dataesr/scientific-paragraphs-categorization huggingface dataset:
Binding We assessed the association of multimodal information by means of a WM binding task that had already been used in several studies in our laboratory, and which measures the ability to associate verbal and spatial features  (Mitchell et al. , 2000a,b; Prabhakaran et al. , 2000; Quinette et al. , 2006 Quinette et al. , , 2013;; Hainselin et al. , 2011;  see Figure  1 ). The task was presented on a computer using SuperLab Pro software, which also recorded responses. In the learning phase, stimuli consisted of four colored uppercase consonants, displayed for 5 s in the center of a 5 × 4 grid, and four colored crosses placed randomly in the remaining 16 squares. Participants were asked to mentally match each consonant with the location represented by the cross of the same color. After a 1-s retention interval, a black letter was displayed in a specific square in the grid, and participants had 4 s to determine whether the letter was in the same place as it had been matched in the learning phase.
Their head was immobilized in a headrest following the orbitomeatal line. The radiotracer was injected via a catheter inserted into a vein in the arm. Transmission scans were obtained with a 68 Ge source. At Time 0, 3-5 mCi (111-185 Mbq) of 18 F-FDG were injected as a bolus, and a 10-min data acquisition session began 50 min post-injection. Full 3D volume acquisition allowed for the reconstruction of 63 planes, with a voxel size of 2. 2 × 2. 2 × 2. 43 mm.
Preprocessing of the images All imaging data were preprocessed and analyzed using statistical parametric mapping software (SPM5; Wellcome Department of Cognitive Neurology) 1 implemented in Matlab (MathWorks, Sherborn, MA, USA). The T1-weighted MRI images were preprocessed using the voxel-based morphometric procedure (VBM), with the VBM5. 1 toolbox, which corresponds to a unified segmentation approach  (Ashburner and Friston, 2005). PET images were first corrected for partial volume effects (PVEs) using PMOD software  (Quarantelli et al. , 2004) , for an optimized voxel-based method. This software allowed us to correct for graymatter (GM) signal loss owing to spill-out onto non-GM tissues, and for GM signal increase caused by spill-in from adjacent white matter. Every reconstructed PET image was coregistered to the corresponding MRI image and spatially normalized to the MNI template by adopting the normalization parameters obtained from the unified segmentation procedure applied to the MRI images.
ACKNOWLEDGMENTS This study was supported by the  Institut de la Longévité et du Vieillissement scientific interest group (GIS) ,  Inserm ,  France Alzheimer  and  Conseil Régional de Basse-Normandie. These funding sources played no role in the study design, the collection, analysis and interpretation of data, the writing of the report, or the decision to submit the article for publication. We are grateful to  Florence Mezenge  for her help with the imaging analyses and to  Dr Shailendra Segobin  for his advice on language.
The mean cognitive score from the MDRS was 141. 25 (range 132-144, SD ¼ 3. 27). Preclinical HD patients had normal scores on all these measures. According to self-report, two preclinical HD patients were left handed. Preclinical HD patients' estimated probability of neurological symptom onset within 5 years was determined from data previously proposed by  Langbehn et al. (2004). A table is provided for each CAG repeat between 36 and 56, and lists the probability of onset within certain time frames for current ages from 0 to 95 years, conditional on the individual being currently presymptomatic  (Langbehn et al. , 2004). Probability of onset within 5 years was determined for each gene carrier based on their CAG repeat and current age (in percentage: range 2-66, mean ¼ 23. 31, SD ¼ 20). HD patients were recruited from the Huntington's patient population receiving annual medical and neuropsychological monitoring in the Department of Neurology of the University Hospital of Angers.
Two hypotheses can be raised to try to explain these unexpected results. The first refers to a methodological point: although cognitive and affective ToM was assessed using objective measures, cognitive and affective empathy was evaluated with self-report questionnaires. However, several studies have shown that HD patients may have impaired self-awareness of cognitive or emotional abilities  (Hoth et al. , 2007; Duff et al. , 2010). So this difference in data collection may explain in particular why clinical HD patients reported no deficit in cognitive empathy, whereas objective measure highlighted affective ToM impairment. This is a significant limitation of our study, which helps indirectly to confirm that HD patients may show anosognosia and corroborate the results of some publications which demonstrated recently some differences between objective and subjective measures of empathy  (Devlin et al.
