dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Masashi Nakatani ,  Abhishek Srivastava ,  Arthur Szlam ,  Tiberiu Tesileanu , and the members of the  Cornell Creative Machines Lab  for insightful discussions. We thank  Sam McKenzie  for helpful comments on earlier versions of the manuscript. This work was supported by the  European Research Council  ( FP7 Program )  ERC Advanced Grant  (PATCH) to V. H. (No. 247300 ) and a  Core Fulbright Visiting Scholar Program fellowship  to J. P.
A search has been made for supersymmetry in a final state containing two photons and missing transverse momentum using the ATLAS detector at the Large Hadron Collider. The search makes use of 3. 2 fb -1 of proton-proton collision data collected at a centre-of-mass energy of 13 TeV in 2015. Using a combination of data-driven and Monte-Carlo-based approaches, the Standard Model background is estimated to be 0. 27 +0. 22  -0. 10 events. No events are observed in the signal region; considering the expected background and its uncertainty, this observation implies a model-independent 95 % CL upper limit of 0. 93 fb (3. 0 events) on the visible cross section due to physics beyond the Standard Model. In the context of a generalized model of gauge-mediated supersymmetry breaking with a bino-like next-to-lightest supersymmetric particle, this leads to a lower limit of 1650 GeV on the mass of a degenerate octet of gluino states, independent of the mass of the lighter bino-like neutralino.
Samples of simulated processes For the GGM models under study, the SUSY mass spectra and branching fractions are calculated using SUSPECT 2. 41  [15]  and SDECAY 1. 3b  [16] , respectively, inside the package Fig. 1  Typical production and decay-chain processes for the gluinopair production GGM model for which the NLSP is a bino-like neutralino SUSY-HIT 1. 3  [17]. The Monte Carlo (MC) SUSY signal samples are produced using Herwig++ 2. 7. 1  [18]  with CTEQ6L1 parton distribution functions (PDFs)  [19]. Signal cross sections are calculated to next-to-leading order (NLO) in the strong coupling constant, including, for the case of strong production, the resummation of soft gluon emission at next-to-leading-logarithmic accuracy (NLO+NLL)  [20] [21] [22] [23] [24]. The nominal cross section and its uncertainty are taken from an envelope of cross-section predictions using different PDF sets and factorization and renormalization scales  [25].
Conclusion A search has been made for a diphoton + E miss T final state using the ATLAS detector at the Large Hadron Collider in 3. 2 fb -1 of proton-proton collision data taken at a centreof-mass energy of 13 TeV in 2015. At least two photon candidates with p T > 75 GeV are required, as well as minimum values of 175 and 1500 GeV of the missing transverse momentum and effective mass of the event, respectively. The resulting signal region targets events with pairproduced high-mass gluinos each decaying to either a highmass or low-mass bino-like neutralino. Using a combination of data-driven and direct Monte Carlo approaches, the SM background is estimated to be 0. 27 +0. 22  -0. 10 events, with most of the expected background arising from the production of a W boson in association with two energetic photons.
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, UK.
Analysis of hmC-Seq data A combinatorial approach was used for high confidence peak calling. Statistically significant peaks of mapped reads were detected by using the model-based analysis of ChIP-Seq (MACS) program  33  on each hmC-Seq file against the matching input file under the stringent condition that satisfies fold enrichment ⩾ 10 and the false discovery rate ⩽ 0. 05%. Replicates were combined by retaining only those peaks that meet the majority rule condition (450% of samples identify a peak) as described previously. 34 To measure the reproducibility at the level of peak calling, irreproducible discovery rate (IDR) analysis  35  was applied to the sets of peaks identified from replicates. Next, peaks were identified using PePr 36 (peak-calling prioritization pipeline) that uses a negative binomial distribution to identify consistent or differential binding sites in ChIP-Seq experiments with biological replicates.
Statistical analyses We analyzed the behavioral data with the statistical program SPSS (IBM, NY, USA) and followed significant effects (Po0. 05) with SPSS post hoc contrasts within the repeated measures analysis of variance module. For the training and footshock phases, the dependent variables were the number of METH infusions during the training days and the punishment sessions. The dependent variables for the extinction tests were total (nonreinforced) active lever presses and inactive lever presses.
