Warm Dark Matter versus Bumpy Power Spectra

In this paper we are exploring the differences between a Warm Dark Matter model and a CDM model where the power on a certain scale is reduced by introducing a narrow negative feature ("dip"). This dip is placed in a way so as to mimic the loss of power in the WDM model: both models have the same integrated power out to the scale where the power of the Dip model rises to the level of the unperturbed CDM spectrum again. Using N-body simulations we show that some of the large-scale clustering patterns of this new model follow more closely the usual CDM scenario while simultaneously suppressing small scale structures (within galactic halos) even more efficiently than WDM. The analysis in the paper shows that the new Dip model appears to be a viable alternative to WDM but it is based on different physics. Where WDM requires the introduction of a new particle species the Dip model is based on a non-standard inflationary period. If we are looking for an alternative to the currently challenged standard LCDM structure formation scenario, neither the LWDM nor the new Dip model can be ruled out based on the analysis presented in this paper. They both make very similar predictions and the degeneracy between them can only be broken with observations yet to come.Comment: 7 pages, 8 figures, replaced with MNRAS accepted version (minor revisions), high-resolution figures at http://astronomy.swin.edu.au/staff/aknebe

Quantum criticality of dipolar spin chains

We show that a chain of Heisenberg spins interacting with long-range dipolar forces in a magnetic field h perpendicular to the chain exhibits a quantum critical point belonging to the two-dimensional Ising universality class. Within linear spin-wave theory the magnon dispersion for small momenta k is [Delta^2 + v_k^2 k^2]^{1/2}, where Delta^2 \propto |h - h_c| and v_k^2 \propto |ln k|. For fields close to h_c linear spin-wave theory breaks down and we investigate the system using density-matrix and functional renormalization group methods. The Ginzburg regime where non-Gaussian fluctuations are important is found to be rather narrow on the ordered side of the transition, and very broad on the disordered side.Comment: 6 pages, 5 figure

Millihertz Quasi-Periodic Oscillations from Marginally Stable Nuclear Burning on an Accreting Neutron Star

We investigate marginally stable nuclear burning on the surface of accreting neutron stars as an explanation for the mHz quasi-periodic oscillations (QPOs) observed from three low mass X-ray binaries. At the boundary between unstable and stable burning, the temperature dependence of the nuclear heating rate and cooling rate almost cancel. The result is an oscillatory mode of burning, with an oscillation period close to the geometric mean of the thermal and accretion timescales for the burning layer. We describe a simple one-zone model which illustrates this basic physics, and then present detailed multizone hydrodynamical calculations of nuclear burning close to the stability boundary using the KEPLER code. Our models naturally explain the characteristic 2 minute period of the mHz QPOs, and why they are seen only in a very narrow range of X-ray luminosities. The oscillation period is sensitive to the accreted hydrogen fraction and the surface gravity, suggesting a new way to probe these parameters. A major puzzle is that the accretion rate at which the oscillations appear in the theoretical models is an order of magnitude larger than the rate implied by the X-ray luminosity when the mHz QPOs are seen. We discuss the implications for our general understanding of nuclear burning on accreting neutron stars. One possibility is that the accreted material covers only part of the neutron star surface at luminosities Lx > ~1E37 erg/s.Comment: 10 pages, 9 figures, submitted to Ap

Precision nomenclature for the new genomics

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism\u27s genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis

Derivative corrections to the Born-Infeld action through beta-function calculations in N=2 boundary superspace

We calculate the beta-functions for an open string sigma-model in the presence of a U(1) background. Passing to N=2 boundary superspace, in which the background is fully characterized by a scalar potential, significantly facilitates the calculation. Performing the calculation through three loops yields the equations of motion up to five derivatives on the fieldstrengths, which upon integration gives the bosonic sector of the effective action for a single D-brane in trivial bulk background fields through four derivatives and to all orders in alpha'. Finally, the present calculation shows that demanding ultra-violet finiteness of the non-linear sigma-model can be reformulated as the requirement that the background is a deformed stable holomorphic U(1) bundle.Comment: 25 pages, numerous figure

Expression and reactivation of HIV in a chemokine induced model of HIV latency in primary resting CD4+ T cells

