pinecone/core-2020-05-10-deduplication huggingface dataset:
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Comprehensive analyses of cancer genomes promise to inform prognoses and precise cancer treatments. A major barrier, however, is inaccessibility of metastatic tissue. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming the challenges of isolating rare cells and sequencing low-input material. Here we report an integrated process to isolate, qualify and sequence whole exomes of CTCs with high fidelity using a census-based sequencing strategy. Power calculations suggest that mapping of >99.995% of the standard exome is possible in CTCs. We validated our process in two patients with prostate cancer, including one for whom we sequenced CTCs, a lymph node metastasis and nine cores of the primary tumor. Fifty-one of 73 CTC mutations (70%) were present in matched tissue. Moreover, we identified 10 early trunk and 56 metastatic trunk mutations in the non-CTC tumor samples and found 90% and 73% of these mutations, respectively, in CTC exomes. This study establishes a foundation for CTC genomics in the clinic.National Science Foundation (U.S.). Graduate Research FellowshipNational Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051)Janssen Pharmaceutical Ltd.Klarman Family Foundatio
Lattice-Based Spatio-temporal Prediction

With the rapidly increasing deployment of sensor networks, large amounts of time series data are generated. One of the main challenges when dealing with such data is performing accurate predictions in order to address a broad class of application problems, ranging from mobile broadband network (MBN) optimization to preventive maintenance. To this end, time series prediction has been widely addressed by the statistics community. Nevertheless, such approaches fail in performing well when the data are more context-dependent than history-dependent. In this paper, we investigate how latent attributes can be built upon the time series in order to define a spatio-temporal context for predictions. Moreover, such attributes are often hierarchical, leading to multiple potential contexts at different levels of granularity for performing a given prediction. In support of this scenario, we propose the Lattice-Based Spatio-Temporal Ensemble Prediction (LBSTEP) approach, which allows modeling the problem as a multidimensional spatio-temporal prediction. Given an ensemble prediction model, we propose a solution for determining the most appropriate spatio-temporal context that maximizes the global prediction metrics of a set of the time series. LBSTEP is evaluated with a real-world MBN dataset, which exemplifies the intended general application domain of time series data with a strong spatio-temporal component. The experimental results shows that the proposed contextual and multi-granular view of the prediction problem is effective, in terms of both several optimization metrics and the model calculation
Regularized characteristic boundary condition for the Lattice Boltzmann methods at high Reynolds number flows

This paper reports the investigations done to adapt the Characteristic Boundary Conditions (CBC) to the Lattice-Boltzmann formalism for high Reynolds number applications. Three CBC formalisms are implemented and tested in an open source LBM code: the baseline one-dimension inviscid (BL-LODI) approach, its extension including the effects of the transverse terms (CBC-2D) and a local streamline approach in which the problem is reformulated in the incident wave framework (LS-LODI). Then all implementations of the CBC methods are tested for a variety of test cases, ranging from canonical problems (such as 2D plane and spherical waves and 2D vortices) to a 2D NACA profile at high Reynolds number (Re = 100,000), representative of aeronautic applications. The LS-LODI approach provides the best results for pure acoustics waves (plane and spherical waves). However, it is not well suited to the outflow of a convected vortex for which the CBC-2D associated with a relaxation on density and transverse waves provides the best results. As regards numerical stability, a regularized adaptation is necessary to increase the Reynolds number. The so-called regularized FD adaptation, a modified regularized approach where the off-equilibrium part of the stress tensor is computed thanks to a finite difference scheme, is the only tested adaptation that can handle the high Reynolds computation
Electronic and atomic structure of complex defects in Al- and Ga-highly doped ZnO films

Point defects in Ga- and Al-doped ZnO thin films are studied by means of first principles electronic structure calculations. Candidate defects are identified to explain recently observed differences in electrical and spectroscopical behavior of both systems. Substitutional doping in Ga-ZnO explain the metallic behavior of the electrical properties. Complexes of interstitial oxygen with substitutional Ga can behave as acceptor and cause partial compensation, as well as gap states below the conduction band minimum as observed in photoemission experiments. Zn vacancies can also act as compensating acceptors. On the other hand, the semiconducting behavior of Al-ZnO and the small variation in the optical gap compared with pure ZnO, can be explained by almost complete compensation between acceptor Zn vacancies and substitutional Al donors. Interstitial Al can also be donor levels and can be the origin of the small band observed in photoemission experiments below the Fermi level. Combinations of substitutional Al with interstitial oxygen can act simultaneously as compensating acceptor and generator o the mentioned photoemission band. The theoretical calculations have been done using density functional theory (DFT) within the generalized gradient approximation with onsite Coulomb interaction. In selected cases, DFT calculations with semilocal-exact exchange hybrid functionals have been performed. Results explain photoelectron spectra of Ga-ZnO and Al-ZnO at the corresponding doping levels
Evaluating the efficiency of the leadership training programmes in Spain

