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Search Results: 1 - 10 of 8355 matches for " Oliver SP Davis "
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Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation
Sophia J Docherty, Oliver SP Davis, Claire MA Haworth, Robert Plomin, Jonathan Mill
Epigenetics & Chromatin , 2009, DOI: 10.1186/1756-8935-2-3
Abstract: Compared with data generated from 89 individual samples, our analysis of 205 CpG sites spanning nine independent regions of the genome demonstrates that DNA pools can be used to provide an accurate and reliable quantitative estimate of average group DNA methylation. Comparison of data generated from the pooled DNA samples with results averaged across the individual samples comprising each pool revealed highly significant correlations for individual CpG sites across all nine regions, with an average overall correlation across all regions and pools of 0.95 (95% bootstrapped confidence intervals: 0.94 to 0.96).In this study we demonstrate the validity of using pooled DNA samples to accurately assess group DNA methylation averages. Such an approach can be readily applied to the assessment of disease phenotypes reducing the time, cost and amount of DNA starting material required for large-scale epigenetic analyses.Epigenetics refers to the reversible regulation of various genomic functions mediated through partially stable modifications of DNA and chromatin histones. Epigenetic processes are essential for normal cellular development and differentiation, and allow the regulation of gene function through non-mutagenic mechanisms. Of particular interest is the phenomenon of cytosine methylation, occurring at position 5 of the cytosine pyrimidine ring in CpG dinucleotides. This process is intrinsically linked to the regulation of gene expression, with many genes demonstrating an inverse correlation between the degree of DNA methylation and the level of expression [1]. The methylation of these CpG sites, over-represented in CpG islands in the promoter regulatory regions of many genes, disrupts the binding of transcription factors and attracts methyl-binding proteins that are associated with gene silencing and chromatin compaction. DNA methylation plays a vital role in normal cellular function, and aberrant methylation signatures have thus been implicated in a growing number o
Genetics of Learning Abilities and Disabilities: Recent Developments from the UK and Possible Directions for Research in China
学习能力与学习障碍的遗传学:英国的近期发展和中国的研究的可能方向(英文)

Robert Plomin,Claire MA Haworth,Oliver SP Davis,
Robert Plomin
,Claire M.A. Haworth,Oliver S.P. Davis

