dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods Patient population and data collection. Clinical trials. Data were prospectively collected in ST-segment elevation myocardial infarction (STEMI) patients involved in four clinical trials for which local ethics committees had approved the protocols (ethic committee of the Hospices Civils de Lyon for PC, PC-CsA and PCNR and ethic committee of Angers University Hospital for RIPOST-MI) in which all patients had given written informed consent. All studies were performed in accordance with the Declaration of Helsinki (revised version, 1996), the European Guidelines for Good Clinical Practice (version 11, July 1990), and French laws. PC (ischemic postconditioning) studies  33, 34. The first study was a prospective, randomized, multicenter, open-label, controlled study. It was a proof-of-concept clinical trial aiming at demonstrating the safety and efficacy of ischemic postconditioning at the time of reperfusion by primary percutaneous coronary intervention (PCI) in STEMI patients presenting within 6 hours a STEMI symptoms onset and with an occluded (TIMI 0 flow grade) left anterior descending (LAD) coronary artery or right coronary artery without evidence of coronary collaterals.
38 patients were included, 21 were assigned to the control group and 17 to the ischemic postconditioning group. PC-CsA study  39. This clinical trial from the Ovize group was a prospective, multicenter, randomized, single-blinded, controlled study aiming at determining the effect of the mitochondrial permeability transition pore inhibitor Cyclosporine A (CsA) on infarct size in a population of STEMI patients similar to that of the above-described PC studies. The primary endpoint was infarct size measured by AUC of CK and cTnI, the secondary endpoint was infarct size assessed by CMR imaging performed at day 5 following acute myocardial infarction. Data were reported for 58 patients, 30 randomized in the control group and 28 in the CsA group. PCNR study  22, 40. This prospective, multicenter, randomized open-label, controlled study aimed at evaluating the effect of ischemic postconditioning on no-reflow, myocardial oedema and infarct size in a population of STEMI patients, similar to the patients included in the above-reported PC studies.
In all studies, blood samples were collected prior to PCI, every 4 h in the first 24 h following PCI, and every 6 h over the following 48 h. CK and cTnI data were obtained from PC, PC-CsA and PCNR trials and were pooled for the kinetic modelling. CK-MB levels were obtained from the RIPOST-MI study only. Data splitting. Data from "RIPOST-MI" trial studies, which were made of CK-MB measurements, were assessed separately. Three full data sets, i. e. with CK, cTnI and CK-MB variables, were built. With the aim of evaluating the predictive performances of kinetic models, data sets were randomly assigned into learning (2/3 patients) and validation (1/3 patients) subsets. Learning and validation subsets were used for internal and external validation kinetic models, respectively. Biomarker kinetic analysis.
Research Design and Methodology The data analyzed in this article come from three recent research conducted recently in the Province of Québec, Canada. A qualitative research approach was chosen so as to access interviewees' perceptions  [27, 28]. The data collected through semi-structured interviews were aimed among others at identifying the factors that were facilitating or harming the mandate received by principals and their assistants to implement a new results-based and accountable management system. In doing so, this research also aimed to identify the skills and competencies required by school principals to accomplish their mandate. Specifically, these data were collected from key informants coming from nineteen school boards. Interviews were conducted with superintendent teams from five school boards; individual superintendents and assistant superintendents from twelve other school boards; twelve school board educational directors; seventeen human resources directors; thirty-three coaches of new school principals and assistant school principals; twenty-seven experienced school principals; and thirty-six new school principals and assistant school principals.
Patients and data collection Medical records were retrospectively screened to identify all patients hospitalized with confirmed NSTIs (International Classification of Diseases, 10 th Revision) from January 1, 2008, to July 31, 2013. The following operative findings were used for definitive diagnosis: the presence of grayish necrotic fascia and/or adjacent subcutaneous soft tissues, lack of bleeding of those tissues during dissection, and the presence of foul smelling pus. The variables that were examined included age, sex, ethnic group, type and number of comorbidities, diagnosis at admission, time from admission to first operative debridement, portal of entry of infection, anatomical site of infection (central or peripheral), and type of symptoms at the time of admission. Tissue samples obtained at the first surgical treatment were cultured and their results were recorded.
