3,293 research outputs found
Comparison of Power Dependence of Microwave Surface Resistance of Unpatterned and Patterned YBCO Thin Film
The effect of the patterning process on the nonlinearity of the microwave
surface resistance of YBCO thin films is investigated. With the use of a
sapphire dielectric resonator and a stripline resonator, the microwave of
YBCO thin films was measured before and after the patterning process, as a
function of temperature and the rf peak magnetic field in the film. The
microwave loss was also modeled, assuming a dependence of
on current density . Experimental and modeled results
show that the patterning has no observable effect on the microwave residual
or on the power dependence of .Comment: Submitted to IEEE Trans. MT
ArborX: A Performance Portable Geometric Search Library
Searching for geometric objects that are close in space is a fundamental
component of many applications. The performance of search algorithms comes to
the forefront as the size of a problem increases both in terms of total object
count as well as in the total number of search queries performed. Scientific
applications requiring modern leadership-class supercomputers also pose an
additional requirement of performance portability, i.e. being able to
efficiently utilize a variety of hardware architectures. In this paper, we
introduce a new open-source C++ search library, ArborX, which we have designed
for modern supercomputing architectures. We examine scalable search algorithms
with a focus on performance, including a highly efficient parallel bounding
volume hierarchy implementation, and propose a flexible interface making it
easy to integrate with existing applications. We demonstrate the performance
portability of ArborX on multi-core CPUs and GPUs, and compare it to the
state-of-the-art libraries such as Boost.Geometry.Index and nanoflann
Power in Pairs: Assessing the Statistical Value of Paired Samples in Tests for Differential Expression
Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study.
Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of subject-level confounding factors. In the design scenarios considered, the statistical power in a fully-paired design is substantially (and in many cases several times) greater than in an unpaired design.
Conclusions: For the many biological systems and research questions where paired samples are feasible and relevant, substantial statistical power gains can be achieved at the study design stage when genomics researchers plan on using paired samples from the largest possible proportion of subjects. Any cost savings in a study design with unpaired samples are likely accompanied by underpowered and possibly biased results
Exploring multilocus associations of inflammation genes and colorectal cancer risk using hapConstructor
<p>Abstract</p> <p>Background</p> <p>In candidate-gene association studies of single nucleotide polymorphisms (SNPs), multilocus analyses are frequently of high dimensionality when considering haplotypes or haplotype pairs (diplotypes) and differing modes of expression. Often, while candidate genes are selected based on their biological involvement in a given pathway, little is known about the functionality of SNPs to guide association studies. Investigators face the challenge of exploring multiple SNP models to elucidate which variants, independently or in combination, might be associated with a disease of interest. A data mining module, hapConstructor (freely-available in Genie software) performs systematic construction and association testing of multilocus genotype data in a Monte Carlo framework. Our objective was to assess its utility to guide statistical analyses of haplotypes within a candidate region (or combined genotypes across candidate genes) beyond that offered by a standard logistic regression approach.</p> <p>Methods</p> <p>We applied the hapConstructor method to a multilocus investigation of candidate genes involved in pro-inflammatory cytokine IL6 production, <it>IKBKB</it>, <it>IL6</it>, and <it>NFKB1 </it>(16 SNPs total) hypothesized to operate together to alter colorectal cancer risk. Data come from two U.S. multicenter studies, one of colon cancer (1,556 cases and 1,956 matched controls) and one of rectal cancer (754 cases and 959 matched controls).</p> <p>Results</p> <p>HapConstrcutor enabled us to identify important associations that were further analyzed in logistic regression models to simultaneously adjust for confounders. The most significant finding (nominal <it>P </it>= 0.0004; false discovery rate <it>q </it>= 0.037) was a combined genotype association across <it>IKBKB </it>SNP rs5029748 (1 or 2 variant alleles), <it>IL6 </it>rs1800797 (1 or 2 variant alleles), and <it>NFKB1 </it>rs4648110 (2 variant alleles) which conferred an ~80% decreased risk of colon cancer.</p> <p>Conclusions</p> <p>Strengths of hapConstructor were: systematic identification of multiple loci within and across genes important in CRC risk; false discovery rate assessment; and efficient guidance of subsequent logistic regression analyses.</p
Genetic Variation in Selenoprotein Genes, Lifestyle, and Risk of Colon and Rectal Cancer