Leadership abilities, and especially social abilities related to emotional intelligence are key factors to team management and the performance increase it generates in companies. For this reason, leadership training is an essential part of development plans in organizations. Also applying learning to work place is equally important. Evaluating learning transfer is a critical condition in order to measure training results and to assess training efficacy within organizations. This article presents the results of an analysis of the factors affecting the transfer of the learning acquired within various leadership programs, in several Spanish companies, by means of the LTSI questionnaire developed by Holton and Bates (1998, 2000). The results show a clear intention to transfer learning, but a low level of support offered by the organization so as to enable trainees to apply learning. In addition, the trainees assessed exhibit an obvious lack of personal capacity to transfer what they learne
Measurement of four-jet differential cross sections in root s = 8 TeV proton-proton collisions using the ATLAS detector

Differential cross sections for the production of at least four jets have been measured in proton-proton collisions at √s=8 TeV at the Large Hadron Collider using the ATLAS detector. Events are selected if the four anti-ktR = 0.4 jets with the largest transverse momentum (pT) within the rapidity range |y| < 2.8 are well separated (ΔR4jmin > 0.65), all have pT > 64 GeV, and include at least one jet with pT > 100 GeV. The dataset corresponds to an integrated luminosity of 20.3 fb⁻¹. The cross sections, corrected for detector effects, are compared to leading-order and next-to-leading-order calculations as a function of the jet momenta, invariant masses, minimum and maximum opening angles and other kinematic variables.G. Aad ... P. Jackson ... L. Lee ... A. Petridis ... N. Soni ... M.J. White ... et al. (ATLAS Collaboration
The Influence of Various Factors on the Progress in Training of International Learners of the Preparatory Department (on the Example of the Course "Computer Science")

The task of research different factors affecting on the progress in training of students is actual. Two main factors as training the course in native language and knowledge of the language in which the course is studied were considered to solve this problem. The research is aimed at learners of the Preparatory Department studying in a non-native language (Russian) and takes into account the characteristics of such contingent of students. The study was made in the course "Computer science" with the help of methods of mathematical statistics. This research was conducted to improve the methods and to change the approaches in teaching the pre-university programs
Non-parametric reconstruction of an inflaton potential from Einstein–Cartan–Sciama–Kibble gravity with particle production

AbstractThe coupling between spin and torsion in the Einstein–Cartan–Sciama–Kibble theory of gravity generates gravitational repulsion at very high densities, which prevents a singularity in a black hole and may create there a new universe. We show that quantum particle production in such a universe near the last bounce, which represents the Big Bang, gives the dynamics that solves the horizon, flatness, and homogeneity problems in cosmology. For a particular range of the particle production coefficient, we obtain a nearly constant Hubble parameter that gives an exponential expansion of the universe with more than 60 e-folds, which lasts about ∼10−42 s. This scenario can thus explain cosmic inflation without requiring a fundamental scalar field and reheating. From the obtained time dependence of the scale factor, we follow the prescription of Ellis and Madsen to reconstruct in a non-parametric way a scalar field potential which gives the same dynamics of the early universe. This potential gives the slow-roll parameters of cosmic inflation, from which we calculate the tensor-to-scalar ratio, the scalar spectral index of density perturbations, and its running as functions of the production coefficient. We find that these quantities do not significantly depend on the scale factor at the Big Bounce. Our predictions for these quantities are consistent with the Planck 2015 observations
The high density effects in heavy-quark production at pA colliders

AbstractIn this Letter we investigate the role of the high density effects in the heavy-quark production cross section in pA processes at RHIC and LHC. We use, as initial condition, a gluon distribution consistent with fixed target nuclear data and the Glauber–Mueller approach to describe the high density effects. We show that this process can be used as a probe of the presence of the high density effects. Moreover, we include these effects in the calculation of the heavy-quark production in AA collisions, verifying that they cannot be disregarded both in the estimates of quarkonium suppression and in the initial conditions of the quark–gluon plasma
Search for new resonances decaying via WZ to leptons in proton–proton collisions at s=8TeV

AbstractA search is performed in proton–proton collisions at s=8 TeV for exotic particles decaying via WZ to fully leptonic final states with electrons, muons, and neutrinos. The data set corresponds to an integrated luminosity of 19.5 fb−1. No significant excess is observed above the expected standard model background. Upper bounds at 95% confidence level are set on the production cross section of a W′ boson as predicted by an extended gauge model, and on the W′WZ coupling. The expected and observed mass limits for a W′ boson, as predicted by this model, are 1.55 and 1.47 TeV, respectively. Stringent limits are also set in the context of low-scale technicolor models under a range of assumptions for the model parameters
The Helicobacter Eradication Aspirin Trial (HEAT): A Large Simple Randomised Controlled Trial Using Novel Methodology in Primary Care

