pinecone/core-2020-05-10-deduplication huggingface dataset:
Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′

AbstractN-Methylpyrrole (Py)–N-methylimidazole (Im) polyamides are small organic molecules that can recognize predetermined DNA sequences with high sequence specificity. As many eukaryotic promoter regions contain highly GC-rich sequences, it is valuable to synthesize and characterize Py–Im polyamides that recognize GC-rich motifs. In this study, we synthesized four hairpin Py–Im polyamides 1–4, which recognize 5′-GCGC-3′ and investigated their binding behavior with surface plasmon resonance assay. Py–Im polyamides 2–4 contain two, one, and one β-alanine units, replacing the Py units of 1, respectively. The binding affinities of 2–4 to the target DNA increased 430, 390, and 610-fold, respectively, over that of 1. The association and dissociation rates of 2 to the target DNA were improved by 11 and 37-fold, respectively, compared with those of 1. Interestingly, the association and dissociation rates of 3 and 4 were higher than those of 2, even though the binding affinities of 2, 3, and 4 to the target DNA were comparable to each other. The binding affinity of 2 to DNA with a 2bp mismatch was reduced by 29-fold, compared with that to the matched DNA. Moreover, the binding affinities of 3 and 4 to the same mismatched DNA were reduced by 270 and 110-fold, respectively, indicating that 3 and 4 have greater specificities than 2 and are suitable as DNA-binding modules for engineered epigenetic regulation
Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

AbstractBackgroundUnderstanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.MethodsIn a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.FindingsWe identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p=0.0017 and p=0.016 respectively) and were further validated in a third cohort with long-term follow-up (p=0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p=0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.InterpretationFor the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts
Next-to-leading order QCD corrections to HZW± production at 14 TeV LHC

AbstractSince the precise study of Higgs gauge couplings is important to test the Standard Model (SM), we calculate the complete next-to-leading order QCD (NLO QCD) correction to the pp→HZW± production in the SM at 14 TeV LHC. Our results show that the NLO QCD correction can enhance the leading-order cross section of pp→HZW± by 45%, when mH=125.3 GeV. We also study the dependence of the LO and NLO corrected cross sections on the renormalization and factorization scale μ. Besides, due to the unbalance of parton distribution functions, we investigate the charge asymmetry of W± in the production of pp→HZW±, which can reach 32.94% for μ=(mH+mZ+mW)/2 at 14 TeV LHC
Biological Overlap of Attention-Deficit/Hyperactivity Disorder and Autism Spectrum Disorder: Evidence From Copy Number Variants

ObjectiveAttention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) often co-occur and share genetic risks. The aim of this analysis was to determine more broadly whether ADHD and ASD share biological underpinnings.MethodWe compared copy number variant (CNV) data from 727 children with ADHD and 5,081 population controls to data from 996 individuals with ASD and an independent set of 1,287 controls. Using pathway analyses, we investigated whether CNVs observed in individuals with ADHD have an impact on genes in the same biological pathways as on those observed in individuals with ASD.ResultsThe results suggest that the biological pathways affected by CNVs in ADHD overlap with those affected by CNVs in ASD more than would be expected by chance. Moreover, this was true even when specific CNV regions common to both disorders were excluded from the analysis. After correction for multiple testing, genes involved in 3 biological processes (nicotinic acetylcholine receptor signalling pathway, cell division, and response to drug) showed significant enrichment for case CNV hits in the combined ADHD and ASD sample.ConclusionThe results of this study indicate the presence of significant overlap of shared biological processes disrupted by large rare CNVs in children with these 2 neurodevelopmental conditions
Spinning σ-model solitons in 2+1 anti-de Sitter space

AbstractWe obtain numerical solutions for rotating topological solitons of the nonlinear σ-model in three-dimensional anti-de Sitter space. Two types of solutions, i) and ii), are found. The σ-model fields are everywhere well defined for both types of solutions, but they differ in their space–time domains. Any time slice of the space–time for the type i) solution has a causal singularity, despite the fact that all scalars constructed from the curvature tensor are bounded functions. No evidence of a horizon is seen for any of the solutions, and therefore the type i) solutions have naked singularities. On the other hand, the space–time domain, along with the fields, for the type ii) solutions are singularity free. Multiple families of solutions exhibiting bifurcation phenomena are found for this case
High Oral Carriage of Non-albicans Candida spp. among HIV-infected individuals

