Direct detection of supersymmetric dark matter- Theoretical rates for transitions to excited states

The recent WMAP data have confirmed that exotic dark matter together with the vacuum energy (cosmological constant) dominate in the flat Universe. Supersymmetry provides a natural dark matter candidate, the lightest supersymmetric particle (LSP). Thus the direct dark matter detection is central to particle physics and cosmology. Most of the research on this issue has hitherto focused on the detection of the recoiling nucleus. In this paper we study transitions to the excited states, focusing on the first excited state at 50 keV of Iodine A=127. We find that the transition rate to this excited state is about 10 percent of the transition to the ground state. So, in principle, the extra signature of the gammai ray following its de-excitation can be exploited experimentally.Comment: LaTex, 13 pages, 3 postscript figures, 1 table, to appear in IJMP

DeepBrain: Functional Representation of Neural In-Situ Hybridization Images for Gene Ontology Classification Using Deep Convolutional Autoencoders

This paper presents a novel deep learning-based method for learning a functional representation of mammalian neural images. The method uses a deep convolutional denoising autoencoder (CDAE) for generating an invariant, compact representation of in situ hybridization (ISH) images. While most existing methods for bio-imaging analysis were not developed to handle images with highly complex anatomical structures, the results presented in this paper show that functional representation extracted by CDAE can help learn features of functional gene ontology categories for their classification in a highly accurate manner. Using this CDAE representation, our method outperforms the previous state-of-the-art classification rate, by improving the average AUC from 0.92 to 0.98, i.e., achieving 75% reduction in error. The method operates on input images that were downsampled significantly with respect to the original ones to make it computationally feasible

Shape resonance for the anisotropic superconducting gaps near a Lifshitz transition: the effect of electron hopping between layers

The multigap superconductivity modulated by quantum confinement effects in a superlattice of quantum wells is presented. Our theoretical BCS approach captures the low-energy physics of a shape resonance in the superconducting gaps when the chemical potential is tuned near a Lifshitz transition. We focus on the case of weak Cooper-pairing coupling channels and strong pair exchange interaction driven by repulsive Coulomb interaction that allows to use the BCS theory in the weak-coupling regime neglecting retardation effects like in quantum condensates of ultracold gases. The calculated matrix element effects in the pairing interaction are shown to yield a complex physics near the particular quantum critical points due to Lifshitz transitions in multigap superconductivity. Strong deviations of the ratio $2\Delta/T_c$ from the standard BCS value as a function of the position of the chemical potential relative to the Lifshitz transition point measured by the Lifshitz parameter are found. The response of the condensate phase to the tuning of the Lifshitz parameter is compared with the response of ultracold gases in the BCS-BEC crossover tuned by an external magnetic field. The results provide the description of the condensates in this regime where matrix element effects play a key role.Comment: 12 pages, 6 figure

The Density Matrix Renormalization Group for finite Fermi systems

The Density Matrix Renormalization Group (DMRG) was introduced by Steven White in 1992 as a method for accurately describing the properties of one-dimensional quantum lattices. The method, as originally introduced, was based on the iterative inclusion of sites on a real-space lattice. Based on its enormous success in that domain, it was subsequently proposed that the DMRG could be modified for use on finite Fermi systems, through the replacement of real-space lattice sites by an appropriately ordered set of single-particle levels. Since then, there has been an enormous amount of work on the subject, ranging from efforts to clarify the optimal means of implementing the algorithm to extensive applications in a variety of fields. In this article, we review these recent developments. Following a description of the real-space DMRG method, we discuss the key steps that were undertaken to modify it for use on finite Fermi systems and then describe its applications to Quantum Chemistry, ultrasmall superconducting grains, finite nuclei and two-dimensional electron systems. We also describe a recent development which permits symmetries to be taken into account consistently throughout the DMRG algorithm. We close with an outlook for future applications of the method.Comment: 48 pages, 17 figures Corrections made to equation 19 and table

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

The main adaptive immune response to bacteria is mediated by B cells and CD4+ T-cells. However, some bacterial proteins reach the cytosol of host cells and are exposed to the host CD8+ T-cells response. Both gram-negative and gram-positive bacteria can translocate proteins to the cytosol through type III and IV secretion and ESX-1 systems, respectively. The translocated proteins are often essential for the bacterium survival. Once injected, these proteins can be degraded and presented on MHC-I molecules to CD8+ T-cells. The CD8+ T-cells, in turn, can induce cell death and destroy the bacteria's habitat. In viruses, escape mutations arise to avoid this detection. The accumulation of escape mutations in bacteria has never been systematically studied. We show for the first time that such mutations are systematically present in most bacteria tested. We combine multiple bioinformatic algorithms to compute CD8+ T-cell epitope libraries of bacteria with secretion systems that translocate proteins to the host cytosol. In all bacteria tested, proteins not translocated to the cytosol show no escape mutations in their CD8+ T-cell epitopes. However, proteins translocated to the cytosol show clear escape mutations and have low epitope densities for most tested HLA alleles. The low epitope densities suggest that bacteria, like viruses, are evolutionarily selected to ensure their survival in the presence of CD8+ T-cells. In contrast with most other translocated proteins examined, Pseudomonas aeruginosa's ExoU, which ultimately induces host cell death, was found to have high epitope density. This finding suggests a novel mechanism for the manipulation of CD8+ T-cells by pathogens. The ExoU effector may have evolved to maintain high epitope density enabling it to efficiently induce CD8+ T-cell mediated cell death. These results were tested using multiple epitope prediction algorithms, and were found to be consistent for most proteins tested

