dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We are grateful to  Dr Dietmar Schwahn  ( Forschungszentrum Ju ¨lich ) for stimulating discussions and support of this project, and to  Manfred Heiderich ,  Simon Staringer ,  Michael Wagener ,  Lydia Fleischhauer-Fuss ,  Harald Kleines ,  Vladimir Ossovyi  and  Dr Nikolas Arend  ( Forschungszentrum Ju ¨lich ) for their technical support during installation and commissioning of the chopper at  KWS-2.
Materials and methods Type specimens of all nearly described species of Eugenia from Madagascar have been examined. All Malagasy specimens of Eugenia housed at MO (abbreviations following Th iers (2015)) have been viewed by  NS (through May 2014) , as have all duplicates housed at his institution  (KSP). Specimens housed at G and P have been studied by MC and PP. Duplicates of many specimens housed at KSP also have been consulted by NS. Specimens cited here also were compared against all material of Eugenia from the Comoros and Mascarenes housed at MO through May 2014. All specimens housed at MO should have duplicates at P and TAN given existing exchange agreements, although none at TAN have been seen by the authors. Accession numbers of specimens (where indicated) follow the herbarium acronym with a hyphen, whereas barcode numbers are enclosed in square brackets.
Species descriptions include all information that can be interpreted with confi dence and, given available information, are more or less in parallel. Th e species concept and criteria follow previous applications  (Snow 1997; Snow et al. 2003). Terminology largely follows earlier works for Malagasy Eugenia (e. g. ,  Snow et al. 2012 ) but with greater consistency regarding general terminology (Beentjie 2010). Terms specifi c to Myrtaceae have been minimized, but may include anthopodium, metaxyphyll, brachyblast, bracteole, monad, and triad, given their descriptive utility in Myrtaceae (see  Briggs and Johnson 1979). Th e collection number cited for each specimen follows immediately after the senior collector, in accordance with most database systems now in use. Geocoordinates in square brackets were determined retrospectively by various workers.
Hotlinks to holotypes on Tropicos® are included in lieu of illustrations of the new species. In addition, scanned images for all barcoded specimens from P are available online through the MNHN Vascular Plant Database (http://science. mnhn. fr/institution/ mnhn/collection/p/item/search/form). Photos of living material are included when available. Th e conservation status of each species was assessed following  IUCN Red List Categories and Criteria (IUCN 2012). Th e calculations of Area of Occupancy (AOO), Extent of Occurrence (EOO) and number of subpopulations follow the methodology of  Callmander et al. (2007) , using a grid cell size to calculate AOO of 3 × 3 km.
Acknowledgments Th e fi rst author thanks colleagues at  Missouri Botanical Garden in St. Louis (MO)  for loans of specimens, access to collections, and general assistance; in particular,  Zachary Rogers ,  Jennifer Kuhl , and  James Solomon. We also thank  MO  for permission to use holotype images on Tropicos® (http://www. tropicos. org). MC is grateful to  Laurent Gautier  and  Fabienne Th  onney for their help at G. Tabita Randrianarivony  assisted with formulation of the specifi c epithet for Eugenia tiampoka, and  Lalao Andriamahefarivo  provided valuable advice on Malagasy vernacular names. Peter Wilson  (NSW),  Kanchi Gandhi  (GH) and especially  Roy Gereau  (MO) wrote or advised on the Latin descriptions and epithets. General discussions of  Malagasy Myrtaceae  with  James Byng  and  George Schatz  have been helpful.
Record-keeping Sea-ice scientists still use non-standardized, ad hoc systems for identifying samples, but if we are to establish comprehensive, accessible, and useful sea-ice biogeochemical databases, then instituting basic standards to classify samples will be necessary. These metadata requirements apply not only to observations at the time of sampling, but also to sample processing and preparing data sets for archiving. In an effort to begin to meet the need for standardized record-keeping, we encourage researchers to always identify their samples with the following information: For each core, a standard data sheet should be prepared, giving the important metadata, information on how the core was processed, and what subsamples were taken for what analyses (Figure  7 ); eventually these sheets should be also populated with the analysis results for archiving.
Genetic community assessments Since 2001, investigators have extracted environmental DNA from sea ice for various sequencing or prokaryotic community fingerprinting applications, enabling determination of prokaryotic community composition, structure, and metabolic potential within sea-ice samples (Table  2 ). In a few cases, RNA has been extracted with DNA to determine the structure and function of the active prokaryotic community. Samples are often size-fractionated with filters of different pore sizes to separate major components of the community before nucleic acid extraction. To facilitate intercomparison with the GOS (Global Ocean Sampling Expedition) dataset, we recommend standard pore sizes of 0. 1, 0. 8, and 3. 0 µm  (Rusch et al. , 2007) , although there is little evidence that these cutoffs correspond to natural ecological boundaries in sea ice.
