dataesr/scientific-paragraphs-categorization huggingface dataset:
Suite au traitement automatique des textes et au filtrage manuel des occurrences de candidats termes, les enrichissements des données sont stockés au format XML-TEI complété par la proposition StandOff-Proposal, en cours de validation par le consortium TEI. La StandOff-Proposal permet de dissocier aisément le contenu textuel et l'ensemble des annotations. Ces traitements sont réalisés à l'aide de la plateforme de traitement spécifique au projet TermITH qui a fait l'objet d'un dépôt sur GitHub <https://github. com/simonmeoni/termITH-tool>. A partir des données enrichies, trois critères ont guidé l'extraction des noms et des adjectifs qui composent les N_Adj examinés : -ils sont communs à au moins deux des trois disciplines prises en compte dans l'expérience ; -ils apparaissent dans des candidats termes de forme N_Adj ; -les occurrences de ces candidats termes ont été jugées disciplinaires lors du filtrage manuel.
Les ressources terminologiques de référence pour chaque discipline ont été constituées par l'INIST. Elles proviennent du vocabulaire utilisé pour l'indexation des bases de données bibliographiques Francis et Pascal. Pour opérer cette confrontation, les noms et les adjectifs sélectionnés sont recherchés par leur forme dans le lexique transdisciplinaire et dans les ressources terminologiques. Lorsqu'ils sont absents de ces lexiques, ils sont considérés comme relevant de la langue générale et reçoivent l'étiquette LG. Lorsqu'ils apparaissent dans le lexique scientifique transdisciplinaire ou dans les ressources terminologiques, leurs sens, tels qu'ils sont décrits explicitement dans le lexique scientifique transdisciplinaire ou tels qu'ils peuvent être inférés dans les ressources terminologiques, sont comparés manuellement au sens qu'ils ont dans l'occurrence N_Adj candidate où ils figurent.
Données cliniques Concernant la population Marfan, une base de données implémentées à chaque consultation et répondant aux exigences de la CNIL (numéro de déclaration 1229912 v 0) a permi le relevé et l'analyse des données suivantes: le sexe, l'âge, la taille, le poids, la surface corporelle (obtenue selon la formule de Du Bois et Du Bois  [47] ), la présence de facteurs de risque, la prise de traitements tels que Beta-bloquants, Inhibiteurs de l'enzyme de conversion (IEC) ou antagonistes des récepteurs de l'angiotensine II (ARA2), la date de réalisation du scanner, le gène muté, la date et le type de chirurgie de l'aorte, de dissection aortique ou de décès. Concernant la population contrôle, les données ont été récupérées via les compte-rendus de consultation réalisées à l'Hôpital Bichat et sur les compte-rendus des scanners réalisées dans le service de radiologie de l'Hôpital Bichat.
Using SAXSQuant software (Anton Paar), the 2D image was integrated into one-dimensional scattering intensities I(q) as a function of the magnitude of the scattering vector q = (4π/λ) sin(θ), where 2θ is the total scattering angle. All data were calibrated by normalizing the attenuated primary intensity and then were corrected for the background scattering from the empty capillary and the solvent, and for slit-smearing effects by a desmearing procedure from SAXSQuant software using the Lake method. After correction, intensities were scaled into absolute units using water as a reference material. Liquid crystals were put in a paste cell, before being placed inside an evacuated chamber equipped with a temperature controlled sample holder unit. Mesoporous materials were put between two sheets of Kapton® placed in a powder cell before being introduced inside the evacuated chamber.
All data were corrected for the background scattering from the Kapton® and for slit-smearing effects by a desmearing procedure from SAXSQuant software using the Lake method. N 2 adsorption and desorption isotherms were determined on a Micromeritics TRISTAR 3000 sorptometer at -196 °C. The pore diameter and the pore size distribution were determined by the BJH (Barret, Joyner, Halenda)  [46]  method applied to the adsorption branch of the isotherm.
REMERCIEMENTS Aux membres de mon jury de thèse, à mes Maîtres, qui sont pour moi des exemples et des références en pathologies neuro-vasculaires. A mon président de thèse, le Professeur Emmanuel HOUDART, Je vous suis extrêmement reconnaissante d'avoir accepté de présider le jury de soutenance de ma thèse. Votre expérience, votre expertise dans le domaine et votre réelle vocation de médecin clinicien thérapeute au service des malades m'ont apportée une vision différente de cette spécialité. Autour de votre intérêt pour les conséquences éthiques du considérable développement des techniques d'imagerie et de traitement endovasculaire et de votre rigueur de travail face à des pathologies complexes, s'est progressivement constituée une véritable école Houdarienne, dont je suis fière d'avoir pu faire partie.
