dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We would like to thank  Marie-Christine Groleau ,  Fabrice Jean-Pierre ,  Valentin Popa ,  Julie Wilkin  and  Vincent Peck  for the technical assistance. This work was supported by the iFor  Consortium (NSERC) and ministère des Forêts, de la Faune et des Parcs Quebec (DGPSP)  to CG. AAD was supported by a  Wladimir A. Smirnoff Fellowship.
The whole RNA-Seq data analysis was done using the Eoulsan software version 1. 1. 6 (Jourdren et al. , 2012)  with the following parameters. Before mapping, polyN read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using the Bowtie mapper (version 0. 12. 7) (Langmead et al. , 2009)  using the-best and -k 2 parameters. Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Mus musculus GFF3 genome annotation from UCSC (mm10) was used. All overlapping regions between alignments and referenced exons were counted. Data normalization and differential analysis was performed using the DESeq package version 1.
, 2012) , two distinct WT RNAs libraries, from C57BL6 and C57BL6/Balbc (Cx30 +/+ ) mice, were prepared. We then compared the Cx30 ∆/∆ and WT transcriptomes and selected changes observed in Cx30 ∆/∆ brain vessels whatever the genetic background. Genes with less than 50 reads and/or with fold change less than 2 were not considered. Selected transcriptional variations were further validated by qPCR on independent brain vessel preparations. Consistently with the above data (Figure  1 ), transcription of junctional molecules as well as pathways implicated in BBB integrity were not modified in absence of Cx30. Among the transcriptional events detected in the Cx30 ∆/∆ brain vascular transcriptome, we confirmed the strong upregulation of Sgcg encoding γ-SG, a member of the dystrophin-glycoprotein complex (DGC) connecting cytoskeleton and the extracellular matrix  (Ozawa et al.
METHODS: DATA COLLECTION, MANAGEMENT AND ANALYSIS Data collection and management The study data are recorded in a web-based eCRF. They are extracted from the medical records of each patient (source data) by the ICU staff. The data manager, in cooperation with the coordinating investigator, establishes the trial database by exporting data from the eCRFs. Any protocol deviations are recorded in either the eCRF or the medical records; both are checked by a clinical research assistant to ensure that all protocol deviations and adverse events are in the database.
According to French law, the eCRF and creation of the database were approved by the appropriate committees (CCTIRS, Comité Consultatif sur le Traitement de l'Information en matière de Recherche dans le domaine de la Santé, N 14 779, on 23 December 2014; and CNIL, Commission Nationale de l'Informatique et des Libertés, N°M MS/VCS/AR1412251, on 16 February 2015).
In clinical practice, clinicians recognise that BoNT-A treatment can often be effective in the treatment of long-term spasticity, even in the presence of contractures. However, this is best achieved when patients and treatment goals are selected appropriately  [9]  and the appropriate concomitant therapies are available  [13]. The Upper Limb International Spasticity (ULIS) programme was established to describe real-life clinical practice and patient-centred outcomes in the treatment of post-stroke ULS with BoNT-A. The second stage of the programme (ULIS-II, NCT01020500) was a large, international, observational cohort study, conducted across 84 centres in 22 countries  [14, 15]. The primary objective of the ULIS-II study was to assess responder rates, as defined by the achievement of the primary person-centred goal using GAS, and to establish a consistent and reproducible approach to the recording of goals and goal attainment as measured by GAS  [14].
Findings from the study showed that the most common primary goals were improvements in passive function (caring for the affected limb), active function (using the affected limb), reduction of spasticity-related pain and prevention of contractures, with these goals achieved by 72%-86% of patients  [15]. Importantly, the achievement of goals related to pain and passive function showed the highest rates of achievement (84%-86%), suggesting that these may be "best response" goal areas for intervention with BoNT-A. In this post-hoc analysis of the ULIS-II study, we further interrogate the dataset to determine the patient-and/or therapy-related factors that may influence goal setting and achievement rates, including baseline patient characteristics, the interval between stroke and first-ever BoNT-A injection, presence or absence of contractures and the type and intensity of therapeutic input (TI).