AbstractBackgroundNon-albicans Candida (NAC) spp. in immunocompromised patients are linked to invasive infections with narrow treatment choice. This study aimed at comparing the oral colonization of NAC spp. between HIV and non-HIV infected individuals in Mwanza, Tanzania.MethodOral rinse of 351 HIV-infected and 639 non-HIV infected individuals were collected between March and July 2015. Phenotypic identifications of Candida spp. was done using Candida Chromogenic agar and confirmed by MALDI-TOF MS.ResultsNAC spp. were detected in 36/351 (10.3%) HIV-infected individuals compared to 28/639 (4.4%) of non-HIV infected individuals; P=0.0003. In HIV infected individuals, commonly isolated NAC spp. were Candida tropicalis, 10(2.8%), C. krusei (Issatschenki orientalis) 9(2.6%) and C. glabrata 8(2.3%). While for non-HIV infected individuals C. dubliniensis 8(1.3%) and C. tropicalis 5(0.9%) were commonly detected. As CD4 count/μl decreases by one unit the risk of being colonized by NAC spp. among HIV infected individuals increases by 1% (OR 1.01, 95% CI; 1.001-1.004, P=0.001).ConclusionThe prevalence of NAC spp. is high among HIV-infected individuals with low CD4 count placing them at higher risk of invasive infections. Further studies to investigate the role of NAC spp. in causing invasive infections among immunocompromised patients are recommended
Search for the standard model Higgs boson decaying to W+W− in the fully leptonic final state in pp collisions at s=7 TeV

AbstractA search for the standard model Higgs boson decaying to W+W− in pp collisions at s=7 TeV is reported. The data are collected at the LHC with the CMS detector, and correspond to an integrated luminosity of 4.6 fb−1. The W+W− candidates are selected in events with two charged leptons and large missing transverse energy. No significant excess of events above the standard model background expectations is observed, and upper limits on the Higgs boson production relative to the standard model Higgs expectation are derived. The standard model Higgs boson is excluded in the mass range 129–270 GeV at 95% confidence level
Fast spectral solution of the generalized Enskog equation for dense gases

AbstractWe propose a fast spectral method for solving the generalized Enskog equation for dense gases. For elastic collisions, the method solves the Enskog collision operator with a computational cost of O(Md−1Ndlog⁡N), where d is the dimension of the velocity space, and Md−1 and Nd are the number of solid angle and velocity space discretizations, respectively. For inelastic collisions, the cost is N times higher. The accuracy of this fast spectral method is assessed by comparing our numerical results with analytical solutions of the spatially-homogeneous relaxation of heated granular gases. We also compare our results for force-driven Poiseuille flow and Fourier flow with those from molecular dynamics and Monte Carlo simulations. Although it is phenomenological, the generalized Enskog equation is capable of capturing the flow dynamics of dense granular gases, and the fast spectral method is accurate and efficient. As example applications, Fourier and Couette flows of a dense granular gas are investigated. In addition to the temperature profile, both the density and the high-energy tails in the velocity distribution functions are found to be strongly influenced by the restitution coefficient
Neutral meson production in pp and Pb–Pb collisions at LHC

AbstractThe ALICE detector at the LHC studies π0 and η meson production by two complementary methods, using electromagnetic calorimeters and the central tracking system for converted photons. Production spectra of π0 and η mesons were measured with ALICE in pp collisions at LHC energies at mid-rapidity in a wide transverse momentum range. The spectrum and the nuclear modification factor RAA of π0 measured in Pb–Pb collisions at different centralities, show a clear pattern of strong suppression in a hot QCD medium with respect to pp collisions
Coach-Swimmer Communications Based on Wrist Mounted 2.4GHz Accelerometer Sensor

AbstractTwo way real time communications during swimming is important for coaches and swimmers in order to reach optimum performance. This paper presents a 2.4GHz wireless communication system to send acceleration data to a coach tablet at the pool side and allow active interactions between swimmers and their coaches. The radio frequency signal does not propagate effectively underwater because of the high attenuation. Therefore the wireless transmitter sends data only when the swimmer's wrist is outside the water. The y-axis acceleration data provides stroke rate SR, stroke length and swim velocity. The experimental results showed that the link is operational 28% per stroke in freestyle swimming. This is more than enough to send important data from the swimmer and reply with the coach's feedback
Seasonal persistence of faecal indicator organisms in soil following dairy slurry application to land by surface broadcasting and shallow injection

