5,942 research outputs found
A method for continuous-range sequence analysis with jensen-shannon divergence
Mutual Information (MI) is a useful Information Theory tool for the recognition of mutual dependence between data sets. Several methods have been developed fore estimation of MI when both data sets are of the discrete type or when both are of the continuous type. However, MI estimation between a discrete range data set and a continuous range data set has not received so much attention. We therefore present here a method for the estimation of MI for this case, based on the kernel density approximation. This calculation may be of interest in diverse contexts. Since MI is closely related to the Jensen Shannon divergence, the method developed here is of particular interest in the problems of sequence segmentation and set comparisons.Fil: Re, Miguel Angel. Universidad Nacional de CĂłrdoba. Facultad de MatemĂĄtica, Astronomia y FĂsica. SecciĂłn FĂsica. Grupo de FĂsica de la Atmosfera; ArgentinaFil: Aguirre Varela, Guillermo Gabriel. Universidad Nacional de CĂłrdoba. Facultad de MatemĂĄtica, Astronomia y FĂsica. SecciĂłn FĂsica. Grupo de FĂsica de la Atmosfera; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂŠcnicas. Centro CientĂfico TecnolĂłgico Conicet - CĂłrdoba. Instituto de FĂsica Enrique Gaviola. Universidad Nacional de CĂłrdoba. Instituto de FĂsica Enrique Gaviola; Argentin
Identification and characterization of a novel non-structural protein of bluetongue virus
Bluetongue virus (BTV) is the causative agent of a major disease of livestock (bluetongue). For over two decades, it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins. The non-structural proteins (NS1, NS2, NS3/NS3a) play different key roles during the viral replication cycle. In this study we show that BTV expresses a fourth non-structural protein (that we designated NS4) encoded by an open reading frame in segment 9 overlapping the open reading frame encoding VP6. NS4 is 77â79 amino acid residues in length and highly conserved among several BTV serotypes/strains. NS4 was expressed early post-infection and localized in the nucleoli of BTV infected cells. By reverse genetics, we showed that NS4 is dispensable for BTV replication in vitro, both in mammalian and insect cells, and does not affect viral virulence in murine models of bluetongue infection. Interestingly, NS4 conferred a replication advantage to BTV-8, but not to BTV-1, in cells in an interferon (IFN)-induced antiviral state. However, the BTV-1 NS4 conferred a replication advantage both to a BTV-8 reassortant containing the entire segment 9 of BTV-1 and to a BTV-8 mutant with the NS4 identical to the homologous BTV-1 protein. Collectively, this study suggests that NS4 plays an important role in virus-host interaction and is one of the mechanisms played, at least by BTV-8, to counteract the antiviral response of the host. In addition, the distinct nucleolar localization of NS4, being expressed by a virus that replicates exclusively in the cytoplasm, offers new avenues to investigate the multiple roles played by the nucleolus in the biology of the cell
Intercalibration of the barrel electromagnetic calorimeter of the CMS experiment at start-up
Calibration of the relative response of the individual channels of the barrel electromagnetic calorimeter of the CMS detector was accomplished, before installation, with cosmic ray muons and test beams. One fourth of the calorimeter was exposed to a beam of high energy electrons and the relative calibration of the channels, the intercalibration, was found to be reproducible to a precision of about 0.3%. Additionally, data were collected with cosmic rays for the entire ECAL barrel during the commissioning phase. By comparing the intercalibration constants obtained with the electron beam data with those from the cosmic ray data, it is demonstrated that the latter provide an intercalibration precision of 1.5% over most of the barrel ECAL. The best intercalibration precision is expected to come from the analysis of events collected in situ during the LHC operation. Using data collected with both electrons and pion beams, several aspects of the intercalibration procedures based on electrons or neutral pions were investigated
Radiation hardness qualification of PbWO4 scintillation crystals for the CMS Electromagnetic Calorimeter
This is the Pre-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2010 IOPEnsuring the radiation hardness of PbWO4 crystals was one of the main priorities during the construction of the electromagnetic calorimeter of the CMS experiment at CERN. The production on an industrial scale of radiation hard crystals and their certification over a period of several years represented a difficult challenge both for CMS and for the crystal suppliers. The present article reviews the related scientific and technological problems encountered
A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations
The development of modern and affordable sequencing technologies has allowed the
study of viral populations to an unprecedented depth. This is of particular
interest for the study of within-host RNA viral populations, where variation due
to error-prone polymerases can lead to immune escape, antiviral resistance and
adaptation to new host species. Methods to sequence RNA virus genomes include
reverse transcription (RT) and polymerase chain reaction (PCR). RT-PCR is a
molecular biology technique widely used to amplify DNA from an RNA template. The
method itself relies on the in vitro synthesis of copy DNA from
RNA followed by multiple cycles of DNA amplification. However, this method
introduces artefactual errors that can act as confounding factors when the
sequence data are analysed. Although there are a growing number of published
studies exploring the intra- and inter-host evolutionary dynamics of RNA
viruses, the complexity of the methods used to generate sequences makes it
difficult to produce probabilistic statements about the likely sources of
observed sequence variants. This complexity is further compounded as both the
depth of sequencing and the length of the genome segment of interest increase.
Here we develop a Bayesian method to characterise and differentiate between
likely structures for the background viral population. This approach can then be
used to identify nucleotide sites that show evidence of change in the
within-host viral population structure, either over time or relative to a
reference sequence (e.g. an inoculum or another source of infection), or both,
without having to build complex evolutionary models. Identification of these
sites can help to inform the design of more focussed experiments using molecular
biology tools, such as site-directed mutagenesis, to assess the function of
specific amino acids. We illustrate the method by applying to datasets from
experimental transmission of equine influenza, and a pre-clinical vaccine trial
for HIV-1
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
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