6,432 research outputs found
Representation of Markov chains by random maps: existence and regularity conditions
We systematically investigate the problem of representing Markov chains by
families of random maps, and which regularity of these maps can be achieved
depending on the properties of the probability measures. Our key idea is to use
techniques from optimal transport to select optimal such maps. Optimal
transport theory also tells us how convexity properties of the supports of the
measures translate into regularity properties of the maps via Legendre
transforms. Thus, from this scheme, we cannot only deduce the representation by
measurable random maps, but we can also obtain conditions for the
representation by continuous random maps. Finally, we present conditions for
the representation of Markov chain by random diffeomorphisms.Comment: 22 pages, several changes from the previous version including
extended discussion of many detail
Scalar Bilepton Dark Matter
In this work we show that 3-3-1 model with right-handed neutrinos has a
natural weakly interacting massive particle (WIMP) dark mater candidate. It is
a complex scalar with mass of order of some hundreds of GeV which carries two
units of lepton number, a scalar bilepton. This makes it a very peculiar WIMP,
very distinct from Supersymmetric or Extra-dimension candidates. Besides,
although we have to make some reasonable assumptions concerning the several
parameters in the model, no fine tunning is required in order to get the
correct dark matter abundance. We also analyze the prospects for WIMP direct
detection by considering recent and projected sensitivities for WIMP-nucleon
elastic cross section from CDMS and XENON Collaborations.Comment: 21 pages, 8 figures, uses iopart.cls, same text as published version
with a small different arrangement of figure
The genome sequence of the highly acetic acid-tolerant zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant
In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH. The analysis of the genome sequence described in this work indicates that strain ISA1307 is an interspecies hybrid between Z. bailii and a closely related species. The genome sequence of ISA1307 is distributed through 154 scaffolds and has a size of around 21.2 Mb, corresponding to 96% of the genome size estimated by flow cytometry. Annotation of ISA1307 genome includes 4385 duplicated genes (~90% of the total number of predicted genes) and 1155 predicted single-copy genes. The functional categories including a higher number of genes are 'Metabolism and generation of energy', 'Protein folding, modification and targeting' and 'Biogenesis of cellular components'. The knowledge of the genome sequence of the ISA1307 strain is expected to contribute to accelerate systems-level understanding of stress resistance mechanisms in Z. bailii and to inspire and guide novel biotechnological applications of this yeast species/strain in fermentation processes, given its high resilience to acidic stress. The availability of the ISA1307 genome sequence also paves the way to a better understanding of the genetic mechanisms underlying the generation and selection of more robust hybrid yeast strains in the stressful environment of wine fermentations.This research was supported by FCT and FEDER through POFC-COMPETE [contracts PEst-OE/EQB/ LA0023/2011_ research line: Systems and Synthetic Biology PTDC/AGR-ALI/102608/2008, PEst-C/BIA/ UI4050/2011, and post-doctoral grant to M.P. (SFRH/BPD/73306/2010) and PhD grants to J.F.G. (SFRH/ BD/80065/2011) and F.C.R. (SFRH/BD/82226/2011)]. U.G. acknowledges the Austrian Science Fund (FWF, special research project F3705)
Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions
Improvements in sequencing technologies and reduced experimental costs have
resulted in a vast number of studies generating high-throughput data. Although
the number of methods to analyze these "omics" data has also increased,
computational complexity and lack of documentation hinder researchers from
analyzing their high-throughput data to its true potential. In this chapter we
detail our data-driven, transkingdom network (TransNet) analysis protocol to
integrate and interrogate multi-omics data. This systems biology approach has
allowed us to successfully identify important causal relationships between
different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of
data
From favorable atomic configurations to supershell structures: a new interpretation of conductance histograms
Title: From favorable atomic configurations to supershell structures: a new
interpretation of conductance histograms Authors: A. Hasmy (IVIC), E. Medina
(IVIC), P.A. Serena (CSIC,IVIC) Comments: 7 pages, 3 figures,
cond-mat.anwar.10825 Subj-class: Soft Condensed MatterComment: 7 pages, 3 figuresSubject: fput HMS.tex HMS-FIG1.ps HMS-FIG2.ps