AbstractDairy farming generates large volumes of liquid manure (slurry), which is ultimately recycled to agricultural land as a valuable source of plant nutrients. Different methods of slurry application to land exist; some spread the slurry to the sward surface whereas others deliver the slurry under the sward and into the soil, thus helping to reduce greenhouse gas (GHG) emissions from agriculture. The aim of this study was to investigate the impact of two slurry application methods (surface broadcast versus shallow injection) on the survival of faecal indicator organisms (FIOs) delivered via dairy slurry to replicated grassland plots across contrasting seasons. A significant increase in FIO persistence (measured by the half-life of E. coli and intestinal enterococci) was observed when slurry was applied to grassland via shallow injection, and FIO decay rates were significantly higher for FIOs applied to grassland in spring relative to summer and autumn. Significant differences in the behaviour of E. coli and intestinal enterococci over time were also observed, with E. coli half-lives influenced more strongly by season of application relative to the intestinal enterococci population. While shallow injection of slurry can reduce agricultural GHG emissions to air it can also prolong the persistence of FIOs in soil, potentially increasing the risk of their subsequent transfer to water. Awareness of (and evidence for) the potential for ‘pollution-swapping’ is critical in order to guard against unintended environmental impacts of agricultural management decisions
The moving rubber hand illusion revisited: Comparing movements and visuotactile stimulation to induce illusory ownership

AbstractThe rubber hand illusion is a perceptual illusion in which a model hand is experienced as part of one’s own body. In the present study we directly compared the classical illusion, based on visuotactile stimulation, with a rubber hand illusion based on active and passive movements. We examined the question of which combinations of sensory and motor cues are the most potent in inducing the illusion by subjective ratings and an objective measure (proprioceptive drift). In particular, we were interested in whether the combination of afferent and efferent signals in active movements results in the same illusion as in the purely passive modes. Our results show that the illusion is equally strong in all three cases. This demonstrates that different combinations of sensory input can lead to a very similar phenomenological experience and indicates that the illusion can be induced by any combination of multisensory information
A note on the dual of N=1 super-Yang–Mills theory

AbstractWe refine the dictionary of the gauge/gravity correspondence realizing N=1 super-Yang–Mills by means of D5-branes wrapped on a resolved Calabi–Yau space. This is done by fixing an ambiguity on the correct interpretation of the holographic dual of the running gauge coupling and amounts to identify a specific 2-cycle in the dual ten-dimensional supergravity background. In doing so, we also discuss the role played in this context by gauge transformations in the relevant seven-dimensional gauged supergravity. While all nice properties of the duality are maintained, this modification of the dictionary has some interesting physical consequences and solves a puzzle recently raised in the literature. In this refined framework, it is also straightforward to see how the correspondence naturally realizes a geometric transition
Well-posedness of the Einstein–Euler system in asymptotically flat spacetimes: The constraint equations

AbstractThis paper deals with the construction of initial data for the coupled Einstein–Euler system. We consider the condition where the energy density might vanish or tend to zero at infinity, and where the pressure is a fractional power of the energy density. In order to achieve our goals we use a type of weighted Sobolev space of fractional order.The common Lichnerowicz–York scaling method (Choquet-Bruhat and York, 1980 [9]; Cantor, 1979 [7]) for solving the constraint equations cannot be applied here directly. The basic problem is that the matter sources are scaled conformally and the fluid variables have to be recovered from the conformally transformed matter sources. This problem has been addressed, although in a different context, by Dain and Nagy (2002) [11]. We show that if the matter variables are restricted to a certain region, then the Einstein constraint equations have a unique solution in the weighted Sobolev spaces of fractional order. The regularity depends upon the fractional power of the equation of state
Disassembly of the JIP1/JNK molecular scaffold by caspase-3-mediated cleavage of JIP1 during apoptosis

AbstractWe report here the cleavage of the c-Jun N-terminal Kinase (JNK) pathway scaffold protein, JNK Interacting Protein-1 (JIP1), by caspases during both Tumour Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL) and staurosporine-induced apoptosis in HeLa cells. During the initiation of apoptosis, maximal JNK activation is observed when JIP1 is intact, whereas cleavage of JIP1 correlates with JNK inactivation and progression of apoptosis. JIP1 is cleaved by caspase-3 at two sites, leading to disassembly of the JIP1/JNK complex. Inhibition of JIP1 cleavage by the caspase-3 inhibitor DEVD.fmk inhibits this disassembly, and is accompanied by sustained JNK activation. These data suggest that TRAIL and staurosporine induce JNK activation in a caspase-3-independent manner and that caspase-3-mediated JIP1 cleavage plays a role in JNK inactivation via scaffold disassembly during the execution phase of apoptosis. Caspase-mediated cleavage of JIP scaffold proteins may therefore represent an important mechanism for modulation of JNK signalling during apoptotic cell death
Analysis of events with b-jets and a pair of leptons of the same charge in pp collisions at √s = 8 TeV with the ATLAS detector

