1,736 research outputs found
Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: Implications for genome-wide association studies
Background: As availability of primary cells can be limited for genetic studies of human disease, lymphoblastoid cell lines (LCL) are common sources of genomic DNA. LCL are created in a transformation process that entails in vitro infection of human B-lymphocytes with the Epstein-Barr Virus (EBV). Methodology/Principal Findings: To test for genotypic errors potentially induced by the Epstein-Barr Virus transformation process, we compared single nucleotide polymorphism (SNP) genotype calls in peripheral blood mononuclear cells (PBMC) and LCL from the same individuals. The average mismatch rate across 19 comparisons was 0.12% for SNPs with a population call rate of at least 95%, and 0.03% at SNPs with a call rate of at least 99%. Mismatch rates were not correlated across genotype subarrays run on all sample pairs. Conclusions/Significance: Genotypic discrepancies found in PBMC and LCL pairs were not significantly different than control pairs, and were not correlated across subarrays. These results suggest that mismatch rates are minimal with stringent quality control, and that most genotypic discrepancies are due to technical artifacts rather than the EBV transformation process. Thus, LCL likely constitute a reliable DNA source for host genotype analysis. © 2009 Herbeck et al
Evaluation of a blocking ELISA for the detection of antibodies against Lawsonia intracellularis in pig sera
<p>Abstract</p> <p>Background</p> <p><it>Lawsonia intracellularis </it>is a common cause of chronic diarrhoea and poor performance in young growing pigs. Diagnosis of this obligate intracellular bacterium is based on the demonstration of the microbe or microbial DNA in tissue specimens or faecal samples, or the demonstration of <it>L. intracellularis</it>-specific antibodies in sera. The aim of the present study was to evaluate a blocking ELISA in the detection of serum antibodies to <it>L. intracellularis</it>, by comparison to the previously widely used immunofluorescent antibody test (IFAT).</p> <p>Methods</p> <p>Sera were collected from 176 pigs aged 8-12 weeks originating from 24 herds with or without problems with diarrhoea and poor performance in young growing pigs. Sera were analyzed by the blocking ELISA and by IFAT. Bayesian modelling techniques were used to account for the absence of a gold standard test and the results of the blocking ELISA was modelled against the IFAT test with a "2 dependent tests, 2 populations, no gold standard" model.</p> <p>Results</p> <p>At the finally selected cut-off value of percent inhibition (PI) 35, the diagnostic sensitivity of the blocking ELISA was 72% and the diagnostic specificity was 93%. The positive predictive value was 0.82 and the negative predictive value was 0.89, at the observed prevalence of 33.5%.</p> <p>Conclusion</p> <p>The sensitivity and specificity as evaluated by Bayesian statistic techniques differed from that previously reported. Properties of diagnostic tests may well vary between countries, laboratories and among populations of animals. In the absence of a true gold standard, the importance of validating new methods by appropriate statistical methods and with respect to the target population must be emphasized.</p
Quantum enhanced positioning and clock synchronization
A wide variety of positioning and ranging procedures are based on repeatedly
sending electromagnetic pulses through space and measuring their time of
arrival. This paper shows that quantum entanglement and squeezing can be
employed to overcome the classical power/bandwidth limits on these procedures,
enhancing their accuracy. Frequency entangled pulses could be used to construct
quantum positioning systems (QPS), to perform clock synchronization, or to do
ranging (quantum radar): all of these techniques exhibit a similar enhancement
compared with analogous protocols that use classical light. Quantum
entanglement and squeezing have been exploited in the context of
interferometry, frequency measurements, lithography, and algorithms. Here, the
problem of positioning a party (say Alice) with respect to a fixed array of
reference points will be analyzed.Comment: 4 pages, 2 figures. Accepted for publication by Natur
Black Hole Hair Removal: Non-linear Analysis
BMPV black holes in flat transverse space and in Taub-NUT space have
identical near horizon geometries but different microscopic degeneracies. It
has been proposed that this difference can be accounted for by different
contribution to the degeneracies of these black holes from hair modes, --
degrees of freedom living outside the horizon. In this paper we explicitly
construct the hair modes of these two black holes as finite bosonic and
fermionic deformations of the black hole solution satisfying the full
non-linear equations of motion of supergravity and preserving the supersymmetry
of the original solutions. Special care is taken to ensure that these solutions
do not have any curvature singularity at the future horizon when viewed as the
full ten dimensional geometry. We show that after removing the contribution due
to the hair degrees of freedom from the microscopic partition function, the
