pinecone/core-2020-05-10-deduplication huggingface dataset:
Towards the introduction of the 'Immunoscore' in the classification of malignant tumours

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                  137112.pdf (publisher's version ) (Open Access)The American Joint Committee on Cancer/Union Internationale Contre le Cancer (AJCC/UICC) TNM staging system provides the most reliable guidelines for the routine prognostication and treatment of colorectal carcinoma. This traditional tumour staging summarizes data on tumour burden (T), the presence of cancer cells in draining and regional lymph nodes (N) and evidence for distant metastases (M). However, it is now recognized that the clinical outcome can vary significantly among patients within the same stage. The current classification provides limited prognostic information and does not predict response to therapy. Multiple ways to classify cancer and to distinguish different subtypes of colorectal cancer have been proposed, including morphology, cell origin, molecular pathways, mutation status and gene expression-based stratification. These parameters rely on tumour-cell characteristics. Extensive literature has investigated the host immune response against cancer and demonstrated the prognostic impact of the in situ immune cell infiltrate in tumours. A methodology named 'Immunoscore' has been defined to quantify the in situ immune infiltrate. In colorectal cancer, the Immunoscore may add to the significance of the current AJCC/UICC TNM classification, since it has been demonstrated to be a prognostic factor superior to the AJCC/UICC TNM classification. An international consortium has been initiated to validate and promote the Immunoscore in routine clinical settings. The results of this international consortium may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM-I (TNM-Immune)
Lung Cancer Screening CT-Based Prediction of Cardiovascular Events

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                  140532.pdf (publisher's version ) (Open Access)OBJECTIVES: The aim of this study was to derivate and validate a prediction model for cardiovascular events based on quantification of coronary and aortic calcium volume in lung cancer screening chest computed tomography (CT). BACKGROUND: CT-based lung cancer screening in heavy smokers is a very timely topic. Given that the heavily smoking screening population is also at risk for cardiovascular disease, CT-based screening may provide the opportunity to additionally identify participants at high cardiovascular risk. METHODS: Inspiratory screening CT of the chest was obtained in 3,648 screening participants. Next, smoking characteristics, patient demographics, and physician-diagnosed cardiovascular events were collected from 10 years before the screening CT (i.e., cardiovascular history) until 3 years after the screening CT (i.e., follow-up time). Cox proportional hazards analysis was used to derivate and validate a prediction model for cardiovascular risk. Age, smoking status, smoking history, and cardiovascular history, together with automatically quantified coronary and aortic calcium volume from the screening CT, were included as independent predictors. The primary outcome measure was the discriminatory value of the model. RESULTS: Incident cardiovascular events occurred in 145 of 1,834 males (derivation cohort) and 118 of 1,725 males and 2 of 89 females (validation cohort). The model showed good discrimination in the validation cohort with a C-statistic of 0.71 (95\% confidence interval: 0.67 to 0.76). When high risk was defined as a 3-year risk of 6\% and higher, 589 of 1,725 males were regarded as high risk and 72 of 118 of all events were correctly predicted by the model. CONCLUSIONS: Quantification of coronary and aortic calcium volumes in lung cancer screening CT images-information that is readily available-can be used to predict cardiovascular risk. Such an approach might prove useful in the reduction of cardiovascular morbidity and mortality and may enhance the cost-effectiveness of CT-based screening in heavy smokers
A case study investigating the impact of the London 2012 Olympic and Paralympic Games on participation in two non-traditional English sports, Judo and Fencing.