DNA hydroxymethylation At 2 h following the SA and footshock regimen, the animals were killed and genomic DNA was extracted from the NAc. Isolated DNA was immunoprecipitated using an antibody against hydroxymethylated cytosine. Immunoprecipitated DNA was made into sequencing libraries and subjected to next-generation sequencing. Reads generated from sequencing underwent quality control measures (see Supplementary Methods) and were aligned to the rat genome (UCSC (University of California, Santa Cruz) Genome Browser rn5). The MACS2 peak-calling program was used to convert loci with enriched reads as peaks. We considered peaks that satisfied fold enrichment ⩾ 10 and the false discovery rate ⩽ 0. 05. In addition, we chose peaks that exist for more than three of the six animals per group. Using the criteria described above, comparisons were performed between SR and CT (SRvsCT), SS and CT (SSvsCT) and SR and SS (SRvsSS) groups.
The hMeDIP Seq data set has been deposited and is freely available at http://www. ncbi. nlm. nih. gov/bioproject/310210. Figure  2  and Supplementary Table  S1  show the results of the overall DNA hydroxymethylation experiments. We found significant differentially hydroxymethylated peaks between SRvsCT, SSvsCT and SRvsSS comparisons. There were 475 (427 hyper-and 48 hypo-hydroxymethylated) peaks that showed differential DNA hydroxymethylation regions in the SRvsCT comparison, 808 (797 hyper and 11 hypo) peaks in the SSvsCT comparison and 992 (598 hyper and 394 hypo) peaks in the SRvsSS comparison (Figure  3  and Supplementary Figures  S1  and S2 ). The Venn diagrams also show the overlaps among the three comparisons for the number of total genes (Figure  2a ) and intragenic genes (Figure  2b ).
Computation times The numerical tools pertaining to the current study have been implemented using the multi-paradigm numerical computing environment Matlab (R2015). This choice is motivated by the fact that this software offers efficient and powerful tools and functionalities in order to optimize the numerical implemen-R tation. The simulations presented in this paper are all performed on a personal computer with 2. 00 GHz of CPU frequency and 6. 00 Go of RAM memory. The CPU time re-Fig. 7  Effect of the relative thickness of the elastomer layer on the enhancement of ductility of the bilayer (predictions based on bifurcation theory) mathematical formulations of the two approaches (M-K and bifurcation): if the amount of initial imperfection is set to 0 in the imperfection model, the problem reduces to the bifurcation analysis.
Materials On 30 June 2009, an Airbus A310 of Yemenia Airlines (flight IY26) en route from Sanaa (Yemen) to Moroni (Comoros) crashed in the Indian Ocean while approaching Moroni at 1:51 a. m. local time  [23]. The accident caused 152 deaths, with only one survivor  [23]. One hundred thirteen victims were recovered from two sites: (i) Comoros (n = 89; PMSI = 60 days) and (ii) Tanzania (n = 24; PMSI = 7 days). It was determined that most victims perished from polytrauma (69 %), while others died either from undetermined causes (26 %) or from polytrauma but with the possibility of drowning unable to be excluded (5 %). These proportions of causes of death are consistent with published cases of deaths from aircraft crashes  [1, 24, 25]. Data concerning the crash and the victims were analysed from administrative investigation reports, autopsy file reports (n = 113), autopsy photos (n = 3 579) and underwater videos of the plane wreck (hours = 322) provided by the relevant authority (The Forensic and Criminal Intelligence Agency of the French Gendarmerie).
The morphology of the lesions was further characterised using four quantitative parameters (area, perimeter, major axis, and ratio of major axis/minor axis, used as a proxy for shape) that were digitally measured and calculated from the autopsy photos by using ImageJ, an open-source software developed to analyse photographs in medical contexts  [29]. The landmark-based method of lesion measurement was validated by an intraclass correlation coefficient test (ICC 1. 0)  [30]. The two observers (a hospital emergency physician and a graduate student in forensic anthropology) had comparable experience with ImageJ software and they independently measured the same set of 20 randomly selected autopsy photos.
Statistical analysis Statistical analysis of the dataset was carried out using the programme R, Version 3. 2. 1  [31]. First, normality of the distributions of the number of lesions per corpse, area, perimeter, major axis, and ratio of major axis/minor axis was tested with a Shapiro-Wilk test. The hypothesis of a normal distribution was rejected for each variable that was either multimodal or positively skewed (number of lesions per corpse 0. 9; area 4. 7; perimeter 1. 8; major axis 1. 8; ratio of major axis/minor axis -0. 3). Given the skewness of the distributions, the median is reported as summary statistics. Frequency of lesions by sexes-only for the victims for which sex was determined at postmortem analysis-was tested with a Kolmogorov-Smirnov test. Chi-square (χ 2 ) tests were performed to analyse the frequencies of type of lesion and tooth notches on edges of lesion.
