with high order sparse matrices A, which arise in grid approximations of multidimensional boundary value problems, are based mainly on accelerated iterative processes with easily invertible preconditioning matrices presented in the form of approximate (incomplete) factorization of the original matrix A. We consider some recent algorithmic approaches, theoretical foundations, experimental data and open questions for incomplete factorization of Stiltijes matrices which are {open_quotes}the best{close_quotes} ones in the sense that they have the most advanced results. Special attention is given to solving the elliptic differential equations with strongly variable coefficients, singular perturbated diffusion-convection and parabolic equations.
Derzelle, Sylviane; Girault, Guillaume; Roest, Hendrik Ido Jan; Koene, Miriam
2015-06-01
Bacillus anthracis, the causative agent of anthrax, has been widely described as a clonal species. Here we report the use of both canonical SNP analysis and whole-genome sequencing to characterize the phylogenetic lineages of B. anthracis from the Netherlands. Eleven strains isolated over a 25-years period (1968-1993) were paired-end sequenced using parallel sequencing technology. Five canSNP groups or lineages, i.e. A.Br.001/002 (n=6), A.Br.Aust94 (n=2), A.Br.008/011 (n=1), A.Br.011/009 (n=1) and A.Br.Vollum (n=1) were identified. Comparative analyses, with a focus on SNPs discovery, were carried out using a total of 52 B. anthracis genomes. A phylogeographic "Dutch" cluster within the dominant A.Br.001/002 group was discovered, involving isolates from a single outbreak. Diagnostic SNPs specific to the newly identified sub-groups were developed into high-resolution melting SNP discriminative assays for the purpose of rapid molecular epidemiology. Phylogenetic relationships with strains from other parts of the world are discussed.
Nishibori, M; Hayashi, T; Tsudzuki, M; Yamamoto, Y; Yasue, H
2001-12-01
The Japanese quail (Coturnix japonica; JQ) is one of the domesticated fowl species of Japan. To provide DNA sequence information for examination of its phylogenetic position in the order Galliformes, the complete sequence of the JQ mitochondria was determined. Sequence analysis revealed that the JQ mitochondrial genome is a circular DNA of 16 697 basepairs (bp), which is smaller than the chicken mitochondrial DNA of 16 775 bp, but the genomic structure of JQ mitochondria was the same as that of the chicken. The sequence homologies of all mitochondrial genes including those for 12S and 16S ribosomal RNA (rRNA), between Japanese quail and chicken ranged from 78.0 to 89.9%. Because the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes had been reported in five species [Phasianus colchicus (ring-neck pheasant: RP), Gallus gallus domesticus (chicken: CH), Perdix perdix (grey partridge: GP), Bambusicola thoracia (Chinese bamboo partridge: CP), and Aythya americana (redhead: RH)], the concatenated nucleotide sequences (2184 bp) and amino acid sequences of these two genes were used in a phylogenetic analysis of JQ against these five species using a maximum likelihood (ML) method. Using the first and second bases of the codons, and the third base of the codons indicated a phylogenic tree of [RH, (RP, GP), (JQ, (CH, CP))]. A phylogenic tree of [RH, JQ, (RP, GP), (CH, CP)] was determined using amino acid sequences. Because the local bootstrap values for the JQ branch in these trees are not high, additional sequence is necessary for construction of a reliable tree.
Directory of Open Access Journals (Sweden)
Roberto Amato
Full Text Available Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or F(ST. We performed a genome-wide estimation of F(ST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of F(ST values between autosomes and heterochromosomes. When we compared the F(ST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of F(ST, while several pathways related to cell signalling, growth and morphogenesis showed high F(ST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.
Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Fagerness, Jesen A.; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Cardona Silgado, Julio C.; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M.J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Mesa Restrepo, Sandra C.; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlos N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosário, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Valencia Duarte, Ana V.; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Walkup, John; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G.M.; Yao, Yin; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Rouleau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson; Stewart, S. Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.
2014-01-01
Obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS) are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. Here, we report a combined genome-wide association study (GWAS) of TS and OCD in 2723 cases (1310 with OCD, 834 with TS, 579 with OCD plus TS/chronic tics (CT)), 5667 ancestry-matched controls, and 290 OCD parent-child trios. Although no individual single nucleotide polymorphisms (SNPs) achieved genome-wide significance, the GWAS signals were enriched for SNPs strongly associated with variations in brain gene expression levels, i.e. expression quantitative loci (eQTLs), suggesting the presence of true functional variants that contribute to risk of these disorders. Polygenic score analyses identified a significant polygenic component for OCD (p=2×10−4), predicting 3.2% of the phenotypic variance in an independent data set. In contrast, TS had a smaller, non-significant polygenic component, predicting only 0.6% of the phenotypic variance (p=0.06). No significant polygenic signal was detected across the two disorders, although the sample is likely underpowered to detect a modest shared signal. Furthermore, the OCD polygenic signal was significantly attenuated when cases with both OCD and TS/CT were included in the analysis (p=0.01). Previous work has shown that TS and OCD have some degree of shared genetic variation. However, the data from this study suggest that there are also distinct components to the genetic architectures of TS and OCD. Furthermore, OCD with co-occurring TS/CT may have different underlying genetic susceptibility compared to OCD alone. PMID:25158072
Edge fluctuations of eigenvalues of Wigner matrices
Döring, Hanna
2012-01-01
We establish a moderate deviation principle (MDP) for the number of eigenvalues of a Wigner matrix in an interval close to the edge of the spectrum. Moreover we prove a MDP for the $i$th largest eigenvalue close to the edge. The proof relies on fine asymptotics of the variance of the eigenvalue counting function of GUE matrices due to Gustavsson. The extension to large families of Wigner matrices is based on the Tao and Vu Four Moment Theorem. Possible extensions to other random matrix ensembles are commented.
Forecasting Covariance Matrices: A Mixed Frequency Approach
DEFF Research Database (Denmark)
Halbleib, Roxana; Voev, Valeri
This paper proposes a new method for forecasting covariance matrices of financial returns. The model mixes volatility forecasts from a dynamic model of daily realized volatilities estimated with high-frequency data with correlation forecasts based on daily data. This new approach allows...... for flexible dependence patterns for volatilities and correlations, and can be applied to covariance matrices of large dimensions. The separate modeling of volatility and correlation forecasts considerably reduces the estimation and measurement error implied by the joint estimation and modeling of covariance...... matrix dynamics. Our empirical results show that the new mixing approach provides superior forecasts compared to multivariate volatility specifications using single sources of information....
Almost Hadamard matrices: general theory and examples
Banica, Teodor; Zyczkowski, Karol
2012-01-01
We develop a general theory of "almost Hadamard matrices". These are by definition the matrices $H\\in M_N(\\mathbb R)$ having the property that $U=H/\\sqrt{N}$ is orthogonal, and is a local maximum of the 1-norm on O(N). Our study includes a detailed discussion of the circulant case ($H_{ij}=\\gamma_{j-i}$) and of the two-entry case ($H_{ij}\\in\\{x,y\\}$), with the construction of several families of examples, and some 1-norm computations.
Extremal spacings of random unitary matrices
Smaczynski, Marek; Kus, Marek; Zyczkowski, Karol
2012-01-01
Extremal spacings between unimodular eigenvalues of random unitary matrices of size N pertaining to circular ensembles are investigated. Probability distributions for the minimal spacing for various ensembles are derived for N=4. We show that for large matrices the average minimal spacing s_min of a random unitary matrix behaves as N^(-1/(1+B)) for B equal to 0,1 and 2 for circular Poisson, orthogonal and unitary ensembles, respectively. For these ensembles also asymptotic probability distributions P(s_min) are obtained and the statistics of the largest spacing s_max are investigated.
Age differences on Raven's Coloured Progressive Matrices.
Panek, P E; Stoner, S B
1980-06-01
Raven's Coloured Progressive Matrices was administered to 150 subjects (75 males, 75 females) ranging in age from 20 to 86 yr. Subjects were placed into one of three age groups: adult (M age = 27.04 yr.), middle-age (M age = 53.36 yr.), old (M age = 73.78 yr.), with 25 males and 25 females in each age group. Significant differences between age groups on the matrices were obtained after partialing out the effects of educational level, while sex of subject was not significant.
Super Special Codes using Super Matrices
Kandasamy, W B Vasantha; Ilanthenral, K
2010-01-01
The new classes of super special codes are constructed in this book using the specially constructed super special vector spaces. These codes mainly use the super matrices. These codes can be realized as a special type of concatenated codes. This book has four chapters. In chapter one basic properties of codes and super matrices are given. A new type of super special vector space is constructed in chapter two of this book. Three new classes of super special codes namely, super special row code, super special column code and super special codes are introduced in chapter three. Applications of these codes are given in the final chapter.
Determinación y propiedades de H-matrices
SCOTT GUILLEARD, JOSÉ ANTONIO
2015-01-01
[EN] The essential topic of this memory is the study of H-matrices as they were introduced by Ostrowski and hereinafter extended and developed by different authors. In this study three slopes are outlined: 1) the iterative or automatic determination of H-matrices, 2) the properties inherent in the H-matrices and 3) the matrices related to H-matrices. H-matrices acquire every time major relevancy due to the fact that they arise in numerous applications so much in Mathematics,...
LAZAR STANKOV; KARL SCHWEIZER
2007-01-01
This paper examines the effects of complexity-enhancing manipulations of two cognitive tasks – Swaps and Triplet Numbers tests (Stankov, 2000) – on their relationship with Raven’s Progressive Matrices test representing aspects of fluid intelligence. The complexity manipulations involved four treatment levels, each requiring an increasing number of components and relationships among these components. The accuracy, speed of processing, and confidence measures were decomposed into experimental a...
Universal portfolios generated by Toeplitz matrices
Tan, Choon Peng; Chu, Sin Yen; Pan, Wei Yeing
2014-06-01
Performance of universal portfolios generated by Toeplitz matrices is studied in this paper. The general structure of the companion matrix of the generating Toeplitz matrix is determined. Empirical performance of the threeband and nine-band Toeplitz universal portfolios on real stock data is presented. Pseudo Toeplitz universal portfolios are studied with promising empirical achievement of wealth demonstrated.
Parametrizations of Positive Matrices With Applications
Tseng, M C; Ramakrishna, V; Zhou, Hong
2006-01-01
This paper reviews some characterizations of positive matrices and discusses which lead to useful parametrizations. It is argued that one of them, which we dub the Schur-Constantinescu parametrization is particularly useful. Two new applications of it are given. One shows all block-Toeplitz states are PPT. The other application is to relaxation rates.
Generation Speed in Raven's Progressive Matrices Test.
Verguts, Tom; De Boeck, Paul; Maris, Eric
1999-01-01
Studied the role of response fluency on results of the Raven's Advanced Progressive Matrices (APM) Test by comparing scores on a test of generation speed (speed of generating rules that govern the items) with APM test performance for 127 Belgian undergraduates. Discusses the importance of generation speed in intelligence. (SLD)
Deconvolution and Regularization with Toeplitz Matrices
DEFF Research Database (Denmark)
Hansen, Per Christian
2002-01-01
of these discretized deconvolution problems, with emphasis on methods that take the special structure of the matrix into account. Wherever possible, analogies to classical DFT-based deconvolution problems are drawn. Among other things, we present direct methods for regularization with Toeplitz matrices, and we show...
Extremal norms of graphs and matrices
Nikiforov, Vladimir
2010-01-01
In the recent years, the trace norm of graphs has been extensively studied under the name of graph energy. In this paper some of this research is extended to more general matrix norms, like the Schatten p-norms and the Ky Fan k-norms. Whenever possible the results are given both for graphs and general matrices.
Numerical Methods for Structured Matrices and Applications
Bini, Dario A; Olshevsky, Vadim; Tyrtsyhnikov, Eugene; van Barel, Marc
2010-01-01
This cross-disciplinary volume brings together theoretical mathematicians, engineers and numerical analysts and publishes surveys and research articles related to the topics where Georg Heinig had made outstanding achievements. In particular, this includes contributions from the fields of structured matrices, fast algorithms, operator theory, and applications to system theory and signal processing.
Generation speed in Raven's Progressive Matrices Test
Verguts, T.; Boeck, P. De; Maris, E.G.G.
1999-01-01
In this paper, we investigate the role of response fluency on a well-known intelligence test, Raven's (1962) Advanced Progressive Matrices (APM) test. Critical in solving this test is finding rules that govern the items. Response fluency is conceptualized as generation speed or the speed at which a
Positivity of Matrices with Generalized Matrix Functions
Institute of Scientific and Technical Information of China (English)
Fuzhen ZHANG
2012-01-01
Using an elementary fact on matrices we show by a unified approach the positivity of a partitioned positive semidefinite matrix with each square block replaced by a compound matrix,an elementary symmetric function or a generalized matrix function.In addition,we present a refined version of the Thompson determinant compression theorem.
Robust stability of interval parameter matrices
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
This note is devoted to the problem of robust stability of interval parameter matrices. Based on some basic facts relating the H∞ norm of a transfer function to the Riccati matrix inequality and Hamilton matrix, several test conditions with parameter perturbation bounds are obtained.
Spectral averaging techniques for Jacobi matrices
del Rio, Rafael; Schulz-Baldes, Hermann
2008-01-01
Spectral averaging techniques for one-dimensional discrete Schroedinger operators are revisited and extended. In particular, simultaneous averaging over several parameters is discussed. Special focus is put on proving lower bounds on the density of the averaged spectral measures. These Wegner type estimates are used to analyze stability properties for the spectral types of Jacobi matrices under local perturbations.
Hierarchical matrix approximation of large covariance matrices
Litvinenko, Alexander
2015-11-30
We approximate large non-structured Matérn covariance matrices of size n×n in the H-matrix format with a log-linear computational cost and storage O(kn log n), where rank k ≪ n is a small integer. Applications are: spatial statistics, machine learning and image analysis, kriging and optimal design.
Correspondence Analysis of Archeological Abundance Matrices
de Leeuw, Jan
2007-01-01
In this chapter we discuss the Correspondence Analysis (CA) techniques used in other chapters of this book. CA is presented as a multivariate exploratory technique, as a proximity analysis technique based on Benzecri distances, as a technique to decompose the total chi-square of frequency matrices, and as a least squares method to ﬁt association or ordination models.
Moment matrices, border bases and radical computation
Mourrain, B.; Lasserre, J.B.; Laurent, M.; Rostalski, P.; Trebuchet, P.
2011-01-01
In this paper, we describe new methods to compute the radical (resp. real radical) of an ideal, assuming it complex (resp. real) variety is nte. The aim is to combine approaches for solving a system of polynomial equations with dual methods which involve moment matrices and semi-denite programming.
Moment matrices, border bases and radical computation
Mourrain, B.; Lasserre, J.B.; Laurent, M.; Rostalski, P.; Trebuchet, P.
2013-01-01
In this paper, we describe new methods to compute the radical (resp. real radical) of an ideal, assuming it complex (resp. real) variety is nte. The aim is to combine approaches for solving a system of polynomial equations with dual methods which involve moment matrices and semi-denite programming.
Spectral properties of random triangular matrices
Basu, Riddhipratim; Ganguly, Shirshendu; Hazra, Rajat Subhra
2011-01-01
We provide a relatively elementary proof of the existence of the limiting spectral distribution (LSD) of symmetric triangular patterned matrices and also show their joint convergence. We also derive the expressions for the moments of the LSD of the symmetric triangular Wigner matrix using properties of Catalan words.
Affine processes on positive semidefinite matrices
Cuchiero, Christa; Mayerhofer, Eberhard; Teichmann, Josef
2009-01-01
This paper provides the mathematical foundation for stochastically continuous affine processes on the cone of positive semidefinite symmetric matrices. These matrix-valued affine processes have arisen from a large and growing range of useful applications in finance, including multi-asset option pricing with stochastic volatility and correlation structures, and fixed-income models with stochastically correlated risk factors and default intensities.