BACKGROUND: Associations between selenium and cancer have directed attention to role of selenoproteins in the carcinogenic process. METHODS: We used data from two population-based case-control studies of colon (n = 1555 cases, 1956 controls) and rectal (n = 754 cases, 959 controls) cancer. We evaluated the association between genetic variation in TXNRD1, TXNRD2, TXNRD3, C11orf31 (SelH), SelW, SelN1, SelS, SepX, and SeP15 with colorectal cancer risk. RESULTS: After adjustment for multiple comparisons, several associations were observed. Two SNPs in TXNRD3 were associated with rectal cancer (rs11718498 dominant OR 1.42 95% CI 1.16,1.74 pACT 0.0036 and rs9637365 recessive 0.70 95% CI 0.55,0.90 pACT 0.0208). Four SNPs in SepN1 were associated with rectal cancer (rs11247735 recessive OR 1.30 95% CI 1.04,1.63 pACT 0.0410; rs2072749 GGvsAA OR 0.53 95% CI 0.36,0.80 pACT 0.0159; rs4659382 recessive OR 0.58 95% CI 0.39,0.86 pACT 0.0247; rs718391 dominant OR 0.76 95% CI 0.62,0.94 pACT 0.0300). Interaction between these genes and exposures that could influence these genes showed numerous significant associations after adjustment for multiple comparisons. Two SNPs in TXNRD1 and four SNPs in TXNRD2 interacted with aspirin/NSAID to influence colon cancer; one SNP in TXNRD1, two SNPs in TXNRD2, and one SNP in TXNRD3 interacted with aspirin/NSAIDs to influence rectal cancer. Five SNPs in TXNRD2 and one in SelS, SeP15, and SelW1 interacted with estrogen to modify colon cancer risk; one SNP in SelW1 interacted with estrogen to alter rectal cancer risk. Several SNPs in this candidate pathway influenced survival after diagnosis with colon cancer (SeP15 and SepX1 increased HRR) and rectal cancer (SepX1 increased HRR). CONCLUSIONS: Findings support an association between selenoprotein genes and colon and rectal cancer development and survival after diagnosis. Given the interactions observed, it is likely that the impact of cancer susceptibility from genotype is modified by lifestyle
Corridors of barchan dunes: stability and size selection
Barchans are crescentic dunes propagating on a solid ground. They form dune
fields in the shape of elongated corridors in which the size and spacing
between dunes are rather well selected. We show that even very realistic models
for solitary dunes do not reproduce these corridors. Instead, two instabilities
take place. First, barchans receive a sand flux at their back proportional to
their width while the sand escapes only from their horns. Large dunes
proportionally capture more than they loose sand, while the situation is
reversed for small ones: therefore, solitary dunes cannot remain in a steady
state. Second, the propagation speed of dunes decreases with the size of the
dune: this leads -- through the collision process -- to a coarsening of barchan
fields. We show that these phenomena are not specific to the model, but result
from general and robust mechanisms. The length scales needed for these
instabilities to develop are derived and discussed. They turn out to be much
smaller than the dune field length. As a conclusion, there should exist further
- yet unknown - mechanisms regulating and selecting the size of dunes.Comment: 13 pages, 13 figures. New version resubmitted to Phys. Rev. E.
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The Quark-Gluon-Plasma Liquid
The quark-gluon plasma close to the critical temperature is a strongly
interacting system. Using strongly coupled, classical, non-relativistic plasmas
as an analogy, we argue that the quark-gluon plasma is in the liquid phase.
This allows to understand experimental observations in ultrarelativistic
heavy-ion collisions and to interpret lattice QCD results. It also supports the
indications of the presence of a strongly coupled QGP in ultrarelativistic
heavy-ion collisions.Comment: 8 pages, 2 figures, final version, to bepublished in J. Phys.
Dynamical Properties and Plasmon Dispersion of a Weakly Degenerate Correlated One-Component Plasma
Classical Molecular Dynamics (MD) simulations for a one-component plasma
(OCP) are presented. Quantum effects are included in the form of the Kelbg
potential. Results for the dynamical structure factor are compared with the
Vlasov and RPA (random phase approximation) theories. The influence of the
coupling parameter , degeneracy parameter and the form
of the pair interaction on the optical plasmon dispersion is investigated. An
improved analytical approximation for the dispersion of Langmuir waves is
presented.Comment: 23 pages, includes 7 ps/eps-figures and 2 table
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Partnerships and Public Service: Normative Issues for Journalists in Converged Newsrooms
As media companies test and implement newsroom “convergence,” growing numbers of journalists are producing content not only for their own employer but also for other media outlets with which that employer has a business relationship. This article, based on case studies in four converged news markets, explores journalists’ perceptions of normative pressures in this new media environment, particularly in relation to the overarching concept of public service. The findings suggest that although journalists do not see convergence itself as posing significant ethical problems, they do raise concerns related to specific components of public service, including a devotion to accuracy, an avoidance of sensationalism, and independence from economic pressures
Word frequency in fast priming: Evidence for immediate cognitive control of eye movements during reading
Numerous studies have demonstrated effects of word frequency on eye movements during reading, but the precise timing of this influence has remained unclear. The fast priming paradigm (Sereno & Rayner, 1992) was previously used to study influences of related versus unrelated primes on the target word. Here, we used this procedure to investigate whether the frequency of the prime word has a direct influence on eye movements during reading when the prime-target relation is not manipulated. We found that with average prime intervals of 32 ms readers made longer single fixation durations on the target word in the low than in the high frequency prime condition. Distributional analyses demonstrated that the effect of prime frequency on single fixation durations occurred very early, supporting theories of immediate cognitive control of eye movements. Finding prime frequency effects only 207 ms after visibility of the prime and for prime durations of 32 ms yields new time constraints for cognitive processes controlling eye movements during reading. Our variant of the fast priming paradigm provides a new approach to test early influences of word processing on eye movement control during reading
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