An analysis is presented of events containing jets including at least one b-tagged jet, sizeable missing transverse momentum, and at least two leptons including a pair of the same electric charge, with the scalar sum of the jet and lepton transverse momenta being large. A data sample with an integrated luminosity of 20.3 fb[superscript −1] of pp collisions at  s√= 8  TeV recorded by the ATLAS detector at the Large Hadron Collider is used. Standard Model processes rarely produce these final states, but there are several models of physics beyond the Standard Model that predict an enhanced rate of production of such events; the ones considered here are production of vector-like quarks, enhanced four-top-quark production, pair production of chiral b′-quarks, and production of two positively charged top quarks. Eleven signal regions are defined; subsets of these regions are combined when searching for each class of models. In the three signal regions primarily sensitive to positively charged top quark pair production, the data yield is consistent with the background expectation. There are more data events than expected from background in the set of eight signal regions defined for searching for vector-like quarks and chiral b′-quarks, but the significance of the discrepancy is less than two standard deviations. The discrepancy reaches 2.5 standard deviations in the set of five signal regions defined for searching for four-top-quark production. The results are used to set 95% CL limits on various models.United States. Dept. of EnergyNational Science Foundation (U.S.)Brookhaven National Laborator
Measurement of the tt¯W and tt¯Z production cross sections in pp collisions at √s =8 TeV with the ATLAS detector

The production cross sections of top-quark pairs in association with massive vector bosons have been measured using data from pp collisions at √s = 8 TeV. The dataset corresponds to an integrated luminosity of 20.3 fb[superscript −1] collected by the ATLAS detector in 2012 at the LHC. Final states with two, three or four leptons are considered. A fit to the data considering the  t[bar over t]W and  t[bar over t]Z processes simultaneously yields a significance of 5.0σ (4.2σ) over the background-only hypothesis for  t[bar over t]W  (t[bar over t]Z ) production. The measured cross sections are  σ[subscript t[bar over t]W] = 369[superscript +100][subscript −91] fb and σ[subscript t[bar over t]Z]=176[superscript +58][subscript −52] fb. The background-only hypothesis with neither  t[bar over t]W nor  t[bar over t]Z  production is excluded at 7.1σ. All measurements are consistent with next-to-leading-order calculations for the  t[bar over t]W and  t[bar over t]Z  processes.United States. Department of EnergyNational Science Foundation (U.S.
On the information content of discrete phylogenetic characters

Phylogenetic inference aims to reconstruct the evolutionary relationships of
different species based on genetic (or other) data. Discrete characters are a
particular type of data, which contain information on how the species should be
grouped together. However, it has long been known that some characters contain
more information than others. For instance, a character that assigns the same
state to each species groups all of them together and so provides no insight
into the relationships of the species considered. At the other extreme, a
character that assigns a different state to each species also conveys no
phylogenetic signal. In this manuscript, we study a natural combinatorial
measure of the information content of an individual character and analyse
properties of characters that provide the maximum phylogenetic information,
particularly, the number of states such a character uses and how the different
states have to be distributed among the species or taxa of the phylogenetic
tree.Comment: 16 pages, 7 figures. Final version has now appeared in Journal of
  Mathematical Biology (December 2017)
  https://link.springer.com/article/10.1007/s00285-017-1198-
Search for new physics in the monophoton final state in proton-proton
  collisions at sqrt(s) = 13 TeV

A search is conducted for new physics in a final state containing a photon
and missing transverse momentum in proton-proton collisions at sqrt(s) = 13
TeV. The data collected by the CMS experiment at the CERN LHC correspond to an
integrated luminosity of 12.9 inverse femtobarns. No deviations are observed
relative to the predictions of the standard model. The results are interpreted
as exclusion limits on the dark matter production cross sections and parameters
in models containing extra spatial dimensions. Improved limits are set with
respect to previous searches using the monophoton final state. In particular,
the limits on the extra dimension model parameters are the most stringent to
date in this channel.Comment: Replaced with the published version. Added the journal reference and
  DOI. All the figures and tables can be found at
  http://cms-results.web.cern.ch/cms-results/public-results/publications/EXO-16-039
  (CMS Public Pages