pinecone/core-2020-05-10-deduplication huggingface dataset:
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

AbstractGut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader–Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n=17) and simple obesity (n=21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation.Research in contextPoorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children genetically obese with Prader–Willi syndrome shared a similar dysbiosis in their gut microbiota with those having diet-related obesity. A diet rich in non-digestible but fermentable carbohydrates significantly promoted beneficial groups of bacteria and reduced toxin-producers, which contributes to the alleviation of metabolic deteriorations in obesity regardless of the primary driving forces
The site of interference in the saccadic Stroop effect

AbstractIn two experiments, the source of competition in the saccadic Stroop effect was investigated. Colored strings of letters were presented at fixation with colored patches in the surround. The task of the participants was to make an eye movement to the patch in the same color as the central string of letters. Three types of cues were compared: Either the string of letters composed a word indicating a direction (the saccadic Stroop condition), or it was a set of arrow signs, or a peripheral stimulus appeared. Whereas response times and saccade errors were similarly influenced by the different types of cues, saccade trajectory deviations away from the cue were found only for peripheral onsets. A second experiment demonstrated that the absence of the curvature effects for direction words was not due to insufficient time to process the words. The results raise doubts on whether the saccadic Stroop effect is effectively an oculomotor effect and could pose a challenge to models of saccade target selection
The Role of Focal Therapy in the Management of Localised Prostate Cancer: A Systematic Review

AbstractContextThe incidence of localised prostate cancer is increasing worldwide. In light of recent evidence, current, radical, whole-gland treatments for organ-confined disease have being questioned with respect to their side effects, cancer control, and cost. Focal therapy may be an effective alternative strategy.ObjectiveTo systematically review the existing literature on baseline characteristics of the target population; preoperative evaluation to localise disease; and perioperative, functional, and disease control outcomes following focal therapy.Evidence acquisitionMedline (through PubMed), Embase, Web of Science, and Cochrane Review databases were searched from inception to 31 October 2012. In addition, registered but not yet published trials were retrieved. Studies evaluating tissue-preserving therapies in men with biopsy-proven prostate cancer in the primary or salvage setting were included.Evidence synthesisA total of 2350 cases were treated to date across 30 studies. Most studies were retrospective with variable standards of reporting, although there was an increasing number of prospective registered trials. Focal therapy was mainly delivered to men with low and intermediate disease, although some high-risk cases were treated that had known, unilateral, significant cancer. In most of the cases, biopsy findings were correlated to specific preoperative imaging, such as multiparametric magnetic resonance imaging or Doppler ultrasound to determine eligibility. Follow-up varied between 0 and 11.1 yr. In treatment-naïve prostates, pad-free continence ranged from 95% to 100%, erectile function ranged from 54% to 100%, and absence of clinically significant cancer ranged from 83% to 100%. In focal salvage cases for radiotherapy failure, the same outcomes were achieved in 87.2–100%, 29–40%, and 92% of cases, respectively. Biochemical disease-free survival was reported using a number of definitions that were not validated in the focal-therapy setting.ConclusionsOur systematic review highlights that, when focal therapy is delivered with intention to treat, the perioperative, functional, and disease control outcomes are encouraging within a short- to medium-term follow-up. Focal therapy is a strategy by which the overtreatment burden of the current prostate cancer pathway could be reduced, but robust comparative effectiveness studies are now required
Search for the Xb and other hidden-beauty states in the π+π−ϒ(1S) channel at ATLAS

AbstractThis Letter presents a search for a hidden-beauty counterpart of the X(3872) in the mass ranges of 10.05–10.31 GeV and 10.40–11.00 GeV, in the channel Xb→π+π−ϒ(1S)(→μ+μ−), using 16.2 fb−1 of s=8 TeV pp collision data collected by the ATLAS detector at the LHC. No evidence for new narrow states is found, and upper limits are set on the product of the Xb cross section and branching fraction, relative to those of the ϒ(2S), at the 95% confidence level using the CLS approach. These limits range from 0.8% to 4.0%, depending on mass. For masses above 10.1 GeV, the expected upper limits from this analysis are the most restrictive to date. Searches for production of the ϒ(13DJ), ϒ(10860), and ϒ(11020) states also reveal no significant signals
The North Atlantic Ocean as habitat for Calanus finmarchicus: Environmental factors and life history traits

