dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work was supported by the  French national research Agency  ( ANR-10-GENM-017-PhyloFish  to JB,  ANR-13-BSV7-0015-Maternal Legacy  to JB, and  ANR-13-ISV7-0005-PhyloSex  to YG) and by the  National Institutes of Health  ( R01 OD011116  and  R24 OD011199  to JHP). The authors thank the following persons for their precious help in providing fish and / or fish samples :  Allyse Ferrara  and  Quenton Fontenot  ( Nicholls State University, USA ) for bowfin and spotted gar,  Benjamin Geoffroy  and  Agnes Bardonnet  ( UMR INRA/UPPA, St Pée-sur-Nivelle, France ) for European eel,  Denis Clavé  ( Migado, Mouleydier, France ) for Aliss shad,  Marc Legendre  and  Jean-Christophe Avarre  ( IRD, Montpellier, France ) for Panga,  Sylvie Retaux  ( CNRS-DECA, Gif-sur-Yvette, France ) for Mexican tetra,  Pascal Fontaine  ( Lorraine University, Nancy, France ) for Northern pike and European perch,  Hugo Verreycken  ( INBO, Brussels, Belgium ) for Eastern mudminnow,  Martin Gerber  ( Fédération de pêche du Bas-Rhin, Obenheim, France ) for Grayling,  Cyrille Chataigner  ( salmoniculture de Rives, Thonon-les-Bains, France ) for European whitefish,  Louis Bertnatchez  ( Laval University, Canada ) for American whitefish and for leptocephalus European eel larval stage,  Goro Yoshizaki  ( Tokyo University of Marine Science and Technology, Tokyo, Japan ) for Sweetfish, and  Hervé Migaud  ( Institute of Aquaculture, Stirling, Scotland ) for Atlantic cod.
Availability and requirements The PhyloFish database is available online at http:// phylofish. sigenae. org/index. html. All sequences described in this paper can be downloaded from that site. RNA-seq raw sequence data from the Hiseq2000 sequencer have been deposited into the NCBI SRA under accessions SRP044781 (zebrafish), SRP044782 (spotted gar), SRP044783 (bowfin), SRP044784 (medaka), SRP045098.
Whole genome sequencing and SNPs discovery Total DNA were subjected to paired-end whole genome sequencing on the Illumina MiSeq platform (Illumina Inc. , San Diego, CA, USA). The number of reads that passed Illumina quality filters varied from 0. 9 to 1. 4 million. Chromosomal, pXO1 and pXO2 sequences of the Ames Ancestor strain or the RA3 strain were used as references for genome and plasmids assembly [GenBank: AE017334. 2, AE017336. 2 and AE017335. 3, CP009697. 1, CP009696. 1 and CP009695. 1, respectively]. Paired-end reads were mapped to the Ames Ancestor genome using the Bowtie 2 tool and its default parameters  (Langmead and Salzberg, 2012). Whole-genome SNPs discovery and variant calling were performed for each alignment using the SAMtools package  (Li et al. , 2009). Individual lists of SNPs were compiled and data filtered to remove SNP positions at ribosomal operons and 31 VNTR loci.
Comparative genomics and in silico canSNP genotyping In order to identify additional strains affiliated to the A. Br. Aust94 lineage, all publicly available B. anthracis genomes were retrieved from database and in silico genotyped. Briefly, the complete or draft genome assemblies from a hundred of strains were used to generate artificial sets of overlapping, 200 bp-long reads (with a 4-fold genome coverage). Each set of reads were aligned to the Ames Ancestor sequences using the same pipeline as described for the paired-end reads of the Swiss isolates. Genotypes were next determined based on 12 published canonical SNPs  (Van Ert et al. , 2007)  and a few additional SNPs  (Birdsell et al. , 2012; Girault et al. , 2014b; Khmaladze et al. , 2014). Sixty strains, representing the genetic diversity observed in B.
