Development of Clostridium difficile R20291ΔPaLoc model strains and in vitro methodologies reveals CdtR is required for the production of CDT to cytotoxic levels

Assessing the regulation of Clostridium difficile transferase (CDT), is complicated by the presence of a Pathogenicity locus (PaLoc) which encodes Toxins A and B. Here we developed R20291ΔPaLoc model strains and cell-based assays to quantify CDT-mediated virulence. Their application demonstrated that the transcriptional regulator, CdtR, was required for CDT-mediated cytotoxicity

Crop supply dynamics and the illusion of partial adjustment

We use field-level data to estimate the response of corn and soybean acreage to price shocks. Our sample contains more than eight million observations derived from satellite imagery and includes every field in Iowa, Illinois, and Indiana. We estimate that aggregate crop acreage responds more to price shocks in the short run than in the long run, and we show theoretically how the benefits of crop rotation generate this response pattern. In essence, farmers who change crops due to a price shock have an incentive to switch back to the previous crop to capture the benefits of crop rotation. Our result contradicts the long-held belief that agricultural supply responds gradually to price shocks through partial adjustment. We would not have obtained this result had we used county-level panel data. Standard econometric methods applied to county-level data produce estimates consistent with partial adjustment. We show that this apparent partial adjustment is illusory, and we demonstrate how it arises from the fact that fields in the same county are more similar to each other than to fields in other counties. This result underscores the importance of using models with appropriate micro-foundations and cautions against inferring micro-level rigidities from inertia in aggregate panel data. Our preferred estimate of the own-price long-run elasticity of corn acreage is 0.29 and the cross-price elasticity is -0.22. The corresponding elasticities for soybean acreage are 0.26 and -0.33. Our estimated short-run elasticities are 37 percent larger than their long-run counterparts

Inhomogeneities in dusty universe - a possible alternative to dark energy?

There have been of late renewed debates on the role of inhomogeneities to explain the observed late acceleration of the universe. We have looked into the problem analytically with the help of the well known spherically symmetric but inhomogeneous Lemaitre-Tolman-Bondi(LTB) model generalised to higher dimensions. It is observed that in contrast to the claim made by Kolb et al the presence of inhomogeneities as well as extra dimensions can not reverse the signature of the deceleration parameter if the matter field obeys the energy conditions. The well known Raychaudhuri equation also points to the same result. Without solving the field equations explicitly it can, however, be shown that although the total deceleration is positive everywhere nevertheless it does not exclude the possibility of having radial acceleration, even in the pure dust universe, if the angular scale factor is decelerating fast enough and vice versa. Moreover it is found that introduction of extra dimensions can not reverse the scenario. To the contrary it actually helps the decelerating process.Comment: 14 pages, 4 figure

Magnetic Anisotropy in the Molecular Complex V15

We apply degenerate perturbation theory to investigate the effects of magnetic anisotropy in the magnetic molecule V15. Magnetic anisotropy is introduced via Dzyaloshinskii-Moriya (DM) interaction in the full Hilbert space of the system. Our model provides an explanation for the rounding of transitions in the magnetization as a function of applied field at low temperature, from which an estimate for the DM interaction is found. We find that the calculated energy differences of the lowest energy states are consistent with the available data. Our model also offers a novel explanation for the hysteretic nature of the time-dependent magnetization data.Comment: Final versio

Genomic adaptations of Campylobacter jejuni to long-term human colonization

Background Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract. Results There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation. Conclusions This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter