dataesr/scientific-paragraphs-categorization huggingface dataset:
Molecular phylogenetic and haplotype network analyses New sequence data of COI, histone H3, and ITS region, generated in this study from 87 coral samples representing 11 species, were combined with published sequences of the families Lobophylliidae, Merulinidae Verrill, 1865, Diploastraeidae  Chevalier & Beau-Contributions to Zoology, 85 (4) -2016 vais, 1987 , and Montastraeidae Yabe & Sugiyama, 1941 , resulting in an alignment composed of 50 nominal species. Plesiastrea versipora was selected as outgroup because of its divergence from the Lobophylliidae, Merulinidae, Diploastraeidae, and Montastraeidae  (Fukami et al. , 2008; Benzoni et al. , 2011; Huang et al. , 2011; Budd et al. , 2012). The final concatenated dataset of aligned sequences of the three molecular fragments had a total length of 1939 bp (COI: 580 bp, histone H3: 318 bp, ITS region: 1041 bp).
The ITS region was the most variable, with 191 variable sites (148 positions parsimony-informative PI), the COI gene fragment showed 87 bp variable sites (57 positions PI), and the histone H3 sequences featured 90 bp variable sites (84 positions PI). The three single gene trees did not show any supported topological conflicts, although the resolution differed notably among the three topologies (Figs S3-S5). Nevertheless, each of the analyzed specimens belonged to the same molecular clade in all of the three phylogenetic reconstructions. Bayesian, maximum likelihood, and maximum parsimony topologies were highly concordant and node support values were high across the ingroup and outgroup. The phylogram based on the concatenated (COI, histone H3, and ITS region) molecular datasets was broadly consistent with previously published phylogeny reconstructions  (Huang et al.
Finally, we recommend also the inclusion of microstructural data to the presented molecular and micromorphological observations in future works as they were demonstrated to be useful and diagnostic in previous systematic revisions  (Budd et al. , 2012; Kitahara et al. , 2012b; Huang et al. , 2014a : Arrigoni et al. , 2014c; Janiszewska et al. , 2015). S11. Coralla of some of the specimens of Micromussa pacifica sp. nov. (referred to as Homophyllia cf. australis in text) examined in this study showing the intra-specific macromorphological variability of this species. Specimen code close to the images. All specimens are included in the phylogeny reconstruction in Fig. 3 (clade A ). S12. Coralla of some of the specimens of Homophyllia australis examined in this study showing the intra-specific macromorphological variability of this species.
Acknowledgements New Caledonia data and specimens were obtained during the  CORALCAL4  (http://dx. doi. org/10. 17600/12100060 ), BIBE-LOT  (http://dx. doi. org/10. 17600/14003700 ), CORALCAL5  (http://dx. doi. org/10. 17600/15004300 ),and  CHEST  (http://dx. doi. org/10. 17600/15004500 )expeditions on the RV Alis. We are grateful to the  Captain  and the crew for their valuable help during the campaigns and their knowledge of the Neocaledonian reefs during fieldwork. The participation of F. B. and B. W. H. was possible thanks to the kind help and support of  C. Payri  and B. Dreyfus. We are also grateful to  J. L. Menou ,  J. Butscher ,  G. Lasne ,  E. Folcher , and  A. Arnaud. We are grateful to  E. Karsenti  (EMBL),  É. Bourgois  ( Tara Expeditions ), and the  OCEANS Consortium  for sampling in Gambier Island during the Tara Oceans expedition.
We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA,  VIB ,  Stazione Zoologica Anton Dohrn, UNIMIB ,  ANR  ( projects POSEIDON/ANR-09-BLAN-0348 ,  BIOMARKS/ANR-08-BDVA-003 ,  PRO-METHEUS/ANR-09-GENM-031 , and  TARA-GIRUS/ ANR-09-PCS-GENM-218 ),  EU   FP7  (MicroB3/No. 287589 ), FWO ,  BIO5 , Biosphere 2, agnès b. , the  Veolia Environment Foundation ,  Region Bretagne ,  World Courier ,  Illumina, Cap L'Orient , the  EDF Foundation EDF Diversiterre , the  Prince Albert II de Monaco Foundation ,  Etienne Bourgois , and the Tara schooner along with its captain and crew. Tara Oceans  would not exist without continuous support from 23 institutes (http://oceans. taraexpeditions. org). This article is contribution number  44  of the Tara Oceans Expedition 2009-2012.