New advances in quantifying aerosol fluxes require simultaneous analyses of sea-ice components, with careful attention to the local meteorology, so that the measured aerosols can be linked to their upwind source regions. Of particular interest is the role of halogens in atmospheric chemistry of the polar regions  (Simpson et al. , 2007; Abbatt et al. , 2012) , including the function of Br in tropospheric ozone and mercury depletion and the possible importance of iodine in new particle formation. High concentrations of BrO observed in satellite datasets during the polar spring, in particular, suggest that halogens originate at the sea-ice surface; the available studies of halocarbons in sea ice, to date, have confirmed variable and often high concentrations of biogenic halocarbons in ice, brines, and overlying snow  (Sturges et al.
Acknowledgments This manuscript is a product of SCOR working group 140 on Biogeochemical Exchange Processes at  Sea-Ice Interfaces (BEPSII) ; we thank BEPSII chairs  Jacqueline Stefels  and  Nadja Steiner  and SCOR executive director  Ed Urban  for their practical and moral support of this endeavour. This manuscript was first conceived at an  EU   COST Action  735 workshop held in Amsterdam in April 2011; in addition to COST 735, we thank the other participants of the "methods" break-out group at that meeting, namely  Gerhard Dieckmann ,  Christoph Garbe , and  Claire Hughes. Our editors,  Steve Ackley  and  Jody Deming , and our reviewers,  Mats Granskog  and two anonymous reviewers, provided invaluable advice that not only identified and helped fill in some gaps, but also suggested additional ways to make what is by nature a rather dry subject (methods) at least a bit more interesting and accessible.
Data are represented as percentage of G1 or S-phase cells in each condition. EdU labelling of NPCs. E17. 5 NPCs were cultured in monolayer with rh-BMP7 and rh-FGF9 (50 and 100 ng ml À 1 , R&D systems) in KSFM. Cultures were incubated with 20 mM EdU (Click-iT EdU Alexa-Fluor 488 Imaging Kit, Life Technologies) 4 h after growth factor stimulation and pulse-chased for 20 h. Fixation, permeabilization and Click-iT reaction was performed according to manufacturer's instructions. Cultures were incubated with anti-pHH3 (1:100, Cell Signaling) antibody for 1 h and Alexa-Fluor-568 secondary antibody was used to visualize the staining. Nuclei were stained with Hoechst 33342 (Life Technologies). Images (5-10)were taken per well for each condition with a minimum of three biological replicates from two independent experiments (n ¼ 2).
Pooled images were analysed by Image-J and number of EdU þ (S-phase) and/or pHH3 þ (Mitosis or M-phase) nuclei were counted and divided by the total number of nuclei to determine the percentage of cells in S-and M-phases. Data are represented as percentage of S-or M-phase cells in each condition. Morphometrics and statistical analyses. (i) Kidney weight measurements were normalized to body weights to account for any differences in overall body size. Kidney size measurements were determined by calculating the cross-sectional area of the pole-to-pole distance on dissected whole kidneys using SPOT 5. 1 imaging software. Measured kidney weights and sizes of individual animals per group are represented in scatter plots. (ii) Quantitation of NPC number and proliferation was performed manually for a minimum of five serial sections 100 mM apart per kidney per genotype and the total number of individual or tamoxifen-treated mice (n) analysed per time point is indicated in the figures.
Acknowledgements We thank  Dr Jun Ninomiya-Tsuji  for TAK1 and JUN constructs,  Dr Michael Schneider  and  Dr Laurie Glimcher  for Tak1 c/c mice and  Dr Axel Behrens  for Jun c/c mice. This work was supported by  National Institutes of Diabetes and Digestive and Kidney Disease  Grant  R01DK078161  (L. O. ). Core facilities support was provided by  Maine Medical Center Research Institute  core facilities for molecular phenotyping and progenitor cell analysis (supported by  National Institutes of General Medicine (NIGMS)   5P30 GM106391 ),  Histopathology  ( NIGMS 5P30 GM106391  and  5P30 GM103392 ),  Transgenics and Gene Targeting  ( NIGMS 5P30 GM103392 ) and  Cell Culture /Viral Vectors  ( NIGMS 5P30 GM103392 ).