The hosting of the London 2012 Olympic and Paralympic Games (LOPG)\ud
brought with it detailed legacy plans aiming to ‘Inspire a Generation’. The idea\ud
that hosting a sports mega-event will encourage the host population to engage in\ud
more physical activity is commonly used by governments to justify the large\ud
investments they make. The aim of this research paper was to investigate the\ud
impact that hosting the 2012 Games had on grass-root sports participation within\ud
the host nation. This paper focuses on two non-traditional English sports, Fencing\ud
and Judo and investigated the changes in mass sports participation. The\ud
membership rate analysis of our sample highlighted an overall increase in participation\ud
between 2007 and 2013, in both Judo and Fencing. The data gathered\ud
from the interviews with the head office staff at the National Governing Bodies\ud
(NGBs) and local club coaches suggested that the grass-root participation programmes\ud
were the most effective way of increasing participation, rather than the\ud
reliance, solely on the inspiration effect from hosting the LOPG itself. The study\ud
highlighted the importance of strengthening communication between local voluntary\ud
clubs and the NGB, to ensure sports could promote themselves and capitalise\ud
on this global sporting phenomenon, which provided unprecedented media\ud
coverage and opportunities for these non-traditional sports. This case study provides\ud
initial results relating to the effect that a major international multi-sport\ud
event can have in the development of non-traditional sports in the host population,\ud
in terms of membership variations, participation programmes and organisational\ud
dynamics
Search for scalar top quark pair production in natural gauge mediated supersymmetry models with the ATLAS detector in pp collisions at root s=7 TeV

The results of a search for pair production of the lighter scalar partners of top quarks ((t) over bar (1)) in 2.05 fb(-1) of pp collisions at root s = 7 TeV using the ATLAS experiment at the LHC are reported. Scalar top quarks are searched for in events with two same flavour opposite-sign leptons (e, mu) with invariant mass consistent with the Z boson mass, large missing transverse momentum and jets in the final state. At least one of the jets is identified as originating from a b-quark. No excess over Standard Model expectations is found. The results are interpreted in the framework of R-parity conserving, gauge mediated Supersymmetry breaking 'natural' scenarios, where the neutralino ((chi) over bar (0)(1)) is the next-to-lightest supersymmetric particle. Scalar top quark masses up to 310 GeV are excluded for 115 GeV m(<(chi) over bar1)(0) 230 GeV at 95% confidence level, reaching an exclusion of m(<(t) over bar1) 330 GeV for m(<(chi) over bar1)(0) = 190 GeV. Scalar top quark masses below 240 GeV are excluded for all values of m((chi) over bar1)(0) > m(z)
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 root 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 similar 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
Search for squarks and gluinos using final states with jets and missing transverse momentum with the ATLAS detector in root s=7 TeV proton-proton collisions

A search for squarks and gluinos in final states containing jets, missing transverse momentum and no electrons or muons is presented. The data were recorded by the ATLAS experiment in root s = 7 TeV proton-proton collisions at the Large Hadron Collider. No excess above the Standard Model background expectation was observed in 35 pb(-1) of analysed data. Gluino masses below 500 GeV are excluded at the 95% confidence level in simplified models containing only squarks of the first two generations, a gluino octet and a massless neutralino. The exclusion increases to 870 GeV for equal mass squarks and gluinos. In MSUGRA/CMSSM models with tan beta = 3, A(0) = 0 and mu > 0, squarks and gluinos of equal mass are excluded below 775 GeV. These are the most stringent limits to date
A new twist to coiled coil.

International audienceSpectrin repeats have been largely considered as passive linkers or spacers with little functional role other than to convey flexibility to a protein. Whilst this is undoubtedly part of their function, it is by no means all. Whilst the overt structure of all spectrin repeats is a simple triple-helical coiled coil, the linkages between repeats and the surface properties of repeats vary widely. Spectrin repeats in different proteins can act as dimerisation interfaces, platforms for the recruitment of signalling molecules, and as a site for the interaction with cytoskeletal elements and even direct association with membrane lipids. In the case of dystrophin several of these functions overlap in the space of a few repeats
The Good, the Bad, and the Ugly: Statistical quality assessment of SZ detections