Coral collecting by A. H. B. was funded by the  ARC Centre of Excellence for Coral Reef Studies. We are grateful to  P. Gentile  for technical help with SEM and  P. Galli  for laboratory support at UNIMIB. R. A. gratefully acknowledges the  National Science Council of Taiwan for Summer Program in Taiwan 2013. This work is supported by  King Abdullah University of Science and Technology's Red Sea Research Center (CCF. grant  FCC/1/1973-07  to M. L. B. ).
When combined with the cross section measurements at other center of mass energies the present measurement can be used to improve PDF constraints. The data presented in this paper are collected at low instantaneous luminosity conditions with, on average, 1. 2 primary interactions per triggered event. The measured cross section is compared to the prediction from a next-to-leading-order (NLO) QCD calculation, performed using the NLOJET++ (v. 4. 1. 3) generator  [17, 18]  implemented in the FASTNLO (v. 2. 1. 0) framework  [19]. NP contributions to the cross section are taken into account in the theoretical prediction; electroweak contributions are negligible  [20].
Results The measured inclusive jet cross section and the theoretical predictions are compared in Figs. 1 2 3. In Fig. 1 , the double-differential cross section is plotted as a function of jet p T and |y|. The theoretical prediction obtained with the CT10 PDF set is shown as well. A more detailed comparison for all |y| bins is presented in Fig. 2 , where the ratios of data to theory using the CT10 PDF set are shown. Within the uncertainties, the data are well described by NLO QCD in the full kinematic range explored. In Fig. 3 , the data, with NP corrections, are compared in a similar manner to the predictions from other PDF sets, normalized to the CT10 prediction. In general, all predictions describe the data well. Within experimental and theoretical (not shown) uncertainties, only the comparison to the prediction from the ABM11 PDF set exhibits slight differences between the data and theory, an effect that has been observed also in other measurements, e.
Summary A measurement of the double-differential inclusive jet cross section was presented. The data were collected by the CMS detector in pp collisions at √ s = 2. 76 TeV, with an integrated luminosity of 5. 43 pb -1. The measurement covers the jet kinematic ranges of 74 ≤ p T < 592 GeV and |y| < 3. 0. A detailed study of the experimental and theoretical uncertainties has been performed. Contributions to the experimental systematic uncertainty were evaluated from the jet energy corrections, jet energy resolution, and integrated luminosity. Jet energy corrections dominate the experimental uncertainty, followed by smaller contributions from jet energy resolution and luminosity. The theoretical uncertainty is dominated by the missing higher-order corrections that were estimated by varying the renormalization and factorization scales, and the PDF uncertainty; the contribution of nonperturbative correction uncertainty is small.
MATERIALS AND METHODS We focused on two 21 base pair (bp) duplex DNA sequences, A and B (Figure  1 ), investigated experimentally by Gates et al. (7). All classical molecular dynamics (MD) simulations were performed using the Amber 12 suite of programs  (26). We started with reference DNA duplexes featuring an abasic site at the 11th nucleobase position (Ap11). Since no experimental structure has been reported for the ICL-containing duplex DNA, the two duplexes were built using the nab module of Amber, with conformational parameters characteristic of B-DNA. The parmbsc0 force field was used for DNA, the force field parameters for the Ap site were generated using Antechamber and atomic point charges were assigned using the RESP procedure. They are comparable to parameters similarly derived in the literature  (27) (28) (29) , and we verified that a similar behavior is obtained with the parmbsc1(30) force field, which is the current reference and most tested set of parameters for undamaged DNA  (31).
Finally, we compute global bending and twist stiffness of the damaged and undamaged oligomers. The calculations are done exactly as in  (38). Briefly, a quadratic model analogous to Equations (  1 ) and (  2 ) is used, with coordinates involving bending angles toward the grooves and toward the backbone together with total twist. The first two diagonal entries of the 3 × 3 stiffness matrix are stiffness constants for groove and backbone bending, respectively, from which the equivalent isotropic bending stiffness is computed as their harmonic average. The results in Table  2  again indicate exceptionally small stiffness of the oligomer containing ICL B. Overall, our data indicate that the two lesions exhibit quite different hydrogen bonding and stacking patterns and affect the DNA properties in a different way.
