ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Articles  (388)
  • Other Sources
  • Oxford University Press  (364)
  • Soil Science Society of America  (24)
Collection
  • Articles  (388)
  • Other Sources
Source
Keywords
Publisher
Years
Journal
Topic
  • 11
    facet.materialart.
    Unknown
    Glycosyl rotation and distortion by key residues in Endocellulase Cel6A from Theromobifida fusca (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-11
    Description: Endocellulases are one kind of the important biodegrading cellulose enzymes. Experimental results show that a rotated and distorted preactivated structure exists before the substrate entering the transition state. The molecular dynamic simulation of endocellulase Cel6A models revealed a correlation between the rotation and distortion of pyranoside ring in –1 glycosyl unit of the substrate. The two key residues, Tyr73 and Ser189, in Cal6A cooperate to rotate and distort the pyranoside ring in the cellulose hydrolysis.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 12
    facet.materialart.
    Unknown
    H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-10
    Description: DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase , but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 13
    facet.materialart.
    Unknown
    Efficient computation of smoothing splines via adaptive basis sampling (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-21
    Description: Smoothing splines provide flexible nonparametric regression estimators. However, the high computational cost of smoothing splines for large datasets has hindered their wide application. In this article, we develop a new method, named adaptive basis sampling, for efficient computation of smoothing splines in super-large samples. Except for the univariate case where the Reinsch algorithm is applicable, a smoothing spline for a regression problem with sample size n can be expressed as a linear combination of n basis functions and its computational complexity is generally O ( n 3 ). We achieve a more scalable computation in the multivariate case by evaluating the smoothing spline using a smaller set of basis functions, obtained by an adaptive sampling scheme that uses values of the response variable. Our asymptotic analysis shows that smoothing splines computed via adaptive basis sampling converge to the true function at the same rate as full basis smoothing splines. Using simulation studies and a large-scale deep earth core-mantle boundary imaging study, we show that the proposed method outperforms a sampling method that does not use the values of response variables.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 14
    facet.materialart.
    Unknown
    Likelihood-based complex trait association testing for arbitrary depth sequencing data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-11
    Description: : In next generation sequencing (NGS)-based genetic studies, researchers typically perform genotype calling first and then apply standard genotype-based methods for association testing. However, such a two-step approach ignores genotype calling uncertainty in the association testing step and may incur power loss and/or inflated type-I error. In the recent literature, a few robust and efficient likelihood based methods including both likelihood ratio test (LRT) and score test have been proposed to carry out association testing without intermediate genotype calling. These methods take genotype calling uncertainty into account by directly incorporating genotype likelihood function (GLF) of NGS data into association analysis. However, existing LRT methods are computationally demanding or do not allow covariate adjustment; while existing score tests are not applicable to markers with low minor allele frequency (MAF). We provide an LRT allowing flexible covariate adjustment, develop a statistically more powerful score test and propose a combination strategy (UNC combo) to leverage the advantages of both tests. We have carried out extensive simulations to evaluate the performance of our proposed LRT and score test. Simulations and real data analysis demonstrate the advantages of our proposed combination strategy: it offers a satisfactory trade-off in terms of computational efficiency, applicability (accommodating both common variants and variants with low MAF) and statistical power, particularly for the analysis of quantitative trait where the power gain can be up to ~60% when the causal variant is of low frequency (MAF 〈 0.01). Availability and implementation : UNC combo and the associated R files, including documentation, examples, are available at http://www.unc.edu/~yunmli/UNCcombo/ Contact: yunli@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 15
    facet.materialart.
    Unknown
    Distributed robust consensus control for nonlinear multi-agent systems by using output regulation approach (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-15
    Description: This paper deals with the distributed robust output regulation problem for the multi-agent systems with general nonlinear dynamics and uncertainty parameters. Assume that the information of active leaders or environmental disturbances cannot be completely measurable for all other agents. By employing the centre manifold theory and characteristics of the agents’ communication, the nonlinear distributed dynamic feedback controllers are designed to make the agents asymptotically track the references or reject the disturbance signals, which are generated by the exosystem. Two numerical examples are provided to show the effectiveness of the main results.
    Print ISSN: 0265-0754
    Electronic ISSN: 1471-6887
    Topics: Mathematics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 16
    facet.materialart.
