pinecone/core-2020-05-10-deduplication huggingface dataset:
Tug-of-war between driver and passenger mutations in cancer and other adaptive processes

Cancer progression is an example of a rapid adaptive process where evolving new traits is essential for survival and requires a high mutation rate. Precancerous cells acquire a few key mutations that drive rapid population growth and carcinogenesis. Cancer genomics demonstrates that these few driver mutations occur alongside thousands of random passenger mutations—a natural consequence of cancer’s elevated mutation rate. Some passengers are deleterious to cancer cells, yet have been largely ignored in cancer research. In population genetics, however, the accumulation of mildly deleterious mutations has been shown to cause population meltdown. Here we develop a stochastic population model where beneficial drivers engage in a tug-of-war with frequent mildly deleterious passengers. These passengers present a barrier to cancer progression describable by a critical population size, below which most lesions fail to progress, and a critical mutation rate, above which cancers melt down. We find support for this model in cancer age–incidence and cancer genomics data that also allow us to estimate the fitness advantage of drivers and fitness costs of passengers. We identify two regimes of adaptive evolutionary dynamics and use these regimes to understand successes and failures of different treatment strategies. A tumor’s load of deleterious passengers can explain previously paradoxical treatment outcomes and suggest that it could potentially serve as a biomarker of response to mutagenic therapies. The collective deleterious effect of passengers is currently an unexploited therapeutic target. We discuss how their effects might be exacerbated by current and future therapies.National Cancer Institute (U.S.) (Grant U54CA143874)MIT Department of Physics Pappalardo Progra
Search for new physics in the dijet mass distribution using 1 fb(-1) of pp collision data at root s = 7 TeV collected by the ATLAS detector

Invariant mass distributions of jet pairs (dijets) produced in LHC proton–proton collisions at a centre-of-mass energy √s = 7 TeV have been studied using a data set corresponding to an integrated luminosity of 1.0 fb⁻¹ recorded in 2011 by ATLAS. Dijet masses up to ∼4 TeV are observed in the data, and no evidence of resonance production over background is found. Limits are set at 95% C.L. for several new physics hypotheses: excited quarks are excluded for masses below 299 TeV, axigluons are excluded for masses below 3.32 TeV, and colour octet scalar resonances are excluded for masses below 1.92 TeV.G. Aad ... P. Jackson ... L. Lee ... A. Petridis ... N. Soni ... M. J. White ... et al. (ATLAS Collaboration
Sum-rates of asynchronous GFDMA and SC-FDMA for 5G uplink

The fifth generation (5G) of mobile communication envisions ultralow latency less than 1 ms for radio interface. To this end, frameless asynchronous multiple access may be needed to allow users to transmit instantly without waiting for the next frame start. In this paper, generalized frequency division multiple-access (GFDMA), one of the promising multiple-access candidates for 5G mobile, is compared with the conventional single-carrier FDMA (SC-FDMA) in terms of the uplink sum rate when both techniques are adapted for the asynchronous scenario. In particular, a waveform windowing technique is applied to both schemes to mitigate the inter-user interference due to non-zero out-of-band emission.ope
Azimuthal decorrelation of jets widely separated in rapidity in pp collisions at √s = 7 TeV

Journal of High Energy Physics 2016.8 (2016): 139 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)Artículo escrito por un elevado número de autores, sólo se referencian, el nombre del grupo de colaboración y los autores que firman como pertenecientes a la UAMThe decorrelation in the azimuthal angle between the most forward and the  most backward jets (Mueller-Navelet jets) is measured in data collected in pp collisions  with the CMS detector at the LHC at √  s = 7 TeV. The measurement is presented in the  form of distributions of azimuthal-angle differences, ∆φ, between the Mueller-Navelet jets,  the average cosines of (π − ∆φ), 2(π − ∆φ), and 3(π − ∆φ), and ratios of these cosines.  The jets are required to have transverse momenta, pT, in excess of 35 GeV and rapidities,  |y|, of less than 4.7. The results are presented as a function of the rapidity separation,  ∆y, between the Mueller-Navelet jets, reaching ∆y up to 9.4 for the first time. The results  are compared to predictions of various Monte Carlo event generators and to analytical  predictions based on the DGLAP and BFKL parton evolution scheme
Influence of metalworking defect in knee cruciate ligament screws as a possible origin of infections