Malware Analysis Using Visualized Image Matrices
Directory of Open Access Journals (Sweden)
KyoungSoo Han
2014-01-01
Full Text Available This paper proposes a novel malware visual analysis method that contains not only a visualization method to convert binary files into images, but also a similarity calculation method between these images. The proposed method generates RGB-colored pixels on image matrices using the opcode sequences extracted from malware samples and calculates the similarities for the image matrices. Particularly, our proposed methods are available for packed malware samples by applying them to the execution traces extracted through dynamic analysis. When the images are generated, we can reduce the overheads by extracting the opcode sequences only from the blocks that include the instructions related to staple behaviors such as functions and application programming interface (API calls. In addition, we propose a technique that generates a representative image for each malware family in order to reduce the number of comparisons for the classification of unknown samples and the colored pixel information in the image matrices is used to calculate the similarities between the images. Our experimental results show that the image matrices of malware can effectively be used to classify malware families both statically and dynamically with accuracy of 0.9896 and 0.9732, respectively.
Directory of Open Access Journals (Sweden)
Malihe Masomian
Full Text Available Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.
Richards, R Souza; Adams, I P; Kreuze, J F; De Souza, J; Cuellar, W; Dullemans, A M; Van Der Vlugt, R A A; Glover, R; Hany, U; Dickinson, M; Boonham, N
2014-04-01
The complete nucleotide sequences of RNA 1 and RNA 2 of the nepovirus potato black ringspot virus (PBRSV) from two different isolates were determined, as well as partial sequences from two additional isolates. RNA1 is 7,579-7,598 nucleotides long and contains one single open reading frame (ORF), which is translated into a large polyprotein with 2,325 amino acids and a molecular weight of 257 kDa. The complete sequence of RNA2 ranges from 3857 to 3918 nt between the different isolates. It encodes a polyprotein of 1079-1082 amino acids with a molecular weight of 120 kDa. Sequence comparison using the Pro-Pol region and CP showed that all four isolates formed two distinct groups, corresponding to potato and arracacha, that were closely related to each other and also to tobacco ringspot virus (TRSV). Comparing our data to those obtained with other nepoviruses, our results confirm that PBRSV belongs to a distinct species and is a member of subgroup A in the genus Nepovirus based on its RNA2 size, genome organization, and nucleotide sequence.
Klinger, Christen M; Ramirez-Macias, Inmaculada; Herman, Emily K; Turkewitz, Aaron P; Field, Mark C; Dacks, Joel B
With advances in DNA sequencing technology, it is increasingly common and tractable to informatically look for genes of interest in the genomic databases of parasitic organisms and infer cellular states. Assignment of a putative gene function based on homology to functionally characterized genes in other organisms, though powerful, relies on the implicit assumption of functional homology, i.e. that orthology indicates conserved function. Eukaryotes reveal a dazzling array of cellular features and structural organization, suggesting a concomitant diversity in their underlying molecular machinery. Significantly, examples of novel functions for pre-existing or new paralogues are not uncommon. Do these examples undermine the basic assumption of functional homology, especially in parasitic protists, which are often highly derived? Here we examine the extent to which functional homology exists between organisms spanning the eukaryotic lineage. By comparing membrane trafficking proteins between parasitic protists and traditional model organisms, where direct functional evidence is available, we find that function is indeed largely conserved between orthologues, albeit with significant adaptation arising from the unique biological features within each lineage. Copyright Â© 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
Johan Buitendag
2005-10-01
Full Text Available The author presents a review article on the book, Brave new world? Theology, ethics and the human genome, edited by Celia Deane-Drummond and published in 2003 by T&T Clark International in London. After a rather elaborate exposition, he appraises the collection of essays in terms of the dialogue between theology and the natural sciences. As an acid test, he assesses the challenge Kant, however, dealt with, namely to combine and to separate the right things. Kant pushed this to extremes and ended up with both solipsism and dualism. This article tackles the challenge differently and concludes that theology is an a posteriori science and that by means of différance, knowledge of the noumenon is indeed possible. The author therefore appreciates the different contributions in the book in this light. Deane-Drummond’s proposal that a virtue ethic should be complemented by certain biblical values is therefore viewed rather sceptically. This remains a transcendental enterprise where epistemology precedes ontology.
Relations between performance on the advance matrices and the EPI in high-intelligence subjects.
Gibson, H B
1975-11-01
This study continues the investigation of the relationship between performance on tests of intelligence, and the personality parameters of the Eysenckian theoretical framework. Candidates for admission to an honours degree course (n = 281) were given the Advanced Progressive Matrices as a screening device. Those admitted to the course were on later occasions given both forms of the Eysenck Personality Inventory (EPI). In view of problems of test-retest on the EPI, scores were analysed in a novel fashion to give three groups: 'introverts', 'extraverts' and 'ambiverts'. The 'introverts' scored significantly highest on the Matrices, but the scores of the 'ambiverts' were lowest. Neuroticism showed little interaction with other variables. These results are discussed in terms of the theory of reactive inhibition. New data on the Advanced Progressive Matrices are given which are significantly higher than the published university norms.
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
Directory of Open Access Journals (Sweden)
Xing-Xing Shen
2016-12-01
Full Text Available Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence and two data matrices (amino acids or the first two codon positions yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.
Karoui, Noureddine El
2009-01-01
We place ourselves in the setting of high-dimensional statistical inference, where the number of variables $p$ in a data set of interest is of the same order of magnitude as the number of observations $n$. More formally, we study the asymptotic properties of correlation and covariance matrices, in the setting where $p/n\\to\\rho\\in(0,\\infty),$ for general population covariance. We show that, for a large class of models studied in random matrix theory, spectral properties of large-dimensional correlation matrices are similar to those of large-dimensional covarance matrices. We also derive a Mar\\u{c}enko--Pastur-type system of equations for the limiting spectral distribution of covariance matrices computed from data with elliptical distributions and generalizations of this family. The motivation for this study comes partly from the possible relevance of such distributional assumptions to problems in econometrics and portfolio optimization, as well as robustness questions for certain classical random matrix result...
Oligomers Modulate Interfibril Branching and Mass Transport Properties of Collagen Matrices
Whittington, Catherine F.; Brandner, Eric; Teo, Ka Yaw; Han, Bumsoo; Nauman, Eric; Voytik-Harbin, Sherry L.
2013-01-01
Mass transport within collagen-based matrices is critical to tissue development, repair, and pathogenesis as well as the design of next generation tissue engineering strategies. This work shows how collagen precursors, specified by intermolecular cross-link composition, provide independent control of collagen matrix mechanical and transport properties. Collagen matrices were prepared from tissue-extracted monomers or oligomers. Viscoelastic behavior was measured in oscillatory shear and unconfined compression. Matrix permeability and diffusivity were measured using gravity-driven permeametry and integrated optical imaging, respectively. Both collagen types showed an increase in stiffness and permeability hindrance with increasing collagen concentration (fibril density); however, different physical property-concentration relationships were noted. Diffusivity wasn’t affected by concentration for either collagen type over the range tested. In general, oligomer matrices exhibited a substantial increase in stiffness and only a modest decrease in transport properties when compared to monomer matrices prepared at the same concentration. The observed differences in viscoelastic and transport properties were largely attributed to increased levels of interfibril branching within oligomer matrices. The ability to relate physical properties to relevant microstructure parameters, including fibril density and interfibril branching, is expected to advance the understanding of cell-matrix signaling as well as facilitate model-based prediction and design of matrix-based therapeutic strategies. PMID:23842082
Influence of dairy matrices on nutrient release in a simulated gastrointestinal environment.
Lamothe, Sophie; Rémillard, Nathalie; Tremblay, Julie; Britten, Michel
2017-02-01
The objective of this study was to compare the kinetics of the release of nutrients (peptides and fatty acids) from different dairy matrices (milks, yogurts, and cheeses) in a simulated gastrointestinal environment. Prior to processing, different heat and homogenization treatments were applied to milks, and different drainage pH levels were used to control calcium concentration in cheeses. The dairy matrices were then subjected to simulated digestion. Matrix degradation, protein hydrolysis, and fat hydrolysis were analyzed during the gastric and intestinal digestion phases. Intense heat treatment of milk induced faster digestion of proteins in the gastric environment. Cheeses were more resistant to protein and lipid digestion than liquid or semi-solid matrices were. No direct relationship could be established between disintegration kinetics and cheese rheological properties. Fatty acid release in the intestinal phase was much faster when matrices were produced from homogenized milk. For cheeses, greater fatty acid release could not be related to faster matrix disintegration, suggesting that the lipid droplet size dispersion was more important than matrix breakdown was for the modulation of lipid digestion kinetics. Calcium soaps were produced in the intestinal environment, and their concentration was higher during the digestion of cheeses in comparison with milks and yogurts. These results suggest that processing-induced modifications to the composition, microstructure, and rheological properties of dairy matrices could be used to control nutrient delivery. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.
Institute of Scientific and Technical Information of China (English)
YANG Li-ming; WANG Yi-hao; PENG Yu; MIN Jiang-tao; HANG Su-qin; ZHU Wei-yun
2016-01-01
To investigate the roles ofEscherichia coli in the pathogenesis of postpartum uterine diseases in dairy cows, a total of 145E. coli isolates were recovered from 18 healthy cows (61 isolates) and 25 cows with clinical endometritis (84 isolates) at 25–35 days after parturition. Genomic characteristics including phylogenetic grouping, genetic diversity and virulence genes of E. coli isolates were screened to proifle the characteristics related to uterine infections. The susceptibility of the bacteria against 23 antibiotics was also evaluated to support prevention and treatment of clinical cases. Genetic diversity ofE. coli identiifed by random ampliifcation of polymorphic DNA (RAPD) revealed 103 clonal types, including 3 common types to unaffected cows and endometritis cows, 39 types speciifc to healthy cows and 61 types in endometritis subjects. In addition, the isolates from endometritis uteri showed more genetic variability compared with that of healthy cows. Ac-cording to the ifndings of phylogenetic grouping, theE. coli isolates were assigned to group A (35.9%), B1 (59.3%) and D (4.8%). The expression of 10 of 20 virulence gens were detected positively, and onlyifmH gene was revealed signiifcantly (P<0.05) associated with endometritis. From antimicrobial susceptibility test,E. coli was found highly resistant to tetracy-cline, ampicilin, carbenicilin and amoxicilin, but sensitive to amikacin, netilmicin, tobramycin, cefepime and ceftazidime. In conclusion,E. coliwere extensively observed in both healthy and endometritis cows, and presented a large clonal types, however, ifmH was the only gene observed associated with clinical endometritis. Our results suggest that the drugs like amikacin, netilmicin, tobramycin and cefepime could be considered for preventing and treating clinical endometritis in the practical management of dairy cow.
The primitive matrices of sandwich semigroups of generalized circulant Boolean matrices
Institute of Scientific and Technical Information of China (English)
LIU Jian-ping; CHEN Jin-song
2013-01-01
Let Gn(C) be the sandwich semigroup of generalized circulant Boolean matrices with the sandwich matrix C and GC (Jn) the set of all primitive matrices in Gn(C). In this paper, some necessary and suﬃ cient conditions for A in the semigroup Gn(C) to be primitive are given. We also show that GC (Jn) is a subsemigroup of Gn(C).
Structure - property relations of high-temperature composite polymer matrices
Energy Technology Data Exchange (ETDEWEB)
Morgan, R.J.; Jurek, R.J.; Larive, D.E. [Michigan Molecular Institute, Midland, MI (United States); Tung, C.M. [Northrop Corp., Hawthorne, CA (United States); Donnellan, T. [Naval Air Development Center, Warminster, PA (United States)
1993-12-31
The structure-deformation-failure mode-mechanical property relations of high-temperature thermoplastic polyimide and thermoset bismaleimide (BMI) polymeric matrices and their composites will be discussed. In the case of polyimides, the effects of test temperature, thermal history, strain rate, type of filler, and filler volume fraction on structure - property relations will be discussed. For BMIs we report systematic Fourier transform infrared spectroscopy and differential scanning calorimetry studies of the cure reactions as a function of chemical composition and time - temperature cure conditions and then describe the resultant cross-linked network structure based on our understanding of the cure reactions. The optimization of the BMI matrix toughness will be considered in terms of network structure and process-induced matrix microcracking. We also describe optimization of composite prepreg, lamination and postcure conditions based on cure kinetics, and their relationship to the BMI viscosity-time-temperature profiles. The critical processing-performance limitations of high-temperature polymer matrices will be critically discussed, and toughening approaches to address these limitations, such as toughness over a wide temperature range, will be presented. 7 refs., 2 figs., 1 tab.
Detailed assessment of homology detection using different substitution matrices
Institute of Scientific and Technical Information of China (English)
LI Jing; WANG Wei
2006-01-01
Homology detection plays a key role in bioinformatics, whereas substitution matrix is one of the most important components in homology detection. Thus, besides the improvement of alignment algorithms, another effective way to enhance the accuracy of homology detection is to use proper substitution matrices or even construct new matrices.A study on the features of various matrices and on the comparison of the performances between different matrices in homology detection enable us to choose the most proper or optimal matrix for some specific applications. In this paper, by taking BLOSUM matrices as an example, some detailed features of matrices in homology detection are studied by calculating the distributions of numbers of recognized proteins over different sequence identities and sequence lengths. Our results clearly showed that different matrices have different preferences and abilities to the recognition of remote homologous proteins. Furthermore, detailed features of the various matrices can be used to improve the accuracy of homology detection.
Electrospun human keratin matrices as templates for tissue regeneration.
Sow, Wan Ting; Lui, Yuan Siang; Ng, Kee Woei
2013-04-01
The aim of this work was to study the feasibility of fabricating human hair keratin matrices through electrospinning and to evaluate the potential of these matrices for tissue regeneration. Keratin was extracted from human hair using Na2S and blended with poly(ethylene oxide) in the weight ratio of 60:1 for electrospinning. Physical morphology and chemical properties of the matrices were characterized using scanning electron microscopy and Fourier transform infrared spectroscopy, respectively. Cell viability and morphology of murine and human fibroblasts cultured on the matrices were evaluated through the Live/Dead(®) assay and scanning electron microscopy. Electrospun keratin matrices were successfully produced without affecting the chemical conformation of keratin. Fibroblasts cultured on keratin matrices showed healthy morphology and penetration into matrices at day 7. Electrospun human hair keratin matrices provide a bioinductive and structural environment for cell growth and are thus attractive as alternative templates for tissue regeneration.
Visualization of results from genomic evaluations.
Cole, J B; VanRaden, P M
2010-06-01
Genomic predictions of estimated breeding values (EBV) for dairy cattle include effects of tens of thousands of markers distributed over 30 chromosomes for many traits. There are so many numbers that data are difficult to compare, levels of detail are obscured, and data cannot easily be tabulated. Well-designed graphics can present more information in a smaller area than text or tables and provide insight into the data. Subtle differences can be detected more easily among graphics than among data grids, allowing information to be presented with greater density. Genomic data can be visualized at several levels, such as the distribution of marker effects across the genome and relationships among markers on the same chromosome. All markers affecting a trait can be plotted on the same ordinate to visualize the distribution of marker effects across the genome, colors or textures can be used to differentiate between chromosomes, and stacked graphs can be constructed to compare interesting groups of traits. Chromosomal EBV can be presented as high-resolution graphics embedded in text to provide an overview of individual animals for comparison to potential mates. Small multiples of chromosomal genetic correlation matrices from which nonsignificant values have been excluded can be used to identify interesting patterns of association among traits, such as that on chromosome 18 associated with calving traits, conformation, and economic merit. Line plots of marker effects for recessive traits can be used to quickly locate chromosomal regions in which causative mutations are probably located, identifying areas of interest for further study. These graphics are easily produced automatically and added to online query systems, providing users with novel information at little cost.