SNP discrimination assays by HRM We designed High Resolution Melting (HRM) assays for three novel specific SNPs using Primer 3 + software [http://www. bioinformatics. nl/cgi-bin/primer3plus/primer3plus. cgi/]. The positions of these SNPs in the Ames Ancestor genome and the primers sequences used are listed in Table  2. Amplification was performed on the ViiA7 TM Real-Time PCR System (Life Technologies) using the LightCycler 1 480 High Resolution Melting Master Mix (Roche Diagnostics) as previously described  (Derzelle, 2015).
Whole genome SNPs discovery and global phylogenomic analysis Five Swiss strains, previously assigned by MLVA-8 and canSNP typing to the rare European B. Br. CNEVA sub-branch (n = 4) or the worldwide spread A. Br. Aust94 lineage (n = 1)  (Pilo et al. , 2008) , were characterized by whole genome SNP analysis. Paired-end sequencing were performed using the Illumina technology, yielding 0. 5-1. 7 million reads per strain. Filter-passed reads were mapped to the Ames Ancestor reference genome for comparative analysis and SNP discovery. Data available for 40 additional genomes, from diverse geographic origins and lineages of B. anthracis, were also included (e. g. , 25 strains belonging to the nine A groups, eleven to the two branches of clade B, four to clade C). The genome sequence of Bacillus cereus strain AH820 was used as outgroup for phylogeny rooting (Table  1 ).
The observation that Asian strains, represented by the Korean soil isolate HYU01  (Kim et al. , 2014) , are branching out from the B. Br. 001/002 group leading to southern African strains early after the B sub-branches split (at a distance of 111 versus 424 SNPs) is consistent with this hypothesis (Fig. 1 ). However, it has to be taken into account that this branch could have been introduced to Asia more recently by contaminated animals or animal products. African strains of the B. Br. 001/002 lineage are characterized by relatively long branches (451-535 SNPs) as compared to the B. anthracis strains are noted by the strain number. Data taken from: (Statistische Erhebungen und Schätzungen über Landwirtschaft und Ernährung. Bearbeitet vom Schweizerischen Bauernsekretariat. 43. Jahresheft, Ausgabe 1966).
Br. 014/013 node has been reported to contain many strains from Africa, especially Namibia or South of Africa, China and Australia  (Khmaladze et al. , 2014) , but none of them were sequenced at that time. To obtain an accurate placement of the Swiss strain along the B. anthracis SNP tree, we further screened public databases for additional A. Br. Aust94 genomic sequences. The whole genome SNP phylogenetic tree drawn from 13 A. Br. Aust94 strains placed the JF3853 genome at the top of a new branch that branches off the basal node of the lineage, i. e. A. Br. 014 (Fig. 3 ). Four novel nodes (A. Br. 034-A. Br. 037) along the branch terminating in the "exotic" Swiss strain (located at a distance of 221 SNPs) were identified. SNPs specific to these genetic groups are listed in Supplementary data.
Biological data We analyzed β diversity in assemblages of algae and sessile invertebrates from rocky substrates at 2 depths on coastlines in the Ligurian, Tyrrhenian, Adriatic, Ionian and Central Mediterranean Seas (Fig. 1 ). Data for littoral areas (0 to -0. 2 m relative to mean low water level) were obtained for 60 replicated sites (5100 quadrats) from surveys carried out between 2000 and 2008. A total of 86 sites (4150 quadrats) in the shallow sublittoral (5 to 7 m) were sampled between 1999 and 2011. At littoral sites, visual estimates of species cover were made directly in the field using 20 × 20 cm (0. 04 m 2 ) quadrats. For the sublittoral, an area of 16 × 25 cm (0. 04 m 2 ) was photographically sampled, and then species cover was visually estimated from slides under magnification. For comparative regional analyses, sites were assigned to 2 regions.