A mucormycosis outbreak in a a clinic of Paraná city after Arthroscopic knee anterior cruciate ligament reconstruction forced to suspend these interventions. The the main candidates as the infection source were the implanted screws. These screws were metallurgically analyzed.  Microscopic defects like burrs and bending`s were found within the screw´s allen heads. According to Spector et al. (2013) these defects protect microorganisms and make difficult to eliminate them. The aim of this work was to demonstrate the implication of metal working defects in the titanium fixing screws as a reservoir of contaminated machining oil which could be the possible transmitting vehicle in the outbreak of bone mucormycosis. The genetic relatedness of the isolated strains was established demonstrating that the screws were the infection sources.Fil: Spector, Mario. Universidad Tecnológica Nacional. Facultad Regional Paraná; ArgentinaFil: García Effron, Guillermo. Universidad Nacional del Litoral. Facultad de Bioquímica y Ciencias Biológicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Peretti, Leandro Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe. Instituto de Desarrollo Tecnológico para la Industria Química (i); Argentina. Universidad Tecnológica Nacional. Facultad Regional Paraná; Argentin
Charged-particle multiplicities in pp interactions at s=900 GeV measured with the ATLAS detector at the LHC

AbstractThe first measurements from proton–proton collisions recorded with the ATLAS detector at the LHC are presented. Data were collected in December 2009 using a minimum-bias trigger during collisions at a centre-of-mass energy of 900 GeV. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity, and the relationship between mean transverse momentum and charged-particle multiplicity are measured for events with at least one charged particle in the kinematic range |η|<2.5 and pT>500 MeV. The measurements are compared to Monte Carlo models of proton–proton collisions and to results from other experiments at the same centre-of-mass energy. The charged-particle multiplicity per event and unit of pseudorapidity at η=0 is measured to be 1.333±0.003(stat.)±0.040(syst.), which is 5–15% higher than the Monte Carlo models predict
Modelling particle scale leach kinetics based on X-ray computed micro-tomography images

AbstractThe apparent leach kinetics for an ore particle within a heap leaching system depend on the chemical conditions in the fluids around the particle, the mass transport within the particle and the reaction kinetics at the surface of each mineral grain. The apparent rate kinetics thus depend upon the distribution of the mineral grains, in terms of both size and position, within the individual ore particles, as well as the evolution of this distribution. Traditionally this behaviour has been modelled using simplified relationships such as the shrinking core model. In this paper a method for simulating this evolution and the resultant kinetics based directly on 3D XMT images of the internal structure of the particles is presented. The model includes mass transport through the gangue matrix, surface reaction kinetics and the dissolution and subsequent evolution of the individual mineral grains within the ore particle. Different minerals and mineral associations will result in different surface reaction kinetics. One of the key inputs into this model is thus the distribution of the surface rate kinetics. A method for experimentally determining this distribution is presented. The simulation results are compared to the evolution of real particles as they undergo leaching as measured using a time sequence of 3D XMT images of a leaching column. It was found that these simulations are able to accurately predict both the overall leaching trends, as well as the leaching behaviour of mineral grains in classes based on their size and distance to the particle surface. The leaching behaviour did not follow that of a simple shrinking core approximation, with the actual spatial and size distribution of the grains, as well as the distribution of their surface rate kinetics, all impacting the apparent leach kinetics. For the copper ore particles used in this work the best fit to the experiments was achieved at an intermediate value of the dimensionless group that characterises the relative importance of surface kinetics to diffusion indicating that both need to be considered for accurate modelling. This paper thus demonstrates that using 3D XMT to provide both structural and kinetic data and incorporating this information into a particle scale simulator provides an improved basis for predicting particle scale leach performance
Groundwater Salinization in a Coastal Multilayer Aquifer: Preliminary Results on Origins and Mechanisms- Example of Recife (Brazil)

