Brain Gene Expression Analysis: a MATLAB toolbox for the analysis of brain-wide gene-expression data

The Allen Brain Atlas project (ABA) generated a genome-scale collection of gene-expression profiles using in-situ hybridization. These profiles were co-registered to the three-dimensional Allen Reference Atlas (ARA) of the adult mouse brain. A set of more than 4,000 such volumetric data are available for the full brain, at a resolution of 200 microns. These data are presented in a voxel-by-gene matrix. The ARA comes with several systems of annotation, hierarchical (40 cortical regions, 209 sub-cortical regions in the whole brain), or non-hierarchical (12 regions in the left hemisphere, with refinement into 94 regions, and cortical layers). The high-dimensional nature of this unique dataset and the possible connection between anatomy and gene expression pose challenges to data analysis. We developed the Brain Gene Expression Analysis Toolbox (downloadable at: www.brainarchitecture.org). The key functionalities include: determination of marker genes for brain regions, statistical analysis of brain-wide co-expression patterns, and the computation of brain-wide correlation maps with cell-type specific microarray data. The auxiliary dataset consisting of cell-type-specific transcriptomes (chapter 4) will be made available in the second version of the toolbox

Chronic inflammation as a manifestation of defects in immunoregulatory networks: implications for novel therapies based on microbial products

Based on a unifying theory presented here, it is predicted that the immune defects resulting in chronic inflammation rather than effective immune responses could be rectified by the therapeutic use of agents prepared from micro-organisms. With appropriate molecular patterns, these should be able to induce protective immunoregulatory networks or to reprogramme defective ones. In contrast to acute inflammation, chronic inflammation appears to have no beneficial role, but is a state of sustained immune reactivity in the presence or progression of a disease process. This results in an escalating cycle of tissue damage followed by unproductive tissue repair, breaks in self-tolerance, malignant transformation or deleterious changes in tissue morphology and function. Such inappropriate immune reactivity is an underlying characteristic, either in initiation or maintenance, of a diverse range of disease states including chronic infection, autoimmunity, allergy, cancer, vascular disease and metabolic alterations. Evidence is presented that the inappropriate immune reactivity is due, at least to some extent, to failures in the establishment of immunoregulatory networks as a result of hygiene-related factors. Such networks are the result of activation of antigen-presenting cells, principally dendritic cells, by molecular patterns of micro-organisms encountered sequentially during life and establishing the "biography" of the immune system.Fil: Bottasso, Oscar Adelmo. Universidad Nacional de Rosario. Facultad de Ciencias Médicas. Instituto de Inmunología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Docena, Guillermo H.. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Criotecnología de Alimentos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Criotecnología de Alimentos; ArgentinaFil: Stanford, J. L.. University College London; Estados UnidosFil: Grange, J. M.. University College London; Estados Unido

Fission widths of hot nuclei from Langevin dynamics

Fission dynamics of excited nuclei is studied in the framework of Langevin equation. The one body wall-and-window friction is used as the dissipative force in the Langevin equation. In addition to the usual wall formula friction, the chaos weighted wall formula developed earlier to account for nonintegrability of single-particle motion within the nuclear volume is also considered here. The fission rate calculated with the chaos weighted wall formula is found to be faster by about a factor of two than that obtained with the usual wall friction. The systematic dependence of fission width on temperature and spin of the fissioning nucleus is investigated and a simple parametric form of fission width is obtained.Comment: RevTex, 12 pages including 9 Postscript figure

Towards mirror symmetry \`a la SYZ for generalized Calabi-Yau manifolds

Fibrations of flux backgrounds by supersymmetric cycles are investigated. For an internal six-manifold M with static SU(2) structure and mirror \hat{M}, it is argued that the product M x \hat{M} is doubly fibered by supersymmetric three-tori, with both sets of fibers transverse to M and \hat{M}. The mirror map is then realized by T-dualizing the fibers. Mirror-symmetric properties of the fluxes, both geometric and non-geometric, are shown to agree with previous conjectures based on the requirement of mirror symmetry for Killing prepotentials. The fibers are conjectured to be destabilized by fluxes on generic SU(3)xSU(3) backgrounds, though they may survive at type-jumping points. T-dualizing the surviving fibers ensures the exchange of pure spinors under mirror symmetry.Comment: 30 pages, 3 figures, LaTeX; v2: references adde

Modeling of mode-locking in a laser with spatially separate gain media

We present a novel laser mode-locking scheme and discuss its unusual properties and feasibility using a theoretical model. A large set of single-frequency continuous-wave lasers oscillate by amplification in spatially separated gain media. They are mutually phase-locked by nonlinear feedback from a common saturable absorber. As a result, ultra short pulses are generated. The new scheme offers three significant benefits: the light that is amplified in each medium is continuous wave, thereby avoiding issues related to group velocity dispersion and nonlinear effects that can perturb the pulse shape. The set of frequencies on which the laser oscillates, and therefore the pulse repetition rate, is controlled by the geometry of resonator-internal optical elements, not by the cavity length. Finally, the bandwidth of the laser can be controlled by switching gain modules on and off. This scheme offers a route to mode-locked lasers with high average output power, repetition rates that can be scaled into the THz range, and a bandwidth that can be dynamically controlled. The approach is particularly suited for implementation using semiconductor diode laser arrays.Comment: 13 pages, 5 figures, submitted to Optics Expres

Heterotic type IIA duality with fluxes - towards the complete story

In this paper we study the heterotic type IIA duality when fluxes are turned on. We show that many of the known fluxes are dual to each other and claim that certain fluxes on the heterotic side require that the type IIA picture is lifted to M or even F-theory compactifications with geometric fluxes.Comment: 31 pages, references adde