    Unknown
    No Genome-Wide Protein Sequence Convergence for Echolocation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-25
    Description: Toothed whales and two groups of bats independently acquired echolocation, the ability to locate and identify objects by reflected sound. Echolocation requires physiologically complex and coordinated vocal, auditory, and neural functions, but the molecular basis of the capacity for echolocation is not well understood. A recent study suggested that convergent amino acid substitutions widespread in the proteins of echolocators underlay the convergent origins of mammalian echolocation. Here, we show that genomic signatures of molecular convergence between echolocating lineages are generally no stronger than those between echolocating and comparable nonecholocating lineages. The same is true for the group of 29 hearing-related proteins claimed to be enriched with molecular convergence. Reexamining the previous selection test reveals several flaws and invalidates the asserted evidence for adaptive convergence. Together, these findings indicate that the reported genomic signatures of convergence largely reflect the background level of sequence convergence unrelated to the origins of echolocation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 17
    facet.materialart.
    Unknown
    Simultaneous optical monitoring of BL Lacertae object S5 0716+714 with high temporal resolution (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: We have monitored the BL Lacertae object S5 0716+714 simultaneously in the B , R and I bands on three nights in 2014 November. The average time resolution is quite high (73, 34 and 58 s for the filters B , R and I ), which can help us trace the profile of the variation and search for the short inter-band time delay. Intra-day variability was about 0.1 mag on the first two nights and more than 0.3 mag on the third. A bluer-when-brighter colour behaviour was found. A clear loop path can be seen on the colour–magnitude diagram of the third night, revealing possible time delays between variations at high and low energies. It is the first time that the intra-day spectral hysteresis loop has been found so obviously in the optical band. We used the interpolated cross-correlation function method to further confirm the time delay and calculated the values of lag between light curves at different wavelengths on each night. On the third night, variations in the R and B bands are approximately 1.5 min lagging behind the I band. Such optical time delay is probably due to the interplay of different processes of electrons in the jet of the blazar.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 18
    facet.materialart.
    Unknown
    Approximation to invariant manifolds under pseudo-hyperbolicity (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-10
    Description: As known from the theory of centre manifolds, it is important to approximate invariant manifolds when discussing high order terms of the reduced systems in the investigation of bifurcations. In this paper, we give a method to approximate invariant manifolds which are obtained under pseudo-hyperbolicity. This method enables us to avoid the trouble of increasing dimension of the so-called approximate inertial manifold for smaller thickness of attractive neighbourhood. Unlike centre manifolds, exponential expansion and contraction may exist on such manifolds. Consequently, the technique of the contraction principle cannot be used directly. We not only overcome the difficulty so as to approximate such $C^{1}$ manifolds at a possibly higher order but also estimate, for non-local bifurcations, the lower bound of their locality radius such that the approximation is valid. Our approximation is demonstrated by examples of a wave equation and an ordinary differential equation.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 19
    facet.materialart.
    Unknown
    Are Convergent and Parallel Amino Acid Substitutions in Protein Evolution More Prevalent Than Neutral Expectations? (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-18
    Description: Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of reports of molecular convergence in the last decade raises the intriguing question of whether molecular convergence occurs substantially more frequently than expected under neutral evolution. We here address this question using all one-to-one orthologous proteins encoded by the genomes of 12 fruit fly species and those encoded by 17 mammals. We found that the expected amount of molecular convergence varies greatly depending on the specific neutral substitution model assumed at each amino acid site and that the observed amount of molecular convergence is explainable by neutral models incorporating site-specific information of acceptable amino acids. Interestingly, the total number of convergent and parallel substitutions between two lineages, relative to the neutral expectation, decreases with the genetic distance between the two lineages, regardless of the model used in computing the neutral expectation. We hypothesize that this trend results from differences in the amino acids acceptable at a given site among different clades of a phylogeny, due to prevalent epistasis, and provide simulation as well as empirical evidence for this hypothesis. Together, our study finds no genomic evidence for higher-than-neutral levels of molecular convergence, but suggests the presence of abundant epistasis that decreases the likelihood of molecular convergence between distantly related lineages.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 20
    facet.materialart.
    Unknown
    Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...