Approach between the abasic site and vicinal purines Our simulation of Ap-contanining 21-bp duplexes provide a dynamic view of the approach between Ap11 and the vicinal purines A31 and G33. It differs significantly from the distances inferred from X-ray structures of undamaged DNA (e. g. PDB ID code 3BSE (  7 )) or on 'frozen' molecular models, which both neglect the rearrangement the duplex undergoes upon formation of an Ap site. Our simulations go beyond these inspections, as we can infer approaching distances between the Ap site and proximal purines, as we also reported for other interstrand cross-links such as dCyd341  (13, 41). The two reactants exhibit different eases of approach: Ap11 gets closer to G33 spontaneously within ∼50 ns, prefiguring the cross-link Ap-dG. Interestingly, Ap and A31 in sequence B do not approach whereas the corresponding lesion Ap-dA was found experimentally to present a much higher yield of formation.
ACKNOWLEDGEMENTS This work was performed within the framework of the  LABEX PRIMES  ( ANR-11-LABX-0063 ) of  Université de Lyon , within the  program 'Investissements d'Avenir'  ( ANR-11-IDEX-0007 ) operated by the  French National Research Agency (ANR). Calculations were performed using the local HPC resources of PSMN at  ENS-Lyon. E. B. is grateful for a PhD fellowship from the  French Ministry of Higher Education and Research. T. D. and F. L. were supported by the  Grant Agency of the Czech Republic  ( 14-21893S ).
FUNDING Université de Lyon [LABEX PRIMES  ( ANR-11-LABX-0063 )];  French National Research Agency (ANR)  [' Investissements d'Avenir'  ( ANR-11-IDEX-0007 )];  Grant Agency of the Czech Republic  [ 14-21893S ]. Funding for open access charge: LABEX  PRIMES  [ ANR-11-LABX0063  of  Université de Lyon ].
Objectives: to evaluate orthogeriatric and nurse-led fracture liaison service (FLS) models of post-hip fracture care in terms of impact on mortality (30 days and 1 year) and second hip fracture (2 years). Setting: Hospital Episode Statistics database linked to Office for National Statistics mortality records for 11 acute hospitals in a region of England. Population: patients aged over 60 years admitted for a primary hip fracture from 2003 to 2013. Methods: each hospital was analysed separately and acted as its own control in a before-after time-series design in which the appointment of an orthogeriatrician or set-up/expansion of an FLS was evaluated. Multivariable Cox regression (mortality) and competing risk survival models (second hip fracture) were used. Fixed effects meta-analysis was used to pool estimates of impact for interventions of the same type.
Materials and methods Information on hip fracture hospital admissions was obtained from the UK hospital episode statistics (HES) database. Mortality data from the Office for National Statistics (ONS) were linked and extracted using an encrypted patient identifier. All patient episodes containing an ICD10-code indicating hip fracture (S72. 0, S72. 1, S72. 2, S72. 9) as the primary diagnosis and with a start date occurring within the study period (1st April 2003-31st March 2013) were identified (Supplementary data, Appendix 1, available in Age and Ageing online). Provider codes and treatment site codes were used to identify episodes occurring within the 11 NHS hospitals admitting hip fracture patients in the region of interest. The primary outcome of interest was time to second hip fracture within 2 years of a primary hip fracture.
We approached relevant health professionals within each hospital with a questionnaire we developed to allow the characterisation of pre-specified elements of secondary fracture prevention services over the study period. The proportion for each financial year was directly standardised using the age and sex structure of the total primary hip fracture population within each hospital (for hospital-specific proportions) and the region as a whole (for whole region proportion). c Impact of intervention on hip fracture rate not evaluated due to insufficient post-/pre-intervention data (either owing to another change in service delivery occurring too close to the intervention or the end of study period (given a 1-year lag would need to be used following an intervention to allow it to take effect)).
Strengths and limitations A major strength of the present analysis is the use of a natural experimental design where each hospital acted as its own control in a before-after impact analysis. The comprehensive nature of the HES database allowed for case-mix adjustment and a robust definition of primary hip fracture. A priori service evaluation findings provided details on the timing and nature of all major changes to service delivery of post-hip fracture care and secondary fracture prevention during the study period. Our analysis is subject to various limitations. We were only able to consider second fractures if associated with a separate hospital spell. Also, confounding events may have coincided with interventions of interest although we consider this unlikely given estimates were consistent across hospitals and for interventions at different time points.
