Search results for "theory [gamma rays]"
showing 10 items of 976 documents
dAPE: a web server to detect homorepeats and follow their evolution.
2016
Abstract Summary Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats. Availability and Implementation dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx. Supplementary information Supplementary data are available at Bioinformatics online.
AFS: identification and quantification of species composition by metagenomic sequencing
2017
Abstract Summary DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. Using Illumina data from a reference sausage comprising four species, we reveal that AFS is independent of the sequencing assay and library preparation protocol. Cost-sav…
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …
REGGAE : a novel approach for the identification of key transcriptional regulators
2019
Abstract Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines assoc…
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
2018
Abstract Motivation Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy. Therefore, an important issue is to understand if, and to what extent, the structural differences in the chromatin organization between in vit…
Digital Competence for the improvement of Special Education Teaching
2016
The increasing digitization and globalization of the media, the broad diversification of media products, with the value-and ethical issues that it raises, proposes and confirms the reasons why media education is to be considered as an indispensable task for anyone involved in education. Thanks to specific educational interventions and appropriate evaluation tools for self-assessment, future educators should be helped to acquire the appropriate media skills necessary to develop the capacity to responsibly and autonomously choose proper media to design their media education courses. The media competence enhances teachers’ ability to creatively modify learning spaces and to design a variety of…
Modeling mass transfer in fracture flows with the time domain-random walk method
2019
The time domain-random walk method was developed further for simulating mass transfer in fracture flows together with matrix diffusion in surrounding porous media. Specifically, a time domain-random walk scheme was developed for numerically approximating solutions of the advection-diffusion equation when the diffusion coefficient exhibits significant spatial variation or even discontinuities. The proposed scheme relies on second-order accurate, central-difference approximations of the advective and diffusive fluxes. The scheme was verified by comparing simulated results against analytical solutions in flow configurations involving a rectangular channel connected on one side with a porous ma…
OPERADS AND JET MODULES
2005
Let $A$ be an algebra over an operad in a cocomplete closed symmetric monoidal category. We study the category of $A$-modules. We define certain symmetric product functors of such modules generalising the tensor product of modules over commutative algebras, which we use to define the notion of a jet module. This in turn generalises the notion of a jet module over a module over a classical commutative algebra. We are able to define Atiyah classes (i.e. obstructions to the existence of connections) in this generalised context. We use certain model structures on the category of $A$-modules to study the properties of these Atiyah classes. The purpose of the paper is not to present any really de…
Sourcing on the internet: Examining the relations among different phases of online inquiry
2021
This study examined students’ engagement in sourcing throughout online inquiry, that is, when they specified the information need, formulated search queries, evaluated online texts, and composed a written product. Participants were 167 upper secondary school students. Students completed an online inquiry task in a restricted online environment that utilized authentic online texts. Students’ prior topic knowledge and reading fluency was measured and controlled for in the analysis. The results showed that students engaged in sourcing even in the earliest phases of online inquiry. A sequential regression analysis indicated that the more frequently students engaged in sourcing in specifying the…