Environmental covariates A suite of satellite-derived oceanographic variables were selected as environmental predictors of β diversity. Level 3 Moderate Resolution Imaging Spectro-radiometer (MODIS) data with spatial resolution of ~4 km at the equator and with daily temporal resolution were acquired from NASA's Goddard Space Flight Centre (http://oceancolor. gsfc. nasa. gov/). Cumulative climatologies between the years 2000 (the earliest available MODIS data) and 2011 were derived for night-time sea surface temperature (SST), sea surface salinity (Salinity), net primary productivity (NPP)  (Behrenfeld & Falkowski 1997) , diffuse light attenuation coefficient at 490 nm (k d 490), Chlorophyll a concentration (CHL) and concentration of colored dissolved organic matter (CDOM). For each of the satellite products the mean, standard deviation around the mean, mean annual range and highest monthly mean were calculated over the full time-series for each pixel corresponding to a single sampling site.
The GLS is derived from standard regression, but differs in the incorporation of the spatial structure directly into the residuals, assuming in this study an exponential relationship between the error term and geographic distance  (Diniz Filho & Bini 2005). All statistical analyses were done using R version 3. 1. 2 (R Development Core Team 2014) (packages 'vegan', 'nlme', 'spacemakeR', 'simba', 'spam') with code obtained from  Millar et al. (2011)  and  Chase et al. (2011).
Acknowledgements. This work was supported by the  European Community 's  7th Framework Programme  ( FP7/ 2007-2013 ) under Grant Agreement No. 287844  for the project ' Towards COast  to  COast NETworks  of marine protected areas (from the shore to the high and deep sea), coupled with sea-based wind energy potential (CoCoNet)'. The funding body had no role in study design, data collection and analysis, or preparation of the manuscript. Author contributions: A. R. and L. B. C. conceived the work and conducted the analysis; M. A. conducted the biophysical modelling; A. R. led the writing of the manuscript. All authors contributed data and reviewed the manuscript. We acknowledge and appreciate the effort of our reviewers for their invaluable assistance in improving the manuscript.
Primer and Probe Design for RT-RPA To identify the most conserved regions in the CHIKV genome for primer and probe design of the RPA assay, we first analyzed an alignment of fifty CHIKV full genome sequences from the RNA virus database (http://bioafrica. mrc. ac. za/rnavirusdb/) using GENEIOUS  [34]. The nsP1 gene region from nucleotide position 131-306 nt was chosen for final RT-RPA assay design. In total, 196 Genbank CHIKV sequences containing the conserved nsP1 region were re-aligned using GENEIOUS. Based on the alignment, two forward primers, two reverse primers and a single probe (Table  3 ) covering all known variants of CHIKV sequences were selected.
Through centrifugation of tubes, the magnesium acetate was dropped into each reaction simultaneously to trigger the RT-RPA reaction. The reaction tubes were vortexed, centrifuged and then placed in the ESE Quant Tubescanner (Qiagen Lake Constance GmbH, Stockach, Germany) for real-time monitoring of fluorescence. The reaction was performed at 39°C for 15 minutes, with brief mixing and centrifugation of reaction tubes after four minutes. The resulting amplification curves were analyzed by ESEQuant Tube Scanner software Version 1. 0 and threshold values were determined by slope validation i. e. slope (mV/ min) values were compared in order to distinguish positive from negative results.
Acknowledgements The work was supported by  Cellule Energie du CNRS  ( SOL-HYBTRANS  Project) and the  University of Rennes 1 (Action Incitative , Défis Scientifiques Emergents 2015). J. E. 's work is supported by the  Fondation d'entreprises banque Populaire de l'Ouest  under Grant  PEROPHOT 2015.
6 EGTA, 4 Na 2 -ATP, 0. 4 Na-GTP, 10 Na-phosphocreatine, and 2. 5 MgCl 2. For cortical layer 4 neurons, the internal solution contained (in mM) 125 K-gluconate, 10 KCl, 10 HEPES, 0. 2 EGTA, 4 Na 2 -ATP, 0. 3 Na-GTP, 14 Na-phosphocreatine, and 1. 8 MgCl 2. For both solution, pH was adjusted to 7. 3 with CsOH or KOH, respectively, and the osmolarity was 300 mOsm. For all recording conditions, only cells with access resistance < 18 M and a change of resistance < 25% over the course of the experiment were analyzed. Data were filtered with a Hum Bug (Quest Scientific, Canada), digitized at 2 kHz (Digidata 1444A, Molecular Devices, Sunnyvale, CA, USA), and acquired using Clampex 10. 2 software (Molecular Devices).
Cortical neurons were identified as excitatory cells, Regular-Spiking (RS) or Fast-Spiking (FS) interneurons, according to their electrophysiological properties (see Supplementary Figure  2 ). In some cases, at the end of the experiments TC slices were incubated overnight in phosphate buffer saline solution (PBS) containing 4% PFA at 4 • C and mounted between microscope slides and coverslips using Mowiol to image the correct localization of virus-induced expression of hChR2-mCherry with an AxioImager Z1 apotome and AxioVision software (Carl Zeiss, France).
, Lawrence, KS, USA). The electrical activity recorded by extradural electrodes was filtered at 50 Hz, sampled at 400 Hz and recorded by a computer equipped with Sirenia R software (Pinnacle Technology Inc. ). A 30 min period of baseline recording before ADX71743 injection (i. p. ; volume of injection: 100 µl/10 g mouse weight of a 100 mg/kg suspension in 50% v/v H 2 0 and hydroxyl-propyl-β-cyclodextrin) allowed detection of EEG abnormalities independent of experimental manipulations. Control animals were injected with vehicle alone. EEG recordings were performed together with monitoring animal behavior. The symptoms developing after injection were classified into different phases as described by  (Weiergraber et al. , 2006) ): phase 0 corresponds to normal exploration and posture; phase 1 corresponds to an "absence-like" non-convulsive state, with reduced motility and typical prostrated position of the animal; phase 2 shows partial clonus of head, vibrissae and/or forelimbs; phase 3 consists of a generalized clonus of the extremities, the tail, and sometimes vocalization; this phase can develop into typical "running fits"; phase 4 corresponds to a generalized tonic-clonic seizure with extension of the four paws; this phase is occasionally followed by death by respiratory failure.
Data Analysis Whole-cell recordings were analyzed using Clampfit 10. 2 software (Molecular Devices). Response amplitudes, short-term plasticity ratios, mIPSCs properties and tonic current amplitudes were compared between WT and mGlu7a AAA mice using the Mann-Whitney test or repeated measures ANOVA ( * P < 0. 05, * * P < 0. 01, * * * P < 0. 001). Normalized IP1 concentrations obtained from TR-FRET experiments were compared using an unpaired t-student test ( * P < 0. 05, * * P < 0. 01, * * * P < 0. 001). All averaged data are presented as mean ± SEM. Eelectroencephalography signals were analyzed using Matlab 2013b software (Matworks Inc. ). Short time Fourier transform analysis was realized using the Signal Processing toolbox (Spectrogram function) and applied to the EEG data in order to obtain the energy of the signal as a function of frequency and time  (Freeman and Quiroga, 2013).
ACKNOWLEDGMENTS We thank the IGF/IGH RAM animal facility,  N. Marchi  and the  IPAM  platform for help with the EEG recording and analysis, the ARPEGE platform at IGF for advice on TR-FRET experiments,  K. Deisseroth  for the hChR2-mCherry construct,  H. Adesnik ,  M. Bagnall ,  L. Ceolin ,  S. Dadak ,  F. De Bock ,  R. Lambert , and  J. Ster  for useful discussion.