AbstractBackgroundClinical trials measuring the effect of an intervention on clinical outcomes are more influential than those investigating surrogate measures but are costly. We developed methods to reduce costs substantially by using existing data in primary care systems, to ask whether Helicobacter pylori eradication would reduce the incidence of hospitalisation for ulcer bleeding in aspirin users.MethodsThe Helicobacter Eradication Aspirin Trial (HEAT) is a National Institute of Health Research-funded, double-blind placebo controlled randomised trial of the effects of H. pylori eradication on subsequent ulcer bleeding in infected individuals taking aspirin daily, conducted in practices across the whole of England, Wales and Northern Ireland. A bespoke web-based trial management system developed for the trial (and housed within the secure NHS Data Network) communicates directly with the HEAT Toolkit software downloaded at participating practices, which issues queries searching entry criteria (≥60years, on chronic aspirin ≤325mg daily, not on anti-ulcer therapy or non-steroidal anti-inflammatory drugs) for GP review of eligibility. Trial participation is invited using a highly secure automated online mail management system. Interested patients are seen once for consent and breath testing. Those with a positive test are randomised to eradication treatment (lansoprazole, clarithromycin, metronidazole) or placebo, with drug sent by post. Events are tracked by upload of accumulating information in the GP database, patient contact, review of National Hospital Episode Statistics and Office of National Statistics data.ResultsHEAT is the largest Clinical Research Network-supported drug trial, with 115,660 invitation letters sent from 850 practices, 22,922 volunteers, and 3038 H. pylori positive patients randomised to active or placebo treatment after 2.5years of recruitment. 178 practices have performed their first follow-up data search to identify 21 potential endpoints to date.DiscussionHEAT is important medically, because aspirin is so widely used, and methodologically, as a successful trial would show that large-scale studies of important clinical outcomes can be conducted at a fraction of the cost of those conducted by industry, which in turn will help to ensure that trials of primarily medical rather than commercial interest can be conducted successfully in the UK
Drosophila myc Regulates Cellular Growth during Development

AbstractTranscription factors of the Myc proto-oncogene family promote cell division, but how they do this is poorly understood. Here we address the functions of Drosophila Myc (dMyc) during development. Using mosaic analysis in the fly wing, we show that loss of dMyc retards cellular growth (accumulation of cell mass) and reduces cell size, whereas dMyc overproduction increases growth rates and cell size. dMyc-induced growth promotes G1/S progression but fails to accelerate cell division because G2/M progression is independently controlled by Cdc25/String. We also show that the secreted signal Wingless patterns growth in the wing primordium by modulating dMyc expression. Our results indicate that dMyc links patterning signals to cell division by regulating primary targets involved in cellular growth and metabolism
More on the universality of the Volkov–Akulov action under N=1 nonlinear supersymmetry

AbstractWe discuss further the universality of the Volkov–Akulov (VA) action of a Nambu–Goldstone (NG) fermion for the spontaneous breaking of supersymmetry (SUSY). We show general relations between the standard VA action and nonlinear (NL) SUSY actions including apparently (pathological) higher derivatives of the NG fermion. Composite fields of the NG fermions are found, which transform homogeneously under NL SUSY transformations of VA. Consequently, we obtain NL SUSY invariant constraints which connect our NL SUSY actions with the VA action. The constraints are explicitly solved and we show examples of the NL SUSY actions which are equivalent to the VA action
Full one-loop electroweak radiative corrections to single Higgs production in e+e−

AbstractWe present the full O(α) electroweak radiative corrections to single Higgs production in e+e−. This takes into account the full one-loop corrections as well as the effects of hard photon radiation. We include both the fusion and Higgsstrahlung processes. The computation is performed with the help of GRACE-loop where we have implemented a generalised non-linear gauge fixing condition. The latter includes 5 gauge parameters that can be used for checks on our results. Besides the UV, IR finiteness and gauge parameter independence checks prove also powerful to test our implementation of the 5-point function. We find that for a 500 GeV machine and a light Higgs of mass 150 GeV, the total O(α) correction is small when the results are expressed in terms of αQED. The total correction decreases slightly for higher energies. For moderate centre of mass energies the total O(α) decreases as the Higgs mass increases, reaching −10% for MH=350 GeV and s=500 GeV. In order to quantify the genuine weak corrections we have subtracted the universal virtual and bremsstrahlung correction from the full O(α). We find, for MH=150 GeV, a weak correction slowly decreasing from −2% to −4% as the energy increases from s=300 GeV to s=1 TeV after expressing the tree-level results in terms of Gμ
Total knee arthroplasty with computer-assisted navigation: an analysis of 200 cases