partition functions of the two black holes agree.Comment: 40 pages, LaTe
A New Portfolio Formation Approach to Mispricing of Marketing Performance Indicators: an Application to Customer Satisfaction
The trans-Planckian problem as a guiding principle
We use the avoidance of the trans-Planckian problem of Hawking radiation as a
guiding principle in searching for a compelling scenario for the evaporation of
black holes or black-hole-like objects. We argue that there exist only three
possible scenarios, depending on whether the classical notion of long-lived
horizon is preserved by high-energy physics and on whether the dark and compact
astrophysical objects that we observe have long-lived horizons in the first
place. Along the way, we find that (i) a theory with high-energy superluminal
signalling and a long-lived trapping horizon would be extremely unstable in
astrophysical terms and that (ii) stellar pulsations of objects hovering right
outside but extremely close to their gravitational radius can result in a
mechanism for Hawking-like emission.Comment: 20 pages, 4 figures. v2: minor clarifications. Published versio
Derivations and automorphisms of free nilpotent Lie algebras and their quotiens
Let \n_{d,t} be the free nilpotent Lie algebra of type and nilindex
. Starting out with the derivation algebra and the automorphism group of
\n_{d,t}, we get a natural description of derivations and automorphisms of
any generic nilpotent Lie algebra of the same type and nilindex. Moreover,
along the paper we discuss several examples to illustrate the obtained results.Comment: 13 page
Does publication bias inflate the apparent efficacy of psychological treatment for major depressive disorder? A systematic review and meta-analysis of US national institutes of health-funded trials
Background The efficacy of antidepressant medication has been shown empirically to be overestimated due to publication bias, but this has only been inferred statistically with regard to psychological treatment for depression. We assessed directly the extent of study publication bias in trials examining the efficacy of psychological treatment for depression. Methods and Findings We identified US National Institutes of Health grants awarded to fund randomized clinical trials comparing psychological treatment to control conditions or other treatments in patients diagnosed with major depressive disorder for the period 1972–2008, and we determined whether those grants led to publications. For studies that were not published, data were requested from investigators and included in the meta-analyses. Thirteen (23.6%) of the 55 funded grants that began trials did not result in publications, and two others never started. Among comparisons to control conditions, adding unpublished studies (Hedges’ g = 0.20; CI95% -0.11~0.51; k = 6) to published studies (g = 0.52; 0.37~0.68; k = 20) reduced the psychotherapy effect size point estimate (g = 0.39; 0.08~0.70) by 25%. Moreover, these findings may overestimate the "true" effect of psychological treatment for depression as outcome reporting bias could not be examined quantitatively. Conclusion The efficacy of psychological interventions for depression has been overestimated in the published literature, just as it has been for pharmacotherapy. Both are efficacious but not to the extent that the published literature would suggest. Funding agencies and journals should archive both original protocols and raw data from treatment trials to allow the detection and correction of outcome reporting bias. Clinicians, guidelines developers, and decision makers should be aware that the published literature overestimates the effects of the predominant treatments for depression
Understanding the threats posed by non-native species: public vs. conservation managers.
Public perception is a key factor influencing current conservation policy. Therefore, it is important to determine the influence of the public, end-users and scientists on the prioritisation of conservation issues and the direct implications for policy makers. Here, we assessed public attitudes and the perception of conservation managers to five non-native species in the UK, with these supplemented by those of an ecosystem user, freshwater anglers. We found that threat perception was not influenced by the volume of scientific research or by the actual threats posed by the specific non-native species. Media interest also reflected public perception and vice versa. Anglers were most concerned with perceived threats to their recreational activities but their concerns did not correspond to the greatest demonstrated ecological threat. The perception of conservation managers was an amalgamation of public and angler opinions but was mismatched to quantified ecological risks of the species. As this suggests that invasive species management in the UK is vulnerable to a knowledge gap, researchers must consider the intrinsic characteristics of their study species to determine whether raising public perception will be effective. The case study of the topmouth gudgeon Pseudorasbora parva reveals that media pressure and political debate has greater capacity to ignite policy changes and impact studies on non-native species than scientific evidence alone
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