Acknowledgments The authors are particularly grateful to the  Forensic and Criminal Intelligence Agency of the French Gendarmerie  ( Institut de Recherche Criminelle de la Gendarmerie Nationale: IRCGN ) for giving access to the study material. They also sincerely wish to thank  Dr Yannis Papastamatiou  for kindly sharing his expertise and data. They are grateful to  Mr Oliver Crimmen  and his collaborators at the  Natural History Museum of London, Mrs Zora Gabsi at the Natural History Museum  of.
Model Description We use the GEOS-Chem CTM version 9-02 (http://www. geos-chem. org/) driven by assimilated meteorological data GEOS-FP from NASA Global Modeling and Assimilation Office (GMAO). The GEOS-FP data have 1-hourly and 3-hourly temporal resolution, 47 vertical layers, and 0. 25° 0. 3125° horizontal resolution. We degrade the horizontal resolution to 2° 2. 5° for input to GEOS-Chem. We initialize the model with a 6-month spin-up followed by simulation of Jan-Apr 2014. Aerosol types simulated in GEOS-Chem include carbonaceous aerosols, sulfate-nitrate-ammonium aerosols, sea salts, and mineral dust. The simulation of carbonaceous aerosols was originally described by  Park et al. (2003). Black carbon and primary organic aerosol (POA) are emitted by fuel (fossil fuel and biofuel) combustion and open fires.
Acknowledgments. The work has been supported by the  Max Planck Society (MPG). We acknowledge the support by the  Instituto Nacional de Pesquisas da Amazônia (INPA). We would like to thank all the people involved in the technical, logistical, and scientific support of the  ATTO  project, in particular  Jürgen Kesselmeier ,  Reiner Ditz ,  Matthias Sörgel ,  Thomas Disper ,  Uwe Schultz ,  Steffen Schmidt ,  Thomas Seifert ,  Andrew Crozier ,  Antonio Ocimar Manzi ,  Hermes Braga Xavier ,  Elton Mendes da Silva ,  Nagib Alberto de Castro Souza ,  Adir Vasconcelos Brandã  o,  Amauri Rodriguê s Perreira ,  Antonio Huxley Melo Nascimento ,  Thiago de Lima Xavier ,  Josué Ferreira de Souza ,  Roberta Pereira de Souza ,  Bruno Takeshi , and  Wallace Rabelo Costa. We acknowledge the support by the  German Federal Ministry of Education and Research  ( BMBF  contract  01LB1001A ) and the  Brazilian Ministé rio da Ciê ncia, Tecnologia e Inovaç ã o (MCTI/FINEP  contract  01.
Methods The Delphi method This consensus project was executed following the Delphi method  [19]. In short, a systematic literature search was conducted after which experts were selected and invited to participate. An online survey using online questionnaire software (www. SurveyMonkey. com) was constructed and presented to participants in three consecutive rounds. Only experts that completed all previous rounds were reinvited to participate in the subsequent round. After each round, the questionnaire was modified based on the comments provided by experts and aggregated results of the previous round were anonymously presented to allow the experts to re-evaluate their answers without peer-pressure. Subsequently, a face-to-face meeting was held to discuss the results of the online survey. A systematic literature search of the PubMed database was performed on February 18, 2016 (see Fig.
Acknowledgements. The data will be made available through the National Snow and Ice Data Center (NSIDC; http://nsidc. org);the contact person is  Kevin Schaefer  (kevin. schaefer@nsidc. org). This study was supported by the  Permafrost Carbon Vulnerability Research Coordination Network , which is funded by the  National Science Foundation. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the  US Government. E. J. Burke  was supported by the  Joint UK DECC/Defra Met Office Hadley Centre Climate Programme  ( GA01101 ) and the  European Union Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement no. 282700. This research was also sponsored by the following Chinese foundations: (1) the  National Basic Research Program of China  (grant no.