Patient outcomes were also documented, which included number of operative debridements, need for amputation, the duration of hospitalization, time spent in intensive care unit (ICU), and the in-hospital mortality rate. Data from medical records were considered missing when they were not mentioned by the practitioner. The disease was classified into two types according to the culture results. 1  Type II NSTI included all cases caused by Streptococcus pyogenes either alone or in combination with other bacteria. All other cases were categorized as Type I.
Statistical analysis Data were analyzed using STATA Statistical Software: Release 12 (StataCorp LP College Station, TX, USA). Median and range were used for quantitative variables that were not normally distributed, and mean and 95% confidence interval (CI) were used for normally distributed variables. Categorical variables were tabulated using frequencies and percentages. The Chi-square test was used for testing the significance of associations between categorical variables. Group differences were tested using the unpaired Student t test in cases of normal distribution and the nonparametric ManneWhitney U test in cases of skewed distribution. Crude and adjusted relative risks (RRs) and 95% CI were calculated. Multiple logistic regression models were constructed to identify independent factors associated with mortality.
Statistical Analyses and OTU Classification Statistical analyses were performed using the vegan package  (Oksanen et al. , 2013)  in R software version 3. 0. 1. 1 For all OTU-based statistical analyses, the data set was normalized by a Hellinger transformation  (Legendre and Gallagher, 2001)  using the decostand function. For beta-diversity, non-metric multidimensional scaling (NMDS) ordination of Hellinger distances was carried out using the cmdscale function. Heatmaps were constructed with the gplots  (Warnes et al. , 2015)  for the OTUs explaining most of the differences between samples. Principal component analysis (PCA) of the Hellinger transformed data was performed using the prcomp function. The 50 OTUs explaining most of the differences between samples were defined as the OTUs contributing the largest absolute loadings in the first and second dimensions of the PCA  (Breidenbach et al.
, 2016a; Hernández et al. , 2017) , obtained from the rotation output file. Hierarchical clustering of the distance matrix was carried out with the "ward" method using hclust function. The heatmap was constructed using the heatmap. 2 function in gplots package  (Hernández et al. , 2017). For the T-RFLP analysis TRF sizes were rounded to integers and treated as OTUs. Overall signal intensity was standardized according to  Dunbar et al. (2001)  and expressed as fractions. The NMDS (using the function metaMDS and Bray-Curtis dissimilarity index) were done with the vegan package, version 2. 3-0  (Oksanen et al. , 2015).
Annealing temperatures for each pair of primers and amplicon sizes were as follows: mexA, 60 °C, 1375 bp; mexB1, 61 °C, 1684 bp; mexB2, 67 °C, 1638 bp. Sanger sequencing was performed in forward and reverse directions at GATC Biotech (Konstanz, Germany) using the same primers. PAO1 was used as a reference. Molecular graphics for MexA and MexB proteins were rendered using Visual Molecular Dynamics program (VMD  35  ), based on Protein Data Bank (PDB) files 2V4D (MexA  24  ), and 2V50 (MexB  25  ). Direct measurement of efflux activity. Efflux pump functionality was assayed by following the kinetics of efflux of N-phenyl-1-naphthylamine (NPN; Sigma-Aldrich), a MexAB-OprM preferential substrate  11  , which is fluorescent when incorporated in bacterial membranes. As previously described  36  , bacteria were treated with carbonyl cyanide m-chlorophenylhydrazone (CCCP, 10 μ M; Sigma-Aldrich) and then loaded with 20 μ M NPN.
Efflux was initiated by energizing bacteria with 50 mM D-glucose (Sigma-Aldrich). Decay in fluorescence signal was followed over time using a Spectramax ® multiplate reader (Molecular devices, Sunnyvale, CA). Maximal velocity (Vmax) was calculated by the SoftMax ® Pro Microplate Data Acquisition and Analysis Software (version 6. 2). PAO1mexAB (Δ mexAB-mutant) was used as negative control. Cloning and overexpression of porins. Genes encoding different porins i. e. OprD (OccD1), OpdK (OccK1), and OpdF (OccK2) were cloned in a heterologous system of Escherichia coli, which was lacking the main native porins OmpC and OmpF (E. coli K-12 W3110:Δ ompFΔ ompC)  37. The genes opdK and opdF were PCR amplified from PAO1 (with HindIII and NsiI restriction site overhangs) and further cloned into pGOmpF (a vector with the signal sequence of phoE [phosphoporin protein E] attached to the ompF gene  38  ) via HindIII/PstI, thereby replacing only ompF.