U.S. Environmental Protection Agency — Relationships of temperature and CNT mass (SWCNT, MWCNT, MWCNT-COOH) were developed for three environmental matrices (sand, soil and sludge) spiked with known...
Listman, J B; Malison, R T; Sanichwankul, K; Ittiwut, C; Mutirangura, A; Gelernter, J
2011-02-01
In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have nonmutually intelligible languages. To test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2,445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results ofrecent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages.
Higher-Order Singular Systems and Polynomial Matrices
2005-01-01
There is a one-to-one correspondence between the set of quadruples of matrices defining singular linear time-invariant dynamical systems and a subset of the set of polynomial matrices. This correspondence preserves the equivalence relations introduced in both sets (feedback-similarity and strict equivalence): two quadruples of matrices are feedback-equivalent if, and only if, the polynomial matrices associated to them are also strictly equivalent. Los sistemas lineales singulares...
Energy Technology Data Exchange (ETDEWEB)
Zhang, Xiaoxiao; Snijders, Antoine; Segraves, Richard; Zhang,Xiuqing; Niebuhr, Anita; Albertson, Donna; Yang, Huanming; Gray, Joe; Niebuhr, Erik; Bolund, Lars; Pinkel, Dan
2007-07-03
We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.
Relationship of mitochondrial genome characteristic variation and human evolution%线粒体基因组特征性变异与人类进化
Institute of Scientific and Technical Information of China (English)
顾明亮
2010-01-01
It currently remains a puzzle for what signature of natural selection casts in human genome.Mitochondrial DNA (mtDNA) differs from nuclear DNA in many aspects such as lack of recombination and maternal inheritance etc. These essential biological characteristics including the natural selection were detected easily in mtDNA, and thus offer a preponderant and potential tool for the investigation between natural selection and adaptation in human evolutionary history. In this review, we elucidated the progress of relationships between mtDNA specific variation and human evolution based on the mitochondrial genome phylogenesis and analysis of encoding gene variation.%自然选择究竟在人类基因组留下怎样的印记,是我们今天一直想解开的秘密.由于线粒体基因组缺少重组和母系遗传等区别于核基因组的诸多特性,使在基因组水平上一些重要的生物学特征如自然选择等较易被检测.因此,为我们探讨自然选择与人类进化和适应的关系提供了具有巨大优势和潜力的研究工具.在本文中,依据线粒体基因组的系统发生和编码基因的变异分析,系统地阐述了基因组特征性变异与人类进化的关系及研究进展.
Monard, Cécile; Mchergui, Chokri; Nunan, Naoise; Martin-Laurent, Fabrice; Vieublé-Gonod, Laure
2012-09-01
The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of (13) C-glucose and (13) C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (-0.001, -0.01 and -0.316 MPa) in 6 × 6 × 6 mm(3) cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.
Decision Matrices: Tools to Enhance Middle School Engineering Instruction
Gonczi, Amanda L.; Bergman, Brenda G.; Huntoon, Jackie; Allen, Robin; McIntyre, Barb; Turner, Sheri; Davis, Jen; Handler, Rob
2017-01-01
Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an…
19 CFR 10.90 - Master records and metal matrices.
2010-04-01
... 19 Customs Duties 1 2010-04-01 2010-04-01 false Master records and metal matrices. 10.90 Section... Master Records, and Metal Matrices § 10.90 Master records and metal matrices. (a) Consumption entries... made, of each master record or metal matrix covered thereby. (c) A bond on Customs Form 301,...
Decision Matrices: Tools to Enhance Middle School Engineering Instruction
Gonczi, Amanda L.; Bergman, Brenda G.; Huntoon, Jackie; Allen, Robin; McIntyre, Barb; Turner, Sheri; Davis, Jen; Handler, Rob
2017-01-01
Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an…
On Skew Circulant Type Matrices Involving Any Continuous Fibonacci Numbers
Directory of Open Access Journals (Sweden)
Zhaolin Jiang
2014-01-01
inverse matrices of them by constructing the transformation matrices. Furthermore, the maximum column sum matrix norm, the spectral norm, the Euclidean (or Frobenius norm, and the maximum row sum matrix norm and bounds for the spread of these matrices are given, respectively.
Waller, Niels G
2016-01-01
For a fixed set of standardized regression coefficients and a fixed coefficient of determination (R-squared), an infinite number of predictor correlation matrices will satisfy the implied quadratic form. I call such matrices fungible correlation matrices. In this article, I describe an algorithm for generating positive definite (PD), positive semidefinite (PSD), or indefinite (ID) fungible correlation matrices that have a random or fixed smallest eigenvalue. The underlying equations of this algorithm are reviewed from both algebraic and geometric perspectives. Two simulation studies illustrate that fungible correlation matrices can be profitably used in Monte Carlo research. The first study uses PD fungible correlation matrices to compare penalized regression algorithms. The second study uses ID fungible correlation matrices to compare matrix-smoothing algorithms. R code for generating fungible correlation matrices is presented in the supplemental materials.
Salvo, Gabriele; Bacchetta, Gianluigi; Ghahremaninejad, Farrokh; Conti, Elena
2008-12-01
Phylogenetic analyses of three cpDNA markers (matK, rpl16, and trnL-trnF) were performed to evaluate previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morphological, phytochemical, and molecular datasets of Ruteae were then compared to look for possible patterns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phylogenetic patterns between the phytochemical and molecular trees might be best explained in terms of convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies provided support for the clades of the molecular tree, while most of the morphological characters traditionally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states.
Lectures on S-matrices and Integrability
Bombardelli, Diego
2016-01-01
In these notes we review the S-matrix theory in (1+1)-dimensional integrable models, focusing mainly on the relativistic case. Once the main definitions and physical properties are introduced, we discuss the factorization of scattering processes due to integrability. We then focus on the analytic properties of the 2-particle scattering amplitude and illustrate the derivation of the S-matrices for all the possible bound states using the so-called bootstrap principle. General algebraic structures underlying the S-matrix theory and its relation with the form factors axioms are briefly mentioned. Finally, we discuss the S-matrices of sine-Gordon and SU(2), SU(3) chiral Gross-Neveu models. This is part of a collection of lecture notes for the Young Researchers Integrability School, organised by the GATIS network at Durham University on 6-10 July 2015.
Inferring Passenger Type from Commuter Eigentravel Matrices
Legara, Erika Fille
2015-01-01
A sufficient knowledge of the demographics of a commuting public is essential in formulating and implementing more targeted transportation policies, as commuters exhibit different ways of traveling. With the advent of the Automated Fare Collection system (AFC), probing the travel patterns of commuters has become less invasive and more accessible. Consequently, numerous transport studies related to human mobility have shown that these observed patterns allow one to pair individuals with locations and/or activities at certain times of the day. However, classifying commuters using their travel signatures is yet to be thoroughly examined. Here, we contribute to the literature by demonstrating a procedure to characterize passenger types (Adult, Child/Student, and Senior Citizen) based on their three-month travel patterns taken from a smart fare card system. We first establish a method to construct distinct commuter matrices, which we refer to as eigentravel matrices, that capture the characteristic travel routines...
Astronomical Receiver Modelling Using Scattering Matrices
King, O G; Copley, C; Davis, R J; Leahy, J P; Leech, J; Muchovej, S J C; Pearson, T J; Taylor, Angela C
2014-01-01
Proper modelling of astronomical receivers is vital: it describes the systematic errors in the raw data, guides the receiver design process, and assists data calibration. In this paper we describe a method of analytically modelling the full signal and noise behaviour of arbitrarily complex radio receivers. We use electrical scattering matrices to describe the signal behaviour of individual components in the receiver, and noise correlation matrices to describe their noise behaviour. These are combined to produce the full receiver model. We apply this approach to a specified receiver architecture: a hybrid of a continous comparison radiometer and correlation polarimeter designed for the C-Band All-Sky Survey. We produce analytic descriptions of the receiver Mueller matrix and noise temperature, and discuss how imperfections in crucial components affect the raw data. Many of the conclusions drawn are generally applicable to correlation polarimeters and continuous comparison radiometers.
Approximate inverse preconditioners for general sparse matrices
Energy Technology Data Exchange (ETDEWEB)
Chow, E.; Saad, Y. [Univ. of Minnesota, Minneapolis, MN (United States)
1994-12-31
Preconditioned Krylov subspace methods are often very efficient in solving sparse linear matrices that arise from the discretization of elliptic partial differential equations. However, for general sparse indifinite matrices, the usual ILU preconditioners fail, often because of the fact that the resulting factors L and U give rise to unstable forward and backward sweeps. In such cases, alternative preconditioners based on approximate inverses may be attractive. We are currently developing a number of such preconditioners based on iterating on each column to get the approximate inverse. For this approach to be efficient, the iteration must be done in sparse mode, i.e., we must use sparse-matrix by sparse-vector type operatoins. We will discuss a few options and compare their performance on standard problems from the Harwell-Boeing collection.
Asymptotic properties of random matrices and pseudomatrices
Lenczewski, Romuald
2010-01-01
We study the asymptotics of sums of matricially free random variables called random pseudomatrices, and we compare it with that of random matrices with block-identical variances. For objects of both types we find the limit joint distributions of blocks and give their Hilbert space realizations, using operators called `matricially free Gaussian operators'. In particular, if the variance matrices are symmetric, the asymptotics of symmetric blocks of random pseudomatrices agrees with that of symmetric random blocks. We also show that blocks of random pseudomatrices are `asymptotically matricially free' whereas the corresponding symmetric random blocks are `asymptotically symmetrically matricially free', where symmetric matricial freeness is obtained from matricial freeness by an operation of symmetrization. Finally, we show that row blocks of square, lower-block-triangular and block-diagonal pseudomatrices are asymptotically free, monotone independent and boolean independent, respectively.
Non-Hermitean Wishart random matrices (I)
Kanzieper, Eugene
2010-01-01
A non-Hermitean extension of paradigmatic Wishart random matrices is introduced to set up a theoretical framework for statistical analysis of (real, complex and real quaternion) stochastic time series representing two "remote" complex systems. The first paper in a series provides a detailed spectral theory of non-Hermitean Wishart random matrices composed of complex valued entries. The great emphasis is placed on an asymptotic analysis of the mean eigenvalue density for which we derive, among other results, a complex-plane analogue of the Marchenko-Pastur law. A surprising connection with a class of matrix models previously invented in the context of quantum chromodynamics is pointed out. This provides one more evidence of the ubiquity of Random Matrix Theory.
Determinants of adjacency matrices of graphs
Directory of Open Access Journals (Sweden)
Alireza Abdollahi
2012-12-01
Full Text Available We study the set of all determinants of adjacency matrices of graphs with a given number of vertices. Using Brendan McKay's data base of small graphs, determinants of graphs with at most $9$ vertices are computed so that the number of non-isomorphic graphs with given vertices whose determinants are all equal to a number is exhibited in a table. Using an idea of M. Newman, it is proved that if $G$ is a graph with $n$ vertices and ${d_1,dots,d_n}$ is the set of vertex degrees of $G$, then $gcd(2m,d^2$ divides the determinant of the adjacency matrix of $G$, where $d=gcd(d_1,dots,d_n$. Possible determinants of adjacency matrices of graphs with exactly two cycles are obtained.
MULTIFRACTAL STRUCTURE AND PRODUCT OF MATRICES
Institute of Scientific and Technical Information of China (English)
Lau Ka-sing
2003-01-01
There is a well established multifractal theory for self-similar measures generated by non-overlapping contractive similutudes.Our report here concerns those with overlaps.In particular we restrict our attention to the important classes of self-similar measures that have matrix representations.The dimension spectra and the Lq-spectra are analyzed through the product of matrices.There are abnormal behaviors on the multifrac-tal structure and they will be discussed in detail.
Ferrers Matrices Characterized by the Rook Polynomials
Institute of Scientific and Technical Information of China (English)
MAHai-cheng; HUSheng-biao
2003-01-01
In this paper,we show that there exist precisely W(A) Ferrers matrices F(C1,C2,…,cm)such that the rook polynomials is equal to the rook polynomial of Ferrers matrix F(b1,b2,…,bm), where A={b1,b2-1,…,bm-m+1} is a repeated set,W(A) is weight of A.
Hierarchical matrix approximation of large covariance matrices
Litvinenko, Alexander
2015-01-07
We approximate large non-structured covariance matrices in the H-matrix format with a log-linear computational cost and storage O(n log n). We compute inverse, Cholesky decomposition and determinant in H-format. As an example we consider the class of Matern covariance functions, which are very popular in spatial statistics, geostatistics, machine learning and image analysis. Applications are: kriging and optimal design
Hierarchical matrix approximation of large covariance matrices
Litvinenko, Alexander
2015-01-05
We approximate large non-structured covariance matrices in the H-matrix format with a log-linear computational cost and storage O(nlogn). We compute inverse, Cholesky decomposition and determinant in H-format. As an example we consider the class of Matern covariance functions, which are very popular in spatial statistics, geostatistics, machine learning and image analysis. Applications are: kriging and op- timal design.
Connection matrices for ultradiscrete linear problems
Energy Technology Data Exchange (ETDEWEB)
Ormerod, Chris [School of Mathematics and Statistics F07, The University of Sydney, Sydney (Australia)
2007-10-19
We present theory outlining associated linear problems for ultradiscrete equations. The appropriate domain for these problems is the max-plus semiring. Our main result is that despite the restrictive nature of the max-plus semiring, it is still possible to define a theory of connection matrices analogous to that of Birkhoff and his school for systems of linear difference equations. We use such theory to provide evidence for the integrability of an ultradiscrete difference equation.
Functional CLT for sample covariance matrices
Bai, Zhidong; Zhou, Wang; 10.3150/10-BEJ250
2010-01-01
Using Bernstein polynomial approximations, we prove the central limit theorem for linear spectral statistics of sample covariance matrices, indexed by a set of functions with continuous fourth order derivatives on an open interval including $[(1-\\sqrt{y})^2,(1+\\sqrt{y})^2]$, the support of the Mar\\u{c}enko--Pastur law. We also derive the explicit expressions for asymptotic mean and covariance functions.
Index matrices towards an augmented matrix calculus
Atanassov, Krassimir T
2014-01-01
This book presents the very concept of an index matrix and its related augmented matrix calculus in a comprehensive form. It mostly illustrates the exposition with examples related to the generalized nets and intuitionistic fuzzy sets which are examples of an extremely wide array of possible application areas. The present book contains the basic results of the author over index matrices and some of its open problems with the aim to stimulating more researchers to start working in this area.
On the exponentials of some structured matrices
Energy Technology Data Exchange (ETDEWEB)
Ramakrishna, Viswanath; Costa, F [Department of Mathematical Sciences and Center for Signals, Systems and Communications, University of Texas at Dallas, PO Box 830688, Richardson, TX 75083 (United States)
2004-12-03
This paper provides explicit techniques to compute the exponentials of a variety of structured 4 x 4 matrices. The procedures are fully algorithmic and can be used to find the desired exponentials in closed form. With one exception, they require no spectral information about the matrix being exponentiated. They rely on a mixture of Lie theory and one particular Clifford algebra isomorphism. These can be extended, in some cases, to higher dimensions when combined with techniques such as Givens rotations.