Acknowledgments: This research project is a part of the European project  MaCuMBA (Marine Microorganisms: Cultivation Methods for Improving Their Biotechnological Applications ) and has been founded by the  European Union 's  Seventh Framework Programme  ( FP7/2007-2013)  under grant agreement no  311975  and  Brittany region  under grant agreement  8433. Thanks to  Amélie Weil  who cultivated strains after preservation, and  Denis Rousseaux  for giving liquid nitrogen.
Human NES Cells Exhibit the Transcriptional Signature of Early Neural Stem Cells To further characterize NCX-NES cells, we conducted single-cell RNA-seq on 439 expanded NCX-NES cells and 383 cells from 5-6 and 8 pcw donor-matched NCX (Table  S1  and Table  S2 ); 362 and 255 cells, respectively, passed our quality-control pipeline (Supplemental Experimental Procedures). The majority of cells analyzed from the donormatched NCX tissue samples expressed canonical marker genes for neuroepithelial cells and RGCs of the dorsal forebrain (Figure  1F ). NCX-NES cells showed similar expression profiles as their donor-matched NCX cells (Figure  1F ). Neither brain NCX cells nor NCX-NES cells expressed ventral forebrain markers (Figure  1G  and Figure  S2D ). To place the transcriptional profiles of NCX-NES cells within the context of fetal development, we supplemented our donor-matched datasets with single-cell RNA-seq data from 526 cells collected from fetal NCX at 16, 19 and 20 pcw (Figure  1H ); 392 of them cells passed quality control.
Single-cell RNA-seq data also showed that TBK1 is highly expressed in neurons, astrocytes and microglia in the adult brain (Figure  5A ). Consistent with this expression, analysis of a developing human brain transcriptome data set  (Kang et al. , 2011)  revealed a bimodal pattern of TBK1 expression in the NCX, with high expression in the embryonic and early fetal samples and again during postnatal development (Figure  S6B ). To investigate if TBK1 levels changed during ZIKV infection, we conducted droplet digital PCR (ddPCR) on both ZIKV-infected and mock-infected NES cells and organotypic brain slices. No differences in TBK1 levels were found between uninfected and ZIKV-infected (with either the Cambodian or Brazilian ZIKV strains) NES cells or organotypic slices, though expression of TBK1 in the homogeneous NES cell population was greater than in the organotypic brain slices, which are composed of both neural stem/progenitor cells and immature postmitotic neurons (Figure  5B ).
Statistical Analysis The presented data are mean ± SD or SEM from three separate experiments. Differences between the groups were analyzed using the t-test. Values of all significant correlations are given with degree of significance indicated (* p ≤ 0. 05, ** p < 0. 01, *** p < 0. 001). For organotypic slice culture, quantification was performed in up to 4 sections that were representative of at least 3 slices. Cells were counted as described in the respective figure legend. The number of cells with pTBK1 located in centrosomes or mitochondria follows a binomial distribution. Fisher's exact test was performed to compare the control and the infected/treated group. Similarly, to test whether infection changed the number of centrosomes, the cells were binned by the number of centrosomes (1-5), and Fisher's exact test was performed to compare control with infected/treated cells.
Acknowledgments We thank  Carolyn Hain  and for assistance with tissue acquisition and processing and  Brian G. Rash  for technical advice. We also thank  Angeliki Louvi  and  Flora Vaccarino  for sharing equipment, for providing reagents and tissue samples. We thank  Marie Flamand  ( Institut Pasteur ) for supplying NS1-specific antibody  17A12-1G5 ,  Alain Kohl  ( MRC Glasgow ) for providing us with the Brazilian ZIKV strain  PE243 ,  Scott Terhune  ( Medical College of Wisconsin ) and  Felicia Goodrum  ( University of Arizona ) for supplying HCMV-GFP, and  Avinash Phadke  ( Achillion Pharmaceuticals ) for supplying samples of Sofosbuvir and 2´-C-methyladenosine. We also thank the other members of our laboratories for their comments. This work was supported by grants  NS076503 ,  MH103339 ,  MH105972 ,  MH106934 ,  MH060929 ,  NS080388 ,  AG034924 ,  AG047270 ,  DC01919 ,  AI120113  and  AI089826  from the  National Institutes of Health (NIH) ,  SFARI 307705  from the  Simons Foundation , and  15-RMA-YALE-31  from  Connecticut Innovations' Regenerative Medicine Research Fund.