The assembled Frankia sp. strain BMG5. 1 genome was analyzed via the Integrated Microbial Genomes (IMGer) platform of the Joint Genome Institute, Walnut Creek, CA. This whole genome shotgun sequence has been deposited at DDBJ/EMBL/GenBank under accession number JWIO00000000. The version described in this paper is JWIO01000000. The draft genome was compared to that of Candidatus Frankia datiscae to identify those genes different between the two genomes using the default values of 30% amino acid identity over 80% of the length of the shortest sequence on the IMGer platform  33.
Acknowledgments This research was supported by  The Ministere de l'Enseignement Superieur et de la Recherche Scientifique ,  Tunisie  project  LR03ES03. We would like to thank  Prof. Manfred Rohde  ( Helmholz Centre for Infection Biology, Braunschweig, Germany ) for the scanning Electron Microscopy. PN acknowledges funding from the  French ANR (BugsInACell   ANR-13-BSV7-0013-03 ). Partial funding was provided by the  New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number  2617. This work was partially supported by the  USDA National Institute of Food and Agriculture Hatch  Project  022821.
Microarray is a powerful and cheap method to identify and quantify gene expression in particular in a mix of total RNA extracted from biological samples such as the tsetse fly gut, including several organisms (here, the fly tissue and the intestinal microorganisms). Besides, biostatistics and bioinformatics allow comparing the transcriptomes from samples collected from differently treated flies, and thus to identify and quantify differential expressed genes. Here, we describe in details a whole microarray transcriptome dataset produced from tsetse flies symbionts, Sodalis glossinidius and Wigglesworthia glossinidia. The tsetse fly midguts were sampled at key steps of tsetse fly infection by trypanosomes, 3-day and 10-day sampling times to target differentially expressed genes involved, respectively, in early events associated with trypanosome entry into the midgut and with the establishment of infection; 20 days to target the genes involved in events occurring later in the infection process.
Custom-made 60-mers oligonucleotide microarrays The tsetse fly symbiont custom-made density arrays (8 × 15 K format) were designed with 60-mer oligos specific to: * For Sodalis  [2, 3] : genes of the S. glossinidius chromosome (NCBI RefSeq: NC_007712. 1; GenBank accession number AP008232), and genes of the Sodalis four plasmids pSG1 (NCBI RefSeq:NC_007183. 1), pSG2 (NCBI RefSeq: NC_007184. 1), pSG3 (NCBI RefSeq: NC_ 007186. 1), and pSG4 (NCBI RefSeq: NC_007187. 1) [8, 9]. Four unique probes were designed for each gene. * For Wigglesworthia  [4] : genes of the W. glossinidia chromosome (from Glosina morsitans morsitans) (NCBI Reference Sequence: NC_016893. 1) [10]. Ten different probes were used for each gene. To avoid cross-hybridization with non-target genes, for Sodalis and Wigglesworthia custom-microarrays, probes were selected only when they correspond to unique sequences.
The details of the Sodalis and Wigglesworthia array design, sample description, and expression data are available at Gene Expression Omnibus (GEO) under accession numbers respectively, GPL17347 and GSE48361 for Sodalis: (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE48360; http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE48361)  [2, 3] , and GPL18427 and GSE55931 for Wigglesworthia: (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE55931)  [4].
Microarray data analyses Lowest normalization was used for within-array normalization. Quantile normalization was used to make the density distributions similar across arrays  [11]. Only one expression value was then assigned to each biological replicate by averaging the normalized expression values through Cy3 signal intensities. The pictures of microarray data scanned with an Agilent microarray scanner (Agilent Technologies) were extracted with the software (version 10. 5. 1. 1) Agilent Feature Extraction. When in at least three of the four replicates, data show with expression levels greater than the background noise, then they were selected for further analyses. In the case of Sodalis transcriptome analyses, statistics was performed using the TIGR MeV (MultiExperiment Viewer) v4. 5 software (http://www.
Functional annotation of differentially expressed genes Regarding Sodalis transcriptomes, functional annotation of differentially expressed genes (DEGs) was performed using DAVID software  [17]. It was used to assess whether specific biological functions or pathways were overrepresented among the DEGs, based on gene ontology (GO) terms and on the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways (http://www. genome. jp/kegg/). A score based on Fisher's exact test reflected the probability that the prevalence of a particular term within a cluster was a simple matter of chance or not. The p-values were corrected to account for multiple testing  [13] ; a p-values lower than 0. 05 was considered significant. As concerns the Wigglesworthia samples, GO was performed using the GeneSpring database, and Wigglesworthia gene expression data were also analyzed by principle component analysis (PCA)  [18, 19]  performed with GeneSpring on infected (or stimulated) vs.