Acknowledgements This work was supported in part by the  Belgian Région Wallonne (program TEMOEXPAND ). The authors thank  V. Yfantis  for expert technical assistance and  Prof. B. van den Berg  ( Newcastle, UK ) for the kind gift of the pB22-OprD construct. H. C. was Boursier of the  Belgian Fonds pour la Recherche dans l'Industrie et l'Agriculture (FRIA ) and F. V. B. is  Maître de Recherches of the Belgian Fonds de la Recherche Scientifique (F. R. S. -FNRS ).
Biological data were not available for all patients, which decreases the power of the multivariate analysis. However, the median OS between the group of patients with all data available and the group with at least one missing data was similar. In addition, all patients were treated, and baseline characteristics presented were collected around the date of diagnosis (+ /-2 weeks) before the beginning of any treatment. We therefore cannot study whether biomarkers (LDH, AST) are only prognostic factors or whether they are also predictive factors of response to systemic chemotherapy (platinum-etoposide), which was the standard first-line treatment. Nevertheless, an important strength of this study is that biological tests were performed in a single institution, and are therefore more homogeneous.
There were no major differences in the previous and recent WHO classifications for the diagnosis of NEC, while few minor changes in the classification of well-differentiated NET were made during the revision of the WHO classification. Our database is registered and this cohort was approved by CNIL (Commission nationale de l'informatique et des libertés) on 6 November 2015 (no. 15-111). All methods were performed in accordance with the relevant guidelines and regulations. All patients signed an informed consent. Clinical, morphological and histological data. The following clinical features were recorded for all patients at diagnosis: age, gender, and presence or absence of symptoms within the 3 months before diagnosis of NEC. Weight loss was defined as the occurrence of a >5% decrease in weight within the 3 months before diagnosis.
Morphological data collected included primary and metastatic locations, TNM stage, number of metastatic sites, uptake on somatostatin receptor scintigraphy (SRS, recorded as positive/negative) with indium-111-pentetreotide, and uptake on 18 F-fluorodeoxyglucose positron emission tomography (FDG-PET, recorded as positive/negative). Pathological data included cell size (small versus large), Ki-67 index, and presence of necrosis. Immunohistochemistry of CgA and synaptophysin were recorded as positive and negative. Evaluation of Ki-67 expression was performed in at least 2000 tumour cells, according to the current recommendations for GEP-NET  24. Patients were followed (clinically with thoraco-abdomino-pelvic computed-tomography scan) every 2-3 months for 2 years after the diagnosis, then every 6 months.
Biological data. Biological data were collected in our laboratory at the time of diagnosis of NEC + /-2 weeks, and before the first treatment (chemotherapy): serum plasma levels of neuroendocrine markers CgA and NSE, LDH, liver functions tests (ALP, alanin aminotransferase -ALT, AST, total bilirubin), inflammatory markers (albumin, CRP, fibrinogen), haemostatic markers (PT, aPTT, haemoglobin -Hb, and platelets) and complete blood count (leukocytes, lymphocytes, neutrophils). The NLR was calculated and was considered high if NLR ≥ 3  7, 8  or ≥ 4  25. For all statistical analysis of biological data, we first analysed the median value as a cut-off. Based on the literature, CgA 4,23 , NSE  4, 23  , and LDH 3,26 levels were considered high if they were 2 ULN. Thus, all the factors were examined as both continuous and categorical variables (2 ULN).
The Zn isotope composition of several CC groups (CK, CB, CH), as well as individual components such as chondrules and matrix, which are the major reservoirs of Zn, have not yet been analyzed. However, these samples may provide critical clues toward further understanding the origin of the volatile element variations among CC. Here we present Zn isotope data for a comprehensive set of CC, including samples from the CI, CM, CO, CV, CK, CB, and CH classes, to further assess the origin and evolution of volatile elements in the inner Solar System. We also present Zn isotope measurements of individual chondrules from Allende (CV3) and Mokoia (CV3) as well as an aliquot of Allende matrix to investigate the formation of solid materials in the early Solar System and the compositions of the primitive materials that represent the building blocks of the terrestrial planets.