However, the next stage of the ULIS programme (ULIS-III) will provide a larger, longitudinal dataset with several BoNT-A treatment cycles and detailed information about the types of concomitant therapy intervention, which should provide a more definitive description of the differential benefits of BoNT-A application when considering treating ULS patient subgroups with multiple and diverse treatment goals. In conclusion, although the findings presented in this analysis will resonate with what is commonly observed in real-life clinical practice, they serve to provide an important body of exploratory data to confirm that experience. In this capacity, our findings will assist in designing future research which will help in selecting the right patients and appropriate goals for treatment with BoNT-A in ULS.
2004 (Binzel et al. , 2006) )  that have been in use for over a decade. Data reduction and spectral extraction were performed using the Image Reduction and Analysis Facility (IRAF, Tody 1993) provided by the National Optical Astronomy Observatories (NOAO). Correction in regions with strong telluric absorption was performed in IDL using an atmospheric transmission (ATRAN) model by  Lord (1992). More detailed information on the observing and reduction procedures can be found in  Rivkin et al. (2004)  and  DeMeo and Binzel (2008). We present the resulting spectrum of Isberga in Fig. 2.
The correlated flux measurements of (939) Isberga were extracted using the data reduction software package EWS (Expert WorkStation, see Jaffe 2004, for a detailed description). Using the closest calibrator observation in time, calibrated correlated fluxes of (939) Isberga were obtained by multiplying the ratio target/calibration star raw correlated flux counts by the absolutely calibrated infrared flux of the calibrator (see  Matter et al. 2011 Matter et al. , 2013 , for a complete description of the data reduction and calibration procedure). Uncertainties on the correlated flux are estimated considering two contributions. First, a short timescale effect (much shorter than typical observations of ≈2 min), dominated by photon noise from the object and thermal background emission. This statistical uncertainty is estimated by splitting a complete exposure, consisting of several thousand of frames and leading to one correlated flux measurement, into five equal parts and by deriving their standard deviation for every spectral channel.
(2009)  in Fig. 2 ). The spectrum of Isberga was however obtained at a large phase angle of 28 • (Sec. 2. 2), and part of the reddening may be caused by the observing geometry. Spectral observations of Isberga at visible wavelengths and small phase angle will help refine its taxonomic classification and state of space weathering. We determine a visible geometric albedo of p V = 0. 14   veys)  and corresponds to the first quartile of all Bus-DeMeo Scomplex asteroids (based on Fig. 6  by  Mainzer et al. 2011). We finally search for the best-fit (M4AST χ 2 match) meteorite in the Relab spectral database to Isberga spectrum, corrected from the reddening (either due to the phase angle or space weathering. Ordinary chondrites provide the most-promising candidates, as to be expected from the Sq-type classification, and the best-match is found for the H4 Sete Lagoas (sample MH-JFB-021).
Acknowledgments We acknowledge support from the  Faculty  of the  European Space Astronomy Centre (ESAC)  for the visits of  M. Delbo  and  A. "Momo" Matter. The work by P. S. and P. P. was supported by the  Grant Agency of the Czech Republic , Grant  P209/12/0229 , and by Program  RVO 67985815. A. Matter  acknowledges financial support from the  Centre National d' Études Spatiales (CNES). TRAPPIST is a project funded by the  Belgian Fund for Scientific Research (Fonds National de la Recherche Scientifique, F. R. S. -FNRS )  E. Jehin  and  M. Gillon  are  FNRS Research Associates , and  Jean Manfroid  is Research Director of the FNRS. Part of the data utilized in this publication were obtained and made available by the The  MIT-UH-IRTF Joint Campaign for NEO Reconnaissance. The IRTF is operated by the  University of Hawaii  under Cooperative Agreement no.