AbstractThe Recife Metropolitan Region (PE, Brazil) appears as a typical environmental “hot spot” illustrating the problems of southern countries, such as urbanization or rapid industrial and touristic development. All of these factors induce high pressure on water resources, both in terms of quantity and quality in the context of global societal and environmental changes. This paper focuses on the groundwater geochemistry of a costal multilayer aquifer, and aims at investigating the sources and processes of salinization. The preliminary results of 62 groundwater samples from the five main aquifers are reported
Reliable Capacity Planning Despite Uncertain Disassembly, Regeneration and Reassembly Workloads by Using Statistical and Mathematical Approaches – Validation in Subsidiaries of a Global MRO Company with Operations in Asia, Europe and North America

AbstractThe MRO industry faces substantial challenges with regard to the capacity planning of disassembly and reassembly work. This is due to the unknown workloads when regenerating complex investment goods and is caused, in particular, by the uncertain degree of disassembly and the complex challenges of reassembly. Forecasting techniques based on Bayesian networks are developed along with mathematical models which optimize capacity utilization, job order and the resulting costs. The approaches are tested and validated in conjunction with an MRO company with global operations. The results show possibilities for enhancing the planning processes and are found to be transferable on an international scale regardless of sociocultural and process differences
Inclusive jet cross sections in the Breit frame in neutral current deep inelastic scattering at HERA and determination of αs

AbstractInclusive jet differential cross sections have been measured in neutral current deep inelastic e+p scattering for boson virtualities Q2>125 GeV2. The data were taken using the ZEUS detector at HERA and correspond to an integrated luminosity of 38.6 pb−1. Jets were identified in the Breit frame using the longitudinally invariant kT cluster algorithm. Measurements of differential inclusive jet cross sections are presented as functions of jet transverse energy (EBT,jet), jet pseudorapidity and Q2, for jets with EBT,jet>8 GeV. Next-to-leading-order QCD calculations agree well with the measurements both at high Q2 and high EBT,jet. The value of αs(MZ), determined from an analysis of dσ/dQ2 for Q2>500 GeV2, is αs(MZ)=0.1212±0.0017(stat.)+0.0023−0.0031(syst.)+0.0028−0.0027(th.)
Can X(5568) be described as a Bsπ, BK¯ resonant state?

AbstractThe D0 Collaboration has recently seen a resonant-like peak in the Bsπ invariant mass spectrum, claimed to be a new state called X(5568). Using a Bsπ–BK¯ coupled channel analysis, implementing unitarity, and with the interaction derived from Heavy Meson Chiral Perturbation Theory, we are able to reproduce the reported spectrum, with a pole that can be associated to the claimed X(5568) state, and with mass and width in agreement with the ones reported in the experimental analysis. However, if the T-matrix regularization is performed by means of a momentum cutoff, the value for the latter needed to reproduce the spectrum is Λ=2.80±0.04GeV, which is much larger than a “natural” value Λ≃1GeV. In view of this, it is difficult to interpret the nature of this new state. This state would not qualify as a resonance dynamically generated by the unitarity loops. Assuming the observed peak to correspond to a physical state, we make predictions for partners in the D, D⁎, and B⁎ sectors. Their observation (or lack thereof) would shed light into this issue
Deviations from Born-Oppenheimer mass scaling in spectroscopy and ultracold molecular physics

