94 research outputs found
Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis
Pathogenic bacteria present a large disease burden on human health. Control
of these pathogens is hampered by rampant lateral gene transfer, whereby
pathogenic strains may acquire genes conferring resistance to common
antibiotics. Here we introduce tools from topological data analysis to
characterize the frequency and scale of lateral gene transfer in bacteria,
focusing on a set of pathogens of significant public health relevance. As a
case study, we examine the spread of antibiotic resistance in Staphylococcus
aureus. Finally, we consider the possible role of the human microbiome as a
reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on
Advanced Methods of Interactive Data Mining for Personalized Medicin
Quantum walk on distinguishable non-interacting many-particles and indistinguishable two-particle
We present an investigation of many-particle quantum walks in systems of
non-interacting distinguishable particles. Along with a redistribution of the
many-particle density profile we show that the collective evolution of the
many-particle system resembles the single-particle quantum walk evolution when
the number of steps is greater than the number of particles in the system. For
non-uniform initial states we show that the quantum walks can be effectively
used to separate the basis states of the particle in position space and
grouping like state together. We also discuss a two-particle quantum walk on a
two- dimensional lattice and demonstrate an evolution leading to the
localization of both particles at the center of the lattice. Finally we discuss
the outcome of a quantum walk of two indistinguishable particles interacting at
some point during the evolution.Comment: 8 pages, 7 figures, To appear in special issue: "quantum walks" to be
published in Quantum Information Processin
Quantum walks: a comprehensive review
Quantum walks, the quantum mechanical counterpart of classical random walks,
is an advanced tool for building quantum algorithms that has been recently
shown to constitute a universal model of quantum computation. Quantum walks is
now a solid field of research of quantum computation full of exciting open
problems for physicists, computer scientists, mathematicians and engineers.
In this paper we review theoretical advances on the foundations of both
discrete- and continuous-time quantum walks, together with the role that
randomness plays in quantum walks, the connections between the mathematical
models of coined discrete quantum walks and continuous quantum walks, the
quantumness of quantum walks, a summary of papers published on discrete quantum
walks and entanglement as well as a succinct review of experimental proposals
and realizations of discrete-time quantum walks. Furthermore, we have reviewed
several algorithms based on both discrete- and continuous-time quantum walks as
well as a most important result: the computational universality of both
continuous- and discrete- time quantum walks.Comment: Paper accepted for publication in Quantum Information Processing
Journa
D* Production in Deep Inelastic Scattering at HERA
This paper presents measurements of D^{*\pm} production in deep inelastic
scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The
data have been taken with the ZEUS detector at HERA. The decay channel
(+ c.c.) has been used in the study. The
cross section for inclusive D^{*\pm} production with
and is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region
{ GeV and }. Differential cross
sections as functions of p_T(D^{*\pm}), and are
compared with next-to-leading order QCD calculations based on the photon-gluon
fusion production mechanism. After an extrapolation of the cross section to the
full kinematic region in p_T(D^{*\pm}) and (D^{*\pm}), the charm
contribution to the proton structure function is
determined for Bjorken between 2 10 and 5 10.Comment: 17 pages including 4 figure
Observation of Scaling Violations in Scaled Momentum Distributions at HERA
Charged particle production has been measured in deep inelastic scattering
(DIS) events over a large range of and using the ZEUS detector. The
evolution of the scaled momentum, , with in the range 10 to 1280
, has been investigated in the current fragmentation region of the Breit
frame. The results show clear evidence, in a single experiment, for scaling
violations in scaled momenta as a function of .Comment: 21 pages including 4 figures, to be published in Physics Letters B.
Two references adde
Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. For growth it does not require any vitamins. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp., so far. A total of 4666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway possibly involved in heterotrophic growth, and in CO2 fixation during autotrophic growth are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes
Development and external validation of a clinical prediction model for functional impairment after intracranial tumor surgery
OBJECTIVE Decision-making for intracranial tumor surgery requires balancing the oncological benefit against the risk for resection-related impairment. Risk estimates are commonly based on subjective experience and generalized num-bers from the literature, but even experienced surgeons overestimate functional outcome after surgery. Today, there is no reliable and objective way to preoperatively predict an individual patient's risk of experiencing any functional impair-ment. METHODS The authors developed a prediction model for functional impairment at 3 to 6 months after microsurgical resection, defined as a decrease in Karnofsky Performance Status of >= 10 points. Two prospective registries in Swit- zerland and Italy were used for development. External validation was performed in 7 cohorts from Sweden, Norway, Germany, Austria, and the Netherlands. Age, sex, prior surgery, tumor histology and maximum diameter, expected major brain vessel or cranial nerve manipulation, resection in eloquent areas and the posterior fossa, and surgical approach were recorded. Discrimination and calibration metrics were evaluated. RESULTS In the development (2437 patients, 48.2% male; mean age +/- SD: 55 +/- 15 years) and external validation (2427 patients, 42.4% male; mean age +/- SD: 58 +/- 13 years) cohorts, functional impairment rates were 21.5% and 28.5%, respectively. In the development cohort, area under the curve (AUC) values of 0.72 (95% CI 0.69-0.74) were observed. In the pooled external validation cohort, the AUC was 0.72 (95% CI 0.69-0.74), confirming generalizability. Calibration plots indicated fair calibration in both cohorts. The tool has been incorporated into a web-based application available at https://neurosurgery.shinyapps.io/impairment/. CONCLUSIONS Functional impairment after intracranial tumor surgery remains extraordinarily difficult to predict, al- though machine learning can help quantify risk. This externally validated prediction tool can serve as the basis for case by-case discussions and risk-to-benefit estimation of surgical treatment in the individual patient.Scientific Assessment and Innovation in Neurosurgical Treatment Strategie
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