pinecone/core-2020-05-10-deduplication huggingface dataset:
The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions

AbstractThe management of drug–drug interactions (DDIs) is a critical issue resulting from the overwhelming amount of information available on them. Natural Language Processing (NLP) techniques can provide an interesting way to reduce the time spent by healthcare professionals on reviewing biomedical literature. However, NLP techniques rely mostly on the availability of the annotated corpora. While there are several annotated corpora with biological entities and their relationships, there is a lack of corpora annotated with pharmacological substances and DDIs. Moreover, other works in this field have focused in pharmacokinetic (PK) DDIs only, but not in pharmacodynamic (PD) DDIs. To address this problem, we have created a manually annotated corpus consisting of 792 texts selected from the DrugBank database and other 233 Medline abstracts. This fined-grained corpus has been annotated with a total of 18,502 pharmacological substances and 5028 DDIs, including both PK as well as PD interactions. The quality and consistency of the annotation process has been ensured through the creation of annotation guidelines and has been evaluated by the measurement of the inter-annotator agreement between two annotators. The agreement was almost perfect (Kappa up to 0.96 and generally over 0.80), except for the DDIs in the MedLine database (0.55–0.72). The DDI corpus has been used in the SemEval 2013 DDIExtraction challenge as a gold standard for the evaluation of information extraction techniques applied to the recognition of pharmacological substances and the detection of DDIs from biomedical texts. DDIExtraction 2013 has attracted wide attention with a total of 14 teams from 7 different countries. For the task of recognition and classification of pharmacological names, the best system achieved an F1 of 71.5%, while, for the detection and classification of DDIs, the best result was F1 of 65.1%. These results show that the corpus has enough quality to be used for training and testing NLP techniques applied to the field of Pharmacovigilance. The DDI corpus and the annotation guidelines are free for use for academic research and are available at http://labda.inf.uc3m.es/ddicorpus
Tracking millennial-scale Holocene glacial advance and retreat using osmium isotopes: Insights from the Greenland ice sheet

AbstractHigh-resolution Os isotope stratigraphy can aid in reconstructing Pleistocene ice sheet fluctuation and elucidating the role of local and regional weathering fluxes on the marine Os residence time. This paper presents new Os isotope data from ocean cores adjacent to the West Greenland ice sheet that have excellent chronological controls. Cores MSM-520 and DA00-06 represent distal to proximal sites adjacent to two West Greenland ice streams. Core MSM-520 has a steadily decreasing Os signal over the last 10 kyr (187Os/188Os = 1.35–0.81). In contrast, Os isotopes from core DA00-06 (proximal to the calving front of Jakobshavn Isbræ) highlight four stages of ice stream retreat and advance over the past 10 kyr (187Os/188Os = 2.31; 1.68; 2.09; 1.47). Our high-resolution chemostratigraphic records provide vital benchmarks for ice-sheet modelers as we attempt to better constrain the future response of major ice sheets to climate change. Variations in Os isotope composition from sediment and macro-algae (seaweed) sourced from regional and global settings serve to emphasize the overwhelming effect weathering sources have on seawater Os isotope composition. Further, these findings demonstrate that the residence time of Os is shorter than previous estimates of ∼104 yr
Superbubble dynamics in globular cluster infancy. I. How do globular clusters first lose their cold gas?