AbstractHere we present a new, pan-Atlantic compilation and analysis of data on Calanus finmarchicus abundance, demography, dormancy, egg production and mortality in relation to basin-scale patterns of temperature, phytoplankton biomass, circulation and other environmental characteristics in the context of understanding factors determining the distribution and abundance of C. finmarchicus across its North Atlantic habitat. A number of themes emerge: (1) the south-to-north transport of plankton in the northeast Atlantic contrasts with north-to-south transport in the western North Atlantic, which has implications for understanding population responses of C. finmarchicus to climate forcing, (2) recruitment to the youngest copepodite stages occurs during or just after the phytoplankton bloom in the east whereas it occurs after the bloom at many western sites, with up to 3.5months difference in recruitment timing, (3) the deep basin and gyre of the southern Norwegian Sea is the centre of production and overwintering of C. finmarchicus, upon which the surrounding waters depend, whereas, in the Labrador/Irminger Seas production mainly occurs along the margins, such that the deep basins serve as collection areas and refugia for the overwintering populations, rather than as centres of production, (4) the western North Atlantic marginal seas have an important role in sustaining high C. finmarchicus abundance on the nearby coastal shelves, (5) differences in mean temperature and chlorophyll concentration between the western and eastern North Atlantic are reflected in regional differences in female body size and egg production, (6) regional differences in functional responses of egg production rate may reflect genetic differences between western and eastern populations, (7) dormancy duration is generally shorter in the deep waters adjacent to the lower latitude western North Atlantic shelves than in the east, (8) there are differences in stage-specific daily mortality rates between eastern and western shelves and basins, but the survival trajectories for cohort development from CI to CV are similar, and (9) early life stage survival is much lower in regions where C. finmarchicus is found with its congeners, C. glacialis and/or C. hyperboreus. This compilation and analysis provides new knowledge for evaluation and parameterisation of population models of C. finmarchicus and their responses to climate change in the North Atlantic. The strengths and weaknesses of modeling approaches, including a statistical approach based on ecological niche theory and a dynamical approach based on knowledge of spatial population dynamics and life history, are discussed, as well as needs for further research
SIM(1)–VSR Maxwell–Chern–Simons electrodynamics

AbstractIn this paper we propose a very special relativity (VSR)-inspired generalization of the Maxwell–Chern–Simons (MCS) electrodynamics. This proposal is based upon the construction of a proper study of the SIM(1)–VSR gauge-symmetry. It is shown that the VSR nonlocal effects present a significant and healthy departure from the usual MCS theory. The classical dynamics is analysed in full detail, by studying the solution for the electric field and static energy for this configuration. Afterwards, the interaction energy between opposite charges is derived and we show that the VSR effects play an important part in obtaining a (novel) finite expression for the static potential
Exploring plant growth-promotion actinomycetes from vermicompost and rhizosphere soil for yield enhancement in chickpea

AbstractThe main objective of the present study was to isolate and characterize actinomycetes for their plant growth-promotion in chickpea. A total of 89 actinomycetes were screened for their antagonism against fungal pathogens of chickpea by dual culture and metabolite production assays. Four most promising actinomycetes were evaluated for their physiological and plant growth-promotion properties under in vitro and in vivo conditions. All the isolates exhibited good growth at temperatures from 20°C to 40°C, pH range of 7–11 and NaCl concentrations up to 8%. These were also found highly tolerant to Bavistin, slightly tolerant to Thiram and Captan (except VAI-7 and VAI-40) but susceptible to Benlate and Ridomil at field application levels and were found to produce siderophore, cellulase, lipase, protease, chitinase (except VAI-40), hydrocyanic acid (except VAI-7 and VAI-40), indole acetic acid and β-1,3-glucanase. When the four actinomycetes were evaluated for their plant growth-promotion properties under field conditions on chickpea, all exhibited increase in nodule number, shoot weight and yield. The actinomycetes treated plots enhanced total N, available P and organic C over the un-inoculated control. The scanning electron microscope studies exhibited extensive colonization by actinomycetes on the root surface of chickpea. The expression profiles for indole acetic acid, siderophore and β-1,3-glucanase genes exhibited up-regulation for all three traits and in all four isolates. The actinomycetes were identified as Streptomyces but different species in the 16S rDNA analysis. It was concluded that the selected actinomycetes have good plant growth-promotion and biocontrol potentials on chickpea
Leading large-x logarithms of the quark–gluon contributions to inclusive Higgs-boson and lepton-pair production

AbstractWe present all-order expressions for the leading double-logarithmic threshold contributions to the quark–gluon coefficient functions for inclusive Higgs-boson production in the heavy top-quark limit and for Drell–Yan lepton-pair production. These results have been derived using the structure of the unfactorized cross sections in dimensional regularization and the large-x resummation of the gluon–quark and quark–gluon splitting functions. The resummed coefficient functions, which are identical up to colour factor replacements, are similar to their counterparts in deep-inelastic scattering but slightly more complicated
The Role of High-Dimensional Diffusive Search, Stabilization, and Frustration in Protein Folding