The spectrum of kernel random matrices
Karoui, Noureddine El
2010-01-01
We place ourselves in the setting of high-dimensional statistical inference where the number of variables $p$ in a dataset of interest is of the same order of magnitude as the number of observations $n$. We consider the spectrum of certain kernel random matrices, in particular $n\\times n$ matrices whose $(i,j)$th entry is $f(X_i'X_j/p)$ or $f(\\Vert X_i-X_j\\Vert^2/p)$ where $p$ is the dimension of the data, and $X_i$ are independent data vectors. Here $f$ is assumed to be a locally smooth function. The study is motivated by questions arising in statistics and computer science where these matrices are used to perform, among other things, nonlinear versions of principal component analysis. Surprisingly, we show that in high-dimensions, and for the models we analyze, the problem becomes essentially linear--which is at odds with heuristics sometimes used to justify the usage of these methods. The analysis also highlights certain peculiarities of models widely studied in random matrix theory and raises some questio...
Quark flavor mixings from hierarchical mass matrices
Energy Technology Data Exchange (ETDEWEB)
Verma, Rohit [Chinese Academy of Sciences, Institute of High Energy Physics, Beijing (China); Rayat Institute of Engineering and Information Technology, Ropar (India); Zhou, Shun [Chinese Academy of Sciences, Institute of High Energy Physics, Beijing (China); Peking University, Center for High Energy Physics, Beijing (China)
2016-05-15
In this paper, we extend the Fritzsch ansatz of quark mass matrices while retaining their hierarchical structures and show that the main features of the Cabibbo-Kobayashi-Maskawa (CKM) matrix V, including vertical stroke V{sub us} vertical stroke ≅ vertical stroke V{sub cd} vertical stroke, vertical stroke V{sub cb} vertical stroke ≅ vertical stroke V{sub ts} vertical stroke and vertical stroke V{sub ub} vertical stroke / vertical stroke V{sub cb} vertical stroke < vertical stroke V{sub td} vertical stroke / vertical stroke V{sub ts} vertical stroke can be well understood. This agreement is observed especially when the mass matrices have non-vanishing (1, 3) and (3, 1) off-diagonal elements. The phenomenological consequences of these for the allowed texture content and gross structural features of 'hierarchical' quark mass matrices are addressed from a model-independent prospective under the assumption of factorizable phases in these. The approximate and analytical expressions of the CKM matrix elements are derived and a detailed analysis reveals that such structures are in good agreement with the observed quark flavor mixing angles and the CP-violating phase at the 1σ level and call upon a further investigation of the realization of these structures from a top-down prospective. (orig.)
Scattering Matrices and Conductances of Leaky Tori
Pnueli, A.
1994-04-01
Leaky tori are two-dimensional surfaces that extend to infinity but which have finite area. It is a tempting idea to regard them as models of mesoscopic systems connected to very long leads. Because of this analogy-scattering matrices on leaky tori are potentially interesting, and indeed-the scattering matrix on one such object-"the" leaky torus-was studied by M. Gutzwiller, who showed that it has chaotic behavior. M. Antoine, A. Comtet and S. Ouvry generalized Gutzwiller‧s result by calculating the scattering matrix in the presence of a constant magnetic field B perpendicular to the surface. Motivated by these results-we generalize them further. We define scattering matrices for spinless electrons on a general leaky torus in the presence of a constant magnetic field "perpendicular" to the surface. From the properties of these matrices we show the following: (a) For integer values of B, Tij (the transition probability from cusp i to cusp j), and hence also the Büttiker conductances of the surfaces, are B-independent (this cannot be interpreted as a kind of Aharonov-Bohm effect since a magnetic force is acting on the electrons). (b) The Wigner time-delay is a monotonically increasing function of B.
On the Construction of Jointly Superregular Lower Triangular Toeplitz Matrices
DEFF Research Database (Denmark)
Hansen, Jonas; Østergaard, Jan; Kudahl, Johnny
2016-01-01
superregular and product preserving jointly superregular matrices, and extend our explicit constructions of superregular matrices to these cases. Jointly superregular matrices are necessary to achieve optimal decoding capabilities for the case of codes with a rate lower than 1/2, and the product preserving......Superregular matrices have the property that all of their submatrices, which can be full rank are so. Lower triangular superregular matrices are useful for e.g., maximum distance separable convolutional codes as well as for (sequential) network codes. In this work, we provide an explicit design...
The modern origin of matrices and their applications
Debnath, L.
2014-05-01
This paper deals with the modern development of matrices, linear transformations, quadratic forms and their applications to geometry and mechanics, eigenvalues, eigenvectors and characteristic equations with applications. Included are the representations of real and complex numbers, and quaternions by matrices, and isomorphism in order to show that matrices form a ring in abstract algebra. Some special matrices, including Hilbert's matrix, Toeplitz's matrix, Pauli's and Dirac's matrices in quantum mechanics, and Einstein's Pythagorean formula are discussed to illustrate diverse applications of matrix algebra. Included also is a modern piece of information that puts mathematics, science and mathematics education professionals at the forefront of advanced study and research on linear algebra and its applications.
Institute of Scientific and Technical Information of China (English)
Chung-Yung Wang; Jia-Wun Zhang
2014-01-01
This study focuses on estimating O-D （origin-destination） trip demand from link traffic flows. Equality relationship among link traffic flow, path flow, and O-D trip matrices are used to establish a linear equation system. Solution characteristics are analyzed based on the relationship between the rank of the link/path incidence matrix and column variables. And under the solution framework of conditional inverse matrices, a column exchange method and a path flow proportion method have been developed. Network testing results verify that the proposed methods yield good results.
Deterministic sensing matrices in compressive sensing: a survey.
Nguyen, Thu L N; Shin, Yoan
2013-01-01
Compressive sensing is a sampling method which provides a new approach to efficient signal compression and recovery by exploiting the fact that a sparse signal can be suitably reconstructed from very few measurements. One of the most concerns in compressive sensing is the construction of the sensing matrices. While random sensing matrices have been widely studied, only a few deterministic sensing matrices have been considered. These matrices are highly desirable on structure which allows fast implementation with reduced storage requirements. In this paper, a survey of deterministic sensing matrices for compressive sensing is presented. We introduce a basic problem in compressive sensing and some disadvantage of the random sensing matrices. Some recent results on construction of the deterministic sensing matrices are discussed.
Li, S.-F.; Xu, J.-W.; Yang, Q.-L.; Wang, C.H.; Chen, Q.; Chapman, D.C.; Lu, G.
2009-01-01
Based upon morphological characters, Silver carp Hypophthalmichthys molitrix and bighead carp Hypophthalmichthys nobilis (or Aristichthys nobilis) have been classified into either the same genus or two distinct genera. Consequently, the taxonomic relationship of the two species at the generic level remains equivocal. This issue is addressed by sequencing complete mitochondrial genomes of H. molitrix and H. nobilis, comparing their mitogenome organization, structure and sequence similarity, and conducting a comprehensive phylogenetic analysis of cyprinid species. As with other cyprinid fishes, the mitogenomes of the two species were structurally conserved, containing 37 genes including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA (tRNAs) genes and a putative control region (D-loop). Sequence similarity between the two mitogenomes varied in different genes or regions, being highest in the tRNA genes (98??8%), lowest in the control region (89??4%) and intermediate in the protein-coding genes (94??2%). Analyses of the sequence comparison and phylogeny using concatenated protein sequences support the view that the two species belong to the genus Hypophthalmichthys. Further studies using nuclear markers and involving more closely related species, and the systematic combination of traditional biology and molecular biology are needed in order to confirm this conclusion. ?? 2009 The Fisheries Society of the British Isles.
Fernando, R L; Cheng, H; Sun, X; Garrick, D J
2017-06-01
The genetic covariance matrix conditional on pedigree is proportional to the pedigree-based additive relationship matrix (PARM), which is twice the matrix of identity-by-descent (IBD) probabilities. In genomic prediction, IBD probabilities in the PARM, which are expected genetic similarities between relatives that are derived from the pedigree, are substituted by realized similarities that are derived from genotypes to obtain a genomic additive relationship matrix (GARM). Different definitions of similarity lead to different GARMs, and two commonly used GARMS are the matrix G, which is based on an allele substitution effect model, and the matrix T, which is based on an allele effect model. We show that although the two matrices T and G are not proportional, they give identical predictions of differences between breeding values. When genomic information is used for variance component estimation, the GARM Gx is computed from genotype covariates that have been standardized to have unit variance. That approach is equivalent to fitting a random regression model using the same standardized covariates. We show that under Hardy-Weinberg and linkage equilibria (LE) that the genetic variance is kσγ2, where σγ2 is the variance of a randomly sampled element from the vector of k substitution effects. However, if linkage disequilibrium (LD) has been generated through selection, covariances between genotypes at different loci will be negative, and therefore, the additive genetic variance will be lower than kσγ2. When the GARM Gx is assumed to be proportional to the genetic covariance matrix, the parameter being estimated is kσγ2. We have demonstrated by simulation that kσγ2 overestimates the additive genetic variance when LD is generated by selection. We argue that unlike the PARM, GARMs are not proportional to a genetic covariance matrix conditional on the observed causal genotypes. The objective here is to recognize the difference between these covariance matrices and
Bickel, Peter J
2010-01-01
In the first part of this paper we give an elementary proof of the fact that if an infinite matrix $A$, which is invertible as a bounded operator on $\\ell^2$, can be uniformly approximated by banded matrices then so can the inverse of $A$. We give explicit formulas for the banded approximations of $A^{-1}$ as well as bounds on their accuracy and speed of convergence in terms of their band-width. In the second part we apply these results to covariance matrices $\\Sigma$ of Gaussian processes and study mixing and beta mixing of processes in terms of properties of $\\Sigma$. Finally, we note some applications of our results to statistics.
Factor structure of Raven's Coloured Progressive Matrices
Muniz, Monalisa; Gomes, Cristiano Mauro Assis; Pasian, Sonia Regina
2016-01-01
Abstract This study's objective was to verify the factor structure of Raven's Coloured Progressive Matrices (CPM). The database used included the responses of 1,279 children, 50.2% of which were males with an average age of 8.48 years old and a standard deviation of 1.49 yrs. Confirmatory factor analyses were run to test seven models based on CPM theory and on a Brazilian study addressing the test's structure. The results did not confirm the CPM theoretical proposition concerning the scales b...
Generalized Jones matrices for anisotropic media.
Ortega-Quijano, Noé; Arce-Diego, José Luis
2013-03-25
The interaction of arbitrary three-dimensional light beams with optical elements is described by the generalized Jones calculus, which has been formally proposed recently [Azzam, J. Opt. Soc. Am. A 28, 2279 (2011)]. In this work we obtain the parametric expression of the 3×3 differential generalized Jones matrix (dGJM) for arbitrary optical media assuming transverse light waves. The dGJM is intimately connected to the Gell-Mann matrices, and we show that it provides a versatile method for obtaining the macroscopic GJM of media with either sequential or simultaneous anisotropic effects. Explicit parametric expressions of the GJM for some relevant optical elements are provided.
Jones matrices of perfectly conducting metallic polarizers
Boyer, Philippe
2014-01-01
We deduce from Monomode Modal Method the analytical expressions of transmission and reflexion Jones matrices of an infinitely conducting metallic screen periodically pierced by subwavelength holes. The study is restricted to normal incidence and to the case of neglected evanescent fields (far-field) which covers many common cases. When only one non-degenerate mode propagates in cavities, they take identical forms to those of a polarizer, with Fabry-Perot-like spectral resonant factors depending on bigrating parameters. The isotropic or birefringent properties are then obtained when holes support two orthogonal polarization modes. This basic formalism is finally applied to design compact and efficient metallic half-wave plates.
Algebraic Graph Theory Morphisms, Monoids and Matrices
Knauer, Ulrich
2011-01-01
This is a highly self-contained book about algebraic graph theory which iswritten with a view to keep the lively and unconventional atmosphere of a spoken text to communicate the enthusiasm the author feels about this subject. The focus is on homomorphisms and endomorphisms, matrices and eigenvalues. Graph models are extremely useful for almost all applications and applicators as they play an important role as structuring tools. They allow to model net structures -like roads, computers, telephones -instances of abstract data structures -likelists, stacks, trees -and functional or object orient
GenoMatrix: A Software Package for Pedigree-Based and Genomic Prediction Analyses on Complex Traits.
Nazarian, Alireza; Gezan, Salvador Alejandro
2016-07-01
Genomic and pedigree-based best linear unbiased prediction methodologies (G-BLUP and P-BLUP) have proven themselves efficient for partitioning the phenotypic variance of complex traits into its components, estimating the individuals' genetic merits, and predicting unobserved (or yet-to-be observed) phenotypes in many species and fields of study. The GenoMatrix software, presented here, is a user-friendly package to facilitate the process of using genome-wide marker data and parentage information for G-BLUP and P-BLUP analyses on complex traits. It provides users with a collection of applications which help them on a set of tasks from performing quality control on data to constructing and manipulating the genomic and pedigree-based relationship matrices and obtaining their inverses. Such matrices will be then used in downstream analyses by other statistical packages. The package also enables users to obtain predicted values for unobserved individuals based on the genetic values of observed related individuals. GenoMatrix is available to the research community as a Windows 64bit executable and can be downloaded free of charge at: http://compbio.ufl.edu/software/genomatrix/. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Directory of Open Access Journals (Sweden)
Jamal S M Sabir
Full Text Available Date palm is a very important crop in western Asia and northern Africa, and it is the oldest domesticated fruit tree with archaeological records dating back 5000 years. The huge economic value of this crop has generated considerable interest in breeding programs to enhance production of dates. One of the major limitations of these efforts is the uncertainty regarding the number of date palm cultivars, which are currently based on fruit shape, size, color, and taste. Whole mitochondrial and plastid genome sequences were utilized to examine single nucleotide polymorphisms (SNPs of date palms to evaluate the efficacy of this approach for molecular characterization of cultivars. Mitochondrial and plastid genomes of nine Saudi Arabian cultivars were sequenced. For each species about 60 million 100 bp paired-end reads were generated from total genomic DNA using the Illumina HiSeq 2000 platform. For each cultivar, sequences were aligned separately to the published date palm plastid and mitochondrial reference genomes, and SNPs were identified. The results identified cultivar-specific SNPs for eight of the nine cultivars. Two previous SNP analyses of mitochondrial and plastid genomes identified substantial intra-cultivar ( = intra-varietal polymorphisms in organellar genomes but these studies did not properly take into account the fact that nearly half of the plastid genome has been integrated into the mitochondrial genome. Filtering all sequencing reads that mapped to both organellar genomes nearly eliminated mitochondrial heteroplasmy but all plastid SNPs remained heteroplasmic. This investigation provides valuable insights into how to deal with interorganellar DNA transfer in performing SNP analyses from total genomic DNA. The results confirm recent suggestions that plastid heteroplasmy is much more common than previously thought. Finally, low levels of sequence variation in plastid and mitochondrial genomes argue for using nuclear SNPs for
Duncan, Margaret J
2003-01-01
Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.
Energy Technology Data Exchange (ETDEWEB)
Wagner, C.
1996-12-31
In 1992, Wittum introduced the frequency filtering decompositions (FFD), which yield a fast method for the iterative solution of large systems of linear equations. Based on this method, the tangential frequency filtering decompositions (TFFD) have been developed. The TFFD allow the robust and efficient treatment of matrices with strongly varying coefficients. The existence and the convergence of the TFFD can be shown for symmetric and positive definite matrices. For a large class of matrices, it is possible to prove that the convergence rate of the TFFD and of the FFD is independent of the number of unknowns. For both methods, schemes for the construction of frequency filtering decompositions for unsymmetric matrices have been developed. Since, in contrast to Wittums`s FFD, the TFFD needs only one test vector, an adaptive test vector can be used. The TFFD with respect to the adaptive test vector can be combined with other iterative methods, e.g. multi-grid methods, in order to improve the robustness of these methods. The frequency filtering decompositions have been successfully applied to the problem of the decontamination of a heterogeneous porous medium by flushing.
