240 research outputs found
HERBVI - a program for simulation of baryon- and lepton- number violating processes
We describe a Monte Carlo event generator for the simulation of baryon- and
lepton-number violating processes at supercolliders. The package, {\HERBVI}, is
designed as a hard-process generator interfacing to the general hadronic event
simulation program {\HW}. In view of the very high multiplicity of gauge bosons
expected in such processes, particular attention is paid to the efficient
generation of multiparticle phase space. The program also takes account of the
expected colour structure of baryon-number violating vertices, which has
important implications for the hadronization of the final state.Comment: 19 pages, standard LaTeX, no figure
Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis
BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108
The Brighton declaration: the value of non-communicable disease modelling in population health sciences.
The Brighton declaration arose out of a one day workshop
held in Brighton in September 2013 as part of the Society
for Social Medicine annual conference. The workshop
convened UK based non-communicable disease modellers
to discuss the challenges and opportunities for non-communicable
disease modelling in the UK. The declaration
describes the value and importance of non-communicable
disease modelling, both for research and for informing
health policy. The declaration also describes challenges
and issues for non-communicable disease modelling. The
declaration has been endorsed by many non-communicable
disease modellers in the UK.The following academics collaborated with the
authors to finalise this article are and acknowledged as co-signatories
on its content. The authors are extremely grateful for their input.
University of Cambridge: Ali Abbas, Marko Tanio; University of
Edinburgh: Dr Susannah McLean; UK Health Forum: Martin Brown,
Tim Marsh, Marco Mesa-Frias, Lise Retat; Imperial College London:
Anthony Laverty; The London School of Hygiene and Tropical
Medicine: Zaid Chalabi; University College London: Luz Sanchez
Romero; University of Oxford: Anja Mizdrak, Mike Rayner, Marco
Springmann; University of Sheffield: Alan Brennan, James Chilcott,
John Holmes, Petra Meier, John Mooney; University of Southampton:
Grant Aitken. ADMB and OTM are funded by the Wellcome Trust.
PS is funded by the British Heart Foundation. JW is funded by an
MRC Population Health Scientist Fellowship.This is the final published version. The article was originally published in the European Journal of Epidemiology (2014) 29, 867–870, DOI 10.1007/s10654-014-9978-0
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multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis
Background: Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. Results: We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. Conclusion: Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research
Precision measurements of the top quark mass from the Tevatron in the pre-LHC era
The top quark is the heaviest of the six quarks of the Standard Model.
Precise knowledge of its mass is important for imposing constraints on a number
of physics processes, including interactions of the as yet unobserved Higgs
boson. The Higgs boson is the only missing particle of the Standard Model,
central to the electroweak symmetry breaking mechanism and generation of
particle masses. In this Review, experimental measurements of the top quark
mass accomplished at the Tevatron, a proton-antiproton collider located at the
Fermi National Accelerator Laboratory, are described. Topologies of top quark
events and methods used to separate signal events from background sources are
discussed. Data analysis techniques used to extract information about the top
mass value are reviewed. The combination of several most precise measurements
performed with the two Tevatron particle detectors, CDF and \D0, yields a value
of \Mt = 173.2 \pm 0.9 GeV/.Comment: This version contains the most up-to-date top quark mass averag
Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib
New targeted approaches to ovarian clear cell carcinomas (OCCC) are needed, given the limited treatment options in this disease and the poor response to standard chemotherapy. Using a series of high-throughput cell-based drug screens in OCCC tumor cell models, we have identified a synthetic lethal (SL) interaction between the kinase inhibitor dasatinib and a key driver in OCCC, ARID1A mutation. Imposing ARID1A deficiency upon a variety of human or mouse cells induced dasatinib sensitivity, both in vitro and in vivo, suggesting that this is a robust synthetic lethal interaction. The sensitivity of ARID1A-deficient cells to dasatinib was associated with G1 -S cell-cycle arrest and was dependent upon both p21 and Rb. Using focused siRNA screens and kinase profiling, we showed that ARID1A-mutant OCCC tumor cells are addicted to the dasatinib target YES1. This suggests that dasatinib merits investigation for the treatment of patients with ARID1Amutant OCCC. Mol Cancer Ther; 15(7); 1472-84. Ó2016 AACR.</p
QCD
We discuss issues of QCD at the LHC including parton distributions, Monte
Carlo event generators, the available next-to-leading order calculations,
resummation, photon production, small x physics, double parton scattering, and
backgrounds to Higgs production.Comment: 115 pages, Latex, 47 figures, to appear in the Report of the ``1999
CERN Workshop on SM Physics (and more) at the LHC'', S. Catani, M. Dittmar,
D. Soper, W.J. Stirling, S. Tapprogge (convenors
A Joint Search for Gravitational Wave Bursts with AURIGA and LIGO
The first simultaneous operation of the AURIGA detector and the LIGO
observatory was an opportunity to explore real data, joint analysis methods
between two very different types of gravitational wave detectors: resonant bars
and interferometers. This paper describes a coincident gravitational wave burst
search, where data from the LIGO interferometers are cross-correlated at the
time of AURIGA candidate events to identify coherent transients. The analysis
pipeline is tuned with two thresholds, on the signal-to-noise ratio of AURIGA
candidate events and on the significance of the cross-correlation test in LIGO.
The false alarm rate is estimated by introducing time shifts between data sets
and the network detection efficiency is measured with simulated signals with
power in the narrower AURIGA band. In the absence of a detection, we discuss
how to set an upper limit on the rate of gravitational waves and to interpret
it according to different source models. Due to the short amount of analyzed
data and to the high rate of non-Gaussian transients in the detectors noise at
the time, the relevance of this study is methodological: this was the first
joint search for gravitational wave bursts among detectors with such different
spectral sensitivity and the first opportunity for the resonant and
interferometric communities to unify languages and techniques in the pursuit of
their common goal.Comment: 18 pages, IOP, 12 EPS figure
Searching for a Stochastic Background of Gravitational Waves with LIGO
The Laser Interferometer Gravitational-wave Observatory (LIGO) has performed
the fourth science run, S4, with significantly improved interferometer
sensitivities with respect to previous runs. Using data acquired during this
science run, we place a limit on the amplitude of a stochastic background of
gravitational waves. For a frequency independent spectrum, the new limit is
. This is currently the most sensitive
result in the frequency range 51-150 Hz, with a factor of 13 improvement over
the previous LIGO result. We discuss complementarity of the new result with
other constraints on a stochastic background of gravitational waves, and we
investigate implications of the new result for different models of this
background.Comment: 37 pages, 16 figure
Dirt, disease and death: control, resistance and change in the post-emancipation Caribbean
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