360 research outputs found
Efficient Parallel Statistical Model Checking of Biochemical Networks
We consider the problem of verifying stochastic models of biochemical
networks against behavioral properties expressed in temporal logic terms. Exact
probabilistic verification approaches such as, for example, CSL/PCTL model
checking, are undermined by a huge computational demand which rule them out for
most real case studies. Less demanding approaches, such as statistical model
checking, estimate the likelihood that a property is satisfied by sampling
executions out of the stochastic model. We propose a methodology for
efficiently estimating the likelihood that a LTL property P holds of a
stochastic model of a biochemical network. As with other statistical
verification techniques, the methodology we propose uses a stochastic
simulation algorithm for generating execution samples, however there are three
key aspects that improve the efficiency: first, the sample generation is driven
by on-the-fly verification of P which results in optimal overall simulation
time. Second, the confidence interval estimation for the probability of P to
hold is based on an efficient variant of the Wilson method which ensures a
faster convergence. Third, the whole methodology is designed according to a
parallel fashion and a prototype software tool has been implemented that
performs the sampling/verification process in parallel over an HPC
architecture
Black-hole quasinormal modes and scalar glueballs in a finite-temperature AdS/QCD model
We use the holographic AdS/QCD soft-wall model to investigate the spectrum of
scalar glueballs in a finite temperature plasma. In this model, glueballs are
described by a massless scalar field in an AdS_5 black hole with a dilaton
soft-wall background. Using AdS/CFT prescriptions, we compute the boundary
retarded Green's function. The corresponding thermal spectral function shows
quasiparticle peaks at low temperatures. We also compute the quasinormal modes
of the scalar field in the soft-wall black hole geometry. The temperature and
momentum dependences of these modes are analyzed. The positions and widths of
the peaks of the spectral function are related to the frequencies of the
quasinormal modes. Our numerical results are found employing the power series
method and the computation of Breit-Wigner resonances.Comment: Revision: Results unchanged. More discussions on the model and on the
results. References added. 28 pages, 7 figures, 5 table
Gravitational quasinormal modes of AdS black branes in d spacetime dimensions
The AdS/CFT duality has established a mapping between quantities in the bulk
AdS black-hole physics and observables in a boundary finite-temperature field
theory. Such a relationship appears to be valid for an arbitrary number of
spacetime dimensions, extrapolating the original formulations of Maldacena's
correspondence. In the same sense properties like the hydrodynamic behavior of
AdS black-hole fluctuations have been proved to be universal. We investigate in
this work the complete quasinormal spectra of gravitational perturbations of
-dimensional plane-symmetric AdS black holes (black branes). Holographically
the frequencies of the quasinormal modes correspond to the poles of two-point
correlation functions of the field-theory stress-energy tensor. The important
issue of the correct boundary condition to be imposed on the gauge-invariant
perturbation fields at the AdS boundary is studied and elucidated in a fully
-dimensional context. We obtain the dispersion relations of the first few
modes in the low-, intermediate- and high-wavenumber regimes. The sound-wave
(shear-mode) behavior of scalar (vector)-type low-frequency quasinormal mode is
analytically and numerically confirmed. These results are found employing both
a power series method and a direct numerical integration scheme.Comment: added references, typos corrected, minor changes, final version for
JHE
Effective killing of the human pathogen Candida albicans by a specific inhibitor of non-essential mitotic kinesin Kip1p