APPLICATIONS OF STAIR MATRICES AND THEIR GENERALIZATIONS TO ITERATIVE METHODS
Institute of Scientific and Technical Information of China (English)
SHAO Xin-hui; SHEN Hai-long; LI Chang-jun
2006-01-01
Stair matrices and their generalizations are introduced. The definitions and some properties of the matrices were first given by Lu Hao. This class of matrices provide bases of matrix splittings for iterative methods. The remarkable feature of iterative methods based on the new class of matrices is that the methods are easily implemented for parallel computation. In particular, a generalization of the accelerated overrelaxation method (GAOR) is introduced. Some theories of the AOR method are extended to the generalized method to include a wide class of matrices. The convergence of the new method is derived for Hermitian positive definite matrices. Finally, some examples are given in order to show the superiority of the new method.
A CLASS OF DETERMINISTIC CONSTRUCTION OF BINARY COMPRESSED SENSING MATRICES
Institute of Scientific and Technical Information of China (English)
Li Dandan; Liu Xinji; Xia Shutao; Jiang Yong
2012-01-01
Compressed Sensing (CS) is an emerging technology in the field of signal processing,which can recover a sparse signal by taking very few samples and solving a linear programming problem.In this paper,we study the application of Low-Density Parity-Check (LDPC) Codes in CS.Firstly,we find a sufficient condition for a binary matrix to satisfy the Restricted Isometric Property (RIP).Then,by employing the LDPC codes based on Berlekamp-Justesen (B-J) codes,we construct two classes of binary structured matrices and show that these matrices satisfy RIP.Thus,the proposed matrices could be used as sensing matrices for CS.Finally,simulation results show that the performance of the Droposed matrices can be comparable with the widely used random sensing matrices.
Asymmetric random matrices: What do we need them for?
Drozdz, Stanislaw; Ioannides, Andreas A; 10.5506/APhysPolB.42.987
2011-01-01
Complex systems are typically represented by large ensembles of observations. Correlation matrices provide an efficient formal framework to extract information from such multivariate ensembles and identify in a quantifiable way patterns of activity that are reproducible with statistically significant frequency compared to a reference chance probability, usually provided by random matrices as fundamental reference. The character of the problem and especially the symmetries involved must guide the choice of random matrices to be used for the definition of a baseline reference. For standard correlation matrices this is the Wishart ensemble of symmetric random matrices. The real world complexity however often shows asymmetric information flows and therefore more general correlation matrices are required to adequately capture the asymmetry. Here we first summarize the relevant theoretical concepts. We then present some examples of human brain activity where asymmetric time-lagged correlations are evident and hence...
Tensor Dictionary Learning for Positive Definite Matrices.
Sivalingam, Ravishankar; Boley, Daniel; Morellas, Vassilios; Papanikolopoulos, Nikolaos
2015-11-01
Sparse models have proven to be extremely successful in image processing and computer vision. However, a majority of the effort has been focused on sparse representation of vectors and low-rank models for general matrices. The success of sparse modeling, along with popularity of region covariances, has inspired the development of sparse coding approaches for these positive definite descriptors. While in earlier work, the dictionary was formed from all, or a random subset of, the training signals, it is clearly advantageous to learn a concise dictionary from the entire training set. In this paper, we propose a novel approach for dictionary learning over positive definite matrices. The dictionary is learned by alternating minimization between sparse coding and dictionary update stages, and different atom update methods are described. A discriminative version of the dictionary learning approach is also proposed, which simultaneously learns dictionaries for different classes in classification or clustering. Experimental results demonstrate the advantage of learning dictionaries from data both from reconstruction and classification viewpoints. Finally, a software library is presented comprising C++ binaries for all the positive definite sparse coding and dictionary learning approaches presented here.
Bromination of selected pharmaceuticals in water matrices.
Benitez, F Javier; Acero, Juan L; Real, Francisco J; Roldan, Gloria; Casas, Francisco
2011-11-01
The bromination of five selected pharmaceuticals (metoprolol, naproxen, amoxicillin, phenacetin, and hydrochlorothiazide) was studied with these compounds individually dissolved in ultra-pure water. The apparent rate constants for the bromination reaction were determined as a function of the pH, obtaining the sequence amoxicillin>naproxen>hydrochlorothiazide≈phenacetin≈metoprolol. A kinetic mechanism specifying the dissociation reactions and the species formed for each compound according to its pK(a) value and the pH allowed the intrinsic rate constants to be determined for each elementary reaction. There was fairly good agreement between the experimental and calculated values of the apparent rate constants, confirming the goodness of the proposed reaction mechanism. In a second stage, the bromination of the selected pharmaceuticals simultaneously dissolved in three water matrices (a groundwater, a surface water from a public reservoir, and a secondary effluent from a WWTP) was investigated. The pharmaceutical elimination trend agreed with the previously determined rate constants. The influence of the main operating conditions (pH, initial bromine dose, and characteristics of the water matrix) on the degradation of the pharmaceuticals was established. An elimination concentration profile for each pharmaceutical in the water matrices was proposed based on the use of the previously evaluated apparent rate constants, and the theoretical results agreed satisfactorily with experiment. Finally, chlorination experiments performed in the presence of bromide showed that low bromide concentrations slightly accelerate the oxidation of the selected pharmaceuticals during chlorine disinfection.
Moderate deviations for the eigenvalue counting function of Wigner matrices
Doering, Hanna
2011-01-01
We establish a moderate deviation principle (MDP) for the number of eigenvalues of a Wigner matrix in an interval. The proof relies on fine asymptotics of the variance of the eigenvalue counting function of GUE matrices due to Gustavsson. The extension to large families of Wigner matrices is based on the Tao and Vu Four Moment Theorem and applies localization results by Erd\\"os, Yau and Yin. Moreover we investigate families of covariance matrices as well.
Symmetric texture-zero mass matrices and its eigenvalues
Criollo, A
2012-01-01
Within the texture-zeros mechanism, first we provide necessary and sufficient conditions on the characteristic polynomial coefficients so that it has real, simple and positive roots, we traduce these conditions in terms to the invariants of the congruent matrices. Next all symmetric texture-zero mass matrices are counted and classified. Finally we apply in a systematic way the result from the first part to analyze the six, four and two zeros texture matrices presented in the second part.
Wick's theorem and reconstruction schemes for reduced density matrices
Institute of Scientific and Technical Information of China (English)
CHEN Feiwu
2006-01-01
We first obtained a closed form of the Wick's theorem expressed in Grassman wedge product, which is similar to a binomial expansion. With this new expansion, new reconstruction schemes for reduced density matrices are derived rigorously. The higher order reduced density matrices are systematically decomposed into a sum of the lower order reduced density matrices which could be used to solve the contracted Schr(o)dinger equation.
Racah matrices and hidden integrability in evolution of knots
Mironov, A.; Morozov, A.; Morozov, An.; Sleptsov, A.
2016-09-01
We construct a general procedure to extract the exclusive Racah matrices S and S bar from the inclusive 3-strand mixing matrices by the evolution method and apply it to the first simple representations R = [ 1 ], [2], [3] and [ 2 , 2 ]. The matrices S and S bar relate respectively the maps (R ⊗ R) ⊗ R bar ⟶ R with R ⊗ (R ⊗ R bar) ⟶ R and (R ⊗ R bar) ⊗ R ⟶ R with R ⊗ (R bar ⊗ R) ⟶ R. They are building blocks for the colored HOMFLY polynomials of arbitrary arborescent (double fat) knots. Remarkably, the calculation realizes an unexpected integrability property underlying the evolution matrices.
Inverse Eigenvalue Problems for Two Special Acyclic Matrices
Directory of Open Access Journals (Sweden)
Debashish Sharma
2016-03-01
Full Text Available In this paper, we study two inverse eigenvalue problems (IEPs of constructing two special acyclic matrices. The first problem involves the reconstruction of matrices whose graph is a path, from given information on one eigenvector of the required matrix and one eigenvalue of each of its leading principal submatrices. The second problem involves reconstruction of matrices whose graph is a broom, the eigen data being the maximum and minimum eigenvalues of each of the leading principal submatrices of the required matrix. In order to solve the problems, we use the recurrence relations among leading principal minors and the property of simplicity of the extremal eigenvalues of acyclic matrices.
Self-dual interval orders and row-Fishburn matrices
Yan, Sherry H F
2011-01-01
Recently, Jel\\'{i}nek derived that the number of self-dual interval orders of reduced size $n$ is twice the number of row-Fishburn matrices of size $n$ by using generating functions. In this paper, we present a bijective proof of this relation by establishing a bijection between two variations of upper-triangular matrices of nonnegative integers. Using the bijection, we provide a combinatorial proof of the refined relations between self-dual Fishburn matrices and row-Fishburn matrices in answer to a problem proposed by Jel\\'{i}nek.
Applications of combinatorial matrix theory to Laplacian matrices of graphs
Molitierno, Jason J
2012-01-01
On the surface, matrix theory and graph theory seem like very different branches of mathematics. However, adjacency, Laplacian, and incidence matrices are commonly used to represent graphs, and many properties of matrices can give us useful information about the structure of graphs. Applications of Combinatorial Matrix Theory to Laplacian Matrices of Graphs is a compilation of many of the exciting results concerning Laplacian matrices developed since the mid 1970s by well-known mathematicians such as Fallat, Fiedler, Grone, Kirkland, Merris, Mohar, Neumann, Shader, Sunder, and more. The text i
Matrices generadas por adición de díadas (matrices de rango 1): propiedades y aplicaciones
Ortigueira, Manuel D.
1996-01-01
Se estudian las matrices elementales de rango 1 (díadas). Para estas matrices se presentan fórmulas para su factorización, inversión, descomposición en valores propios y valores singulares. Estos resultados son aplicados en análisis recursivo a cualquier matriz, siempre que se descomponga en una suma de matrices de rango 1. Peer Reviewed
Matrices generadas por adición de díadas (matrices de rango 1): propiedades y aplicaciones
Ortigueira, Manuel D.
1996-01-01
Se estudian las matrices elementales de rango 1 (díadas). Para estas matrices se presentan fórmulas para su factorización, inversión, descomposición en valores propios y valores singulares. Estos resultados son aplicados en análisis recursivo a cualquier matriz, siempre que se descomponga en una suma de matrices de rango 1. Peer Reviewed
Błażej, Paweł; Miasojedow, Błażej; Grabińska, Małgorzata; Mackiewicz, Paweł
2015-01-01
Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.
Directory of Open Access Journals (Sweden)
Paweł Błażej
Full Text Available Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.
Investigation of degradation mechanisms in composite matrices
Giori, C.; Yamauchi, T.
1982-01-01
Degradation mechanisms were investigated for graphite/polysulfone and graphite/epoxy laminates exposed to ultraviolet and high-energy electron radiations in vacuum up to 960 equivalent sun hours and 10 to the ninth power rads respectively. Based on GC and combined GC/MS analysis of volatile by-products evolved during irradiation, several free radical mechanisms of composite degradation were identified. The radiation resistance of different matrices was compared in terms of G values and quantum yields for gas formation. All the composite materials evaluated show high electron radiation stability and relatively low ultraviolet stability as indicated by low G values and high quantum for gas formation. Mechanical property measurements of irradiated samples did not reveal significant changes, with the possible exception of UV exposed polysulfone laminates. Hydrogen and methane were identified as the main by-products of irradiation, along with unexpectedly high levels of CO and CO2.
Diameter Preserving Surjection on Alternate Matrices
Institute of Scientific and Technical Information of China (English)
Li Ping HUANG
2009-01-01
Let F be a field with |F| ≥ 3, Km be the set of all m × m (m ≥ 4) alternate matrices over F. The arithmetic distance of A, B ∈ Km is d(A, B) := rank(A- B). If d(A, B) = 2, then A and B are said to be adjacent. The diameter of Km is max{d(A, B) : A, B ∈ Km}. Assume that ψ : Km→ Km is a map. We prove the following are equivalent: (a) ψ is a diameter preserving surjection in both directions, (b) ψ is both an adjacency preserving surjection and a diameter preserving map, (c) ψ is a bijective map which preserves the arithmetic distance.
Spirooxazine Photoisomerization and Relaxation in Polymer Matrices
Directory of Open Access Journals (Sweden)
Maria Larkowska
2011-01-01
Full Text Available 9′-Hydroxy-1,3,3-trimethylspiro[indoline-2,3′[3H]naphtha[2,1-b]-1,4oxazine] (SPO-7OH was used in studies of photochromic transformations in polymer matrices. Illumination with UV lamp caused opening the spirostructure of the oxazine with formation of open merocyanine species absorbing at ca. 610 nm. The kinetic studies of thermal relaxation of the open form showed that this process can be described with a biexponential function including both photochemical reaction and rheological behaviour of the polymeric environment. Basing on Arrhenius plot of the rate constant ascribed to the photochemical reaction, the activation energy was determined, which was 66.1 and 84.7 kJ/mole for poly(methyl methacrylate-co-butyl methacrylate and poly(vinylpyrrolidone matrix, respectively.
Carbon nanomaterials in silica aerogel matrices
Energy Technology Data Exchange (ETDEWEB)
Hamilton, Christopher E [Los Alamos National Laboratory; Chavez, Manuel E [Los Alamos National Laboratory; Duque, Juan G [Los Alamos National Laboratory; Gupta, Gautam [Los Alamos National Laboratory; Doorn, Stephen K [Los Alamos National Laboratory; Dattelbaum, Andrew M [Los Alamos National Laboratory; Obrey, Kimberly A D [Los Alamos National Laboratory
2010-01-01
Silica aerogels are ultra low-density, high surface area materials that are extremely good thermal insulators and have numerous technical applications. However, their mechanical properties are not ideal, as they are brittle and prone to shattering. Conversely, single-walled carbon nanotubes (SWCNTs) and graphene-based materials, such as graphene oxide, have extremely high tensile strength and possess novel electronic properties. By introducing SWCNTs or graphene-based materials into aerogel matrices, it is possible to produce composites with the desirable properties of both constituents. We have successfully dispersed SWCNTs and graphene-based materials into silica gels. Subsequent supercritical drying results in monolithic low-density composites having improved mechanical properties. These nanocomposite aerogels have great potential for use in a wide range of applications.
Momentum representation for equilibrium reduced density matrices
Golovko, V A
2011-01-01
The hierarchy of equations for reduced density matrices that describes a thermodynamically equilibrium quantum system obtained earlier by the author is investigated in the momentum representation. In the paper it is shown that the use of the momentum representation opens up new opportunities in studies of macroscopic quantum systems both nonsuperfluid and superfluid. It is found that the distribution over momenta in a quantum fluid is not a Bose or Fermi distribution even in the limit of practically noninteracting particles. The distribution looks like a Maxwellian one although, strictly speaking, it is not Maxwellian. The momentum distribution in a quantum crystal depends upon the interaction potential and the crystalline structure. The momentum distribution in a superfluid contains a delta function. The momentum distribution for the condensate in a superfluid crystal consists of delta peaks that are arranged periodically in momentum space. The periodical structure remains if the condensate crystal is not su...
Statistical properties of random scattering matrices
Seba, P; Zakrzewski, J A; Seba, Petr; Zyczkowski, Karol; Zakrzewski, Jakub
1996-01-01
We discuss the properties of eigenphases of S--matrices in random models simulating classically chaotic scattering. The energy dependence of the eigenphases is investigated and the corresponding velocity and curvature distributions are obtained both theoretically and numerically. A simple formula describing the velocity distribution (and hence the distribution of the Wigner time delay) is derived, which is capable to explain the algebraic tail of the time delay distribution observed recently in microwave experiments. A dependence of the eigenphases on other external parameters is also discussed. We show that in the semiclassical limit (large number of channels) the curvature distribution of S--matrix eigenphases is the same as that corresponding to the curvature distribution of the underlying Hamiltonian and is given by the generalized Cauchy distribution.