NCC 5-538  with the  National Aeronautics and Space Administration, Office of Space Science, Planetary Astronomy Program. The MIT component of this work is supported by  NASA  grant  09-NEOO009-0001 , and by the  National Science Foundation  under Grants Nos. 0506716  and  0907766. FED acknowledges funding from  NASA  under grant number  NNX12AL26G  and  Hubble Fellowship  grant  HST-HF-51319. 01-A. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of NASA or the  National Science Foundation. This research utilizes spectra acquired by  Jeffery F. Bell  with the  NASA RELAB facility at Brown University.
g. p+A → π + + X ). This Sanford-Wang (SW) parametrization has the following functional form: d 2 σ dpd ( p, θ) = exp[c 1 -c 3 p c 4 p c 5 b -c 6 θ ( p -c 7 p b cos c 8 θ )] p c 2 1 - p p b , ( 3 ) where X denotes any system of other particles in the final state; p b is the proton beam momentum in GeV/c; p and θ are the π + momentum and angle in units of GeV/c and radians, respectively; d 2 σ/(dpd ) is expressed in units of mb/(GeV/c sr); d ≡ 2π d(cos θ ); and the parameters c 1 ,. , c 8 are obtained from fits to meson production data. HARP data were fitted using this empirical SW parametrization. This is a useful tool to compare and combine different data sets. A global SW parametrization for forward production of charged pions as an approximation of all the studied datasets is provided in Ref.
[26]. It can serve as a tool for quick yields estimates. The next HARP analysis was devoted to the measurement of the double-differential production cross section of π ± in the collision of 12 GeV/c protons (see Fig. 1 ) and pions with a thin 5% λ I carbon target  [18]. These measurements are important for a precise calculation of the atmospheric neutrino flux  [7]  and for a prediction of the development of EAS  [4]. Simulations predict that collisions of protons with a carbon target are very similar to proton interactions with air. This hypothesis could be directly tested with the HARP data. Measurements with cryogenic O 2 and N 2 targets  [19] , also shown in Fig. 1 , confirm that p+C data can indeed be used to predict pion production in p+O 2 and p+N 2 interactions. It is important to emphasize that a systematic campaign of measurements was performed by HARP: all thin target ISVHECRI 2014   3 ) with parameters given in Ref.
A much higher statistics available in the 2009 data makes it possible to use finer { p, θ} binning. An improved statistics of the 2009 data also allows for the first measurements of negatively charged kaons within NA61/SHINE. The corresponding results are shown in Fig. 6    prediction of the intrinsic electron neutrino component and the high energy tail of the T2K beam  [51]. Preliminary results for proton yields were also obtained, see Fig. 6  (right). Clearly, some hadron production models have difficulties in describing these measurements. The analysis of neutral strange particles (K 0 s and ) production using V 0 -like topology of their decays has been developed  [59, 63]  and the results are now published  [64]. New preliminary results from the analysis of the 2009 dataset have been also released recently.
During the 2009 run, NA61/SHINE also recorded data with negatively charged pion beams at 158 and 350 GeV/c on a thin carbon target to provide particle-production data for the tuning of hadronic interaction models used in air-shower simulations and first preliminary results have already been released  [71, 72]. They are summarized below. The results on the production of charged hadrons in π -+C interactions at 158 and 350 GeV/c are presented in Fig. 7. These spectra were obtained within a fiducial phase space of the NA61/SHINE detector, for which the detection and selection efficiency for charged tracks is close to unity, and corrected for feed-down and track loss using the average correction predicted by the VENUS and EPOS event generators after simulation of the detector response. The trigger bias is corrected for by studying the track loss in a sub-sample of unbiased beam-trigger data.
Figure10illustrates the preliminary results obtained in the analysis of a larger-statistics 2009 p+RT@31GeV/c dataset [75]. Fully corrected yields of π + for two bins of polar angle ([100,140] mrad and [140,180] mrad) measured in 6 longitudinal intervals are shown and compared to FLUKA2011 predictions. The data presented in Refs. [55, 56, 74]  provide important information used for improved calculation of the T2K neutrino flux [51]. New NA61/SHINE measurements described here will allow to reach even a better precision.