non-infected (or non-stimulated) conditions at the different experimental infection times. Quantitative real-time PCR (qPCR) analysis cDNA was synthesized from 5 μg of total RNA from each biological replicates using random hexamers and Superscript II reverse-transcriptase (Invitrogen, France). qPCR was then tested on some Sodalis genes that were differentially expressed in microarray experiments between the different groups of flies analyzed to confirm the results. Primers specific to the chosen genes were designed using Primer-Blast software (http://www. ncbi. nlm. nih. gov/tools/ primer-blast/). qPCR reactions were then performed in an Mx3005P QPCR System (Agilent Technologies) using the Brillant II Sybrgreen qPCR Kit (Agilent technologies) with 2 μl of cDNA in a 25-μl total volume. qPCR was analyzed using the qPCR Stratagene MxPro 3005P data analysis software.
Image acquisition was done either using a confocal imaging set up (Zeiss LSM 510 upright microscope, Zeiss, Germany), equipped with a Plan-Apochromat 63x/1. 4 Oil M27 objective or a epifluorescence widefield imaging setup (Zeiss Axioplan 2 upright + Axiocam MRc5 digital camera)). Image recording was performed with the appropriate software (Zen black Software or Axiovision LE46-Zeiss). The following antibodies were used: anti-CXADR (HPA030411, Atlas Antibodies, Stockholm, Sweden), anti-CXADR (H300, sc15405, Santa Cruz Biotechnology, Heidelberg, Germany) anti-NIDOGEN (Clone ELM1, Millipore, Darmstadt, Germany), anti-NEPHRIN (GP-N2, Progen, Heidelberg, Germany), anti-ZO-1 (Clone ZO1-1A12, Life Technologies, Karlsruhe, Germany), anti-β-Actin (Clone AC-15, Sigma, Schnelldorf, Germany), anit-CD2AP (generous gift by Andrey Shaw, Washington University, St.
Acknowledgments We would like to thank  Charlotte Meyer ,  Betina Kiefer ,  Sigrun Nestel  and  Temel Kilic  for their expert technical assistance. This study was supported by the  German Research Foundation (DFG) :  CRC 1140  (to FG, TBH),  Heisenberg program  and  CRC 992  (to TBH); by the  Else Kröner Stiftung  (to FG and TBH); by the  Fritz-Thyssen-Stiftung  (to FG and TBH); by the  European Research Council  ( ERC grant  to TBH); by the  BMBF-Joint transnational  Grant (TBH) and by the  Excellence Initiative of the German Federal and State Governments  ( EXC 294  to TBH).
This study was supported by the  German Research Foundation (DFG) :  CRC 1140  (to FG, TBH),  Heisenberg program  and  CRC 992  (to TBH); by the  Else Kröner Stiftung  (to FG and TBH); by the  Fritz-Thyssen-Stiftung  (to FG and TBH); by the  European Research Council  ( ERC grant  to TBH); by the  BMBF-Joint transnational  Grant (TBH) and by the  Excellence Initiative of the German Federal and State Governments  ( EXC 294  to TBH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
High spatial resolution and short acquisition time are the major advantages of the current CTA studies. This technology allows visualisation of a greater volume per unit time, resulting in reduced pulsation and stairstep artefacts. CTA has the ability to generate threedimensional multiplanar and volume-rendered images. Assessment of the renal arteries should be performed using vascular windows on a dedicated three-dimensional workstation. It is imperative to review the data sets using multiple reconstruction formats, including multiplanar reformatted images, shaded surface display and maximum-intensity projections. The use of all these reformats in addition to the axial Braw data^has been shown to improve the sensitivity and specificity of this imaging modality  [25]. Although the diagnosis of cervico-encephalic FMD can be suspected with Doppler ultrasound in case of vascular loops, ectasia, intimal flap or aliasing, it is most frequently established with cross-sectional imaging, using CTA of the supra-aortic trunks (SAT), MRA or in some cases conventional angiography.
Experimental procedures The experimental trials were performed in an outdoor cycling stadium in the hot/humid conditions of Guadeloupe, French West Indies (WBGT: mean±SD outdoor temperature: 27. 6°C ±0. 8°C, dry bulb temperature: 32. 5±1. 2°C; 57%±0. 05% RH and wind: 25. 9 km. h -1 ±0. 7 km. h -1 ). HR was monitored continuously using a portable telemetry unit (Suunto Memory Belt, Suunto, Vantaa, Finland) with recording every 10 seconds, and the data were analyzed with Suunto software. T co was assessed via the gastrointestinal temperature using ingestible temperature measurement pills (CorTemp, HQ, Inc. , Palmetto, FL, USA). The athletes were instructed to ingest these pills 6 to 8 h before all experimental trials to ensure the pill was out of the stomach, thereby avoiding variability in T co due to pill movement or fluid/food consumption.