Matrices over runtime systems at exascale
Agullo, Emmanuel
2012-11-01
The goal of Matrices Over Runtime Systems at Exascale (MORSE) project is to design dense and sparse linear algebra methods that achieve the fastest possible time to an accurate solution on large-scale multicore systems with GPU accelerators, using all the processing power that future high end systems can make available. In this poster, we propose a framework for describing linear algebra algorithms at a high level of abstraction and delegating the actual execution to a runtime system in order to design software whose performance is portable accross architectures. We illustrate our methodology on three classes of problems: dense linear algebra, sparse direct methods and fast multipole methods. The resulting codes have been incorporated into Magma, Pastix and ScalFMM solvers, respectively. © 2012 IEEE.
Unbiased community detection for correlation matrices
MacMahon, Mel
2013-01-01
A challenging problem in the study of large complex systems is that of resolving, without prior information, the emergent mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented at identifying such modules and suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, the attempts made so far have merely replaced network data with correlation matrices, a procedure that we show to be fundamentally biased due to its inconsistency with the null hypotheses underlying the existing algorithms. Here we introduce, via a consistent redefinition of null models based on Random Matrix Theory, the unbiased correlation-based counterparts of the most popular community detection techniques. After successfully benchmarking our methods, we apply them to s...
A convergence analysis of SOR iterative methods for linear systems with weak H-matrices
Directory of Open Access Journals (Sweden)
Zhang Cheng-yi
2016-01-01
Full Text Available It is well known that SOR iterative methods are convergent for linear systems, whose coefficient matrices are strictly or irreducibly diagonally dominant matrices and strong H-matrices (whose comparison matrices are nonsingular M-matrices. However, the same can not be true in case of those iterative methods for linear systems with weak H-matrices (whose comparison matrices are singular M-matrices. This paper proposes some necessary and sufficient conditions such that SOR iterative methods are convergent for linear systems with weak H-matrices. Furthermore, some numerical examples are given to demonstrate the convergence results obtained in this paper.
Houser, Dorian S; Champagne, Cory D; Crocker, Daniel E; Kellar, Nicholas M; Cockrem, John; Romano, Tracy; Booth, Rebecca K; Wasser, Samuel K
2016-01-01
Knowledge regarding stress hormones and how they vary in response to seasonality, gender, age, and reproductive status for any marine mammal is limited. Furthermore, stress hormones may be measured in more than one matrix (e.g., feces, blood, blubber), but the relationships between levels of a given hormone across these matrices are unknown, further complicating the interpretations of hormones measured in samples collected from wild animals. A study is underway to address these issues in a population of bottlenose dolphins trained for voluntary participation in sample collections from different matrices and across season and time of day.
Dirac matrices for Chern-Simons gravity
Izaurieta, Fernando; Ramírez, Ricardo; Rodríguez, Eduardo
2012-10-01
A genuine gauge theory for the Poincaré, de Sitter or anti-de Sitter algebras can be constructed in (2n - 1)-dimensional spacetime by means of the Chern-Simons form, yielding a gravitational theory that differs from General Relativity but shares many of its properties, such as second order field equations for the metric. The particular form of the Lagrangian is determined by a rank n, symmetric tensor invariant under the relevant algebra. In practice, the calculation of this invariant tensor can be reduced to the computation of the trace of the symmetrized product of n Dirac Gamma matrices Γab in 2n-dimensional spacetime. While straightforward in principle, this calculation can become extremely cumbersome in practice. For large enough n, existing computer algebra packages take an inordinate long time to produce the answer or plainly fail having used up all available memory. In this talk we show that the general formula for the trace of the symmetrized product of 2n Gamma matrices Γab can be written as a certain sum over the integer partitions s of n, with every term being multiplied by a numerical cofficient αs. We then give a general algorithm that computes the α-coefficients as the solution of a linear system of equations generated by evaluating the general formula for different sets of tensors Bab with random numerical entries. A recurrence relation between different coefficients is shown to hold and is used in a second, "minimal" algorithm to greatly speed up the computations. Runtime of the minimal algorithm stays below 1 min on a typical desktop computer for up to n = 25, which easily covers all foreseeable applications of the trace formula.
Dirac matrices for Chern-Simons gravity
Energy Technology Data Exchange (ETDEWEB)
Izaurieta, Fernando; Ramirez, Ricardo; Rodriguez, Eduardo [Departamento de Matematica y Fisica Aplicadas, Universidad Catolica de la Santisima Concepcion, Alonso de Ribera 2850, 4090541 Concepcion (Chile)
2012-10-06
A genuine gauge theory for the Poincare, de Sitter or anti-de Sitter algebras can be constructed in (2n- 1)-dimensional spacetime by means of the Chern-Simons form, yielding a gravitational theory that differs from General Relativity but shares many of its properties, such as second order field equations for the metric. The particular form of the Lagrangian is determined by a rank n, symmetric tensor invariant under the relevant algebra. In practice, the calculation of this invariant tensor can be reduced to the computation of the trace of the symmetrized product of n Dirac Gamma matrices {Gamma}{sub ab} in 2n-dimensional spacetime. While straightforward in principle, this calculation can become extremely cumbersome in practice. For large enough n, existing computer algebra packages take an inordinate long time to produce the answer or plainly fail having used up all available memory. In this talk we show that the general formula for the trace of the symmetrized product of 2n Gamma matrices {Gamma}{sub ab} can be written as a certain sum over the integer partitions s of n, with every term being multiplied by a numerical cofficient {alpha}{sub s}. We then give a general algorithm that computes the {alpha}-coefficients as the solution of a linear system of equations generated by evaluating the general formula for different sets of tensors B{sup ab} with random numerical entries. A recurrence relation between different coefficients is shown to hold and is used in a second, 'minimal' algorithm to greatly speed up the computations. Runtime of the minimal algorithm stays below 1 min on a typical desktop computer for up to n = 25, which easily covers all foreseeable applications of the trace formula.
Transformation of full 4 × 4 Mueller matrices: a quantitative technique for biomedical diagnosis
He, Honghui; Chang, Jintao; He, Chao; Ma, Hui
2016-03-01
Polarization images contain abundant microstructural information of samples. Recently, as a comprehensive description of the structural and optical properties of complex media, the Mueller matrix imaging has been widely applied to biomedical studies, especially cancer detections. In previous works, we proposed a technique to transform the backscattering 3 × 3 Mueller matrices into a group of quantitative parameters with clear relationships to specific microstructures. In this paper, we extend this transformation method to full 4 × 4 Mueller matrices of both the back and forward scattering directions. Using the experimental results of phantoms and Monte Carlo simulation based on the sphere-cylinder birefringence model, we fit the Mueller matrix elements to trigonometric curves in polar coordinates and obtain a new set of transformation parameters, which can be expressed as analytical functions of 16 Mueller matrix elements. Both the experimental and simulated results demonstrate that the transformation parameters have simple relationships to the characteristic microstructural properties, including the densities and orientations of fibrous structures, the sizes of the scatterers, and the depolarization power of the samples. We also apply the transformation parameters of full 4 × 4 Mueller matrices to human liver cancerous tissues. Preliminary imaging results show that the parameters can quantitatively reflect the formation of fibrous birefringent tissues accompanying the cancerous processes. The findings presented in this study can be useful for in vivo or in vitro polarization imaging of tissues for diagnostic applications.
A drug release study from hydroxypropylmethylcellulose (HPMC) matrices using QSPR modeling.
Ghafourian, Taravat; Gafourian, Taravat; Safari, Arezoo; Adibkia, Khosro; Parviz, Fatemeh; Nokhodchi, Ali
2007-12-01
This investigation is aimed at characterization of the mode of release from two different substitution types of HPMC and the effect of chemical structure of drugs using the QSPR (Quantitative - Structure-Property Relationship) technique. To this end, release profiles of HPMC matrices of several drugs containing the same formulation and compressed at a constant pressure were studied. QSPR method was used to establish statistically significant relationships between release parameters and the structural descriptors. Structural descriptors consisted of molecular mechanical, quantum mechanical and graph-theoretical parameters, as well as the partition coefficient and the aqueous solubility of the drugs. The results showed that the most important factors determining the release profile from both HPMC K4M and HPMC E4M matrices were the aqueous solubility of drugs (which could be substituted efficiently by dipole moment) and the size of the drug molecules. Comparison of drug release from matrices prepared using the two grades of HPMC showed very distinct differences for some drugs, as evaluated by the similarity factor. The results indicated that the source of the difference could be sought in the drug properties (as exemplified by the aqueous solubility and surface area) as well as the rate of erosion (that depends mainly on the polymer type).
Yu, Hon-Tsen; Ma, Gwo-Chin; Lee, Dong-Jay; Chin, Shih-Chien; Chen, Ting-Li; Tsao, Hsien-Shao; Lin, Wen-Hsiang; Wu, Sheng-Hai; Lin, Chyi-Chyang; Chen, Ming
2012-05-01
The objective was to apply a novel modification of a genome-wide, comparative cytogenetic technique (comparative genomic hybridization, comparative genomic hybridization (CGH)), to study species belonging to the myrmecophagous (ant/termite eating) mammalian orders/superorders (Pholidota, Tubulidentata, Carnivora, and Xenarthra), as a model for other applications in mammalian systematics and conservation biology. In this study, CGH was applied to high-quality metaphase spreads of pangolin (Pholidota), using probes of sloth and canine (Xenarthra and Carnivora, respectively) genomic DNA labeled with different fluorophores, thereby facilitating analysis of the visible color spectrum on pangolin karyotypes. Our results posited that pholidotes are closer to carnivores than to xenarthrans, which confirmed the current consensus that myrmecophagy in these mammalian lineages was more likely because of homoplasy (convergent evolution) than being an ancestral character. Since the modified CGH technique used is genome-wide, has chromosome-level resolution, and does not need full genome sequencing, it has considerable potential in systematics and other fields. Copyright © 2012 Elsevier Inc. All rights reserved.
A Lex-BFS-based recognition algorithm for Robinsonian matrices
Laurent, M.; Seminaroti, M.; Paschos, V.; Widmayer, P.
2015-01-01
Robinsonian matrices arise in the classical seriation problem and play an important role in many applications where unsorted similarity (or dissimilarity) information must be re- ordered. We present a new polynomial time algorithm to recognize Robinsonian matrices based on a new characterization of
A Lex-BFS-based recognition algorithm for Robinsonian matrices
M. Laurent (Monique); M. Seminaroti (Matteo); V. Paschos; P. Widmayer
2015-01-01
htmlabstractRobinsonian matrices arise in the classical seriation problem and play an important role in many applications where unsorted similarity (or dissimilarity) information must be re- ordered. We present a new polynomial time algorithm to recognize Robinsonian matrices based on a new characte
Mutation classes of skew-symmetrizable 3x3 matrices
Seven, Ahmet
2010-01-01
In this paper, we determine representatives for the mutation classes of skew-symmetrizable 3x3 matrices and associated graphs using a natural minimality condition, generalizing and strengthening results of Beineke-Brustle-Hille and Felikson-Shapiro-Tumarkin. Furthermore, we obtain a new numerical invariant for the mutation operation on skew-symmetrizable matrices of arbitrary size.
The Exponent Set of Central Symmetric Primitive Matrices
Institute of Scientific and Technical Information of China (English)
陈佘喜; 胡亚辉
2004-01-01
This paper first establishes a distance inequality of the associated diagraph of a central symmetric primitive matrix, then characters the exponent set of central symmetric primitive matrices, and proves that the exponent set of central symmetric primitive matrices of order n is {1, 2,… ,n-1}. There is no gap in it.
The Modern Origin of Matrices and Their Applications
Debnath, L.
2014-01-01
This paper deals with the modern development of matrices, linear transformations, quadratic forms and their applications to geometry and mechanics, eigenvalues, eigenvectors and characteristic equations with applications. Included are the representations of real and complex numbers, and quaternions by matrices, and isomorphism in order to show…
A Lex-BFS-based recognition algorithm for Robinsonian matrices
M. Laurent (Monique); M. Seminaroti (Matteo); V. Paschos; P. Widmayer
2015-01-01
htmlabstractRobinsonian matrices arise in the classical seriation problem and play an important role in many applications where unsorted similarity (or dissimilarity) information must be re- ordered. We present a new polynomial time algorithm to recognize Robinsonian matrices based on a new
The determinants of some multilevel Vandermonde and Toeplitz matrices
Energy Technology Data Exchange (ETDEWEB)
Cervellino, A [Laboratory for Neutron Scattering, PSI Villigen and ETH Zuerich, CH-5232 Villigen PSI (Switzerland); Ciccariello, S [Dipartimento di Fisica ' G. Galilei' and Unita INFM, Universita di Padova, Via Marzolo 8, I-35131 Padova (Italy)
2005-11-11
The closed algebraic expressions of the determinants of some multivariate (multilevel) Vandermonde matrices and the associated Toeplitz/Karle-Hauptman matrices are worked out. The formula can usefully be applied to evaluate the determinant of the Karle-Hauptman matrix generated by a principal basic set of reflections, the knowledge of which determines the full diffraction pattern of an ideal crystal.
Fusion for AdS/CFT boundary S-matrices
Energy Technology Data Exchange (ETDEWEB)
Nepomechie, Rafael I. [Physics Department, University of Miami,P.O. Box 248046, Coral Gables, FL 33124 (United States); Pimenta, Rodrigo A. [Physics Department, University of Miami,P.O. Box 248046, Coral Gables, FL 33124 (United States); Departamento de Física, Universidade Federal de São Carlos,Caixa Postal 676, CEP 13569-905, São Carlos (Brazil)
2015-11-24
We propose a fusion formula for AdS/CFT worldsheet boundary S-matrices. We show that, starting from the fundamental Y=0 boundary S-matrix, this formula correctly reproduces the two-particle bound-state boundary S-matrices.
Revisiting amino acid substitution matrices for identifying distantly related proteins.
Yamada, Kazunori; Tomii, Kentaro
2014-02-01
Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence-profile and profile-profile comparison methods can be improved further. Newly developed matrices and datasets used for this study are available at http://csas.cbrc.jp/Ssearch/.
The Modern Origin of Matrices and Their Applications
Debnath, L.
2014-01-01
This paper deals with the modern development of matrices, linear transformations, quadratic forms and their applications to geometry and mechanics, eigenvalues, eigenvectors and characteristic equations with applications. Included are the representations of real and complex numbers, and quaternions by matrices, and isomorphism in order to show…
Reprint of Testing scattering matrices: a compendium of recipes
Hovenier, J.W.; van der Mee, C.V.M.
2010-01-01
Scattering matrices describe the transformation of the Stokes parameters of a beam of radiation upon scattering of that beam. The problems of testing scattering matrices for scattering by one particle and for single scattering by an assembly of particles are addressed. The treatment concerns
Sarymsakov matrices and coordination tasks for multi-agent systems
Xia, Weiguo; Cao, Ming
2012-01-01
The convergence of products of stochastic matrices has proven to be critical in establishing the effectiveness of distributed coordination algorithms for multi-agent systems. After reviewing some classic and recent results on infinite backward products of stochastic matrices, we provide a new
Random Matrices, Combinatorics, Numerical Linear Algebra and Complex Networks
2012-02-16
Littlewood-Offord theorems and the condition number of random discrete matrices, Annals of Mathematics , to appear. [29] T. Tao and V. Vu, The condition...Wigner. On the distribution of the roots of certain symmetric matrices. Annals of Mathematics , 67(2):325327, 1958. Department of Mathematics, Yale, New Haven, CT 06520 E-mail address: van.vu@yale.edu
On Factorization of Coupled Channel Scattering S Matrices
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
We investigate the problem on how to factorize a coupled channel scattering S matrix into a product of simple S matrices. Simple S matrix solutions are found, respecting unitarity, analyticity and being real analytic. The phase shift and its physical meaning produced by these simple S matrices are discussed.