Kinesins from the bipolar (Kinesin-5) family are conserved in eukaryotic organisms and play critical roles during the earliest stages of mitosis to mediate spindle pole body separation and formation of a bipolar mitotic spindle. To date, genes encoding bipolar kinesins have been reported to be essential in all organisms studied. We report the characterization of CaKip1p, the sole member of this family in the human pathogenic yeast Candida albicans. C. albicans Kip1p appears to localize to the mitotic spindle and loss of CaKip1p function interferes with normal progression through mitosis. Inducible excision of CaKIP1 revealed phenotypes unique to C. albicans, including viable homozygous Cakip1 mutants and an aberrant spindle morphology in which multiple spindle poles accumulate in close proximity to each other. Expression of the C. albicans Kip1 motor domain in Escherichia coli produced a protein with microtubule-stimulated ATPase activity that was inhibited by an aminobenzothiazole (ABT) compound in an ATP-competitive fashion. This inhibition results in ‘rigor-like’, tight association with microtubules in vitro. Upon treatment of C. albicans cells with the ABT compound, cells were killed, and terminal phenotype analysis revealed an aberrant spindle morphology similar to that induced by loss of the CaKIP1 gene. The ABT compound discovered is the first example of a fungal spindle inhibitor targeted to a mitotic kinesin. Our results also show that the non-essential nature and implementation of the bipolar motor in C. albicans differs from that seen in other organisms, and suggest that inhibitors of a non-essential mitotic kinesin may offer promise as cidal agents for antifungal drug discovery
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
An Uncertain Dominion: Irish Psychiatry, Methadone, and the Treatment of Opiate Abuse
This paper investigates some productive ambiguities around the medical
administration of methadone in the Republic of Ireland. The tensions surrounding
methadone maintenance therapy (MMT) are outlined, as well as the sociohistorical
context in which a serious heroin addiction problem in Ireland developed. Irish
psychiatry intervened in this situation, during a time of institutional change, debates
concerning the nature of addiction, moral panics concerning heroin addiction in
Irish society and the recent boom in the Irish economy, known popularly as the
Celtic Tiger. A particular history of this sort illuminates how technologies like
MMT become cosmopolitan, settling into, while changing, local contexts
Q
The Qweak experiment, which took data at Jefferson Lab in the period 2010 - 2012, will precisely determine the weak charge of the proton by measuring the parity-violating asymmetry in elastic e-p scattering at 1.1 GeV using a longitudinally polarized electron beam and a liquid hydrogen target at a low momentum transfer of Q2 = 0.025 (GeV/c)2. The weak charge of the proton is predicted by the Standard Model and any significant deviation would indicate physics beyond the Standard Model. The technical challenges and experimental apparatus for measuring the weak charge of the proton will be discussed, as well as the method of extracting the weak charge of the proton. The results from a small subset of the data, that has been published, will also be presented. Furthermore an update will be given of the current status of the data analysis
The Atacama Cosmology Telescope: A Catalog of >4000 Sunyaev–Zel’dovich Galaxy Clusters
We present a catalog of 4195 optically confirmed Sunyaev–Zel'dovich (SZ) selected galaxy clusters detected with signal-to-noise ratio >4 in 13,211 deg2 of sky surveyed by the Atacama Cosmology Telescope (ACT). Cluster candidates were selected by applying a multifrequency matched filter to 98 and 150 GHz maps constructed from ACT observations obtained from 2008 to 2018 and confirmed using deep, wide-area optical surveys. The clusters span the redshift range 0.04 1 clusters, and a total of 868 systems are new discoveries. Assuming an SZ signal versus mass-scaling relation calibrated from X-ray observations, the sample has a 90% completeness mass limit of M500c > 3.8 × 1014 M⊙, evaluated at z = 0.5, for clusters detected at signal-to-noise ratio >5 in maps filtered at an angular scale of 2farcm4. The survey has a large overlap with deep optical weak-lensing surveys that are being used to calibrate the SZ signal mass-scaling relation, such as the Dark Energy Survey (4566 deg2), the Hyper Suprime-Cam Subaru Strategic Program (469 deg2), and the Kilo Degree Survey (825 deg2). We highlight some noteworthy objects in the sample, including potentially projected systems, clusters with strong lensing features, clusters with active central galaxies or star formation, and systems of multiple clusters that may be physically associated. The cluster catalog will be a useful resource for future cosmological analyses and studying the evolution of the intracluster medium and galaxies in massive clusters over the past 10 Gyr
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