Acknowledgements The HES data were made available by the  NHS Health and Social Care Information Centre. Copyright © 2013, re-used with the permission of The  Health and Social Care Information Centre. All rights reserved. We thank all the members of the  FRiSCy group  for contributing their time and expertise. S. H. and A. J. had full access to all of the study data and take responsibility for the integrity of the data and the accuracy of the data analysis. All authors revised and approved the final version of the article. A. J. and M. K. J. supervised the study and are joint senior authors. The ReFRESH study group consists of A. J. , M. K. J. , N. K. A. , C. C. ,  Prof. Andrew Farmer , D. P. -A,  Dr Jose Leal ,  Prof. Michael Goldacre ,  Prof. Alastair Gray ,  J. L. ,  Dr Rachael Gooberman-Hill  and  Laura Graham.
Data Collection and Definitions Information on patient characteristics, medical history, laboratory and imaging findings, vital signs before treatment, severity of ischemic stroke, and clinical outcome was collected prospectively by using the same structured questionnaire. The severity of the ischemic stroke was assessed by using the NIHSS score at admission and 24 hours later. We defined early neurologic improve-ment as an NIHSS score of 0 -1 at 24 hours or a decrease of at least 4 points in the NIHSS score.
Statistical Analysis Data are presented as means (SD) or medians (interquartile range) for continuous variables and percentages (count) for categoric variables. Normality of distributions was assessed by using histograms and the Shapiro-Wilk test. Bivariate comparisons were performed between the ADAPT and Solitaire groups by using 2 tests for categoric variables (the Fisher exact test was used when the expected cell frequency was Ͻ5) and Student t tests for continuous variables (the Mann-Whitney U test was used for non-Gaussian distributions). Differences in primary and secondary outcomes between the study groups were expressed as relative risks with 95% confidence intervals. We assessed the heterogeneity in outcome effect across centers by using the Breslow-Day test. Comparisons in primary and secondary outcomes were further adjusted for baseline differences (at P Ͻ.
In a posterior power calculation (not taking into account the adjustment), we calculated the smallest significant between-group difference (expressed as effect size by using relative risk) that our study sample size allowed us to detect with a power of 80%. Assuming an incidence of good outcome of 10% and 50% in the reference group (Solitaire), we could respectively detect a relative risk of 2. 34 and 1. 35 (or 0. 43 and 0. 74 for a detrimental effect). We suggest that future studies follow a randomized controlled trial with core imaging performed by an independent neurointerventionalist to further support those findings. We are currently starting the Interest of Direct Aspiration First Pass Technique (ADAPT) for Thrombectomy Revascularisation of Large Vessel Occlusion in Acute Ischaemic Stroke trial, a randomized, controlled, multicentric, blinded-end-point study (ClinicalTrials.
ACKNOWLEDGMENTS We thank  Mary Osborne-Pellegrin  for help in editing the final draft of the manuscript. Disclosures:  Bertrand Lapergue-RELATED : Grant: An institutional grant has been provided by  Penumbra  for ASTER TRIAL (ADAPT versus stent retriever in acute ischemic stroke); Support for Travel to meetings for the study or other purposes: travel support by Medtronic; Payment for lectures (including service of Speakers Bureaus): speaker's honoraria from  Penumbra. Bruno Bartolini-UNRELATED: Consultancy: Stryker Neurovascular. Mikael Mazighi-UNRELATED: Consultancy: Servier , Comments: honoraria for teaching engagements as a consultant; Payment for Lectures (including service on Speakers Bureaus): Covidien; Travel/Accommodations/Meeting Expenses Unrelated to Activities Listed: Bayer A. G.
Aceto et al. (  2016 ) collected a data base of damages from hydro-meteorological events, including flash floods and landslides in the Calabria region. They provide trend analysis on those damaging events. Karagiornos et al. (2016)  propose a method to map the susceptibility of the Greek territory to flash flood including structural building vulnerability but also social vulnerability. Ettinger et al. (2016)  propose a vulnerability function for buildings based on the reconstruction of a flash flood that occurred in Peru, where field data about damages and flooded areas were collected. Portugues et al. (2016) reconstructed an historical event that occurred in 1957 in Valencia (Spain) in terms of hydraulic and geomorphic elements, using historical sources of information (aerial photographs, water marks).