AbstractProteins are polymeric molecules with many degrees of conformational freedom whose internal energetic interactions are typically screened to small distances. Therefore, in the high-dimensional conformation space of a protein, the energy landscape is locally relatively flat, in contrast to low-dimensional representations, where, because of the induced entropic contribution to the full free energy, it appears funnel-like. Proteins explore the conformation space by searching these flat subspaces to find a narrow energetic alley that we call a hypergutter and then explore the next, lower-dimensional, subspace. Such a framework provides an effective representation of the energy landscape and folding kinetics that does justice to the essential characteristic of high-dimensionality of the search-space. It also illuminates the important role of nonnative interactions in defining folding pathways. This principle is here illustrated using a coarse-grained model of a family of three-helix bundle proteins whose conformations, once secondary structure has formed, can be defined by six rotational degrees of freedom. Two folding mechanisms are possible, one of which involves an intermediate. The stabilization of intermediate subspaces (or states in low-dimensional projection) in protein folding can either speed up or slow down the folding rate depending on the amount of native and nonnative contacts made in those subspaces. The folding rate increases due to reduced-dimension pathways arising from the mere presence of intermediate states, but decreases if the contacts in the intermediate are very stable and introduce sizeable topological or energetic frustration that needs to be overcome. Remarkably, the hypergutter framework, although depending on just a few physically meaningful parameters, can reproduce all the types of experimentally observed curvature in chevron plots for realizations of this fold
A search for high-mass resonances decaying to τ+τ− in pp collisions at s=7 TeV with the ATLAS detector

AbstractThis Letter presents a search for high-mass resonances decaying into τ+τ− final states using proton–proton collisions at s=7 TeV produced by the Large Hadron Collider. The data were recorded with the ATLAS detector and correspond to an integrated luminosity of 4.6 fb−1. No statistically significant excess above the Standard Model expectation is observed; 95% credibility upper limits are set on the cross section times branching fraction of Z′ resonances decaying into τ+τ− pairs as a function of the resonance mass. As a result, Z′ bosons of the Sequential Standard Model with masses less than 1.40 TeV are excluded at 95% credibility
Gluon saturation and entropy production in proton–proton collisions

AbstractWe study properties of high energy factorisable gluon densities focusing on saturation effects. In particular we show that the property of saturation of unintegrated gluon density allows for introduction of thermodynamical entropy associated with production of gluons. This is due to the observation that saturation scale acts like a mass of a gluon which related with temperature via thermodynamical relations allows for calculations of entropy. We also show that obtained entropy behaves like multiplicity of produced gluons
Electron–neutrino survival probability from solar-neutrino data

AbstractWith SNO data [SNO Collaboration, nucl-ex/0106015] on electron–neutrino flux from the sun, it is possible to derive the νe survival probability Pee(E) from existing experimental data of Super-Kamiokande, gallium experiments and Homestake. The combined data of SNO and Super-Kamiokande provide boron νe flux and the total flux of all active boron neutrinos, giving thus Pee(E) for boron neutrinos. The Homestake detector, after subtraction of the signal from boron neutrinos, gives the flux of Be+CNO neutrinos, and Pee for the corresponding energy interval, if the produced flux is taken from the Standard Solar Model (SSM). Gallium detectors, GALLEX, SAGE and GNO, detect additionally pp-neutrinos. The pp flux can be calculated subtracting from the gallium signal the rate due to boron, beryllium and CNO neutrinos. The ratio of the measured pp-neutrino flux to that predicted by the SSM gives the survival probability for pp-neutrinos. Comparison with theoretical survival probabilities shows that the best (among known models) fit is given by LMA and LOW solutions
Surface improvement of laser clad Ti–6Al–4V using plain waterjet and pulsed electron beam irradiation

AbstractLaser cladding is a flexible process which can be used to enhance the lifetime of components and repair them when worn. This is especially relevant where components are highly valued, and therefore costly to replace. To date, the surface finish achievable by laser cladding is poor and is characterised by ridges which correspond to the individual beads associated with the process. Increasingly laser cladding is being applied to conformal surfaces which are difficult to process by conventional grinding procedures which may also be ineffective because of discontinuous clad regions. There is therefore a need for a freeform approach which is capable of introducing specific surface finishes to complex components. Hence, in this study, a process chain incorporating plain water jet (PWJ) followed by a pulsed electron beam irradiation was used for the surface modification of laser clad surfaces of Ti–6Al–4V. Initially the surface was characterised by large recesses with peak-trough heights of 200±18μm and waviness of 49μm. Upon processing employing water head pressure of 345MPa impinging the clad surface at an angle 90°, 250mm/min jet traverse speed, 3mm stand-off distance and 0.25mm milling overlap with 2 passes, it was possible to eliminate the peak-trough profile by milling to a depth of 480±10μm. A flat surface characterised by a surface waviness of 14.9μm, 12.6μm Ra and 44μm straightness was achieved. PWJ milled surfaces were characterised by deep cavities, stepped fractured surfaces, cracks and sub-surface tunnels, however, with application of pulsed electron beam irradiation, most of these surface features were eliminated with a relatively smooth surface produced with 6.2μm Ra finish
The Global ECT-MRI Research Collaboration (GEMRIC): Establishing a multi-site investigation of the neural mechanisms underlying response to electroconvulsive therapy.