The European Paediatric Pulmonary Vascular Disease (PVD) Network is a registered, non-profit organisation that strives to define and develop effective, innovative diagnostic methods and treatment options in all forms of paediatric pulmonary hypertensive vascular disease, including specific forms such as pulmonary arterial hypertension (PAH)-congenital heart disease, pulmonary hypertension (PH) associated with bronchopulmonary dysplasia, persistent PH of the newborn, and related cardiac dysfunction. Methods The writing group members conducted searches of the PubMed/MEDLINE bibliographic database (1990-2015) and held five face-to-face meetings with votings. Clinical trials, guidelines, and reviews limited to paediatric data were searched using the terms 'pulmonary hypertensio n' and 5-10 other keywords, as outlined in the other nine articles of this special issue.
I C The initial evaluation should include a comprehensive medical history, thorough physical examination, assignment to a functional class and formal assessment of cardiac function (ECG and echocardiogram). This should be followed by further diagnostic testing to delineate the PH aetiology-ideally prior to the initiation of therapy. The above recommendations of the European Paediatric Pulmonary Vascular Disease Network relate to the grading system currently suggested by the European Society of Cardiology and the American Heart Association and are based on paediatric data only (class, LOE). The complete list of references on the above subtopic can be found in ref. 21 ecommendations on PH diagnostics and monitoring, specifically in neonatal chronic lung disease and persistent PH of the newborn,  27  and PAH associated with congenital heart disease,,  26     Table  8  Recommendations on the evaluation and management of PH in children and adolescents with CHD (CHD-PAH, CHD-PPHVD)  26  Recommendations COR LOE Children/adolescents with clinically confirmed CHD should undergo specific transthoracic echocardiography (TTE) screening for PAH and/or ventricular dysfunction.
Although LSI is capable of rapid measurements over large spatial regions, the data lack quantitative accuracy and are limited to detecting relative changes in blood flow  [12]. One reason for this is the confounding effect of spatial and temporal variations in the tissue absorption and reduced scattering coefficients (µ a and µ s ', respectively) on SFI  [13]. cSFDI can decouple µ a and µ s ' with the use of Spatial Frequency Domain (SFD) techniques, and then potentially use this information to correct for errors imparted on SFI. These SFD methods, which we have previously described in detail  [3, 14] , employ structured coherent illumination. Images of back-scattered reflectance are then acquired at multiple spatial frequencies using a CCD or CMOS detector. Computational models of photon transport are then applied to the measurements to extract µ a and µ s ' from diffuse reflectance images acquired at multiple spatial frequencies.
Materials and methods Single snapshot cSFDI instrument setup (Fig. 1 ) A 120 mW 660 nm laser diode (HL6545MG Opnext Inc. ) was powered and stabilized using a combined laser diode and temperature controller (Newport Corporation). Coherent light from the laser diode was spatially homogenized using a ground glass diffuser and then condensed onto a sinusoidal-patterned slide (Applied Image Inc. ). The pattern was imaged onto the sample using an objective lens in off-axis configuration. The sinusoidal projection pattern had a fixed spatial frequency of 0. 185 mm 1. Data was recorded using a high-speed sCMOS camera (Hamamatsu Photonics, Orca Flash 4. 0) with a cross polarizer placed in front of a 16 mm fixed focal length lens (Edmund Optics). For all experiments mentioned below, the lens aperture was f/5.
Due to the non-trivial nature of the phantom making process, the optical properties are not equally spaced. Calibrated data are used to calculate µa and µs'. Right: Speckle flow index is calculated from the same raw image. A sliding window filter is used to compute the spatial standard deviation and mean intensity. The ratio of these quantities produces the speckle contrast (K) image. Speckle Flow Index (SFI) is then calculated from speckle contrast according to the equation above where T is the integration time.
This range was chosen to reflect red blood cell velocities encountered in microcirculation  [25]. Conventional LSI was performed by projecting planar coherent illumination, while single snapshot cSFDI was performed by projecting spatially modulated coherent illumination. In every other way (aperture, exposure time, optics) the two measurements were completely identical. Fifty sequential frames were acquired at each flow speed. SFI maps were calculated for each frame and averaged over a region of interest that was positioned over the entire length of the tube. Additionally, µ a and µ s ' maps were recovered from one of the single snapshot cSFDI data sets to demonstrate its ability to recover spatial maps of all three sources of optical contrast.