M. Krause1, C. Charbonnel, T. Decressin, G. Meynet, N. Prantzos, and R. Diehl, 'Superbubble dynamics in globular cluster infancy', Astronomy & Astrophysics, Vol. 546, L5 (2012), the version of record is available online at DOI: 10.1051/0004-6361/201220244. Published by EDP Sciences. ?? ESO 2012.The picture of the early evolution of globular clusters has been significantly revised in recent years. Current scenarios require at least two generations of stars of which the first generation (1G), and therefore also the protocluster cloud, has been much more massive than the currently predominating second generation (2G). Fast gas expulsion is thought to unbind the majority of the 1G stars. Gas expulsion is also mandatory to remove metal-enriched supernova ejecta, which are not found in the 2G stars. It has long been thought that the supernovae themselves are the agent of the gas expulsion, based on crude energetics arguments. Here, we assume that gas expulsion happens via the formation of a superbubble, and describe the kinematics by a thin-shell model. We find that supernova-driven shells are destroyed by the Rayleigh-Taylor instability before they reach escape speed for all but perhaps the least massive and most extended clusters. More power is required to expel the gas, which might plausibly be provided by a coherent onset of accretion onto the stellar remnants. The resulting kpc-sized bubbles might be observable in Faraday rotation maps with the planned Square Kilometre Array radio telescope against polarised background radio lobes if a globular cluster would happen to form in front of such a radio lobe
Search for pair production of vector-like T and B quarks in
  single-lepton final states using boosted jet substructure in proton-proton
  collisions at sqrt(s) = 13 TeV

A search for pair production of massive vector-like T and B quarks in
proton-proton collisions at sqrt(s) = 13 TeV is presented. The data set was
collected in 2015 by the CMS experiment at the LHC and corresponds to an
integrated luminosity of up to 2.6 inverse femtobarns. The T and B quarks are
assumed to decay through three possible channels into a heavy boson (either a
W, Z or Higgs boson) and a third generation quark. This search is performed in
final states with one charged lepton and several jets, exploiting techniques to
identify W or Higgs bosons decaying hadronically with large transverse momenta.
No excess over the predicted standard model background is observed. Upper
limits at 95% confidence level on the T quark pair production cross section are
set that exclude T quark masses below 860 GeV in the singlet, and below 830 GeV
in the doublet branching fraction scenario. For other branching fraction
combinations with B(tH) + B(bW) >= 0.4, lower limits on the T quark range from
790 to 940 GeV. Limits are also set on pair production of singlet vector-like B
quarks, which can be excluded up to a mass of 730 GeV. These limits are among
the most stringent to date for vector-like T quarks. The techniques showcased
here for understanding highly-boosted final states are important as the
sensitivity to new particles is extended to higher masses.Comment: Replaced with thet 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/B2G-16-024
  (CMS Public Pages
The FitTrack Index as fitness indicator : a pilot study

BACKGROUND : The FitTrack Index is a web-based programme developed in South Africa and
widely used by athletes to indicate their fitness. A need exists for a self-managed, noninvasive
tool to evaluate and categorise health-related fitness in different population
groups. The aim of this study was to compare the FitTrack Index with a reliable measure of
cardio-respiratory fitness as indicated by maximal oxygen uptake (direct VO2max).
METHODS AND RESULTS : During a 12-week cross-sectional, descriptive pilot study the direct laboratory
tested VO2max indicated a moderate to strong correlation with the FitTrack
Index (Spearman's rho ¼ 0.439, p ¼ 0.089 at baseline; Spearman's rho ¼ 0.853, p < 0.001 after 12
weeks).
CONCLUSIONS : These results suggest that the web-based FitTrack Index may be considered an
appropriate tool to evaluate exercise capacity and cardiovascular fitness in healthy individuals
following an aerobic training programme.Research was partly funded by Momentum, South Africa
(Reference No.: TP1208066080).am2017Biokinetics, Sport and Leisure SciencesSports MedicineStatistic
Search for TeV-scale gravity signatures in high-mass final states with leptons and jets with the ATLAS detector at √s=13 TeV

Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAMA search for physics beyond the Standard Model, in final states with at least one high transverse momentum charged lepton (electron or muon) and two additional high transverse momentum leptons or jets, is performed using 3.2 fb−1 of proton–proton collision data recorded by the ATLAS detector at the Large Hadron Collider in 2015 at √s=13 TeV. The upper end of the distribution of the scalar sum of the transverse momenta of leptons and jets is sensitive to the production of high-mass objects. No excess of events beyond Standard Model predictions is observed. Exclusion limits are set for models of microscopic black holes with two to six extra dimensionsWe acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWFW and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Re-public; DNRF and DNSRC, Denmark; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, HGF, and MPG, Germany; GSRT, Greece; RGC, Hong Kong SAR, China; ISF, ICORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; RCN, Norway; MNiSW and NCN, Poland; FCT, Portugal; MNE/IFA, Romania; MES of Russia and NRC KI, Russian Federation; JINR; MESTD, Serbia; MSSR, Slovakia; ARRS and MIZŠ, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Knut and Alice Wallenberg Foundation, Sweden; SERI, SNSF and Cantons of Bern and Geneva, Switzerland; MOST, Tai-wan; TAEK, Turkey; STFC, United Kingdom; DOE and NSF, United States of America. In addition, individual groups and members have received support from BCKDF, the Canada Council, Canarie, CRC, Compute Canada, FQRNT, and the Ontario Innovation Trust, Canada; EPLANET, ERC, FP7, Horizon 2020 and Marie Skłodowska-Curie Actions, European Union; Investissements d’Avenir Labex and Idex, ANR, Région Auvergne and Fondation Partager le Savoir, France; DFG and AvH Foundation, Germany; Herakleitos, Thales and Aristeia programmes co-financed by EU-ESF and the Greek NSRF; BSF, GIF and Minerva, Israel; BRF, Norway; Generalitat de Catalunya, Generalitat Valenciana, Spain; the Royal Society and Leverhulme Trust, United Kingdom. The crucial computing support from all WLCG partners is acknowledged gratefully, in particular from CERN and the ATLAS Tier-1facilities at TRIUMF (Canada), NDGF (Denmark, Norway, Sweden), CC-IN2P3 (France), KIT/GridKA (Germany), INFN-CNAF (Italy), NL-T1 (Netherlands), PIC (Spain), ASGC (Taiwan), RAL (UK) and BNL (USA) and in the Tier-2 facilities worldwid
Literacy models across nations : literacy and critical literacy in teacher training programs in India

The thrust towards constructivist learning and critical thinking in the National Curricular Framework (2005) of India implies shifts in pedagogical practices. In this context, drawing on grounded theory, focus group interviews were conducted with 40 preservice teachers to ascertain the contextual situation and the likely outcomes of applying critical literacy across the curriculum. Central themes that emerged in the discussion were: being teacher centred/ learner centred, and conformity/autonomy in teaching and learning. The paper argues that within the present Indian context, while there is scope for changes to pedagogy and learning styles, yet these must be adequately contextualised
Organic pollution selective degradation by adsorption on high silica zeolites and regeneration by ozone

This study concerns the treatment of industrial airstreams polluted with volatile organic compounds (VOCs), and focuses on highlighting the experimental feasibility of a new hybrid process combining VOC adsorption on hydrophobic zeolites and regeneration by an ozonated airstream in a single reactor.\ud
A preliminary study of high-silica zeolites has shown the different kinds of interactions between gaseous ozone and two mineral zeolitic adsorbents, a faujasite Y (FauY) and a ZSM-5 type silicalite (SilZ), and the conservation of the solids adsorption properties (capacities and selectivity) after their contact with ozone.\ud
Here, results concerning the contact of gaseous ozone and zeolites saturated with adsorbed VOC are presented. Using temperature measurements inside the fixed bed, oxidation of two models VOC, methyl ethyl ketone (MEK) and toluene (TOL), was observed on both zeolites. Adsorbents were fully regenerated, and the adsorption capacities of the zeolites after their contact with ozone were not affected when used in a discontinuous adsorption / oxidation mode.\ud
In addition, the adsorbed VOC were totally mineralized. Detection and identification of oxidation sub-products traces using mass spectrometer - gas chromatography (formic, oxalic, acetic acids, and acetaldehyde for TOL and 2,3-butanedione and acetic acid for MEK) makes possible the indentification of oxidative species. Moreover, a mass balance on oxygen showed that all the produced ozone was used for organic compounds oxidation. There was no or very little ozone lost via side-effect decomposition/deactivation mechanisms.\ud
At last, using the zeolites selectivity determined in a previous study toward a binary MEK-TOL mixture, the adsorption / ozonation cyclic process enables the recovery of the minor compound and the selective oxidation of the other component.\ud
The great interest of this new process is clearly highlighted, and the technology transfer to industrial operating plants is now studied
Measurements of tt¯ cross sections in association with b jets and inclusive jets and their ratio using dilepton final states in pp collisions at s=13TeV