AbstractWe investigate Born-Oppenheimer breakdown (BOB) effects (beyond the usual mass scaling) for the electronic ground states of a series of homonuclear and heteronuclear alkali-metal diatoms, together with the Sr2 and Yb2 diatomics. Several widely available electronic structure software packages are used to calculate the leading contributions to the total isotope shift for commonly occurring isotopologs of each species. Computed quantities include diagonal Born-Oppenheimer corrections (mass shifts) and isotopic field shifts. Mass shifts dominate for light nuclei up to and including K, but field shifts contribute significantly for Rb and Sr and are dominant for Yb. We compare the ab initio mass-shift functions for Li2, LiK and LiRb with spectroscopically derived ground-state BOB functions from the literature. We find good agreement in the values of the functions for LiK and LiRb at their equilibrium geometries, but significant disagreement with the shapes of the functions for all 3 systems. The differences may be due to contributions of nonadiabatic terms to the empirical BOB functions. We present a semiclassical model for the effect of BOB corrections on the binding energies of near-threshold states and the positions of zero-energy Feshbach resonances
Going south: Latitudinal change in mammalian biodiversity in Miocene Eurasia

AbstractFor palaeontologists, the challenge is to reconstruct biodiversity patterns of the past. Mammal richness in grids is used to assess the stability of biodiversity hotspots and document changes over time in Europe for Mammal Neogene units 3 to 11 (19.5 to 7.6Ma), early to late Miocene. The maps clearly show the patchiness of the fossil record. As the Miocene was an eventful epoch with severe environmental changes, Europe slowly became drier, and more seasonal, both in temperature and precipitation. From the early to middle Miocene an area of high biodiversity moved from higher to lower latitudes, culminating in one of the most remarkable hotspots in the history of mammals: the early late Miocene (Vallesian mammal stage) faunas from the Vallès-Penedès (Catalonia, Spain). Remarkably, the surrounding areas did not exhibit similar richness. During the subsequent Vallesian turnover event (~9.7Ma), the large and small mammal distribution became more equitable and the hotspots less prominent. The richest area was found in the periphery of the humid Miocene ecosystem, which experienced species influx from the drier south. The southward shift was a result of the expansion of the humid area with subsequent closed environments and related mixing of ecosystems, coming to a halt in the late Miocene, when all of Europe became equally open
Flow Velocity Mapping Using Contrast Enhanced High-Frame-Rate Plane Wave Ultrasound and Image Tracking: Methods and Initial in Vitro and in Vivo Evaluation

AbstractUltrasound imaging is the most widely used method for visualising and quantifying blood flow in medical practice, but existing techniques have various limitations in terms of imaging sensitivity, field of view, flow angle dependence, and imaging depth. In this study, we developed an ultrasound imaging velocimetry approach capable of visualising and quantifying dynamic flow, by combining high-frame-rate plane wave ultrasound imaging, microbubble contrast agents, pulse inversion contrast imaging and speckle image tracking algorithms. The system was initially evaluated in vitro on both straight and carotid-mimicking vessels with steady and pulsatile flows and in vivo in the rabbit aorta. Colour and spectral Doppler measurements were also made. Initial flow mapping results were compared with theoretical prediction and reference Doppler measurements and indicate the potential of the new system as a highly sensitive, accurate, angle-independent and full field-of-view velocity mapping tool capable of tracking and quantifying fast and dynamic flows
Chern–Simons AdS5 supergravity in a Randall–Sundrum background

AbstractChern–Simons AdS supergravity theories are gauge theories for the super-AdS group. These theories possess a fermionic symmetry which differs from standard supersymmetry. In this paper, we study five-dimensional Chern–Simons AdS supergravity in a Randall–Sundrum scenario with two Minkowski 3-branes. After making modifications to the D=5 Chern–Simons AdS supergravity action and fermionic symmetry transformations, we obtain a Z2-invariant total action S=S˜bulk+Sbrane and fermionic transformations δ˜ϵ. While δ˜ϵS˜bulk=0, the fermionic symmetry is broken by Sbrane. Our total action reduces to the original Randall–Sundrum model when S˜bulk is restricted to its gravitational sector. We solve the Killing spinor equations for a bosonic configuration with vanishing su(N) and u(1) gauge fields
Precise QCD predictions for the production of Higgs + jet final states