Major depression, currently the world's primary cause of disability, leads to profound personal suffering and increased risk of suicide. Unfortunately, the success of antidepressant treatment varies amongst individuals and can take weeks to months in those who respond. Electroconvulsive therapy (ECT), generally prescribed for the most severely depressed and when standard treatments fail, produces a more rapid response and remains the most effective intervention for severe depression. Exploring the neurobiological effects of ECT is thus an ideal approach to better understand the mechanisms of successful therapeutic response. Though several recent neuroimaging studies show structural and functional changes associated with ECT, not all brain changes associate with clinical outcome. Larger studies that can address individual differences in clinical and treatment parameters may better target biological factors relating to or predictive of ECT-related therapeutic response. We have thus formed the Global ECT-MRI Research Collaboration (GEMRIC) that aims to combine longitudinal neuroimaging as well as clinical, behavioral and other physiological data across multiple independent sites. Here, we summarize the ECT sample characteristics from currently participating sites, and the common data-repository and standardized image analysis pipeline developed for this initiative. This includes data harmonization across sites and MRI platforms, and a method for obtaining unbiased estimates of structural change based on longitudinal measurements with serial MRI scans. The optimized analysis pipeline, together with the large and heterogeneous combined GEMRIC dataset, will provide new opportunities to elucidate the mechanisms of ECT response and the factors mediating and predictive of clinical outcomes, which may ultimately lead to more effective personalized treatment approaches
The low-frequency environment of the Murchison Widefield Array :
                    radio-frequency interference analysis and mitigation

This is the Accepted Manuscript version of the following article: A. R. Offringa, et al., ???The low-frequency environment of the Murchison Widefield Array: radio-frequency interference analysis and mitigation???, Publications of the Astronomical Society of Australia, Vol. 32, March 2015. The final published version is available at: https://doi.org/10.1017/pasa.2015.7 ?? Astronomical Society of Australia 2015The Murchison Widefield Array (MWA) is a new low-frequency interferometric radio telescope built in Western Australia at one of the locations of the future Square Kilometre Array (SKA). We describe the automated radio-frequency interference (RFI) detection strategy implemented for the MWA, which is based on the AOFlagger platform, and present 72-231-MHz RFI statistics from 10 observing nights. RFI detection removes 1.1% of the data. RFI from digital TV (DTV) is observed 3% of the time due to occasional ionospheric or atmospheric propagation. After RFI detection and excision, almost all data can be calibrated and imaged without further RFI mitigation efforts, including observations within the FM and DTV bands. The results are compared to a previously published Low-Frequency Array (LOFAR) RFI survey. The remote location of the MWA results in a substantially cleaner RFI environment compared to LOFAR's radio environment, but adequate detection of RFI is still required before data can be analysed. We include specific recommendations designed to make the SKA more robust to RFI, including: the availability of sufficient computing power for RFI detection; accounting for RFI in the receiver design; a smooth band-pass response; and the capability of RFI detection at high time and frequency resolution (second and kHz-scale respectively)
Measurements of the tt̄ charge asymmetry using the dilepton decay channel in pp collisions at s = 7 TeV

The tt̄ charge asymmetry in proton-proton collisions at s = 7TeV is measured using the dilepton decay channel (ee, eμ, or μμ). The data correspond to a total integrated luminosity of 5.0 fb-1, collected by the CMS experiment at the LHC. The tt̄ and lepton charge asymmetries, defined as the differences in absolute values of the rapidities between the reconstructed top quarks and antiquarks and of the pseudorapidities between the positive and negative leptons, respectively, are measured to be AC = -0.010 ± 0.017 (stat.) ± 0.008 (syst.) and AC lep = 0.009 ± 0.010 (stat.) ± 0.006 (syst.). The lepton charge asymmetry is also measured as a function of the invariant mass, rapidity, and transverse momentum of the tt̄ system. All measurements are consistent with the expectations of the standard model.The Scientific and Technical Research Council of Turkey, and Turkish Atomic Energy Authorit