Model Parameters Model parameters (Table  2 ) were based on the available literature, and African data wherever possible. Demographic parameters were based on Burkina Faso, a country at the heart of the meningitis belt. Different "who acquires infection from whom" (WAIFW) matrices were used and compared. In the absence of empirical data on population contact patterns, we used evidence on the age distribution of carriers during an MenA epidemic to inform these matrices  [20]. The WAIFW matrix used is shown in Supplementary Figure  1 ; contacts are more intense between individuals in the same age group and particularly so for older children and young adults. It was necessary to estimate values for some parameters where direct evidence was lacking. In exploring the parameter space, it was apparent that there was a strong co-linear relationship between the transmission rate and duration of colonization.
The dates of the beginning and the end of any subsequent pregnancies (miscarriage, abortion, ectopic pregnancy, childbirth) will be recorded. The blinding of the study will be assessed during interviews with the patients during follow up. Patients may reply that (1) they do not know which arm they were assigned to, (ii) they think they underwent hysteroscopy, or (iii) they think they underwent vacuum aspiration. The primary endpoint of the trial is a pregnancy of at least 22 weeks duration in the 2 years of follow up. The progress of the pregnancy will be evaluated according to standard procedures. These data will be collected from a standardized report of the pregnancy and birth (see Additional file 5). In cases of delivery at the same hospital or of additional examinations or surgical procedures, medical records may be used to complete the information.
Handling of missing data Participants lost to follow up will be taken into account on the basis of their last known status and several reminders will be sent. We will check that the participants lost to follow up are equally distributed between the two arms of the trial, which is the usual procedure to deal with such participants in this type of trial. An explanatory calculation may be performed to classify these participants as failures (no pregnancy of more than 22 weeks of gestation within 2 years). Methods based on multiple imputation may also be used.
Secondary endpoints (incidence of miscarriage and ectopic pregnancy in the 2-year follow-up period; surgical complications according to the Clavien-Dindo classification; secondary surgical intervention for the management of intrauterine retention after miscarriage) will be analyzed and compared between the two arms by chi-squared test. All tests will be twotailed. Interim analyses are not planned. Stata version 13 software (Stata Corp. , College Station, TX, USA) will be used for all statistical analyses.
Data collection and management Data for all phases of the study will be collected in a stepwise manner using the secure online internet platform, Cleanweb (https://cleanweb. aphp. fr/Ctms-02/portal/login). Personal information relating to the participants enrolled will be known only to the local investigators. The first letter of the given name and the first letter of the last name, together with the month and year of birth, will be collected for each patient, to protect confidentiality in the database. As neither the investigators nor the sponsor have any competing interests and the study does not focus on the use of drugs, no data monitoring committee is required. Data quality will be monitored by visits to the investigating centers, with a frequency corresponding to the planned follow up of patients in the protocol, inclusions at the various centers and the level of risk attributed to the protocol.
During subsequent visits, the observations will be reviewed as the study progresses, by clinical research assistants, who will be responsible for checking that the data are correctly entered and for validating the data. The principal investigator at each center and the other investigators responsible for including or following up subjects participating in the study will agree to visits from representatives of the promoter, nominated by Assistance Publique-Hôpitaux de Paris (AP-HP), at regular intervals. During these site visits, in accordance with good clinical practice, the following aspects will be audited: respect for the research protocols and the procedures defined in it examination of the source documents, comparing them with the data reported in the online observation notebook, to assure the quality of the results obtained: exactness, missing data, data consistency.
Publication and ownership of the results AP-HP is the owner of all the data obtained, and no use or transmission of these data to a third party is permitted without prior agreement. The individuals who made a genuine contribution to the development and running of the protocol and to the writing up of the results will be the first authors on any resulting publications. The principal investigator and methodologists will be authors on the principal publication. The positions of the intermediate authors will depend on the number of patients included and participation in the writing of the manuscript (including participation in study design, data analysis and the writing and reviewing of the manuscript).