International audienceWe examine three approaches to the problem of source classification in catalogues. Our goal is to determine the confidence withwhich the elements in these catalogues can be distinguished in populations on the basis of their spectral energy distribution (SED).Our analysis is based on the projection of the measurements onto a comprehensive SED model of the main signals in the consideredrange of frequencies. We first consider likelihood analysis, which is halfway between supervised and unsupervised methods. Next, weinvestigate an unsupervised clustering technique. Finally, we consider a supervised classifier based on artificial neural networks. Weillustrate the approach and results using catalogues from various surveys, such as X-rays (MCXC), optical (SDSS), and millimetric(Planck Sunyaev-Zeldovich (SZ)). We show that the results from the statistical classifications of the three methods are in very goodagreement with each other, although the supervised neural network-based classification shows better performance allowing the bestseparation into populations of reliable and unreliable sources in catalogues. The latest method was applied to the SZ sources detectedby the Planck satellite. It led to a classification assessing and thereby agreeing with the reliability assessment published in the PlanckSZ catalogue. Our method could easily be applied to catalogues from future large surveys such as SRG/eROSITA and Euclid
Bronsted and Lewis acidity of modified montmorillonite clay catalysts determined by FT-IR spectroscopy

The surface acidity of different modified montmorillonite clay catalysts, Al(3+)-exchanged montmorillonite (Al(3+)-Mont) and aluminium pillared montmorillonite (AI-PILC) was determined by DRIFTS (diffuse reflectance Fourier transform infrared spectra) using pyridine as probe molecule. The method involved treating the clay sample directly with pyridine, drying the sample at 120 degrees C and recording FT-IR spectra in the region 1650 and 1350 cm(-1). The spectra obtained showed well resolved absorption bands for Lewis and Bronsted acid sites in the clay catalysts. In order to understand the role of acid sites present on clay catalysts, esterification of propionic acid with p-cresol has been studied. The Bronsted acidity data obtained by FT-IR study for modified montmorillonite clay catalysts correlated well with the catalytic activity in the esterification reaction. Among the modified clay catalysts, Al(3+)-Mont and H(+)-Mont clay catalysts showed good activity and AI-PILC showed negligible activity in esterification. The inactivity of AI-PILC catalysts is attributed to the absence of Bronsted acidity. (c) 2008 Elsevier B.V. All rights reserved
$A_4$ and CP symmetry and a model with maximal CP violation

We study a second CP symmetry compatible with the $A_4$ flavor group, which
interchanges the representations $\mathbf{1}'$ and $\mathbf{1}"$. We analyze
the lepton mixing patterns arising from the $A_4$ and CP symmetry broken to
residual subgroups $Z_3$ and $Z_2\times CP$ in the charged lepton and neutrino
sectors respectively. One phenomenologically viable mixing pattern is found,
and it predicts maximal atmospheric mixing angle as well as maximal Dirac CP
phase, trivial Majorana phase and the correlation
$\sin^2\theta_{12}\cos^2\theta_{13}=1/3$. We construct a concrete model based
on the $A_4$ and CP symmetry, the above interesting mixing pattern is achieved,
the observed charged lepton mass hierarchy is reproduced, and the reactor
mixing angle $\theta_{13}$ is of the correct order.Comment: 22 pages, 1 figur
Search for top quark decays via Higgs-boson-mediated flavor-changing
  neutral currents in pp collisions at sqrt(s) = 8 TeV

A search is performed for Higgs-boson-mediated flavor-changing neutral
currents in the decays of top quarks. The search is based on proton-proton
collision data corresponding to an integrated luminosity of 19.7 inverse
femtobarns at a center-of-mass energy of 8 TeV collected with the CMS detector
at the LHC. Events in which a top quark pair is produced with one top quark
decaying into a charm or up quark and a Higgs boson (H), and the other top
quark decaying into a bottom quark and a W boson are selected. The Higgs boson
in these events is assumed to subsequently decay into either dibosons or
difermions. No significant excess is observed above the expected standard model
background, and an upper limit at the 95% confidence level is set on the
branching fraction B(t to Hc) of 0.40% and B(t to Hu) of 0.55%, where the
expected upper limits are 0.43% and 0.40%, respectively. These results
correspond to upper limits on the square of the flavor-changing Higgs boson
Yukawa couplings |lambda[tc]^H|^2 < 6.9E-3 and |lambda[tu]^H|^2 < 9.8E-3.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/TOP-13-017/index.htm
Carry a big stick, or no stick at all: Punishment and endowment heterogeneity in the trust game