The cross sections for the production of tt¯bb¯ and tt¯jj events and their ratio σ tt¯bb¯ /σ tt¯jj are measured using data corresponding to an integrated luminosity of 2.3 fb −1 collected in pp collisions at s=13 TeV with the CMS detector at the LHC. Events with two leptons (e or μ) and at least four reconstructed jets, including at least two identified as b quark jets, in the final state are selected. In the full phase space, the measured ratio is 0.022±0.003(stat)±0.006(syst), the cross section σ tt¯bb¯ is 4.0±0.6(stat)±1.3(syst) pb and σ tt¯jj is 184±6(stat)±33(syst) pb. The measurements are compared with the standard model expectations obtained from a POWHEG simulation at next-to-leading-order interfaced with PYTHIA
Search for anomalous couplings in boosted WW/WZ to l nu q q-bar production in proton-proton collisions at sqrt(s) = 8 TeV

This Letter presents a search for new physics manifested as anomalous triple gauge boson couplings in WW and WZ diboson production in proton-proton collisions. The search is performed using events containing a W boson that decays leptonically and a W or Z boson whose decay products are merged into a single reconstructed jet. The data, collected at sqrt(s) = 8 TeV with the CMS detector at the LHC, correspond to an integrated luminosity of 19 inverse femtobarns. No evidence for anomalous triple gauge couplings is found and the following 95% confidence level limits are set on their values: lambda ([-0.011, 0.011]), Delta kappa[gamma] ([-0.044, 0.063]), and Delta g[1, Z] ([-0.0087, 0.024]). These limits are also translated into their effective field theory equivalents: c[WWW] / Lambda^2 ([-2.7, 2.7] TeV^{; ; -2}; ; ), c[B] / Lambda^2 ([-14, 17] TeV^{; ; -2}; ; ), and c[W] / Lambda^2 ([-2.0, 5.7] TeV^{; ; -2}; ; )
RuxNb1-xO2 catalyst for the oxygen evolution reaction in proton exchange membrane water electrolysers

Bimetallic catalyst system of ruthenium oxide (RuO2) and niobium oxide (Nb2O5) was prepared using the Adams method and the hydrolysis method. Physical and electrochemical characterizations of the catalysts were studied using X-ray diffraction (XRD), Scanning electron microscopy (SEM), cyclic voltammogram (CV) and polarization measurements. Nb2O5 addition to RuO2 was found to increase the stability of RuO2. In Adams method the sodium nitrate was found to be forming complex with Nb2O5 at high temperature reaction. This makes Adams method unsuitable for the synthesis of RuO2eNb2O5 bimetallic system. Hydrolysis method on other hand does not have this problem. But a proper mixture of two oxides was not obtained in hydrolysis method. A lower crystallite size for bimetallic system was obtained with Adams method compared to hydrolysis method. RuO2 prepared by Adams method had higher activity compared to the hydrolysis counterpart in electrolyzer operation with nafion membrane. A cell voltage of 1.62 V was obtained with RuO2 (A) at 1 A/cm2. A higher stability for Ru0.8Nb0.2O2(A) compared to RuO2Web of Scienc
Charge-stripe order and superconductivity in Ir1−xPtxTe2

