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

Intersublevel Polaron Dephasing in Self-Assembled Quantum Dots

Polaron dephasing processes are investigated in InAs/GaAs dots using far-infrared transient four wave mixing (FWM) spectroscopy. We observe an oscillatory behaviour in the FWM signal shortly (< 5 ps) after resonant excitation of the lowest energy conduction band transition due to coherent acoustic phonon generation. The subsequent single exponential decay yields long intraband dephasing times of 90 ps. We find excellent agreement between our measured and calculated FWM dynamics, and show that both real and virtual acoustic phonon processes are necessary to explain the temperature dependence of the polarization decay.Comment: 10 pages, 4 figures, submitted to Phys Rev Let

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.Laboratorio de Investigaciones del Sistema Inmun

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

Prescission neutron multiplicity and fission probability from Langevin dynamics of nuclear fission

A theoretical model of one-body nuclear friction which was developed earlier, namely the chaos-weighted wall formula, is applied to a dynamical description of compound nuclear decay in the framework of the Langevin equation coupled with statistical evaporation of light particles and photons. We have used both the usual wall formula friction and its chaos-weighted version in the Langevin equation to calculate the fission probability and prescission neutron multiplicity for the compound nuclei $^{178}$W, $^{188}$Pt, $^{200}$Pb, $^{213}$Fr, $^{224}$Th, and $^{251}$Es. We have also obtained the contributions of the presaddle and postsaddle neutrons to the total prescission multiplicity. A detailed analysis of our results leads us to conclude that the chaos-weighted wall formula friction can adequately describe the fission dynamics in the presaddle region. This friction, however, turns out to be too weak to describe the postsaddle dynamics properly. This points to the need for a suitable explanation for the enhanced neutron emission in the postsaddle stage of nuclear fission.Comment: RevTex, 14 pages including 5 Postscript figures, results improved by using a different potential, conclusions remain unchanged, to appear in Phys. Rev.

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