2,024 research outputs found
Improved algorithm for neuronal ensemble inference by Monte Carlo method
Neuronal ensemble inference is one of the significant problems in the study
of biological neural networks. Various methods have been proposed for ensemble
inference from their activity data taken experimentally. Here we focus on
Bayesian inference approach for ensembles with generative model, which was
proposed in recent work. However, this method requires large computational
cost, and the result sometimes gets stuck in bad local maximum solution of
Bayesian inference. In this work, we give improved Bayesian inference algorithm
for these problems. We modify ensemble generation rule in Markov chain Monte
Carlo method, and introduce the idea of simulated annealing for hyperparameter
control. We also compare the performance of ensemble inference between our
algorithm and the original one.Comment: 14 pages, 3 figure
Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα
Interleukins 2 and 15 (IL-2 and IL-15) are highly differentiated but related cytokines with overlapping, yet also distinct functions, and established benefits for medical drug use. The present study identified a gene for an ancient third IL-2/15 family member in reptiles and mammals, interleukin 15-like (IL-15L), which hitherto was only reported in fish. IL-15L genes with intact open reading frames (ORFs) and evidence of transcription, and a recent past of purifying selection, were found for cattle, horse, sheep, pig and rabbit. In human and mouse the IL-15L ORF is incapacitated. Although deduced IL-15L proteins share only ~21 % overall amino acid identity with IL-15, they share many of the IL-15 residues important for binding to receptor chain IL-15Rα, and recombinant bovine IL-15L was shown to interact with IL-15Rα indeed. Comparison of sequence motifs indicates that capacity for binding IL-15Rα is an ancestral characteristic of the IL-2/15/15L family, in accordance with a recent study which showed that in fish both IL-2 and IL-15 can bind IL-15Rα. Evidence reveals that the species lineage leading to mammals started out with three similar cytokines IL-2, IL-15 and IL-15L, and that later in evolution (1) IL-2 and IL-2Rα receptor chain acquired a new and specific binding mode and (2) IL-15L was lost in several but not all groups of mammals. The present study forms an important step forward in understanding this potent family of cytokines, and may help to improve future strategies for their application in veterinarian and human medicine
Use of the multiple-locus variable-number tandem repeat fingerprinting method and microfluidic chips for rapid genotyping of Staphylococcus aureus isolates
Heterotic Black Horizons
We show that the supersymmetric near horizon geometry of heterotic black
holes is either an AdS_3 fibration over a 7-dimensional manifold which admits a
G_2 structure compatible with a connection with skew-symmetric torsion, or it
is a product R^{1,1} * S^8, where S^8 is a holonomy Spin(7) manifold,
preserving 2 and 1 supersymmetries respectively. Moreover, we demonstrate that
the AdS_3 class of heterotic horizons can preserve 4, 6 and 8 supersymmetries
provided that the geometry of the base space is further restricted. Similarly
R^{1,1} * S^8 horizons with extended supersymmetry are products of R^{1,1} with
special holonomy manifolds. We have also found that the heterotic horizons with
8 supersymmetries are locally isometric to AdS_3 * S^3 * T^4, AdS_3 * S^3 * K_3
or R^{1,1} * T^4 * K_3, where the radii of AdS_3 and S^3 are equal and the
dilaton is constant.Comment: 35 pages, latex. Minor alterations to equation (3.11) and section
4.1, the conclusions are not affecte
Information transmission in oscillatory neural activity
Periodic neural activity not locked to the stimulus or to motor responses is
usually ignored. Here, we present new tools for modeling and quantifying the
information transmission based on periodic neural activity that occurs with
quasi-random phase relative to the stimulus. We propose a model to reproduce
characteristic features of oscillatory spike trains, such as histograms of
inter-spike intervals and phase locking of spikes to an oscillatory influence.