Acknowledgements We thank the numerous reviewers who provided valuable recommendations to improve the quality of the papers presented in this special issue and the chief editor,  K. Georgakakos  for his advice and help. We also appreciate the help of the editorial office of  J. Hydrology , in particular  Pallavi Das. The work presented in this paper is partly a contribution to the  HyMeX program  and to the  FloodScale ANR project  (contract  ANR   2011 BS56 027 ).
Telemetric Assessments The RPC-1 receiver plates and Data Exchange matrix were connected to a computer running on ART-gold software 3. 1 (Data Sciences International, Saint-Paul, MN, USA). We recorded right hippocampus EEG, T c , and locomotion in all animals and additionally either EMG (6 rats) or left hippocampus EEG (37 rats). The 22 h of recording were split into 5 s epochs (5 s-epochs) to analyze the concomitant telemetric variables (i. e. , T c , locomotion, EEG). The EEG and EMG signals were recorded at a sampling rate of 500 Hz. Only the right EEG signal above hippocampus CA1 was analyzed. Analyzes were carried out only on artifact free 5 s-epochs. According to three reference methods  (Tong and Thakor, 2009) , epochs were considered as artifacted when at least one value of the signal was missing, or when the absolute variation of the signal slope was greater than 0.
075 µV/ms, or when the absolute value of the signal was >5 standard deviations of the mean. After artifacted epochs rejection, the EEG power spectral analysis was performed in each non-artifacted epoch using a Fast Fourier Transform algorithm with Welch estimation (500 points, hamming window, and 50% overlap) perform with Matlab (Mathworks, r2013b version). The telemetric bandwidth being 1-50 Hz according to the manufacturer, only the following bands were considered (δ: 1. 5-4 Hz, Low θ: 4-6. 5 Hz, High θ: 6. 5-9. 5 Hz, α: 9. 5-12 Hz, β1: 13-18 Hz, β2: 18-25 Hz, Slow γ: 25-48 Hz). The absolute power of each band was calculated from EEG spectrum as the area under the spectrum curve. The relative power of each band was expressed in ratio of the total power spectrum in each epoch. When present, the frequency of maximal peak power was identified in each band by an integrated function of Matlab (findpeaks function).
Definition of Active Waking We determine the SLA threshold of active waking vs. inactive waking and sleep in a preliminary analysis carried out on the Baseline 22-h recording of the 6 animals equipped with EMG electrodes. We determine the vigilance level and the SLA value in a high number of 5 s-epochs in order to validate the use of SLA as a biomarker of active wake. The vigilance analysis, i. e. , repartition of epochs into wake, slow wave sleep and paradoxical sleep stages, was performed visually in 5 s-epochs in a blindto-treatment manner using a presentation software running on Matlab. Sleep and waking represented 42. 9 ± 1. 6 and 57. 0 ± 1. 4% of the time, respectively. The waking was further divided into active (15. 1 ± 0. 5%) and inactive (41. 9 ± 0. 9%) waking. A SLA ≥ 1 AU was rarely observed during sleep (298 epochs out of 15,433 epochs), but were predominant during wake (15,135 out of 15,433 epochs).
Statistical Analysis Statistical analyses were performed with Statistica software v7. 1 (StaSoft-France, Maisons-Alfort, France). Two K-mean Group effects performed on stressed animals were based on sBDNF values at Baseline and Recovery to determine the V vs. NV groups. The k-mean algorithm distributed the animals into a given number of subgroups in a way that minimize the intragroup variability and maximize the intergroup variability. In our case, we chose 2 subgroups (i. e. , V and NV animals). Time course was analyzed using repeated measures Analysis of Variance (ANOVA; Time effect) with conditioning effects (Group and Group * Time effects). Time effects corresponded to the effects of measure repetition (i. e. , Baseline, Post-Stress, and Recovery). Group effects corresponded to the effects of group classification (i.
e. , V and NV subgroups). Group * Time effects corresponded to the combined effects of the time and the group classification. When ANOVA revealed a significant effect, a posthoc Bonferroni tests for all couples were carried out. Correlations within subgroups were done using multiple correlation tests. The significance level was set at p < 0. 05. Data are presented as means ± standard error of the mean (SEM). To determine whether observed differences could represent biomarker, data underwent Receiver Operating Characteristic (ROC) curve analyses. The Area Under the ROC Curve (AUC) provides a measure of overall performance of the classifier. AUC with corresponding 95% Confidence Intervals (CI 95 ) were calculated with the statistical software package SPSS 22 for Windows (SPSS Inc. , Chicago, USA).