Claudine DUVIVIER has received travel grants, honoraria or study grants from various pharmaceutical companies, including Bristol-Myers-Squibb, Gilead Sciences, Janssen, Merck and ViiV Healthcare. Pascal PUGLIESE is member of advisory boards for Gilead and BMS. Laurent COTTE has received research grants from ViiV healthcare and MSD, personal fees from Mylan and non-financial support from BMS, Gilead Science, Janssen Cilag, MSD and ViiV healthcare. Alissa NAQVI, Véronique OBRY-ROGUET, Antoine CHERET, and Pierre PRADAT have no conflict of interest to disclose. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. So far, few data are available regarding the antiretroviral regimens currently prescribed in HIV/HCV co-infected patients. The present study was conducted to describe a large cohort of HIV/HCV coinfected patients enrolled in a French multicenter cohort of HIV-infected patients, and to emphasize the specificity of this population regarding potential interactions between DAAs and antiretroviral drugs.
The Dat'AIDS cohort A cross-sectional observational study was conducted at the end of 2012 using the multicenter Dat'AIDS cohort. The Dat'AIDS Cohort represents a collaboration between 10 major French HIV treatment centers using a common electronic medical record for the follow-up of HIV-, hepatitis B virus (HBV)-and HCV-infected adults (NADIS 1 [Fedialis Medica, Marly le Roi, France]), corresponding to a representative sample of the French infected population regarding potential inter-region disparities  [22]. Patient-related data are recorded during medical visits in a structured database, allowing the use of the database for clinical, epidemiological or therapeutic studies. Data quality is ensured by automated checks during data capture, regular controls, annual assessments, and ad hoc processes before any scientific analysis is performed.
Data collected Demographic data, last available CD4 cell count, last available HIV-RNA, HCV genotype (the most recent one in case of reinfection) and the last antiretroviral treatment were recorded. Liver fibrosis was evaluated by liver biopsy and/or elastometry (Fibroscan 1 ) and/or Fibrotest 1 , and results were converted into METAVIR fibrosis score equivalent. For patients with successive fibrosis evaluations, the last score was retained for the study. For patients evaluated by several methods at the same time, the fibrosis score determined by liver biopsy was kept as a priority against elastometry, the latter being prioritized against Fibrotest 1. Fibroscan 1 -based assessment was considered valid if the Inter Quartile Range (IQR) was 30% and the success rate 50%. The fibrosis score was defined as a function of liver stiffness as: 7 kPa: F0-F1; 7-14.
Statistical analysis Discrete variables are presented as number of cases and percentages, and continuous variables are presented as median values and IQR. Characteristics between naïve and pretreated patients were compared using Pearson's Chi-square test for categorical parameters and a t-test for continuous parameters. For all analyses, a two-tailed significance testing and a significance level of 0. 05 were used. Statistical analysis was performed using SPSS version 19 for Windows (SPSS Inc. , Chicago, IL, USA).
Acknowledgments The authors would like to thank  Hervé Bismut  for editorial assistance in the preparation of the manuscript, and the members of the Dat'Aids group:  S. Brégigeon ,  O. Faucher ,  V. Obry-Roguet ,  M. Orticoni ,  M. J. Soavi ,  I. Luquet-Besson ,  E. Ressiot ,  I. Pinot ,  M. J. Ducassou ,  H. Bertone ,  S. Galie ,  S. Trijau ,  A. S. Ritleng ,  A. Ivanova ,  M. Guignard ,  C. E. Cano ,  I. Poizot-Martin  (Marseille);  B. Marchou ,  P. Massip ,  E. Bonnet ,  M. Obadia ,  M. Alvarez ,  L. Porte ,  A. Debard ,  L. Cuzin ,  P. Delobel ,  M. Chauveau ,  D. Garipuy ,  I. Lepain ,  M. Marcel ,  E. Puntis ,  K. Sauné  (Toulouse);  P. Pugliese ,  C. Ceppi ,  E. Cua ,  J. Cottalorda ,  P. Dellamonica ,  E. Demonchy ,  B. Dunais ,  J. Durant ,  C. Etienne ,  S. Ferrando ,  J. G. Fuzibet ,  R.
Sediment leaching reproducibility Given evidence for a potential sample size effect on the Nd isotopic compositions of sediment leachates  (Wilson et al. , 2013) , we tested the effect on Pb isotopic compositions at two core depths (328 cm and 424 cm). We see effects from 200 ppm to 2600 ppm on 206 Pb/ 204 Pb, 207 Pb/ 204 Pb and 208 Pb/ 204 Pb (Figure  S1 ), representing on average ~10 % of the glacial-interglacial variability in the record. Since these tests represent a worst case scenario, they imply a generally reliable recovery of the authigenic Pb isotope signal. We also analysed a subset of nine samples without complete decarbonation before the leaching (Table  S4 ) and these data are in excellent agreement with the decarbonated leachate data. The results of both tests are consistent with a mass balance argument that the recovery of authigenic compositions by sediment leaching should be more robust for Pb than Nd isotopes  (Gutjahr et al.
Our leachate data from sediment cores SK129-CR2 and ODP defined by those ferromanganese nodules (Figure  3 ), as well as extending to more radiogenic compositions during interglacials. The excellent agreement between the two datasets indicates that our record was influenced by the same two Pb sources as those crusts, which appears to confirm both the reliable recovery of an authigenic signal and its bottom water origin. This evidence also argues against a pore water control, or other in-situ controls, because in those cases such a well-defined binary mixing line would not be expected to be replicated between multiple nodules and sediment cores in different sedimentological environments across a large area of the Indian Ocean (Figure  1 ).
Acknowledgments We thank Jo Clegg and Jason Day for help keeping the clean lab and MC-ICP-MS running, and Oliver Shorttle for assistance with Pb isotope data reduction. We also thank two reviewers for their valuable comments which helped us improve the manuscript. The sediment core was collected on board ORV Sagar Kanya of the Ministry of Earth Sciences, India. This study was supported by a NERC studentship to DJW and NERC Grant NE/F006047/1, RG50124 to AMP/AG. Ferromanganese crusts and nodules whose surface layers were analysed for Pb isotopes are also plotted  (von Blanckenburg et al. , 1996, pink diamonds; Vlastelic et al. , 2001 , orange diamonds, their N-Indian domain). Blue arrows show schematic representation of the deep circulation (after  Mantyla and Reid, 1995; You, 2000)  and dotted line shows the extent of the Bengal Fan.
, 1998)  according to an exponential law. The reliability of this approach was optimised by using matrix-and concentration-matched standards and samples  (Rehkamper and Mezger, 2000) , spiking with a constant Pb/Tl ratio (~2) and mixing Pb and Tl immediately prior to analysis  (Kamenov et al. , 2004). The mercury (Hg) beam was also monitored at mass 202, allowing for an interference correction for the 204 Hg on 204 Pb using the natural 204 Hg/ 202 Hg ratio, itself corrected for mass fractionation assessed by Tl and using an exponential law. Concentration-matched NIST-SRM-981 Pb standards were measured after approximately every five samples, and a linear correction was applied to all data measured in each analytical session in order to produce agreement with the accepted composition of NIST-SRM-981 Pb  (Galer and Abouchami, 1998; Abouchami et al.
Detrital sediment Pb isotopic composition of the Lower Meghna Sample BGP 21 was collected from the Lower Meghna during the monsoon period and represents the whole silicate fraction of the suspended load. It was leached with 1 M acetic acid to remove authigenic components before dissolution and measurement of its Pb isotopic composition  (Galy and France-Lanord, 2001). Its Pb isotopic composition is 206 Pb/ 204 Pb = 19. 297 ± 0. 005, 207 Pb/ 204 Pb = 15. 796 ± 0. 005, 208 Pb/ 204 Pb = 39. 72 ± 0. 01 (all 2σ errors). (Butzin et al. , 2005; Cao et al. , 2007)  and was converted to calendar years using the  Fairbanks et al. (2005)  calibration curve 01. 07 (see http://radiocarbon. LDEO. columbia. edu). These data were originally presented in  Piotrowski et al. (2009) , but there was an error in how the reservoir correction was applied which has been corrected here.
Joseph, MI). The first chromatographic separation was done using an SPB-5 capillary column (5% diphenyl-, 95% dimethylpolysiloxane, length 30 m Â internal diameter 0. 32 mm Â film thickness 1 lm; Supelco, St-Germain-en-Laye, France and the second separation using a DB-17 capillary column (50% dimethyl-, 50% diphenylpolysiloxane, length 2. 50 m Â internal diameter 0. 178 mm Â film thickness 0. 30 lm; J&W Agilent, Santa Clara, CA). To achieve reliable identification, the data obtained were cross-matched against spectral databases (NIST/ EPA/NIH 2005 v2. 0d, Gaithersburg, MD; Wiley 275K, 1996; Masslib 1999: MSP Köfel, Koeniz, Switzerland) and comparisons with databases of linear retention indices  (Kondjoyan & Berdagué, 1996). Data were expressed in arbitrary units of area.