The proposed model is based on an inhomogeneous Gamma process governed by a
density function that is a product of the usual stimulus-dependent rate and a
quasi-periodic function. Further, we present an analysis method generalizing
the direct method (Rieke et al, 1999; Brenner et al, 2000) to assess the
information content in such data. We demonstrate these tools on recordings from
relay cells in the lateral geniculate nucleus of the cat.Comment: 18 pages, 8 figures, to appear in Biological Cybernetic
A novel nonhuman primate model for influenza transmission
Studies of influenza transmission are necessary to predict the pandemic potential of emerging influenza viruses. Currently, both ferrets and guinea pigs are used in such studies, but these species are distantly related to humans. Nonhuman primates (NHP) share a close phylogenetic relationship with humans and may provide an enhanced means to model the virological and immunological events in influenza virus transmission. Here, for the first time, it was demonstrated that a human influenza virus isolate can productively infect and be transmitted between common marmosets (Callithrix jacchus), a New World monkey species. We inoculated four marmosets with the 2009 pandemic virus A/California/07/2009 (H1N1pdm) and housed each together with a naïve cage mate. We collected bronchoalveolar lavage and nasal wash samples from all animals at regular intervals for three weeks post-inoculation to track virus replication and sequence evolution. The unadapted 2009 H1N1pdm virus replicated to high titers in all four index animals by 1 day post-infection. Infected animals seroconverted and presented human-like symptoms including sneezing, nasal discharge, labored breathing, and lung damage. Transmission occurred in one cohabitating pair. Deep sequencing detected relatively few genetic changes in H1N1pdm viruses replicating in any infected animal. Together our data suggest that human H1N1pdm viruses require little adaptation to replicate and cause disease in marmosets, and that these viruses can be transmitted between animals. Marmosets may therefore be a viable model for studying influenza virus transmission. © 2013 Moncla et al
The first determination of Generalized Polarizabilities of the proton by a Virtual Compton Scattering experiment
Absolute differential cross sections for the reaction (e+p -> e+p+gamma) have
been measured at a four-momentum transfer with virtuality Q^2=0.33 GeV^2 and
polarization \epsilon = 0.62 in the range 33.6 to 111.5 MeV/c for the momentum
of the outgoing photon in the photon-proton center of mass frame. The
experiment has been performed with the high resolution spectrometers at the
Mainz Microtron MAMI. From the photon angular distributions, two structure
functions which are a linear combination of the generalized polarizabilities
have been determined for the first time.Comment: 4 pages, 3 figure
M-Horizons
We solve the Killing spinor equations and determine the near horizon
geometries of M-theory that preserve at least one supersymmetry. The M-horizon
spatial sections are 9-dimensional manifolds with a Spin(7) structure
restricted by geometric constraints which we give explicitly. We also provide
an alternative characterization of the solutions of the Killing spinor
equation, utilizing the compactness of the horizon section and the field
equations, by proving a Lichnerowicz type of theorem which implies that the
zero modes of a Dirac operator coupled to 4-form fluxes are Killing spinors. We
use this, and the maximum principle, to solve the field equations of the theory
for some special cases and present some examples.Comment: 36 pages, latex. Reference added, minor typos correcte
Characteristic Evolution and Matching
I review the development of numerical evolution codes for general relativity
based upon the characteristic initial value problem. Progress in characteristic
evolution is traced from the early stage of 1D feasibility studies to 2D
axisymmetric codes that accurately simulate the oscillations and gravitational
collapse of relativistic stars and to current 3D codes that provide pieces of a
binary black hole spacetime. Cauchy codes have now been successful at
simulating all aspects of the binary black hole problem inside an artificially
constructed outer boundary. A prime application of characteristic evolution is
to extend such simulations to null infinity where the waveform from the binary
inspiral and merger can be unambiguously computed. This has now been
accomplished by Cauchy-characteristic extraction, where data for the
characteristic evolution is supplied by Cauchy data on an extraction worldtube
inside the artificial outer boundary. The ultimate application of
characteristic evolution is to eliminate the role of this outer boundary by
constructing a global solution via Cauchy-characteristic matching. Progress in
this direction is discussed.Comment: New version to appear in Living Reviews 2012. arXiv admin note:
updated version of arXiv:gr-qc/050809
Emergent Properties of Tumor Microenvironment in a Real-life Model of Multicell Tumor Spheroids
Multicellular tumor spheroids are an important {\it in vitro} model of the
pre-vascular phase of solid tumors, for sizes well below the diagnostic limit:
therefore a biophysical model of spheroids has the ability to shed light on the
internal workings and organization of tumors at a critical phase of their
development. To this end, we have developed a computer program that integrates
the behavior of individual cells and their interactions with other cells and
the surrounding environment. It is based on a quantitative description of
metabolism, growth, proliferation and death of single tumor cells, and on
equations that model biochemical and mechanical cell-cell and cell-environment
interactions. The program reproduces existing experimental data on spheroids,
and yields unique views of their microenvironment. Simulations show complex
internal flows and motions of nutrients, metabolites and cells, that are
otherwise unobservable with current experimental techniques, and give novel
clues on tumor development and strong hints for future therapies.Comment: 20 pages, 10 figures. Accepted for publication in PLOS One. The
published version contains links to a supplementary text and three video
file
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