Spinning disk images were acquired using a Plan-APO Â 40/1. 25 NA objective on a Leica DMI6000B microscope enclosed in a thermostatic chamber (Life Imaging Service) equipped with a CoolSnap HQ2/CCD camera (Princeton Instruments) coupled to a Sutter filter wheel (Roper Scientific) and a Yokogawa CSU-X1-M1spinning disc  57. The Metamorph software (Universal Imaging) was used to collect data and ImageJ (NIH) to analyse and process data. Since the embryo is a round cell with two objects of interest, the two sets of parental DNA, all analysis were performed in two dimensions in the medial plane formed by these two objects. Plasmids and in vitro transcription of cRNAs. We used the following constructs: pspe3-GFP-UtrCH 5 , pRN3-histone-red fluorescent protein (pRN3-histone-RFP)  58  , pRN3-SF9-GFP 36 , pRN3-EB3-GFP 59 , pRN3-EzTD-mCherry-VCA 14 , pRN3-histone-GFP  14  and pGEMHE-mCherry-Myosin-Vb (gift from Melina Schuh, MRC Cambridge, UK)  10, 29.
Great care was taken that all cells stay inside the pipette for the same duration (B100 s). They were then released and the shape recovery was recorded. The curve representing the evolution of the reduced diameter L l À 1 with L the bigger diameter and l the smaller diameter was plotted as a function of time and fitted as an exponential. The characteristic time t was extracted and the viscosity Z was deduced from the formula t ¼ ZRc k with R c as the cell radius and k as the cortical tension. Statistical analysis. The statistical analysis was performed using GraphPad Prism version 6. 00 for MacOS, GraphPad Software, La Jolla, CA, USA (www. graphpad. com). For comparison of several means, the normality of the variables was checked and parametric (Student's t-tests with Welch correction where indicated or one-way analysis of variance) or non-parametric comparison tests were performed with a confidence interval of 95%.
Acknowledgements We wish to thank the members of the Verlhac team,  Sophie Louvet  ( UPMC, Paris, France ),  Keith Jones  (the  University of Southampton, UK ) for helpful discussions and  Melina Schuh  ( MRC Cambridge, UK ) for the gift of the Myosin-Vb plasmid. This work was supported by grants from the  Ligue Nationale Contre le Cancer  ( EL2012/LNCC/MHV ) and from the  Fondation ARC  ( PJA20131200412  to M. -E. T. ). This work has received support under the program Investissements d'Avenir launched by the  French Government  and implemented by the  ANR , with the references:  ANR-10-LABX-54   MEMO LIFE ,  ANR-11-IDEX-0001-02 PSL* Research University.
They measured a reduction in blood flow compared to the control leg by up to 49%. The measure of the skin temperature via infrared thermography is a reliable, non-invasive method. For years, infrared thermography has become a powerful investigation tool for in section in many applications, namely, mechanical, building, sports, and medical applications  [12] [13] [14]. Due to its non-intrusive feature  [15, 16] , infrared thermography (IRT) can be defined as the science of analysis of data from non-contact thermal imaging devices. Many studies using infrared thermography have been devoted to a sport's performance and diagnostic of pathologies in the medical field. Several authors evaluated this tool to validate and to set up measurement protocols  [17] [18] [19]. In particular, Jones and Plassmann  [19]  discussed different ways of using infrared thermography as a diagnostic tool by capturing either a single static thermal image or a sequence of images and using the region of interest (ROI) method to calculate the temperature as well.
Material The skin temperature was measured with the VarioCAM ® hr head and connected to the IRBIS3 ® Infratec software. The infrared thermal camera is a non-invasive tool for measuring temperature, providing the surface temperature of a body. On this camera, we installed a type 1 lens with a focal length of 50 mm  [25]. This allows us to retain 99% of the information 1. 4m away. This distance has been chosen in order to view the body between the shins and the hips. The range of temperature measurement of the VarioCAM ® hr is between ´40 ˝C and 1200 ˝C with an accuracy of ˘2% in the measuring range. The radiometric thermographic system is based on an uncooled microbolometer FPA detector at 640 ˆ480 IR pixels. The camera spectral range is between 7. 5 and 14 µm. In this work, the reflected temperature barely affected results and can be neglected.
Material The skin temperature was measured with the VarioCAM® hr head and connected to the IRBIS3 ® Infratec software. The infrared thermal camera is a non-invasive tool for measuring temperature, providing the surface temperature of a body. On this camera, we installed a type 1 lens with a focal length of 50 mm  [25]. This allows us to retain 99% of the information 1. 4m away. This distance has been chosen in order to view the body between the shins and the hips. The range of temperature measurement of the VarioCAM® hr is between -40 °C and 1200 °C with an accuracy of ±2% in the measuring range. The radiometric thermographic system is based on an uncooled microbolometer FPA detector at 640 × 480 IR pixels. The camera spectral range is between 7. 5 and 14 μm. In this work, the reflected temperature barely affected results and can be neglected.
Patients with hypokalemia and/or hypomagnesemia (which are associated with electrocardiogram abnormalities)  15  were to be supplemented before romidepsin dosing. Additional details for this open-label, single-arm, phase 2 study have been previously described. 12 e study was conducted in accordance with the Declaration of Response was assessed every two cycles by both investigators and an independent review committee (IRC; expert radiologists and hematologic oncologists) according to the 1999 IWG guidelines for NHL (IWG-NHL). 14 All descriptive statistical analyses were performed by using SAS statistical software version 9. 2 (SAS Institute, Cary, NC, USA). Time-to-event data were summarised by Kaplan-Meier methods. Of 131 total patients in the overall study, 27 were diagnosed with AITL. Largely, the baseline characteristics of the 27 patients with AITL (Table  1 ) were similar to those of the overall study population, which were previously reported.
Peaks in common for both replicates were determined using intersectBed  (Quinlan and Hall, 2010) , with at least 25% peak overlap. For de novo motif finding, peak-motifs from RSATools was used with default settings  (Thomas-Chollier et al. , 2012). Enrichment of motifs was calculated by generating 1000 random control samples from the genome and the p-value of the enrichment was defined as the number of times the motif occurred as frequently in the control regions as in the real dataset, over the 1000 samples. The similarity of de novo motifs with known motifs was determined using compare-matrices from RSATools with lower threshold limit 0. 5, against a collection of known motifs  (Higo et al. , 1999; Davuluri et al. , 2003; Steffens et al. , 2004; Weirauch et al. , 2014). The bZIP29 TChAP-seq data have been deposited in the ArrayExpress database (http://www.
Root growth analysis Primary root length and lateral root density were determined 10 DAS. To score root growth defects, plants were grown for 7 DAS on ½MS plates inclined at an angle of approximately 45°. For gravistimulation experiments, roots of 4-day-old light-grown seedlings, germinated on vertical plates, were aligned, reoriented by a 90° angle and placed in the dark. Plates were scanned after 6 h and 20-24 h and the root bending angle was determined using ImageJ software. For root meristem length determination, plants were grown vertical for 5 DAS. After propidium iodide staining, root meristem length was measured from the quiescent center (QC) until the first cortex cell that elongates.
RNA-seq transcriptome analysis and quantitative PCR confirmation For RNA-seq, Promoter_bZIP29:bZIP29-SRDX line 1 and outsegregated WT line 1 plants were grown for 5 DAS on nylon meshes (Prosep), placed on vertical ½MS medium-containing plates. In three biological repeat experiments, root tips (<3 mm) were harvested. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) and treated with RQ1 RNase-Free DNase I (Promega). RNA samples were processed by preparing a Truseq RNA-seq library (Illumina) and sequenced on an Illumina HiSeq 2000 (50 nt single reads) at GATC Biotech Ltd (Cologne, Germany). The quality of the raw data was verified with FASTQC (http://www. bioinformatics. babraham. ac. uk/projects/fastqc/). Sequences were filtered and trimmed using FASTX-Toolkit (http://hannonlab.