Discussion This study is a single-blind randomized controlled trial. The single-blind design was chosen so as to restrict any placebo effect on the occurrence of pregnancy. A double-blind design was not possible because the two arms of the study correspond to surgical interventions. Blinding for the patient will be assessed during follow up, to determine the efficacy of the patient blinding procedure. The validity and reliability of data collection procedures used in the trial could be called into question as follow up is planned to involve telephone conversations or questionnaires sent by email or post during a 2-year period, rather than a review of medical records. However, patients often move house just before or after giving birth. The patient might then give birth at another hospital and would be lost to follow up.
Acknowledgements This study is financially supported by  Assistance Publique -Hôpitaux de Paris  (APHP, 3  Avenue Victoria ,  75004 ,  Paris, France))  ( AOR13087 ). The funders have no role in study design, data collection and analysis, decision to publish, or manuscript preparation. The study team would like to thank  Laurence Bussières ,  Eric Dufour  and  Laurence Lecomte  for their contributions to the study.
Using the truncated cone formula, QF muscle volume was calculated by summing the areas of all the slices, taking into account the slice thickness and the gaps between slices. T 2 maps were generated by a linear fit on a pixel-by-pixel basis using the logarithm of the data to the equation (  1 ): ( ( )) = ( ) -( / ) ( ) S TE S TE T ln ln 1 0 2 where S(TE) is the signal at time equal to TE and S 0 is the equilibrium magnetization. Thereafter, T 2 maps were resized to the T 1 -weighted images resolution. Regions of interest initially drawn on T 1 -weighted images were used to analyze T 2 maps and to determine a mean T 2 value for VL, VM, VI and RF. In addition, histograms representing the voxels numbers with respect to T 2 relaxation times were determined for each muscle at baseline, D2 and D4.
Spatial normalization of the T 2 maps. As described in Fig. 4a , 3D affine coregistration was first performed using FLIRT algorithm of the FSL software (cost function = cross-correlation with 12 degrees of freedom) on the manually segmented masks of the four muscles at D2 and D4 to the manually segmented mask obtained at baseline. The affine transformation estimated by the intra-individual coregistration was then applied to the T 1 -weighted images and T 2 maps. Thereafter, a 3D non-linear coregistration using ANTs library with symmetric diffeomorphic deformation model  43  was performed for all the subjects. The parameters were optimized for large deformations of areas (with SyN option activated, cost function = cross-correlation, gradient step = 0. 5, total-smoothing = 0. 5, gradient-smoothing = 3, N-Time Steps = 1 and trunk = 256).
001. The SPM analysis was used to detect alterations among and within each muscle of the QF ("inter-individual analysis" module of the Fig. 4 ). Localization and quantification of altered muscle areas. First, a polar coordinate system was used to determine the position of each voxel of the T 2 maps obtained after the affine co-registration (intra-individual coregistration). The origin of the localization system was determined as the bone gravity center on the basis of an automatic segmentation of bone, muscle and subcutaneous adipose tissue. The automatic segmentation has been developed in C+ + using OpenCV library as previously published by Positano et al. 50 in order to obtain a fast and fully automatic segmentation. While Positano et al. used a gradient vector flow snake algorithm  51  , we used a more classical polygonal active contour algorithm  52  which determines the boundary between the subcutaneous fat and muscle tissues.
Results Twenty-seven patients were enrolled; median age 64 years (range: 29-77 years). Chronic dosing with patisiran has been generally well tolerated. Three patients experienced serious adverse events unrelated to study drug. Flushing and infusion-related reactions were observed in 22. 2% and 18. 5% of the patients, respectively; these were mild in severity, and did not result in any discontinuations. Sustained mean serum TTR lowering of approximately 80% was achieved, with further mean nadir of up to 88% between doses for approximately 16 months. Stabilization of quality of life (QOL) measures was observed. Among the 20 evaluable patients at the time of data cutoff, neuropathy impairment scores were stable through 12 months with a mean change in mNIS+7 and NIS of -2. 5 and 0. 4 points, respectively; this compares favorably to the 10-18 point increase in neurologic impairment scores estimated at 12 months from prior FAP studies in a patient population with similar baseline NIS.
© 2015 Adams et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http:// creativecommons. org/licenses/by/4. 0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons. org/publicdomain/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated.