Population dynamical behavior of non-autonomous Lotka-Volterra competitive system with random perturbation

In this paper, we consider a non-autonomous stochastic Lotka-Volterra competitive system dxi(t) = xi(t)[(bi(t)¡ nPj=1aij (t)xj (t))dt+¾i(t)dBi(t)], where Bi(t) (i = 1; 2; ¢ ¢ ¢ ; n) are independent standard Brownian motions. Some dynamical properties are discussed and the su±cient conditions for the existence of global positive solutions, stochastic permanence, extinction as well as global attractivity are obtained. In addition, the limit of the average in time of the sample paths of solutions is estimated

The torsion cosmology in Kaluza-Klein theory

We have studied the torsion cosmology model in Kaluza-Klein theory. We considered two simple models in which the torsion vectors are $A_{\mu}=(\alpha,0,0,0)$ and $A_{\mu}=a(t)^2(0,\beta,\beta,\beta)$, respectively. For the first model, the accelerating expansion of the Universe can be not explained without dark energy which is similar to that in the standard cosmology. But for the second model, we find that without dark energy the effect of torsion can give rise to the accelerating expansion of the universe and the alleviation of the well-known age problem of the three old objects for appropriated value of the model parameter $\beta$. These outstanding features of the second torsion cosmology model have been supported by the Type Ia supernovae (SNIa) data.Comment: 12 pages, 2 figures. Accepted for publication in JCA

A minimal set of invariants as a systematic approach to higher order gravity models: Physical and Cosmological Constraints

We compare higher order gravity models to observational constraints from magnitude-redshift supernova data, distance to the last scattering surface of the CMB, and Baryon Acoustic Oscillations. We follow a recently proposed systematic approach to higher order gravity models based on minimal sets of curvature invariants, and select models that pass some physical acceptability conditions (free of ghost instabilities, real and positive propagation speeds, and free of separatrices). Models that satisfy these physical and observational constraints are found in this analysis and do provide fits to the data that are very close to those of the LCDM concordance model. However, we find that the limitation of the models considered here comes from the presence of superluminal mode propagations for the constrained parameter space of the models.Comment: 12 pages, 6 figure

Scalar-Torsion Mode in a Cosmological Model of the Poincar\'{e} Gauge Theory of Gravity

We investigate the equation of state (EoS) of the scalar-torsion mode in Poincar\'{e} gauge theory of gravity. We concentrate on two cases with the constant curvature solution and positive kinetic energy, respectively. In the former, we find that the torsion EoS has different values in the various stages of the universe. In particular, it behaves like the radiation (matter) EoS of $w_r=1/3$ ($w_m=0$) in the radiation (matter) dominant epoch, while in the late time the torsion density is supportive for the accelerating universe. In the latter, our numerical analysis shows that in general the EoS has an asymptotic behavior in the high redshift regime, while it could cross the phantom divide line in the low redshift regime.Comment: 12 pages, 2 figures, title changed, revised version accepted for publication in JCA

GIVE: portable genome browsers for personal websites.

Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome annotation, "linear" quantitative data, and genome interaction data. GIVE includes a graphical interface called HUG (HTML Universal Generator) that automatically generates HTML code for displaying user chosen data, which can be copy-pasted into user's personal website or saved and shared with collaborators. GIVE is available at: https://www.givengine.org/

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

We present biallelic SNVs called from 2,548 samples across 26 populationsfrom the 1000 Genomes Project, called directly on GRCh38. We believethis will be a useful reference resource for those using GRCh38,representing an improvement over the “lift-overs” of the 1000 GenomesProject data that have been available to date and providing a resourcenecessary for the full adoption of GRCh38 by the community. Here, wedescribe how the call set was created and provide benchmarking datadescribing how our call set compares to that produced by the final phase ofthe 1000 Genomes Project on GRCh37

Cosmological Equation of State and Interacting Energies

In this paper we study a model of cosmic evolution, assuming that the different components of the universe could interact between them any time. An effective equation of state (EOS) for the universe has been used as well. A particular function for w, which gives a good agreement between our results and the experimental data, has been studied. Finally, the model obtained has been applied to different important cases

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome- wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material. Methods: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species. Results: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice. Conclusions: Plant-RRBS offers high-throughput and broad, genome- dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations

One loop photon-graviton mixing in an electromagnetic field: Part 2

In part 1 of this series compact integral representations had been obtained for the one-loop photon-graviton amplitude involving a charged spin 0 or spin 1/2 particle in the loop and an arbitrary constant electromagnetic field. In this sequel, we study the structure and magnitude of the various polarization components of this amplitude on-shell. Explicit expressions are obtained for a number of limiting cases.Comment: 31 pages, 3 figure

Cosmological Evolution of a Tachyon-Quintom Model of Dark Energy

In this work we study the cosmological evolution of a dark energy model with two scalar fields, i.e. the tachyon and the phantom tachyon. This model enables the equation of state $w$ to change from $w>-1$ to $w<-1$ in the evolution of the universe. The phase-space analysis for such a system with inverse square potentials shows that there exists a unique stable critical point, which has power-law solutions. In this paper, we also study another form of tachyon-quintom model with two fields, which voluntarily involves the interactions between both fields.Comment: 17 pages, 10 figure