We investigate the effect of costly punishment in a trust game with endowment heterogeneity. Our findings indicate that the difference between the investor and the allocator’s initial endowments determines the effect of punishment on trust and trustworthiness. Punishment fosters trust only when the investor is wealthier than the allocator. Otherwise, punishment fails to promote trusting behavior. As for trustworthiness, the effect is just the opposite. The higher the difference between the investor and the allocator’s initial endowments, the less willing allocators are to pay back. We discuss the consistency of our findings with social preference models (like inequality aversion, reciprocity), the capacity of punishment (i.e., the deterrence hypothesis) and hidden costs of punishment (i.e., models of intrinsic and extrinsic motivation). Our results are hardly coherent with the first two (inequality aversion and deterrence), but roughly consistent with the latter
Study of exclusive two-photon production of W(+)W(-) in pp collisions at sqrt(s) = 7 TeV and constraints on anomalous quartic gauge couplings

A search for exclusive or quasi-exclusive W(+)W(-) production by photon-photon interactions, pp to p(*)W(+)W(-)p(*), at sqrt(s) = 7 TeV is reported using data collected by the CMS detector with an integrated luminosity of 5.05 inverse femtobarns. Events are selected by requiring a mu(+/-)e(-/+) vertex with no additional associated charged tracks and dilepton transverse momentum pt(mu(+/-)e(-/+)) &gt; 30 GeV. Two events passing all selection requirements are observed in the data, compared to a standard model expectation of 2.2 +/- 0.4 signal events with 0.84 +/- 0.15 background. The tail of the dilepton pt distribution is studied for deviations from the standard model. No events are observed with pt &gt; 100 GeV. Model-independent upper limits are computed and compared to predictions involving anomalous quartic gauge couplings. The limits on the parameters a[W, (0, C)]/Lambda^2 with a dipole form factor and an energy cutoff Lambda(cutoff) = 500 GeV are of the order of 10E-4
Automorphisms fixing a variable of K〈x,y,z〉

AbstractWe study automorphisms φ of the free associative algebra K〈x,y,z〉 over a field K such that φ(x),φ(y) are linear with respect to x,y and φ(z)=z. We establish a sufficient and necessary condition for the tameness of these automorphisms in the class of all automorphisms fixing z, which gives an algorithm to recognize the wild ones. In particular, we prove that the well-known Anick automorphism is wild in this sense. This class of automorphisms induces tame automorphisms of the polynomial algebra K[x,y,z]. For n>2 the automorphisms of K〈x1,…,xn,z〉 which fix z and are linear in the xis are tame
High-density lipoprotein cholesterol levels and cardiovascular outcomes in Japanese patients after percutaneous coronary intervention: A report from the CREDO-Kyoto registry cohort-2

AbstractObjectiveTo determine whether low HDL-C is a risk factor for adverse cardiovascular events in patients with known CAD.MethodsWe evaluated 10,391 patients who underwent PCI from January 2005 to December 2007. In total, 3838 (36.9%) patients had low HDL-C (HDL-C <40 mg/dL in males and <50 mg/dL in females) and 6553 (63.1%) patients had normal HDL-C based on measurements on admission.ResultsThe unadjusted 5-year incidence of major adverse cardiac events (MACE: composite of cardiovascular death, myocardial infarction or stroke) was significantly higher in the low HDL-C group than in the normal HDL-C group (17.6% vs. 14.0%, P < 0.0001). However, after adjusting for confounders, low HDL-C was not associated with a higher risk of MACE (adjusted hazard ratio [HR] 1.07, 95% confidence interval (CI) 0.97–1.19; P = 0.19). There was no significant interaction between the effect of low HDL-C on MACE and several subgroup factors including age, sex, clinical presentation of CAD, statins use, serum low-density lipoprotein cholesterol level, and serum triglycerides level.ConclusionLow HDL-C, as compared with normal HDL-C, was not associated with higher 5-year risk of MACE in patients who underwent PCI
Reconnection at three dimensional magnetic null points: Effect of current sheet asymmetry.