Multi-response modelling The multi-response stoichiokinetic model was developed using Matlab R2009a Ò software with the associated optimisation and statistics toolboxes. The system of ordinary differential equation (ODE) obtained was solved using time discretisation by the ode15s solver of Matlab. As the system was placed under transient conditions (during the temperature increase), the resolution of the system required the use of very different time scales. Therefore a solver for stiff systems such as the ode15s was found to be more suitable than the ode45 (that turned out to be unsuccessful)  (Shampine & Reichelt, 1997). The ode15s solver is based on the implementation of the numerical differentiation formulas of order 1-5. The fit of experimental data by the model was made according to the method of maximum likelihood.
Given the number of parameters to be settled, we choose to conduct this recognition procedure under positivity constraint. In fact, the values of the rate constants and activation energy are necessarily positive. Therefore we used the fmincon function from Matlab which allows to bound the vector of parameters to adjust. However, this function also restricts the number of algorithms available for the minimisation procedure. We used the active-set algorithm  (Rakowsha et al. , 1991)  in order to minimise the opposite of the likelihood function. After the fit of the model parameters to the experimental data, the confidence intervals were calculated from the Fisher information matrix. Briefly, the covariance matrix of the estimated parameters is obtained from the inverse of the Fisher information matrix.
Acknowledgments T. T. and D. L. performed synthesis of individual double-walled carbon nanotubes. D. L. , T. M. , M. P. , and J. -L. S. devised and performed Raman experiments. D. L. and  R. A. identified atomic structures of the nanotubes by electron diffraction and HRTEM. M. A. and S. R. devised 2-D membrane theory and made calculations of RBLM frequencies of individual DWNTs. D. L. , M. A. , D. R. , A. O. , T. M. , R. A. , M. P. , J. -L. S. , S. R. , and Yu. Y. actively participated in the data analysis, discussions, and wrote the paper. D. L. , M. A. , D. R. , and S. R. gratefully acknowledge the financial support of  Russian Science Foundation  (Grant No. 15-12-10004 ). R. A. gratefully acknowledges the support of the  Spanish Ministerio de Economia y Competitividad  ( FIS2013-46159-C3-3-P ) and funding from the  European Union   Seventh Framework Program  under Grant No.
In this paper we present a performance analysis of the European lightning location system EUCLID for cloud-to ground flashes/strokes in terms of location accuracy (LA), detection efficiency (DE) and peak current estimation. The performance analysis is based on ground truth data from direct lightning current measurements at the Gaisberg Tower (GBT) and data from E-field and video recordings. The E-field and video recordings were collected in three different regions in Europe, namely in Austria, Belgium and France. The analysis shows a significant improvement of the LA of the EUCLID network over the past 7 years. Currently, the median LA is in the range of 100 m in the center of the network and better than 500 m within the majority of the network. The observed DE in Austria and Belgium is similar, yet a slightly lower DE is determined in a particular region in France, due to malfunctioning of a relevant lightning location sensor during the time of observation.
evaluate the performance of the EUCLID (European Cooperation for Lightning Detection) LLS in terms of LA, DE and the accuracy of the peak current estimate, we are using approaches (A) and (C) in this paper for the collection of ground truth data by using data from the direct lightning current measurement at the Gaisberg Tower (GBT)  (Diendorfer et al. , 2009a) , and video and E-field records of lightning data collected in three different regions (Austria, Belgium and France) in Europe  (Poelman et al. , 2013b) , respectively. Those measurements should be representative for all regions in Europe covered by the EUCLID network with similar sensor baselines. We do not present any data on polarity errors because by comparing LLS data with independent Efield measurement data we have never observed such errors since we started the measurements.
EUCLID network In 2001 several countries (Austria, France, Germany, Italy, Norway and Slovenia) started a cooperation named EU-CLID. The goal of this cooperation is to provide to the end users "European-wide" lightning data of high and nearly homogeneous quality. Since that time also Spain, Portugal, Finland, Sweden and Belgium joined EUCLID. The EUCLID cooperation is special in the sense that it is the merge of independent national networks, and the individual partners are highly motivated to run their local networks with state-ofthe-art lightning detection sensors. All the partners employ dedicated technicians to supervise and maintain the network and to react in short time in case of sensor or communication problems. As of December 2014 the EUCLID net- In addition to the processing carried out by each national LLS, data from all 149 sensors are processed in real-time using a central processor in Austria at ALDIS (Austrian Lightning Detection and Information System), which also provides daily performance analyses reports for each of the sensors.