Topological algebras of rapidly decreasing matrices and generalizations
Glockner, Helge
2010-01-01
It is a folklore fact that the rapidly decreasing matrices of countable size form an associative topological algebra whose set of quasi-invertible elements is open, and such that the quasi-inversion map is continuous. We provide a direct proof, which applies more generally to a large class of algebras of weighted matrices with entries in a Banach algebra.
Zenil-Ferguson, Rosana; Ponciano, José M; Burleigh, J Gordon
2016-07-01
Whole-genome duplications (WGDs) can rapidly increase genome size in angiosperms. Yet their mean genome size is not correlated with ploidy. We compared three hypotheses to explain the constancy of genome size means across ploidies. The genome downsizing hypothesis suggests that genome size will decrease by a given percentage after a WGD. The genome size threshold hypothesis assumes that taxa with large genomes or large monoploid numbers will fail to undergo or survive WGDs. Finally, the genome downsizing and threshold hypothesis suggests that both genome downsizing and thresholds affect the relationship between genome size means and ploidy. We performed nonparametric bootstrap simulations to compare observed angiosperm genome size means among species or genera against simulated genome sizes under the three different hypotheses. We evaluated the hypotheses using a decision theory approach and estimated the expected percentage of genome downsizing. The threshold hypothesis improves the approximations between mean genome size and simulated genome size. At the species level, the genome downsizing with thresholds hypothesis best explains the genome size means with a 15% genome downsizing percentage. In the genus level simulations, the monoploid number threshold hypothesis best explains the data. Thresholds of genome size and monoploid number added to genome downsizing at species level simulations explain the observed means of angiosperm genome sizes, and monoploid number is important for determining the genome size mean at the genus level. © 2016 Botanical Society of America.
Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium
DEFF Research Database (Denmark)
Machado, Henrique; Gram, Lone
2017-01-01
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...... misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan-and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity...
Directory of Open Access Journals (Sweden)
Pavel Etingof
2007-03-01
Full Text Available Following the works by Wiegmann-Zabrodin, Elbau-Felder, Hedenmalm-Makarov, and others, we consider the normal matrix model with an arbitrary potential function, and explain how the problem of finding the support domain for the asymptotic eigenvalue density of such matrices (when the size of the matrices goes to infinity is related to the problem of Hele-Shaw flows on curved surfaces, considered by Entov and the first author in 1990-s. In the case when the potential function is the sum of a rotationally invariant function and the real part of a polynomial of the complex coordinate, we use this relation and the conformal mapping method developed by Entov and the first author to find the shape of the support domain explicitly (up to finitely many undetermined parameters, which are to be found from a finite system of equations. In the case when the rotationally invariant function is βz^2, this is done by Wiegmann-Zabrodin and Elbau-Felder. We apply our results to the generalized normal matrix model, which deals with random block matrices that give rise to *-representations of the deformed preprojective algebra of the affine quiver of type Â_{m-1}. We show that this model is equivalent to the usual normal matrix model in the large N limit. Thus the conformal mapping method can be applied to find explicitly the support domain for the generalized normal matrix model.
Directory of Open Access Journals (Sweden)
Butrymowicz Dariusz
2016-09-01
Full Text Available The theoretical basis for the indirect measurement approach of mean heat transfer coefficient for the packed bed based on the modified single blow technique was presented and discussed in the paper. The methodology of this measurement approach dedicated to the matrix of the rotating regenerative gas heater was discussed in detail. The testing stand consisted of a dedicated experimental tunnel with auxiliary equipment and a measurement system are presented. Selected experimental results are presented and discussed for selected types of matrices of regenerative air preheaters for the wide range of Reynolds number of gas. The agreement between the theoretically predicted and measured temperature profiles was demonstrated. The exemplary dimensionless relationships between Colburn heat transfer factor, Darcy flow resistance factor and Reynolds number were presented for the investigated matrices of the regenerative gas heater.
Time series, correlation matrices and random matrix models
Energy Technology Data Exchange (ETDEWEB)
Vinayak [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, C.P. 62210 Cuernavaca (Mexico); Seligman, Thomas H. [Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, C.P. 62210 Cuernavaca, México and Centro Internacional de Ciencias, C.P. 62210 Cuernavaca (Mexico)
2014-01-08
In this set of five lectures the authors have presented techniques to analyze open classical and quantum systems using correlation matrices. For diverse reasons we shall see that random matrices play an important role to describe a null hypothesis or a minimum information hypothesis for the description of a quantum system or subsystem. In the former case various forms of correlation matrices of time series associated with the classical observables of some system. The fact that such series are necessarily finite, inevitably introduces noise and this finite time influence lead to a random or stochastic component in these time series. By consequence random correlation matrices have a random component, and corresponding ensembles are used. In the latter we use random matrices to describe high temperature environment or uncontrolled perturbations, ensembles of differing chaotic systems etc. The common theme of the lectures is thus the importance of random matrix theory in a wide range of fields in and around physics.
The semi-dynamical reflection equation: solutions and structure matrices
Energy Technology Data Exchange (ETDEWEB)
Avan, J; Zambon, C [Laboratoire de Physique Theorique et Modelisation, Universite de Cergy-Pontoise (CNRS UMR 8089), Saint-Martin 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise Cedex (France)], E-mail: avan@u-cergy.fr, E-mail: cristina.zambon@u-cergy.fr
2008-05-16
Explicit solutions of the non-constant semi-dynamical reflection equation are constructed, together with suitable parametrizations of their structure matrices. Considering the semi-dynamical reflection equation with rational non-constant Arutyunov-Chekhov-Frolov structure matrices, and a specific meromorphic ansatz, it is found that only two sets of the previously found constant solutions are extendible to the non-constant case. In order to simplify future constructions of spin-chain Hamiltonians, a parametrization procedure is applied explicitly to all elements of the semi-dynamical reflection equation available. Interesting expressions for 'twists' and R-matrices entering the parametrization procedure are found. In particular, some expressions for the R-matrices seem to appear here for the first time. In addition, a new set of consistent structure matrices for the semi-dynamical reflection equation is obtained.
Genetical stability and osteogenic ability of mesenchimal stem cells on demineralized bone matrices
Directory of Open Access Journals (Sweden)
A. Pozzuoli
2015-03-01
Full Text Available Aim Tissue engineering is a rapidly expanding field with regard to the use of biomaterials and stem cells in the orthopedic surgery. Many experimental studies have been done to understand the best characteristics of cells, materials and laboratory methods for safe clinical applications. The aim of this study was to compare the ability of 2 different human demineralized bone matrices (DBMs, the one enriched and the other not enriched with hyaluronic acid, to stimulate in vitro the proliferation and the osteogenic differentiation of human adipose-derived stem cells (ADSCs seeded onto an osteoconductive scaffold. Materials and Methods ADSCs were isolated, by enzymatic digestion, from abdominal adipose tissue of 5 patients undergoing cosmetic lipoaspiration surgery. ADSCs were then seeded onto a 3D scaffold in the presence of the two different osteoinductive matrices of human demineralized bone and evaluated for proliferation and osteogenic differentiation. The safety of the methods was verified using array-Comparative Genomic Hybridization (array-CGH. Results ADSCs were able to differentiate in osteogenic sense. Both DBMs showed the ability to induce osteogenic differentiation of the cells. Conclusion array-CGH showed no changes at genome level, thus confirming the safety of materials and methods.
Gramene database: navigating plant comparative genomics resources
Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationship...
Genetic structure of La Cabrera, Spain, from surnames and migration matrices.
Boattini, Alessio; Blanco Villegas, María José; Pettener, Davide
2007-12-01
The genetic structure of La Cabrera (province of Léon, Spain), a highly isolated and inbred population (alpha3 = 0.00482), is analyzed by applying multivariate methods (nonmetric multidimensional scaling, Mantel test, Monmonier's algorithm) to different biodemographic data sets. Isonymy, parent-offspring migration (total, males, females), and marital migration matrices were obtained from 5,714 marriages recorded in 37 parishes (clustered in 4 municipalities) between 1880 and 1989. The aim of the study is to investigate the relationships between the genetic and geographic structures of the area. Endemicity values (diagonal of parent-offspring migration matrices), calculated for both sexes at two hierarchical levels (parishes and municipalities), show that female mobility follows the virilocal migration model at the higher (municipalities) level and the uxorilocal model at the parish level. Analysis of isonymy and parent-offspring migration matrices shows high correspondence between the genetic structure and geographic location of the parishes. In fact, the main reproductive barriers, constructed using Monmonier's algorithm, generally coincide with geographic barriers, highlighting increasing isolation patterns from northwest to southeast. Moreover, the analysis of isonymous relationships, which are influenced by earlier population movements, identifies three parishes whose outlier positions are explained by historical-cultural or geographic reasons. The positive and highly significant values (0.32 migration matrix. When the outlier parishes are omitted from the analysis, the correlation between isonymy and geographic distance increases from 0.35 to 0.46, and the values from the other migration matrices remain unchanged. In conclusion, the combination of different data sets and methods allows a wider and more coherent reconstruction of the historical changes in the genetic structure of the La Cabrera population.
H-MATRICES AND S-DOUBLY DIAGONALLY DOMINANT MATRICES%H-矩阵和S-双对角占优矩阵
Institute of Scientific and Technical Information of China (English)
杨月婷; 徐成贤
2004-01-01
In this paper, the concept of the s-doubly diagonally dominant matrices is introduced and the properties of these matrices are discussed. With the properties of the s-doubly diagonally dominant matrices and the properties of comparison matrices, some equivalent conditions for H-matrices are presented. These conditions generalize and improve existing results about the equivalent conditions for H-matrices. Applications and examples using these new equivalent conditions are also presented, and a new inclusion region of k-multiple eigenvalues of matrices is obtained.
Microbial Genomics Research in China
Institute of Scientific and Technical Information of China (English)
ZHAO Guo-ping
2004-01-01
@@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.
Microbial Genomics Research in China
Institute of Scientific and Technical Information of China (English)
ZHAOGuo-ping
2004-01-01
Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.
Kaphingst, Kimberly A; Blanchard, Melvin; Milam, Laurel; Pokharel, Manusheela; Elrick, Ashley; Goodman, Melody S
2016-01-01
The increasing importance of genomic information in clinical care heightens the need to examine how individuals understand, value, and communicate about this information. Based on a conceptual framework of genomics-related health literacy, we examined whether health literacy was related to knowledge, self-efficacy, and perceived importance of genetics and family health history (FHH) and communication about FHH in a medically underserved population. The analytic sample was composed of 624 patients at a primary care clinic in a large urban hospital. About half of the participants (47%) had limited health literacy; 55% had no education beyond high school, and 58% were Black. In multivariable models, limited health literacy was associated with lower genetic knowledge (β = -0.55, SE = 0.10, p importance of genetic information (OR = 1.95, 95% CI [1.27, 3.00], p = .0022) but lower perceived importance of FHH information (OR = 0.47, 95% CI [0.26, 0.86], p = .013) and more frequent communication with a doctor about FHH (OR = 2.02, 95% CI [1.27, 3.23], p = .0032). The findings highlight the importance of considering domains of genomics-related health literacy (e.g., knowledge, oral literacy) in developing educational strategies for genomic information. Health literacy research is essential to avoid increasing disparities in information and health outcomes as genomic information reaches more patients.
Kaphingst, Kimberly A.; Blanchard, Melvin; Milam, Laurel; Pokharel, Manusheela; Elrick, Ashley; Goodman, Melody S.
2017-01-01
The increasing importance of genomic information in clinical care heightens our need to examine how individuals understand, value, and communicate about this information. Based on a conceptual framework of genomics-related health literacy, we examined whether health literacy was related to knowledge, self-efficacy, and perceived importance of genetics and FHH and communication about FHH in a medically underserved population. The analytic sample was comprised of 624 patients at a primary care clinic at a large urban hospital. About half of participants (47%) had limited health literacy; 55% had no education beyond high school and 58% were Black. In multivariable models, limited health literacy was associated with lower genetic knowledge (β=−0.55; SE=0.10, pcommunication with a doctor about FHH (OR=2.02; 95% CI=1.27,3.23, p=.0032). The findings highlight the importance of considering domains of genomics-related health literacy (e.g., knowledge, oral literacy) in developing educational strategies for genomic information. Health literacy research is essential to avoid increasing disparities in information and health outcomes as genomic information reaches more patients. PMID:27043759
Genome-wide prediction, display and refinement of binding sites with information theory-based models
Directory of Open Access Journals (Sweden)
Leeder J Steven
2003-09-01
Full Text Available Abstract Background We present Delila-genome, a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by scanning genomic sequences with information theory-based (or user-defined weight matrices. Matrices are refined by adding experimentally-defined binding sites to published binding sites. Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. The software can then be used to predict novel sites by rescanning the genome with the refined matrices. Results Parameters for genome scans are entered using a Java-based GUI interface and backend scripts in Perl. Multi-processor CPU load-sharing minimized the average response time for scans of different chromosomes. Scans of human genome assemblies required 4–6 hours for transcription factor binding sites and 10–19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. For large datasets, we applied a data reduction strategy that limited displays of binding sites exceeding a threshold information content to specific chromosomal regions within or adjacent to genes. An HTML document is produced listing binding sites ranked by binding site strength or chromosomal location hyperlinked to the UCSC custom track, other annotation databases and binding site sequences. Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths
Mechanically implementable accommodation matrices for passive force control
Energy Technology Data Exchange (ETDEWEB)
Goswami, A. [Univ. of Pennsylvania, Philadelphia, PA (United States). Center for Human Modeling and Simulation; Peshkin, M. [Northwestern Univ., Evanston, IL (United States). Dept. of Mechanical Engineering
1999-08-01
Robot force control implemented by means of passive mechanical devices has inherent advantages over active implementations with regard to stability, response rapidity, and physical robustness. The class of devices considered in this paper consists of a Stewart platform-type mechanism interconnected with a network of adjustable mechanical elements such as springs and dampers. The control law repertoire of such a device, imagined as a robot wrist, is given by the range of admittance matrices that it may be programmed to possess. This paper focuses on wrists incorporating damper networks for which the admittance matrices reduce to accommodation or inverse-damping matrices. The authors show that a hydraulic network of fully adjustable damper elements may attain any diagonally dominant accommodation matrix. They describe the technique of selecting the individual damping coefficients to design a desired matrix. They identify the set of dominant matrices as a polyhedral convex cone in the space of matrix entries, and show that each dominant matrix can be composed of a positive linear combination of a fixed set of basis matrices. The overall wrist-accommodation matrix is obtained by projecting the accommodation matrix of the damper network through the wrist kinematics. The linear combination of the dominant basis matrices projected through the wrist kinematics generates the entire space of mechanically implementable force-control laws. The authors quantify the versatility of mechanically implementable force-control laws by comparing this space to the space of all matrices.
Poland, Jesse
2015-04-01
The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.
