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Transfer of Biomarkers in the Phobos-Mars System: Hyper-Velocity Impact Investigations using a Light Gas Gun
Efficient chaining of seeds in ordered trees
We consider here the problem of chaining seeds in ordered trees. Seeds are
mappings between two trees Q and T and a chain is a subset of non overlapping
seeds that is consistent with respect to postfix order and ancestrality. This
problem is a natural extension of a similar problem for sequences, and has
applications in computational biology, such as mining a database of RNA
secondary structures. For the chaining problem with a set of m constant size
seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2)
in space
SimSearch: A new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences
http://www.informatik.uni-trier.de/%7Eley/db/conf/iwpacbb/iwpacbb2008.htmlIn this paper, we propose SimSearch, an algorithm implementing a new variant of dynamic programming based on distance series for optimal and near-optimal similarity discovery in biological sequences. The initial phase of SimSearch is devoted to fulfil the binary similarity matrices by signalling the distances between occurrences of the same symbol. The scoring scheme is further applied, when analysed the maximal extension of the pattern. Employing bit parallelism to analyse the global similarity matrixâs upper triangle, the new methodology searches the sequence(s) for all the exact and approximate patterns in regular or reverse order. The algorithm accepts parameterization to work with greater seeds for near-optimal results. Performance tests show significant efficiency improvement over traditional optimal methods based on dynamic programming. Comparing the new algorithmâs efficiency against heuristic based methods, equalizing the required sensitivity, the proposed algorithm remains acceptable.This work has been partially supported by PRODEP
Janus II: a new generation application-driven computer for spin-system simulations
This paper describes the architecture, the development and the implementation
of Janus II, a new generation application-driven number cruncher optimized for
Monte Carlo simulations of spin systems (mainly spin glasses). This domain of
computational physics is a recognized grand challenge of high-performance
computing: the resources necessary to study in detail theoretical models that
can make contact with experimental data are by far beyond those available using
commodity computer systems. On the other hand, several specific features of the
associated algorithms suggest that unconventional computer architectures, which
can be implemented with available electronics technologies, may lead to order
of magnitude increases in performance, reducing to acceptable values on human
scales the time needed to carry out simulation campaigns that would take
centuries on commercially available machines. Janus II is one such machine,
recently developed and commissioned, that builds upon and improves on the
successful JANUS machine, which has been used for physics since 2008 and is
still in operation today. This paper describes in detail the motivations behind
the project, the computational requirements, the architecture and the
implementation of this new machine and compares its expected performances with
those of currently available commercial systems.Comment: 28 pages, 6 figure
Use of dispersion modelling for Environmental Impact Assessment of biological air pollution from composting: Progress, problems and prospects
Š 2017 The Authors With the increase in composting as a sustainable waste management option, biological air pollution (bioaerosols) from composting facilities have become a cause of increasing concern due to their potential health impacts. Estimating community exposure to bioaerosols is problematic due to limitations in current monitoring methods. Atmospheric dispersion modelling can be used to estimate exposure concentrations, however several issues arise from the lack of appropriate bioaerosol data to use as inputs into models, and the complexity of the emission sources at composting facilities. This paper analyses current progress in using dispersion models for bioaerosols, examines the remaining problems and provides recommendations for future prospects in this area. A key finding is the urgent need for guidance for model users to ensure consistent bioaerosol modelling practices
Insights into the expanding phenotypic spectrum of inherited disorders of biogenic amines
Inherited disorders of neurotransmitter metabolism are rare neurodevelopmental diseases presenting with movement disorders and global developmental delay. This study presents the results of the first standardized deep phenotyping approach and describes the clinical and biochemical presentation at disease onset as well as diagnostic approaches of 275 patients from the registry of the International Working Group on Neurotransmitter related Disorders. The results reveal an increased rate of prematurity, a high risk for being small for gestational age and for congenital microcephaly in some disorders. Age at diagnosis and the diagnostic delay are influenced by the diagnostic methods applied and by disease-specific symptoms. The timepoint of investigation was also a significant factor: delay to diagnosis has decreased in recent years, possibly due to novel diagnostic approaches or raised awareness. Although each disorder has a specific biochemical pattern, we observed confounding exceptions to the rule. The data provide comprehensive insights into the phenotypic spectrum of neurotransmitter disorders
The PHENIX Experiment at RHIC
The physics emphases of the PHENIX collaboration and the design and current
status of the PHENIX detector are discussed. The plan of the collaboration for
making the most effective use of the available luminosity in the first years of
RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program
available at http://www.rhic.bnl.gov/phenix
Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV
Results are presented from a search for a W' boson using a dataset
corresponding to 5.0 inverse femtobarns of integrated luminosity collected
during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV.
The W' boson is modeled as a heavy W boson, but different scenarios for the
couplings to fermions are considered, involving both left-handed and
right-handed chiral projections of the fermions, as well as an arbitrary
mixture of the two. The search is performed in the decay channel W' to t b,
leading to a final state signature with a single lepton (e, mu), missing
transverse energy, and jets, at least one of which is tagged as a b-jet. A W'
boson that couples to fermions with the same coupling constant as the W, but to
the right-handed rather than left-handed chiral projections, is excluded for
masses below 1.85 TeV at the 95% confidence level. For the first time using LHC
data, constraints on the W' gauge coupling for a set of left- and right-handed
coupling combinations have been placed. These results represent a significant
improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe
Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV
A search for a Higgs boson decaying into two photons is described. The
analysis is performed using a dataset recorded by the CMS experiment at the LHC
from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an
integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross
section of the standard model Higgs boson decaying to two photons. The expected
exclusion limit at 95% confidence level is between 1.4 and 2.4 times the
standard model cross section in the mass range between 110 and 150 GeV. The
analysis of the data excludes, at 95% confidence level, the standard model
Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The
largest excess of events above the expected standard model background is
observed for a Higgs boson mass hypothesis of 124 GeV with a local significance
of 3.1 sigma. The global significance of observing an excess with a local
significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is
estimated to be 1.8 sigma. More data are required to ascertain the origin of
this excess.Comment: Submitted to Physics Letters
Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV
The Lambda(b) differential production cross section and the cross section
ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum
pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7
TeV using data collected by the CMS experiment at the LHC. The measurements are
based on Lambda(b) decays reconstructed in the exclusive final state J/Psi
Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and
Lambda to proton pion, using a data sample corresponding to an integrated
luminosity of 1.9 inverse femtobarns. The product of the cross section times
the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls
faster than that of b mesons. The measured value of the cross section times the
branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06
+/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for
anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are
statistical and systematic, respectively.Comment: Submitted to Physics Letters
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