AbstractWe compute the cross section and differential distributions for the production of a Standard Model Higgs boson in association with a hadronic jet to next-to-next-to-leading order in quantum chromodynamics (QCD). In Higgs boson studies at the LHC, final states containing one jet are a dominant contribution to the total event rate, and their understanding is crucial for improved determinations of the Higgs boson properties. We observe substantial higher order corrections to transverse momentum spectra and rapidity distributions in Higgs-plus-one-jet final states. Their inclusion stabilises the residual theoretical uncertainty of the predictions around 9%, thereby providing important input to precision studies of the Higgs boson
Alpha induced reaction cross section measurements on 162Er for the astrophysical γ process

AbstractThe cross sections of the Er162(α,γ)Yb166 and Er162(α,n)Yb165 reactions have been measured for the first time. The radiative alpha capture reaction cross section was measured from Ec.m.=16.09 MeV down to Ec.m.=11.21 MeV, close to the astrophysically relevant region (which lies between 7.8 and 11.48 MeV at 3 GK stellar temperature). The Er162(α,n)Yb165 reaction was studied above the reaction threshold between Ec.m.=12.19 and 16.09 MeV. The fact that the Er162(α,γ)Yb166 cross sections were measured below the (α,n) threshold at first time in this mass region opens the opportunity to study directly the α-widths required for the determination of astrophysical reaction rates. The data clearly show that compound nucleus formation in this reaction proceeds differently than previously predicted
Coherent states of the deformed Heisenberg–Weyl algebra in non-commutative space

AbstractIn two-dimensional space a subtle point that for the case of both space–space and momentum–momentum non-commuting, different from the case of only space–space non-commuting, the deformed Heisenberg–Weyl algebra in non-commutative space is not completely equivalent to the undeformed Heisenberg–Weyl algebra in commutative space is clarified. It follows that there is no well-defined procedure to construct the deformed position–position coherent state or the deformed momentum–momentum coherent state from the undeformed position–momentum coherent state. Identifications of the deformed position–position and deformed momentum–momentum coherent states with the lowest energy states of a cold Rydberg atom in special conditions and a free particle, respectively, are demonstrated
A mutation in the silver gene leads to defects in melanosome biogenesis and alterations in the visual system in the zebrafish mutant fading vision

AbstractForward genetic screens have been instrumental in defining molecular components of visual function. The zebrafish mutant fading vision (fdv) has been identified in such a screen due to defects in vision accompanied by hypopigmentation in the retinal pigment epithelium (RPE) and body melanocytes. The RPE forms the outer most layer of the retina, and its function is essential for vision. In fdv mutant larvae, the outer segments of photoreceptors are strongly reduced in length or absent due to defects in RPE cells. Ultrastructural analysis of RPE cells reveals dramatic cellular changes such as an absence of microvilli and vesicular inclusions. The retinoid profile is altered as judged by biochemical analysis, arguing for a partial block in visual pigment regeneration. Surprisingly, homozygous fdv vision mutants survive to adulthood and show, despite a persistence of the hypopigmentation, a partial recovery of retinal morphology. By positional cloning and subsequent morpholino knock-down, we identified a mutation in the silver gene as the molecular defect underlying the fdv phenotype. The Silver protein is required for intralumenal fibril formation in melanosomes by amylogenic cleavage. Our data reveal an unexpected link between melanosome biogenesis and the visual system, undetectable in cell culture
N-terminal amino acid sequences of chloroform/methanol-soluble proteins and albumins from endosperms of wheat, barley and related species Homology with inhibitors of α-amylase and trypsin and with 2 S storage globulins

AbstractThe N-terminal amino acid sequences of two chloroform/methanol soluble globulins from barley and one form wheat are reported. They are homologous with N-terminal sequences previously reported for α-amylase and trypsin inhibitors from cereals and 2 S storage proteins from castor bean and rape. Three albumins were also purified from Aegilops squarrosa and Triticum monococcum. These had N-terminal amino acid sequences most closely related to the α-amylase and trypsin inhibitors. The relationships of this superfamily of seed proteins are discussed