Limits of spiked random matrices II
Bloemendal, Alex
2011-01-01
The top eigenvalues of rank r spiked real Wishart matrices and additively perturbed Gaussian orthogonal ensembles are known to exhibit a phase transition in the large size limit. We show that they have limiting distributions for near-critical perturbations, fully resolving the conjecture of Baik, Ben Arous and P\\'ech\\'e (2005). The starting point is a new (2r+1)-diagonal form that is algebraically natural to the problem; for both models it converges to a certain random Schr\\"odinger operator on the half-line with r x r matrix-valued potential. The perturbation determines the boundary condition, and the low-lying eigenvalues describe the limit jointly over all perturbations in a fixed subspace. We treat the real, complex and quaternion (beta = 1,2,4) cases simultaneously. We also characterize the limit laws in terms of a diffusion related to Dyson's Brownian motion, and further in terms of a linear parabolic PDE; here beta is simply a parameter. At beta = 2 the PDE appears to reconcile with known Painlev\\'e fo...
NOTE ON REGULAR D-OPTIMAL MATRICES
Institute of Scientific and Technical Information of China (English)
李乔良
2003-01-01
Let A be aj ×d (0,1) matrix. It is known that ifj = 2k-1is odd, then det(AAT) ≤(j+1)((j+1)d/4j)j; ifj is even, then det(AAT) ≤ (j+1)((j+2)d/4(j+1))j. A is called a regularD-optimal matrix if it satisfies the equality of the above bounds. In this note, it is proved thatifj = 2k - 1 is odd, then A is a regular D-optimal matrix if and only if A is the adjacent matrixof a (2k - 1, k, (j + 1)d/4j)-BIBD; if j ＝ 2k is even, then A is a regular D-optimal matrix ifand only if A can be obtained from the adjacent matrix B of a (2k + 1, k + 1, (j + 2)d/4(j + 1))-BIBD by deleting any one row from B. Three 21 × 42 regular D-optimal matrices, which wereunknown in [11], are also provided.
Striations in PageRank-Ordered Matrices
Pennycuff, Corey
2016-01-01
Patterns often appear in a variety of large, real-world networks, and interesting physical phenomena are often explained by network topology as in the case of the bow-tie structure of the World Wide Web, or the small world phenomenon in social networks. The discovery and modelling of such regular patterns has a wide application from disease propagation to financial markets. In this work we describe a newly discovered regularly occurring striation pattern found in the PageRank ordering of adjacency matrices that encode real-world networks. We demonstrate that these striations are the result of well-known graph generation processes resulting in regularities that are manifest in the typical neighborhood distribution. The spectral view explored in this paper encodes a tremendous amount about the explicit and implicit topology of a given network, so we also discuss the interesting network properties, outliers and anomalies that a viewer can determine from a brief look at the re-ordered matrix.
On some Toeplitz matrices and their inversions
Directory of Open Access Journals (Sweden)
S. Dutta
2014-10-01
Full Text Available In this article, using the difference operator B(a[m], we introduce a lower triangular Toeplitz matrix T which includes several difference matrices such as Δ(1,Δ(m,B(r,s,B(r,s,t, and B(r̃,s̃,t̃,ũ in different special cases. For any x ∈ w and m∈N0={0,1,2,…}, the difference operator B(a[m] is defined by (B(a[m]xk=ak(0xk+ak-1(1xk-1+ak-2(2xk-2+⋯+ak-m(mxk-m,(k∈N0 where a[m] = {a(0, a(1, …, a(m} and a(i = (ak(i for 0 ⩽ i ⩽ m are convergent sequences of real numbers. We use the convention that any term with negative subscript is equal to zero. The main results of this article relate to the determination and applications of the inverse of the Toeplitz matrix T.
Visualizing complex (hydrological) systems with correlation matrices
Haas, J. C.
2016-12-01
When trying to understand or visualize the connections of different aspects of a complex system, this often requires deeper understanding to start with, or - in the case of geo data - complicated GIS software. To our knowledge, correlation matrices have rarely been used in hydrology (e.g. Stoll et al., 2011; van Loon and Laaha, 2015), yet they do provide an interesting option for data visualization and analysis. We present a simple, python based way - using a river catchment as an example - to visualize correlations and similarities in an easy and colorful way. We apply existing and easy to use python packages from various disciplines not necessarily linked to the Earth sciences and can thus quickly show how different aquifers work or react, and identify outliers, enabling this system to also be used for quality control of large datasets. Going beyond earlier work, we add a temporal and spatial element, enabling us to visualize how a system reacts to local phenomena such as for example a river, or changes over time, by visualizing the passing of time in an animated movie. References: van Loon, A.F., Laaha, G.: Hydrological drought severity explained by climate and catchment characteristics, Journal of Hydrology 526, 3-14, 2015, Drought processes, modeling, and mitigation Stoll, S., Hendricks Franssen, H. J., Barthel, R., Kinzelbach, W.: What can we learn from long-term groundwater data to improve climate change impact studies?, Hydrology and Earth System Sciences 15(12), 3861-3875, 2011
Random matrices as models for the statistics of quantum mechanics
Casati, Giulio; Guarneri, Italo; Mantica, Giorgio
1986-05-01
Random matrices from the Gaussian unitary ensemble generate in a natural way unitary groups of evolution in finite-dimensional spaces. The statistical properties of this time evolution can be investigated by studying the time autocorrelation functions of dynamical variables. We prove general results on the decay properties of such autocorrelation functions in the limit of infinite-dimensional matrices. We discuss the relevance of random matrices as models for the dynamics of quantum systems that are chaotic in the classical limit. Permanent address: Dipartimento di Fisica, Via Celoria 16, 20133 Milano, Italy.
On the asymptotic distribution of block-modified random matrices
Energy Technology Data Exchange (ETDEWEB)
Arizmendi, Octavio, E-mail: octavius@cimat.mx [Department of Probability and Statistics, CIMAT, Guanajuato (Mexico); Nechita, Ion, E-mail: nechita@irsamc.ups-tlse.fr [Zentrum Mathematik, M5, Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany and CNRS, Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, UPS, F-31062 Toulouse (France); Vargas, Carlos, E-mail: obieta@math.tugraz.at [Department of Mathematical Structure Theory, Technische Universität Graz, Steyrergasse 30/III, 8010 Graz (Austria)
2016-01-15
We study random matrices acting on tensor product spaces which have been transformed by a linear block operation. Using operator-valued free probability theory, under some mild assumptions on the linear map acting on the blocks, we compute the asymptotic eigenvalue distribution of the modified matrices in terms of the initial asymptotic distribution. Moreover, using recent results on operator-valued subordination, we present an algorithm that computes, numerically but in full generality, the limiting eigenvalue distribution of the modified matrices. Our analytical results cover many cases of interest in quantum information theory: we unify some known results and we obtain new distributions and various generalizations.
Kerov's interlacing sequences and random matrices
Energy Technology Data Exchange (ETDEWEB)
Bufetov, Alexey, E-mail: alexey.bufetov@gmail.com [Institute for Information Transmission Problems, Independent University of Moscow and Higher School of Economics, Moscow (Russian Federation)
2013-11-15
To a N × N real symmetric matrix Kerov assigns a piecewise linear function whose local minima are the eigenvalues of this matrix and whose local maxima are the eigenvalues of its (N − 1) × (N − 1) submatrix. We study the scaling limit of Kerov's piecewise linear functions for Wigner and Wishart matrices. For Wigner matrices the scaling limit is given by the Verhik-Kerov-Logan-Shepp curve which is known from asymptotic representation theory. For Wishart matrices the scaling limit is also explicitly found, and we explain its relation to the Marchenko-Pastur limit spectral law.
ANOVA like analysis for structured families of stochastic matrices
Dias, Cristina; Santos, Carla; Varadinov, Maria; Mexia, João T.
2016-12-01
Symmetric stochastic matrices width a width a dominant eigenvalue λ and the corresponding eigenvector α appears in many applications. Such matrices can be written as M =λ α αt+E¯. Thus β = λ α will be the structure vector. When the matrices in such families correspond to the treatments of a base design we can carry out a ANOVA like analysis of the action of the treatments in the model on the structured vectors. This analysis can be transversal-when we worked width homologous components and - longitudinal when we consider contrast on the components of each structure vector. The analysis will be briefly considered at the end of our presentation.
Lipschitz correspondence between metric measure spaces and random distance matrices
Gadgil, Siddhartha
2011-01-01
Given a metric space with a Borel probability measure, for each integer $N$ we obtain a probability distribution on $N\\times N$ distance matrices by considering the distances between pairs of points in a sample consisting of $N$ points chosen indepenedently from the metric space with respect to the given measure. We show that this gives an asymptotically bi-Lipschitz relation between metric measure spaces and the corresponding distance matrices. This is an effective version of a result of Vershik that metric measure spaces are determined by associated distributions on infinite random matrices.
User-Friendly Tools for Random Matrices: An Introduction
2012-12-03
The set of positive-semidefinite matrices with size d forms a closed, convex cone in the real- linear space of Hermitian matrices of dimension d...valued function h on matrices that is concave or convex. The expectation of a random matrix can be viewed as a convex combination, and the cone of...hope shatters when we subject it to interrogation. It is not hard to find the reason that (3.3.2) fails. Note that the identity (3.3.1) depends on the
Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium
Henrique Machado; Lone Gram
2017-01-01
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...
Ji, Sun-Gou; Juran, Brian D.; Mucha, Soeren; Folseraas, Trine; Jostins, Luke; Melum, Espen; Kumasaka, Natsuhiko; Atkinson, Elizabeth J.; Schlicht, Erik M; Liu, Jimmy Z.; Shah, Tejas; Gutierrez-Achury, Javier; Boberg, Kirsten M.; Bergquist, Annika; Vermeire, Severine; Eksteen, Bertus; Durie, Peter R.; Farkkila, Martti; Mueller, Tobias; Schramm, Christoph; Sterneck, Martina; Weismueller, Tobias J.; Gotthardt, Daniel Nils; Ellinghaus, David; Braun, Felix; Teufel, Andreas; Laudes, Mattias; Lieb, Wolfgang; Jacobs, Gunnar; Beuers, Ulrich; Weersma, Rinse K.; Wijmenga, Cisca; Marschall, Hanns-Ulrich; Milkiewicz, Piotr; Pares, Albert; Kontula, Kimmo; Chazouilleres, Olivier; Invernizzi, Pietro; Goode, Elizabeth; Spiess, Kelly; Moore, Carmel; Sambrook, Jennifer; Ouwehand, Willem H.; Roberts, David J; Danesh, John; Floreani, Annarosa; Gulamhusein, Aliya F; Eaton, John E; Schreiber, Stefan; Coltescu, Catalina; Bowlus, Christopher L.; Luketic, Velimir A.; Odin, Joseph A; Chopra, Kapil B; Kowdley, Kris V; Chalasani, Naga; Manns, Michael P.; Srivastava, Brijesh; Mells, George; Sandford, Richard N.; Alexander, Graeme; Gaffney, Daniel J; Chapman, Roger W.; Hirschfield, Gideon M.; de Andrade, Mariza; Rushbrook, Simon M.; Franke, Andre; Karlsen, Tom H.; Lazaridis, Konstantinos N.; Anderson, Carl A.
Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; similar to 75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified
Ji, Sun-Gou; Juran, Brian D; Mucha, Sören; Folseraas, Trine; Jostins, Luke; Melum, Espen; Kumasaka, Natsuhiko; Atkinson, Elizabeth J; Schlicht, Erik M; Liu, Jimmy Z; Shah, Tejas; Gutierrez-Achury, Javier; Boberg, Kirsten M; Bergquist, Annika; Vermeire, Severine; Eksteen, Bertus; Durie, Peter R; Farkkila, Martti; Müller, Tobias; Schramm, Christoph; Sterneck, Martina; Weismüller, Tobias J; Gotthardt, Daniel N; Ellinghaus, David; Braun, Felix; Teufel, Andreas; Laudes, Mattias; Lieb, Wolfgang; Jacobs, Gunnar; Beuers, Ulrich; Weersma, Rinse K; Wijmenga, Cisca; Marschall, Hanns-Ulrich; Milkiewicz, Piotr; Pares, Albert; Kontula, Kimmo; Chazouillères, Olivier; Invernizzi, Pietro; Goode, Elizabeth; Spiess, Kelly; Moore, Carmel; Sambrook, Jennifer; Ouwehand, Willem H; Roberts, David J; Danesh, John; Floreani, Annarosa; Gulamhusein, Aliya F; Eaton, John E; Schreiber, Stefan; Coltescu, Catalina; Bowlus, Christopher L; Luketic, Velimir A; Odin, Joseph A; Chopra, Kapil B; Kowdley, Kris V; Chalasani, Naga; Manns, Michael P; Srivastava, Brijesh; Mells, George; Sandford, Richard N; Alexander, Graeme; Gaffney, Daniel J; Chapman, Roger W; Hirschfield, Gideon M; de Andrade, Mariza; Rushbrook, Simon M; Franke, Andre; Karlsen, Tom H; Lazaridis, Konstantinos N; Anderson, Carl A
2016-01-01
Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new ge
Derzelle, S.; Girault, G.; Roest, H.I.J.; Koene, M.G.J.
2015-01-01
Bacillus anthracis, the causative agent of anthrax, has been widely described as a clonal species. Here we report the use of both canonical SNP analysis and whole-genome sequencing to characterize the phylogenetic lineages of B. anthracis from the Netherlands. Eleven strains isolated over a 25-years
Whole-exome/genome sequencing and genomics.
Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne
2013-12-01
As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.
ON THE STIFFNESS OF DEMINERALIZED DENTIN MATRICES
Ryou, Heonjune; Turco, Gianluca; Breschi, Lorenzo; Tay, Franklin R.; Pashley, David H.; Arola, Dwayne
2015-01-01
Resin bonding to dentin requires the use of self-etching primers or acid etching to decalcify the surface and expose a layer of collagen fibrils of the dentin matrix. Acid-etching reduces the stiffness of demineralized dentin from approximately 19 GPa to 1 MPa, requiring that it floats in water to prevent it from collapsing during bonding procedures. Several publications show that crosslinking agents like gluteraladehyde, carbodiimide or grape seed extract can stiffen collagen and improve resin-dentin bond strength. Objective The objective was to assess a new approach for evaluating the changes in stiffness of decalcified dentin by polar solvents and a collagen cross-linker. Methods Fully demineralized dentin beams and sections of etched coronal dentin were subjected to indentation loading using a cylindrical flat indenter in water, and after treatment with ethanol or ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). The stiffness was measured as a function of strain and as a function of loading rate from 1 to 50 µm/sec. Results At a strain of 0.25% the elastic modulus of the fully demineralized dentin was approximately 0.20 MPa. It increased to over 0.90 MPa at strains of 1%. Exposure to ethanol caused an increase in elastic modulus of up to four times. Increasing the loading rate from 1 to 50 µm/sec caused an increase in the apparent modulus of up to three times in both water and ethanol. EDC treatment caused increases in the stiffness in fully demineralized samples and in acid-etched demineralized dentin surfaces in situ. Significance Changes in the mechanical behavior of demineralized collagen matrices can be measured effectively under hydration via indentation with cylindrical flat indenters. This approach can be used for quantifying the effects of bonding treatments on the properties of decalcified dentin after acid etching, as well as to follow the loss of stiffness over time due to enzymatic degradation. PMID:26747822
Super Fuzzy Matrices and Super Fuzzy Models for Social Scientists
Kandasamy, W B Vasantha; Amal, K
2008-01-01
This book introduces the concept of fuzzy super matrices and operations on them. This book will be highly useful to social scientists who wish to work with multi-expert models. Super fuzzy models using Fuzzy Cognitive Maps, Fuzzy Relational Maps, Bidirectional Associative Memories and Fuzzy Associative Memories are defined here. The authors introduce 13 multi-expert models using the notion of fuzzy supermatrices. These models are described with illustrative examples. This book has three chapters. In the first chaper, the basic concepts about super matrices and fuzzy super matrices are recalled. Chapter two introduces the notion of fuzzy super matrices adn their properties. The final chapter introduces many super fuzzy multi expert models.