<p>Abstract</p> <p>Background</p> <p>We recently described that HIV latent infection can be established <it>in vitro </it>following incubation of resting CD4+ T-cells with chemokines that bind to CCR7. The main aim of this study was to fully define the post-integration blocks to virus replication in this model of CCL19-induced HIV latency.</p> <p>Results</p> <p>High levels of integrated HIV DNA but low production of reverse transcriptase (RT) was found in CCL19-treated CD4+ T-cells infected with either wild type (WT) NL4.3 or single round envelope deleted NL4.3 pseudotyped virus (NL4.3- Δenv). Supernatants from CCL19-treated cells infected with either WT NL4.3 or NL4.3- Δenv did not induce luciferase expression in TZM-bl cells, and there was no expression of intracellular p24. Following infection of CCL19-treated CD4+ T-cells with NL4.3 with enhanced green fluorescent protein (EGFP) inserted into the <it>nef </it>open reading frame (NL4.3- Δnef-EGFP), there was no EGFP expression detected. These data are consistent with non-productive latent infection of CCL19-treated infected CD4+ T-cells. Treatment of cells with phytohemagluttinin (PHA)/IL-2 or CCL19, prior to infection with WT NL4.3, resulted in a mean fold change in unspliced (US) RNA at day 4 compared to day 0 of 21.2 and 1.1 respectively (p = 0.01; n = 5), and the mean expression of multiply spliced (MS) RNA was 56,000, and 5,000 copies/million cells respectively (p = 0.01; n = 5). In CCL19-treated infected CD4+ T-cells, MS-RNA was detected in the nucleus and not in the cytoplasm; in contrast to PHA/IL-2 activated infected cells where MS RNA was detected in both. Virus could be recovered from CCL19-treated infected CD4+ T-cells following mitogen stimulation (with PHA and phorbyl myristate acetate (PMA)) as well as TNFα, IL-7, prostratin and vorinostat.</p> <p>Conclusions</p> <p>In this model of CCL19-induced HIV latency, we demonstrate HIV integration without spontaneous production of infectious virus, detection of MS RNA in the nucleus only, and the induction of virus production with multiple activating stimuli. These data are consistent with <it>ex vivo </it>findings from latently infected CD4+ T-cells from patients on combination antiretroviral therapy, and therefore provide further support of this model as an excellent <it>in vitro </it>model of HIV latency.</p

Sequence analysis and editing for bisulphite genomic sequencing projects

Bisulphite genomic sequencing is a widely used technique for detailed analysis of the methylation status of a region of DNA. It relies upon the selective deamination of unmethylated cytosine to uracil after treatment with sodium bisulphite, usually followed by PCR amplification of the chosen target region. Since this two-step procedure replaces all unmethylated cytosine bases with thymine, PCR products derived from unmethylated templates contain only three types of nucleotide, in unequal proportions. This can create a number of technical difficulties (e.g. for some base-calling methods) and impedes manual analysis of sequencing results (since the long runs of T or A residues are difficult to align visually with the parent sequence). To facilitate the detailed analysis of bisulphite PCR products (particularly using multiple cloned templates), we have developed a visually intuitive program that identifies the methylation status of CpG dinucleotides by analysis of raw sequence data files produced by MegaBace or ABI sequencers as well as Staden SCF trace files and plain text files. The program then also collates and presents data derived from independent templates (e.g. separate clones). This results in a considerable reduction in the time required for completion of a detailed genomic methylation project

Streptomyces tardus sp. nov.: A Slow-Growing Actinobacterium Producing Candicidin, Isolated From Sediments of the Trondheim Fjord

Marine environments are home to an extensive number of microorganisms, many of which remain unexplored for taxonomic novelty and functional capabilities. In this study, a slow-growing Streptomyces strain expressing unique genomic and phenotypic characteristics, P38-E01T , was described using a polyphasic taxonomic approach. This strain is part of a collection of over 8,000 marine Actinobacteria isolates collected in the Trondheim fjord of Norway by SINTEF Industry (Trondheim, Norway) and the Norwegian University of Science and Technology (NTNU, Trondheim, Norway). Strain P38-E01T was isolated from the sediments of the Trondheim fjord, and phylogenetic analyses affiliated this strain with the genus Streptomyces, but it was not closely affiliated with other described species. The closest related type strains were Streptomyces daliensis YIM 31724T (98.6%), Streptomyces rimosus subsp. rimosus ATCC 10970T (98.4%), and Streptomyces sclerotialus NRRL ISP-5269T (98.3%). Predominant fatty acids were C16V0 iso, C16V0, and Summed Feature 3, and the predominant respiratory quinones were MK-10(H6), MK-10(H4), and MK9(H4). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hosphatidylglycerol, and phosphoglycolipid. The whole-cell sugars were glucose, ribose, and in minor amounts, mannose. The cell wall peptidoglycan contained LL-diaminopimelic acid. The draft genome has a size of 6.16 Mb, with a %G C C content of 71.4% and is predicted to contain at least 19 biosynthetic gene clusters encoding diverse secondary metabolites. Strain P38-E01T was found to inhibit the growth of the pathogenic yeast Candida albicans ATCC 90028 and a number of Gram-positive bacterial human and plant pathogens. Metabolites extracted from cultures of P38-E01T were analyzed by mass spectrometry, and it was found that the isolate produced the antifungal compound candicidin. Phenotypic and chemotaxonomic signatures, along with phylogenetic analyses, distinguished isolate P38-E01T from its closest neighbors; thus, this isolate represents a novel species of the genus Streptomyces for which the name Streptomyces tardus sp. nov. (P38-E01T D CCM 9049T D DSM 111582T ) is proposed.publishedVersio

Schreier rewriting beyond the classical setting

Using actions of free monoids and free associative algebras, we establish some Schreier-type formulas involving the ranks of actions and the ranks of subactions in free actions or Grassmann-type relations for the ranks of intersections of subactions of free actions. The coset action of the free group is used to establish the generalization of the Schreier formula to the case of subgroups of infinite index. We also study and apply large modules over free associative algebras in the spirit of the paper Olshanskii, A. Yu.; Osin, D.V., Large groups and their periodic quotients, Proc. Amer. Math. Soc., 136 (2008), 753 - 759.Comment: 17 page