心理学报 , 2008,
Abstract: It is exciting to witness the birth of behavioral genetics in China at a time when the field of genetics is exploding with new discoveries. We begin by discussing the potential for Chinese researchers to sidestep the false starts of previous genetic research on behavior and to become leaders rather than followers in behavioral genetics research. Using learning abilities and disabilities as an example, the rest of the paper considers ways in which quantitative genetic research can go beyond the nature versus...
Eigenvalues of sample covariance matrices of non-linear processes with infinite variance
Richard A. Davis,Oliver Pfaffel
Statistics , 2012,
Abstract: We study the $k$-largest eigenvalues of heavy-tailed sample covariance matrices of the form $\bX\bX^\T$ in an asymptotic framework, where the dimension of the data and the sample size tend to infinity. To this end, we assume that the rows of $\bX$ are given by independent copies of some stationary process with regularly varying marginals with index $\alpha\in(0,2)$ satisfying large deviation and mixing conditions. We apply these general results to stochastic volatility and GARCH processes.
Limit Theory for the largest eigenvalues of sample covariance matrices with heavy-tails
Richard A. Davis,Oliver Pfaffel,Robert Stelzer
Statistics , 2011,
Abstract: We study the joint limit distribution of the $k$ largest eigenvalues of a $p\times p$ sample covariance matrix $XX^\T$ based on a large $p\times n$ matrix $X$. The rows of $X$ are given by independent copies of a linear process, $X_{it}=\sum_j c_j Z_{i,t-j}$, with regularly varying noise $(Z_{it})$ with tail index $\alpha\in(0,4)$. It is shown that a point process based on the eigenvalues of $XX^\T$ converges, as $n\to\infty$ and $p\to\infty$ at a suitable rate, in distribution to a Poisson point process with an intensity measure depending on $\alpha$ and $\sum c_j^2$. This result is extended to random coefficient models where the coefficients of the linear processes $(X_{it})$ are given by $c_j(\theta_i)$, for some ergodic sequence $(\theta_i)$, and thus vary in each row of $X$. As a by-product of our techniques we obtain a proof of the corresponding result for matrices with iid entries in cases where $p/n$ goes to zero or infinity and $\alpha\in(0,2)$.
Gene Expression Profiles Resulting from Stable Loss of p53 Mirrors Its Role in Tissue Differentiation
Oliver Couture, Eric Lombardi, Kendra Davis, Emily Hays, Nalini Chandar
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082494
Abstract: The tumor suppressor gene p53 is involved in a variety of cellular activities such as cellular stress responses, cell cycle regulation and differentiation. In our previous studies we have shown p53’s transcription activating role to be important in osteoblast differentiation. There is still a debate in the literature as to whether p53 inhibits or promotes differentiation. We have found p53 heterozygous mice to show a p53 dependency on some bone marker gene expression that is absent in knockout mice. Mice heterozygous for p53 also show a higher incidence of osteosarcomas than p53 knockout mice. This suggests that p53 is able to modify the environment within osteoblasts. In this study we compare changes in gene expression resulting after either a transient or stable reduction in p53. Accordingly we reduced p53 levels transiently and stably in C2C12 cells, which are capable of both myoblast and osteoblast differentiation, and compared the changes in gene expression of candidate genes regulated by the p53 pathway. Using a PCR array to assay for p53 target genes, we have found different expression profiles when comparing stable versus transient knockdown of p53. As expected, several genes with profound changes after transient p53 loss were related to apoptosis and cell cycle regulation. In contrast, stable p53 loss produced a greater change in MyoD and other transcription factors with tissue specific roles, suggesting that long term loss of p53 affects tissue homeostasis to a greater degree than changes resulting from acute loss of p53. These differences in gene expression were validated by measuring promoter activity of different pathway specific genes involved in differentiation. These studies suggest that an important role for p53 is context dependent, with a stable reduction in p53 expression affecting normal tissue physiology more than acute loss of p53.
From observational to dynamic genetics
Claire M. A. Haworth,Oliver S. P. Davis
Frontiers in Genetics , 2014, DOI: 10.3389/fgene.2014.00006
Abstract: Twin and family studies have shown that most traits are at least moderately heritable. But what are the implications of finding genetic influence for the design of intervention and prevention programs? For complex traits, heritability does not mean immutability, and research has shown that genetic influences can change with age, context, and in response to behavioral and drug interventions. The most significant implications for intervention will come when we move from observational genetics to investigating dynamic genetics, including genetically sensitive interventions. Future interventions should be designed to overcome genetic risk and draw upon genetic strengths by changing the environment.
A Cross-Sectional Survey of Bacterial Species in Plaque from Client Owned Dogs with Healthy Gingiva, Gingivitis or Mild Periodontitis
Ian J. Davis, Corrin Wallis, Oliver Deusch, Alison Colyer, Lisa Milella, Nick Loman, Stephen Harris
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083158
Abstract: Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss). In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.

学习能力与学习障碍的遗传学:英国的近期发展和中国的研究的可能方向


robert,plomin,claire,m.a.,haworth,oliver,s.p.,davis
心理学报 , 2008,
Abstract: ?中国的行为遗传学诞生在遗传学突飞猛进的时代,令人振奋。作为一个新兴学科,中国的行为遗传学研究可以避免走前人的弯路,而成为领先而不是滞后的领域。以学习能力的研究为例,计量行为遗传学可以避免“性与养”(naturevs.nurture)的争论而直接研究一些遗传学与心理学里有意义的问题,包括正常与异常、稳定与变动、同质与异质的关系等问题。尤为重要的是超越“性与养”的争论而直接研究遗传对行为的影响。本文也扼要介绍了英国“双生子早期发展”项目的计量行为遗传学和“全基因组关联”对学习能力研究的结果。可以预计,飞速发展的遗传学发现将会持续一些时日,其发展将会对中国和世界的心理学产生更大的影响
étude de la lipogenèse a l'aide d'un acétate marqué au 14C chez des paires de s?urs normales et naines
SP Touchburn
Genetics Selection Evolution , 1971, DOI: 10.1186/1297-9686-3-3-386
Abstract:
Evaluating fracture healing using digital x-ray image analysis: Fracture healing is not easily monitored using currently available techniques
SP Whiley
Continuing Medical Education , 2011,
Abstract:
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