Asymmetric current sheets are likely to be prevalent in both astrophysical and laboratory plasmas with complex three dimensional (3D) magnetic topologies. This work presents kinematic analytical models for spine and fan reconnection at a radially symmetric 3D null (i.e., a null where the eigenvalues associated with the fan plane are equal) with asymmetric current sheets. Asymmetric fan reconnection is characterized by an asymmetric reconnection of flux past each spine line and a bulk flow of plasma across the null point. In contrast, asymmetric spine reconnection is characterized by the reconnection of an equal quantity of flux across the fan plane in both directions. The higher modes of spine reconnection also include localized wedges of vortical flux transport in each half of the fan. In this situation, two definitions for reconnection rate become appropriate: a local reconnection rate quantifying how much flux is genuinely reconnected across the fan plane and a global rate associated with the net flux driven across each semi-plane. Through a scaling analysis, it is shown that when the ohmic dissipation in the layer is assumed to be constant, the increase in the local rate bleeds from the global rate as the sheet deformation is increased. Both models suggest that asymmetry in the current sheet dimensions will have a profound effect on the reconnection rate and manner of flux transport in reconnection involving 3D nulls
A brain imaging repository of normal structural MRI across the life course: Brain Images of Normal Subjects (BRAINS)

AbstractThe Brain Images of Normal Subjects (BRAINS) Imagebank (http://www.brainsimagebank.ac.uk) is an integrated repository project hosted by the University of Edinburgh and sponsored by the Scottish Imaging Network: A Platform for Scientific Excellence (SINAPSE) collaborators. BRAINS provide sharing and archiving of detailed normal human brain imaging and relevant phenotypic data already collected in studies of healthy volunteers across the life-course. It particularly focusses on the extremes of age (currently older age, and in future perinatal) where variability is largest, and which are under-represented in existing databanks.BRAINS is a living imagebank where new data will be added when available. Currently BRAINS contains data from 808 healthy volunteers, from 15 to 81years of age, from 7 projects in 3 centres. Additional completed and ongoing studies of normal individuals from 1st to 10th decades are in preparation and will be included as they become available.BRAINS holds several MRI structural sequences, including T1, T2, T2* and fluid attenuated inversion recovery (FLAIR), available in DICOM (http://dicom.nema.org/); in future Diffusion Tensor Imaging (DTI) will be added where available. Images are linked to a wide range of ‘textual data’, such as age, medical history, physiological measures (e.g. blood pressure), medication use, cognitive ability, and perinatal information for pre/post-natal subjects. The imagebank can be searched to include or exclude ranges of these variables to create better estimates of ‘what is normal’ at different ages
Factorization and regularization by dimensional reduction

AbstractSince an old observation by Beenakker et al., the evaluation of QCD processes in dimensional reduction has repeatedly led to terms that seem to violate the QCD factorization theorem. We reconsider the example of the process gg→tt¯ and show that the factorization problem can be completely resolved. A natural interpretation of the seemingly non-factorizing terms is found, and they are rewritten in a systematic and factorized form. The key to the solution is that the D- and (4−D)-dimensional parts of the 4-dimensional gluon have to be regarded as independent partons
CD24+ Liver Tumor-Initiating Cells Drive Self-Renewal and Tumor Initiation through STAT3-Mediated NANOG Regulation

SummaryTumor-initiating cells (T-ICs) are a subpopulation of chemoresistant tumor cells that have been shown to cause tumor recurrence upon chemotherapy. Identification of T-ICs and their related pathways are therefore priorities for the development of new therapeutic paradigms. We established chemoresistant hepatocellular carcinoma (HCC) xenograft tumors in immunocompromised mice in which an enriched T-IC population was capable of tumor initiation and self-renewal. With this model, we found CD24 to be upregulated in residual chemoresistant tumors when compared with bulk tumor upon cisplatin treatment. CD24+ HCC cells were found to be critical for the maintenance, self-renewal, differentiation, and metastasis of tumors and to significantly impact patients' clinical outcome. With a lentiviral-based knockdown approach, CD24 was found to be a functional liver T-IC marker that drives T-IC genesis through STAT3-mediated NANOG regulation. Our findings point to a CD24 cascade in liver T-ICs that may provide an attractive therapeutic target for HCC patients