A combined resistivity and hard x-ray diffraction study of superconductivity and charge ordering in Ir Ir1-xPtxTe2, as a function of Pt substitution and externally applied hydrostatic pressure, is presented. Experiments are focused on samples near the critical composition x c  ~ 0.045 where competition and switching between charge order and superconductivity is established. We show that charge order as a function of pressure in Ir0.95Pt0.05Te2 is preempted - and hence triggered - by a structural transition. Charge ordering appears uniaxially along the short crystallographic (1, 0, 1) domain axis with a (1/5, 0, 1/5) modulation. Based on these results we draw a charge-order phase diagram and discuss the relation between stripe ordering and superconductivity
Hybrid approaches for multiple-species stochastic reaction–diffusion models

Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model
Stochastic R matrix for Uq(An(¹))

We show that the quantum R matrix for symmetric tensor representations of Uq(An(¹)) satisfies the sum rule required for its stochastic interpretation under a suitable gauge. Its matrix elements at a special point of the spectral parameter are found to factorize into the form that naturally extends Povolotsky's local transition rate in the q -Hahn process for n=1 . Based on these results we formulate new discrete and continuous time integrable Markov processes on a one-dimensional chain in terms of n species of particles obeying asymmetric stochastic dynamics. Bethe ansatz eigenvalues of the Markov matrices are also given
Simultaneous multiple change-point and factor analysis for\ud
high-dimensional time series

We propose the first comprehensive treatment of high-dimensional time series factor models with multiple change-points in their second-order structure. We operate under the most flexible definition of piecewise stationarity, and estimate the number and locations of change-points consistently as well as identifying whether they originate in the common or idiosyncratic components. Through the use of wavelets, we transform the problem of change-point detection in the second-order structure of a high-dimensional time series, into the (relatively easier) problem of change-point detection in the means of high-dimensional panel data. Also, our methodology circumvents the difficult issue of the accurate estimation of the true number of factors in the presence of multiple change-points by adopting a screening procedure. We further show that consistent factor analysis is achieved over each segment defined by the change-points estimated by the proposed methodology. In extensive simulation studies, we observe that factor analysis prior to change-point detection improves the detectability of change-points, and identify and describe an interesting ‘spillover’ effect in which substantial breaks in the idiosyncratic components get, naturally enough, identified as change-points in the common components, which prompts us to regard the corresponding change-points as also acting as a form of ‘factors’. Our methodology is implemented in the R package factorcpt, available from CRAN
Preaxial polydactyly of the foot Clinical and genetic implications for the orthopedic practice based on a literature review and 76 patients

Contains fulltext :
                  191468.pdf (publisher's version ) (Open Access)Background and purpose - Preaxial polydactyly of the foot is a rare malformation and clinicians are often unfamiliar with the associated malformations and syndromes. In order to give guidelines for diagnostics and referral to a clinical geneticist, we provide an overview of the presentation using a literature review and our own patient population. Patients and methods - The literature review was based on the Human Phenotype Ontology (HPO) project. From the HPO dataset, all phenotypes describing preaxial polydactyly were obtained and related diseases were identified and selected. An overview was generated in a heatmap, in which the phenotypic contribution of 12 anatomical groups to each disease is displayed. Clinical cases were obtained from our hospital database and were reviewed in terms of phenotype, genotype, heredity, and diagnosed syndromes. Results - From the HPO dataset, 21 diseases were related to preaxial polydactyly of the foot. The anatomical groups with the highest phenotypic contribution were lower limb, upper limb, and craniofacial. From our clinical database, we included 76 patients with 9 different diseases, of which 27 had a GLI3 mutation. Lower limb malformations (n = 55), upper limb malformations (n = 59), and craniofacial malformations (n = 32) were most frequently observed. Malformations in other anatomical groups were observed in 27 patients. Interpretation - Preaxial polydactyly of the foot often presents with other upper and lower limb malformations. In patients with isolated preaxial polydactyly of the foot, referral to a clinical geneticist is not mandatory. In patients with additional malformations, consultation with a clinical geneticist is recommended. When additional limb malformations are present, analysis of GLI3 is most feasible