Carbonaceous chondrite components were measured at IPGP, while UOC leachates were measured at WUSTL. External reproducibility was assessed through full procedural replicate analyses of the same sample to be 40 ppm for 66 Zn/ 64 Zn and 50 ppm for 68 Zn/ 64 Zn  (Chen et al. , 2013). The Zn isotope composition of the USGS basalt standard BHVO-2 was measured throughout the study; the data are in agreement with currently accepted literature values (see Table  1 ;  Moynier et al. , 2017). Additionally, one sample (Murray) was independently processed through the entire procedure (dissolution, chemical purification, mass spectrometry) at both Washington University in Saint Louis and at the Institut de Physique du Globe in Paris; these replicates yield identical results within analytical error, signifying that the method is reproducible.
The unique impact-plume formation of CH and CB chondrites Two CC classes in the current dataset do not lie on the trend defined by CI-CK; specifically, the CH and CB chondrites have higher δ 66 Zn values than expected based on their low Zn concentrations (on average, 35 ppm and 5 ppm, respectively). This is an indicator that CB and CH chondrites experienced a different formation history compared to the other CC. CB chondrites have high metal content, are highly depleted in volatile elements, and the metal compositions suggest direct condensation from a gas  (Weisberg et al. , 2001). The CB chondrites have chemical and isotopic characteristics that are similar to CH, and both seem to be related to CR  (Weisberg et al. , 2001). Chondrules in CB are highly depleted in moderately volatile elements.
Acknowledgements We thank the Editor,  Derek Vance , as well as 3 anonymous reviewers for their constructive comments that greatly improved the quality of the manuscript. Julien Moureau ,  Pascale Louvat , and  Jessica Dallas  for maintaining the MC-ICP-MS at IPGP. FM acknowledges funding from the  European Research Council  under the  H2020 framework program / ERC  grant agreement # 637503  ( Pristine ) the  ANR  through the  Cradle  project, the  UnivEarthS Labex program at Sorbonne Paris Cité  ( ANR-10-LABX-0023  and  ANR-11-IDEX-0005-02 ). Parts of this work were supported by  IPGP  multidisciplinary program PARI, and by  Region Île-de-France SESAME  Grant no. 12015908. We also are indebted to  Joseph Boesenberg  and  Denton Ebel  ( American Museum of National History, New York ),  Timothy McCoy  ( US National Museum of Natural History, Smithsonian Institution, Washington DC ),  Caroline Smith  (The  Natural History Museum, London ),  Alex Bevan  ( Western Australian Museum, Perth ),  Jim Karner  and  Carl Agee  ( University of New Mexico, Albuquerque ),  Ludovic Ferriere  ( Naturhistorisches Museum, Vienna ),  Philip Heck  (The  Field Museum, Chicago ),  Meenakshi Wadhwa  ( Arizona State University, Tempe ),  Cecilia Satterwhite  ( NASA Johnson Space Center, Houston ) and the  Comité de Gestion (Museum Nationale d'Histoire Naturelle, Paris)  for their generous donations of meteorite samples for this work and their confidence in our analytical and scientific capabilities.
The associated MURE reactor simulation The reactor simulation was performed with the Monte Carlo Code MURE (MCNP Utility for Reactor Evolution). Available at the NEA databank, the MURE code is a precision, open-source code, designed by CNRS/IN2P3 laboratories and written in C++ which automates the preparation, computation of successive MCNP (Monte Carlo N-Particle) calculations and solves the Bateman equations in between, using a Runge-Kutta method, for burnup purpose  [8]. The MURE code is highly flexible to simulate reactors with a variety of refueling schemes, operation history and non-trivial core geometry like research reactors. The SUBATECH laboratory has developed important new functions in MURE to analyze the beta decay properties of the fission products in order to compute the associated antineutrino energy spectrum together with the reactor fuel evolution.