Analysis of Corticomotor Excitability Muscle recordings were performed as previously described with minor modifications  (Hosoido et al. , 2009). For forelimbs and hindlimbs, we analyzed the corticomotor responses evoked in interosseus muscles on the left side following stimulation of the right motor cortex  (Oulad Ben Taib et al. , 2005). We used subcutaneous electrodes (Technomed 017K025) implanted in interosseus muscles. The impedance was kept below 5 K. In previous studies, we determined the ''hot spot'' of the gastrocnemius muscle  (Oulad Ben Taib et al. , 2005). This allowed us to identify the precise location corresponding to the largest motor evoked potential (MEP; confirmed by epidural stimulation with tungsten microelectrodes TM33A05, World Precision Instruments, UK), which was found to be located between 2-4 mm laterally, and between 1 mm anterior and 2 mm posterior (coordinates related to bregma).
Behavioral Data We assessed the effects of intra-nuclear administration of GAD65Ab bilaterally upon the exploration behavior (open field) and upon locomotor activity (beam test). Rats were assessed 6 h after the administration of GAD65Ab, using two digital cameras (Canon ZR40). Displacement times and number of squares crossed were obtained by extracting manually the position of rats from digitally reconstructed images using the APAS system (Ariel Dynamics, USA). The images were filtered using a Sobel filter providing contrasted pictures by emphasizing edges and transitions. The spatial accuracy was 1. 5 mm. The sampling rate was 60 Hz. The reproducibility of the method has been assessed with 2 independent observers (beam test: Pearson product moment correlation = 0. 958; open field: Pearson product moment correlation = 0.
Behavioral Data Effects of GAD65Ab on exploration behavior (open field) and locomotor activity (beam test) were assessed. For exploration behavior the number of squares crossed in an open field by rats infused with b78, b96. 11, Ringer solution, or non-injected animals was analyzed (Figure  8 ). The administration of b78 decreased the exploration behavior of rats in the open field significantly as seen in the number of squares crossed compared to the other groups (P < 0. 001). Gait was moderately irregular. Both groups injected with b96. 11 and Ringer solution showed a slight but significant decrease in exploration behavior as compared to the group without injection (P < 0. 05), however the animals' gait was regular. For assessment of locomotor activity the animals had to traverse an elevated horizontal beam (beam test).
To this aim, we first sampled an extensive range of ticks, with 58 tick species examined, and developed a sensitive detection method that reveals a wider Coxiella diversity than recognized in past studies. Second, instead of relying solely on the 16S rRNA gene, a molecular marker that is notoriously inadequate for inferring reliable fine-scale phylogenies  [32] , we used a novel multilocus typing method, allied to Whole Genome Sequencing (WGS) data, and conducted phylogenetic analyses on a large amount of DNA sequence data. Third, we examined two major ecological features of Coxiella-like organisms, i. e. their ability to be maternally-inherited through the tick egg cytoplasm and to grow in a vertebrate cell environment suitable to C. burnetii. Altogether, this corpus of data has led to the characterization of a large genetic and ecological diversity within the Coxiella genus, far beyond the C.
The overall dataset included 33 to 40 alleles per bacterial gene (Table  2 ) and 51 new multilocus genotypes (43 in Coxiella and eight in Rickettsiella). Within the Coxiella genus, all pairs of 16S rRNA gene sequences are at least 93% identical (Table  2 ) and range in threshold values typically used to delineate other Legionellales genera such as Legionella  [33]  and Rickettsiella  [34]. Each of the infected tick species harbored a specific bacterial genotype or a set of closely related genotypes. None of the Coxiella multi-locus genotypes identified in ticks was identical to those of the 15 C. burnetii reference strains (Table B in S1 Text), although some showed moderate levels of nucleotide identity: pairwise identity between the two groups ranged from 77. 8% to 97. 7%. For each bacterial gene, the genetic diversity was significantly higher in the Coxiella strains of ticks than in C.