HMS-FIG3.p
Matrix assisted laser desorption ionization-time-of-flight mass spectrometry identification of mycobacterium bovis in bovinae
In this study, Matrix Assisted Laser Desorption Ionization-Time-of-Flight (MALDI-TOF) mass spectrometry was used to identify Mycobacterium bovis from cattle and buffalo tissue isolates from the North and South regions of Brazil, grown in solid medium and previously identified by Polymerase Chain Reaction (PCR) based on Region of Difference 4 (RD4), sequencing and spoligotyping. For this purpose, the protein extraction protocol and the mass spectra reference database were optimized for the identification of 80 clinical isolates of mycobacteria. As a result of this optimization, it was possible to identify and differentiate M. bovis from other members of the Mycobacterium tuberculosis complex with 100% specificity, 90.91% sensitivity and 91.25% reliability. MALDI-TOF MS methodology described herein provides successful identification of M. bovis within bovine/bubaline clinical samples, demonstrating its usefulness for bovine tuberculosis diagnosis in the future.Instituto de BiotecnologíaFil: Bacanelli, Gisele. Federal University of Mato Grosso do Sul. Biotechnology and Biodiversity of the Central Western Region Postgraduate Program; BrasilFil: Olarte, Larissa C. Federal University of Mato Grosso do Sul. Biochemistry and Molecular Biology Multicentric Postgraduate Program; BrasilFil: Silva, Marcio Roberto. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Leite; BrasilFil: Rodrigues, Rudielle A. Federal University of Mato Grosso do Sul. Faculty of Veterinary Medicine. Veterinary Sciences Postgraduate Program; BrasilFil: Carneiro, Paulo A. M. Michigan State University. Center for Comparative Epidemiology; Estados UnidosFil: Kannene, John B. Michigan State University. Center for Comparative Epidemiology; Estados UnidosFil: Pasquatti, Taynara N. Dom Bosco Catholic University; BrasilFil: Takatani, Haruo. Agricultural Defense Agency of Amazonas; BrasilFil: Zumarraga, Martin Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Etges, Rodrigo N. Secretary of Agriculture, Livestock and Irrigation; BrasilFil: Araujo, Flabio Ribeiro de. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Corte; BrasilFil: Verbisck, Newton V. Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Gado de Corte; Brasi
A geometrical estimation of saturation of partonic densities
We propose a new criterium for saturation of the density of partons both in
nucleons and nuclei. It is applicable to any multiple scattering model which
would be used to compute the number of strings exchanged in and
collisions. The criterium is based on percolation of strings, and the onset of
percolation is estimated from expectations coming from the study of heavy ion
collisions at high energies. We interpret this onset as an indication of
saturation of the density of partons in the wave function of the hadron. In
order to produce quantitative results, a particular model fitted to describe
present HERA data and generalized to the nuclear case is used. Nevertheless,
with the number of scatterings controlled by the relation between inclusive and
diffractive processes, conclusions are weakly model-dependent as long as
different models are tuned to describe the experimental data. This constitutes
a new approach, based on the eikonal description of soft hadronic collisions,
and different from others which employ either perturbative QCD ideas or
semiclassical methods. It offers an alternative picture for saturation in the
small region.Comment: LaTeX, 15 pages, 2 eps figures included using epsfig; final version,
abstract and discussions enlarged, references added and updated, results
unchanged; more references adde
Network centrality: an introduction
Centrality is a key property of complex networks that influences the behavior
of dynamical processes, like synchronization and epidemic spreading, and can
bring important information about the organization of complex systems, like our
brain and society. There are many metrics to quantify the node centrality in
networks. Here, we review the main centrality measures and discuss their main
features and limitations. The influence of network centrality on epidemic
spreading and synchronization is also pointed out in this chapter. Moreover, we
present the application of centrality measures to understand the function of
complex systems, including biological and cortical networks. Finally, we
discuss some perspectives and challenges to generalize centrality measures for
multilayer and temporal networks.Comment: Book Chapter in "From nonlinear dynamics to complex systems: A
Mathematical modeling approach" by Springe
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