AbstractObjectiveto evaluate the results from surgery with computer-assisted navigation in cases of total knee arthroplasty.Methoda total of 196 patients who underwent total knee arthroplasty with computer-assisted navigation were evaluated. The extension and flexion spaces (gaps) were evaluated during the operation and the alignment after the operation was assessed. The Knee Society Score (KSS) questionnaire for assessing patient's function was applied preoperatively and postoperatively after a mean follow-up of 22 months.Resultsin all, 86.7% of the patients presented good alignment of the mechanical axis (less than 3° of varus or valgus in relation to the mechanical axis) and 96.4% of the patients presented balanced flexion and extension gaps. Before the operation, 97% of the patients presented poor or insufficient KSS, but after the operation, 77.6% presented good or excellent KSS.Conclusionthe navigation system made it possible to achieve aligned and balanced implants, with notable functional improvement among the patients. It was found to be useful in assessing, understanding and improving knowledge in relation to performing arthroplasty procedures
Altered GABAA α5 subunit expression in the hypothalamic paraventricular nucleus of hypertensive and pregnant rats

AbstractA characteristic of both hypertension and pregnancy is increased sympathetic nerve activity. The level of sympathetic activation is determined, in part, by a tonic GABAergic inhibition arising from the hypothalamic paraventricular nucleus (PVN). In hypertension, decreases in GABAergic inhibition and increases in glutamatergic excitation within the PVN contribute to this sympatho-excitation. In late-term pregnancy however, the sympatho-excitation appears to be mediated by decreases in GABAergic inhibition only. This study examined whether changes in subunit expression for GABAA receptors in the PVN could provide a molecular basis for the sympatho-excitation characteristic of hypertension and pregnancy. Hypertension and pregnancy were accompanied by significant decrease in the GABAA receptor α5 subunit in the PVN. We suggest that decreases in the α5 subunit of the GABAA receptor may be important in mediating the sympatho-excitation observed in both hypertension and pregnancy
Bose–Einstein condensation in the Rindler space

AbstractBased on the Unruh effect, we calculate the critical acceleration of the Bose–Einstein condensation in a free complex scalar field at finite density in the Rindler space. Our model corresponds to an ideal gas performing constantly accelerating motion in a Minkowski space–time at zero-temperature, where the gas is composed of the complex scalar particles and it can be thought to be in a thermal-bath with the Unruh temperature. In the accelerating frame, the model will be in the Bose–Einstein condensation state at low acceleration; on the other hand, there will be no condensation at high acceleration by the thermal excitation brought into by the Unruh effect. Our critical acceleration is the one at which the Bose–Einstein condensation begins to appear in the accelerating frame when we decrease the acceleration gradually. To carry out the calculation, we assume that the critical acceleration is much larger than the mass of the particle
Characteristics of polyomavirus BK (BKPyV) infection in primary human urothelial cells

AbstractHigh-level polyomavirus BK (BKPyV) replication in urothelial cells is a hallmark of polyomavirus-associated hemorrhagic cystitis (PyVHC), a painful condition affecting bone marrow transplant recipients. In kidney transplant recipients, replication in tubular epithelial cells is associated with overt disease whereas high-level urothelial replication is clinically silent. We characterized BKPyV replication in primary human urothelial cells (HUCs) and compared it to replication in renal tubular epithelial cells (RPTECs). HUCs were easily infected, as shown by expression of T-antigens, VP1-3, and agnoprotein, and intranuclear virion production. Compared to RPTECs, progeny release was delayed by ≥24h and reduced. BKPyV-infected HUCs rounded up like “decoy cells” and detached without necrosis as shown by delayed cytokeratin-18 release, real-time viability monitoring and imaging. The data show that BKV infection of HUCs and RPTECs is significantly different and support the notion that PyVHC pathogenesis is not solely due to BKPyV replication, but likely requires urotoxic and immunological cofactors
He3(α,γ)Be7 and H3(α,γ)Li7 astrophysical S factors from the no-core shell model with continuum

AbstractThe 3He(α,γ)7Be and 3H(α,γ)7Li astrophysical S factors are calculated within the no-core shell model with continuum using a renormalized chiral nucleon–nucleon interaction. The 3He(α,γ)7Be astrophysical S factors agree reasonably well with the experimental data while the 3H(α,γ)7Li ones are overestimated. The seven-nucleon bound and resonance states and the α + 3He/3H elastic scattering are also studied and compared with experiment. The low-lying resonance properties are rather well reproduced by our approach. At low energies, the s-wave phase shift, which is non-resonant, is overestimated