Differences in the results normalisation arise from the unknown operation history associated to the APOLLO2 simulation and database choices. However, the ratio betwen the neutron fluxes in the thermal and rapid energy ranges are in good agreement, as shown in Ref. [11]. The distribution of the fission rates for the 4 main fissile nuclei: 235 U, 238 U, 239 Pu and 241 Pu is presented in Fig. 2  for a refueling scenario by 1 seventh every 20 days, starting with a core completly filled with fresh fuel. The fission rates are constrained by the power maintained at its nominal value along the evolution. By definition, the equilibrium of the reactor is reached when the fission rates show a periodic pattern repeated every 20 days. This is reached for the different contributions after 260 days, i. e.
Introduction As microsystems are becoming more complex, simulation and modeling become more relevant and widespread in the micropump domain. Zengerle and Richter have shown in 1994 that micropumps could be modeled using the equivalence between fluidic systems and electrical networks  [1]. Bourouina et al. have verified and used this method to design a micropump for medical application  [2, 3]. More recently, thanks to progress in the computational domain, models can be driven using software such as ANSYS for a complete electro-fluid-solid simulation  [4]. Experimental validation of the modeling of a piezoelectric micropump was already reported for a device with no-moving-part valves  [5]  and a valveless  [6]  and piezoelectric peristaltic micropump  [7]. This paper presents a piezoelectric positive-displacement MEMS micropump having two check valves and a fixed stroke volume  [8, 9].
Acknowledgments The authors would like to thank the whole team involved in the  Insulin Micropump Project at Debiotech and ST Microelectronics (MEMS Division, Agrate Brianza, Italy, and Kirkop, Malta). They also explicitly thank  Harald van Lintel ,  Bertrand Boutaud ,  Véronique Vallet , and  Niklaus Schneeberger , who made important contributions to the modeling of this MEMS micropump.
We demonstrate the performance of our framework on a publicly available benchmark dataset, which has been acquired with a mobile mapping system in the city of Delft in the Netherlands. This dataset contains 10. 13 M labeled 3D points among which 17. 6% are labeled as "tree points". The derived results clearly reveal a semantic classification of high accuracy (up to 90. 77%) and an instance-level segmentation of high plausibility, while the simplicity, applicability and efficiency of the involved methods even allow applying the complete framework on a standard laptop computer with a reasonable processing time (less than 2. 5 h).
g. , shown in Figure  1 , a special track within the recent IQmulus Processing Contest IQPC'15 has been initiated  [13]. This special track focuses on two subtasks facing the challenges of an irregular point sampling, a high complexity of real-world scenes and a huge amount of data resulting from the acquisition of larger scenes. The first subtask is given by the binary classification of the 3D points of an MMS point cloud into "tree points" and "other points", whereas the second subtask is given by the separation of the "tree points" into clusters corresponding to individual trees. The joint consideration of both subtasks represents an instance-level segmentation inferring both class labels and instance labels  [19, 20]. To evaluate the performance of respective approaches for both subtasks, a labeled benchmark dataset acquired with a mobile mapping system in the city of Delft in the Netherlands has been released.
This dataset comprises about 10. 13 M labeled 3D points, whereby the reference labels are given at point-level with respect to a binary classification distinguishing "tree points" and "other points". The results of a segmentation of individual trees can easily be verified by visual inspection. Regarding the IQPC'15, a diversity of proposed approaches for both subtasks relies on a voxelization of 3D space. For reasons of accuracy, however, it would be desirable to have an efficient end-to-end processing pipeline for individual tree extraction from MMS point cloud data that is scalable towards the processing of large datasets without involving a voxelization of 3D space. In this paper, we focus on the extraction of individual trees from densely sampled 3D point cloud data. We present a novel two-step framework that addresses (1) semantic classification by assigning semantic class labels to irregularly distributed 3D points and (2) semantic segmentation by separating individual objects within the labeled 3D points.
We demonstrate the performance of our framework by presenting the respective results obtained for the IQPC'15 benchmark dataset. This paper represents an extended version of  [21] , whereby the extension is given by a more comprehensive analysis comprising: • feature subsets that are selected manually, • feature subsets that are derived automatically via feature selection techniques and • an improved segment-based shape analysis relying on semantic rules. In addition to drawing conclusions about which features are most relevant for the given classification task, we focus on increased efficiency via a parallelized memory-efficient implementation, which can be run on a standard laptop computer. After briefly summarizing related work (Section 2), we describe our novel two-step framework for extracting individual trees from densely sampled 3D point cloud data (Section 3).