Coxiella burnetii originated from a tick-borne Coxiella ancestor We constructed a multi-gene phylogeny of the entire Coxiella genus using a dataset that included the Coxiella and Rickettsiella sequences from ticks, the 15 C. burnetii reference genomes, as well as sequences from Legionella spp. and more distant outgroups that were available in Gen-Bank (Table B in S1 Text). The concatenated sequences included 3009 unambiguously aligned base pairs (bp). Prior recombination tests showed that Coxiella and Rickettsiella strains did not exhibit a strictly clonal structure, but rather experienced significant genetic exchanges. We thus applied a sequence-based network approach that does not force relationships to be tree-like but rather incorporates recombination into the phylogenetic reconstruction.
Coxiella sequences were also searched for in the whole genome sequence (WGS) data of R. microplus and I. scapularis (GenBank accession numbers ADMZ02000000 and ABJB000000000, respectively) using the 1,995,281 bp C. burnetii genome (str. Nine Mile I RSA 493, GenBank accession number NC002971) as a probe and the Basic Local Alignment Search Tool (BLAST) with default parameters. Table C in S1 Text reports the number and content of Coxiella contigs that were detected in the R. microplus WGS data.
Molecular and phylogenetic analyses The GBLOCKS program  [63]  with default parameters was used to remove poorly aligned positions and to obtain non-ambiguous sequence alignments. Sequences of individual genes that differed by one or more nucleotides were assigned distinct allele numbers using DNASP  [64] , with the option of excluding sites with alignment gaps and/or missing data. Tick-borne Coxiella strains are defined as each unique combination of alleles. The genetic diversity estimates (P s , number of polymorphic sites; A d , allelic diversity; π, nucleotide diversity; D, average number of nucleotide differences between sequences) were computed using DNASP. Other statistical analyses were carried out using the R statistical package. All sequence alignments were checked for putative recombinant regions using the GENECONV  [65]  and RDP  [66]  methods available in the RDP3 computer analysis package  [67].
Phylogenetic analyses were based on single and concatenated sequences of the five bacterial genes used in the multi-locus typing scheme and on the 50 Coxiella genes found in the R. microplus WGS data. Sequence alignments included Coxiella and Rickettsiella sequences obtained in this study from tick DNA, as well as sequences available in GenBank from reference strains of C. burnetii, Rickettsiella grylli, Legionella pneumophila, L. longbeacheae, and two more distantly related bacteria, Escherichia coli and Salmonella enterica (Table B in S1 Text). The evolutionary models fitting the sequence data most closely were determined using the Akaike information criterion with the program MEGA. For each data set examined, the best-fit approximation was the general time reversible model with gamma distribution and invariant sites (GTR+G+I).
Accession codes Nucleotide sequences of PCR-amplified fragments of tick-borne Coxiella and Rickettsiella genes have been deposited in the GenBank nucleotide database under accession codes KP994768-KP994862 (16S rRNA), KP994678-KP994767 (23S rRNA), KP985445-KP985537 (GroEL), KP985265-KP985357 (rpoB) and KP985358-KP985444 (dnaK).
Acknowledgments We are grateful to  X. Bailly ,  A. Barbour ,  L. Beati ,  T. Boulinier ,  J. L. Chapuis ,  F. Dantas-Torres ,  A. Estrada-Peña ,  M. Gauthier-Clerc ,  L. Gern ,  D. González Acuña ,  J. Gonzalez-Solis ,  U. Guidon ,  A. Guglielmone ,  K. Hansford ,  M. Hipfner ,  A. Jaeger ,  D. Jenny ,  M. Labruna ,  R. Lane, M. S. Latrofa ,  C. Lebarbenchon ,  J. Liu ,  J. Medlock ,  S. Nava ,  A. C. Norte ,  U. E. Schneppat ,  D. Spratt , P.
Financial support was provided by the  CNRS-INEE  ( Programme PEPS-Ecologie de la Santé 2014 , 'SYMPATTIQUES': OD LZ; http://www. cnrs. fr/inee/outils/PEPS2014. htm), French http:// www. institut-polaire. fr/ipev/programmes_de_recherche), the  CNRS-INEE/TAAF  ( Programme Iles Eparses  "PathOrnithoTiques": KDMcC; http://www. cnrs. fr/inee/recherche/programmes/iles_eparses. htm), and the  Agence Nationale de la Recherche  ( ANR-11-BSV7-003-02 :  KDMcC ,  ANR-13-BSV7-0018-01 :  KDMcC ,  ANR-3215AO-3R077 -STEV: FR, PD, CA,  JFT ,  ANR-11-LABX-0048 : FV, OM, LZ, EJ; http://www. agence-nationale-recherche. fr/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.