Repression of Floral Meristem Fate Is Crucial in Shaping Tomato Inflorescence

Tomato is an important crop and hence there is a great interest in understanding the genetic basis of its flowering. Several genes have been identified by mutations and we constructed a set of novel double mutants to understand how these genes interact to shape the inflorescence. It was previously suggested that the branching of the tomato inflorescence depends on the gradual transition from inflorescence meristem (IM) to flower meristem (FM): the extension of this time window allows IM to branch, as seen in the compound inflorescence (s) and falsiflora (fa) mutants that are impaired in FM maturation. We report here that JOINTLESS (J), which encodes a MADS-box protein of the same clade than SHORT VEGETATIVE PHASE (SVP) and AGAMOUS LIKE 24 (AGL24) in Arabidopsis, interferes with this timing and delays FM maturation, therefore promoting IM fate. This was inferred from the fact that j mutation suppresses the high branching inflorescence phenotype of s and fa mutants and was further supported by the expression pattern of J, which is expressed more strongly in IM than in FM. Most interestingly, FA - the orthologue of the Arabidopsis LEAFY (LFY) gene - shows the complementary expression pattern and is more active in FM than in IM. Loss of J function causes premature termination of flower formation in the inflorescence and its reversion to a vegetative program. This phenotype is enhanced in the absence of systemic florigenic protein, encoded by the SINGLE FLOWER TRUSS (SFT) gene, the tomato orthologue of FLOWERING LOCUS T (FT). These results suggest that the formation of an inflorescence in tomato requires the interaction of J and a target of SFT in the meristem, for repressing FA activity and FM fate in the IM

Construction of a Microscopic Model for Yb and Tm Compounds on the Basis of a \mib{j}-\mib{j} Coupling Scheme

We provide a prescription to construct a microscopic model for heavy lanthanide systems such as Yb and Tm compounds by exploiting a $j$-$j$ coupling scheme. Here we consider a situation with a large spin-orbit coupling, in which $j$=5/2 sextet is fully occupied, while $j$=7/2 octet is partially occupied, where $j$ denotes total angular momentum. We evaluate crystalline electric field potentials and Coulomb interactions among the states of the $j$=7/2 octet to construct a local Hamiltonian in the $j$-$j$ coupling scheme. Then, it is found that the local $f$-electron states composed of the $j$=7/2 octet agree quite well with those of seven $f$ orbitals even for a realistic value of the spin-orbit coupling. As an example of the application of the present model, we discuss low-temperature multipole states of Yb- and Tm-based filled skutterudites by analyzing multipole susceptibility of the Anderson model in the $j$-$j$ coupling scheme with the use of a numerical renormalization group technique. From the comparison with the numerical results of the seven-orbital Anderson model, it is concluded that the multipole state is also well reproduced by the $j$-$j$ coupling model, even when we include the hybridization between conduction and $f$ electrons for the realistic value of the spin-orbit coupling. Finally, we briefly discuss future applications of the present prescription for theoretical research on heavy lanthanide compounds.Comment: 12 pages, 8 figures

Geometric methods on low-rank matrix and tensor manifolds

In this chapter we present numerical methods for low-rank matrix and tensor problems that explicitly make use of the geometry of rank constrained matrix and tensor spaces. We focus on two types of problems: The first are optimization problems, like matrix and tensor completion, solving linear systems and eigenvalue problems. Such problems can be solved by numerical optimization for manifolds, called Riemannian optimization methods. We will explain the basic elements of differential geometry in order to apply such methods efficiently to rank constrained matrix and tensor spaces. The second type of problem is ordinary differential equations, defined on matrix and tensor spaces. We show how their solution can be approximated by the dynamical low-rank principle, and discuss several numerical integrators that rely in an essential way on geometric properties that are characteristic to sets of low rank matrices and tensors

Geminivirus-Mediated Delivery of Florigen Promotes Determinate Growth in Aerial Organs and Uncouples Flowering from Photoperiod in Cotton

This article discusses geminivirus-mediated delivery of florigen. Florigen acts as a general growth hormone, advancing determinate growth. The findings extend our understanding of florigen as a general growth hormone and could benefit crop management techniques