Les tests statistiques ont été effectués avec un test bilatéral à intervalle de confiance de 95%. Les données ont été analysées à l'aide du logiciel SAS version 9. 3 (SAS Institute, Cary, NC). Une analyse bivariée des critères de revascularisation de secours dans la population des ACAE a été réalisée en utilisant le test Chi-Square (ou le test exact de Fisher lorsque l'effectif était <5) pour les variables qualitatives non ordinales et le test t de Student pour les variables continues gaussiennes. La distribution des emboles selon leur taille et le site de l'occlusion initiale a été présentée sous la forme d'intervalle interquartile. Enfin, l'impact de l'ACAE, avec manoeuvre de revascularisation de secours, ou non, sur le devenir neurologique à 3 mois, a été illustré selon le même modèle.
Methods: We retrospectively reviewed, in a prospectively collected database, consecutive patients with anterior circulation stroke between January 2012 and December 2016. Angiographic images were analyzed to assess ACAE. The primary outcome was the favorable outcome defined as a 3-months modified Rankin Scale (mRS) of 0-2. Results: Among 690 included patients, ACAE occurred in 65 patients (9. 4%; 95%CI, 7. 2 to 11. 6%). ICA occlusion (tandem or terminal), ASPECTS<7, increasing number of passes and use of SR alone (compared to distal aspiration alone or combined technique) were found as independent predictors of ACAE. Compared to patients without ACAE, patients with ACAE have a lower efficacy outcome rates, with an adjusted OR (95%CI) of 0. 48 (0. 25 to 0. 92) for favorable outcome, 0. 53 (0.
Les données relatives à la procédure endovasculaire étaient aussi répertoriées prospectivement : la réalisation d'une anesthésie générale, l'utilisation d'un cathéter guide à ballon (BGC), la réalisation d'une angioplastie carotidienne au ballon et/ou mise en place d'un stent, l'administration au cours de la procédure d'héparine, le choix du dispositif de thrombectomie, le nombre de passages et le temps de procédure du point de ponction à la reperfusion. La technique de TM choisie était collectée pour le premier passage et sur l'ensemble de la procédure : soit aspiration, soit SR, soit association des dispositifs. L'évaluation de la reperfusion cérébrale au décours de la TM, basée sur le score mTICI ou modified Treatment in Cerebral Ischemia (24), était réalisée en fin de procédure par l'opérateur et validée par un second opérateur senior lors du recueil prospectif dans la base de données.
In the case of the 2P-STED setup, the excitation light was provided by a second Ti:Sapphire laser tuned to 910 nm running at 80 MHz that was synchronized to the OPO pulses. We used water-immersion objectives with long working distances, either from Nikon (CFI Apo 60X W NIR, 1. 0 NA, 2. 8 mm WD)  46  or Olympus (LUMFI 60×, 1. 1 NA, 1. 5 mm WD)  45. The STED pulses were broadened in time by passing them through glass rods and a long optical fiber (20 m) to ensure effective de-excitation and maximal resolution enhancement. Synchronization and optimal pulse delay were achieved with phaselocked loop electronics. The STED beam reflected twice on two different surfaces of a single spatial light modulator (SLM) (Easy3D Module, Abberior Instruments, Göttingen, Germany) to generate doughnut and bottle beams for 2D and 3D-STED microscopy.
5 h. 2 Hz confocal Ca 2+ imaging (12. 5 × 25 µm 2 , pixel size 100 nm) was performed for 2. 5 min and corresponding STED images (12. 5 × 25 × 1. 5 µm 3 , pixel size 19. 53 nm, z plane 250 nm × 6 planes) were acquired subsequently. 8 Hz Ca 2+ imaging (5 × 10 µm 2 , pixel size 78 nm) was performed for 2 min using bidirectional scanning and corresponding STED images (10 × 5 × 1. 2 µm 3 , pixel size 19. 53 nm, z plane 100 nm × 12 planes) were acquired subsequently. STED images were always acquired after Ca 2+ imaging so that Ca 2+ signals were not affected by the STED laser. Image acquisition was controlled by the software Imspector. Organotypic slice experiments except for SUSHI (described in Extracellular labelling for SUSHI) were performed in ACSF containing 125 mM NaCl, 2. 5 mM KCl, 1. 3 mM MgCl 2 , 2 mM CaCl 2 , 26 mM NaHCO 3 , 1.
When the shaft was shorter than 1 µm, the width of the further end of the shaft was used. Image processing and analysis. All STED images were deconvolved by Huygens Professional (SVI) software. Loops were manually identified and their inner perimeter and area were measured using ImageJ. Nodes were manually identified based on their enlarged 3D spherical submicron structure and shafts were identified as hyperthin tubes connecting nodes. To measure the width across these astrocytic components, we used a wavelet-based custom-made ImageJ plugin  50. Distance between nodes was measured as the distance along the shaft from the center of node to the center of the neighboring node. Structures within 20 µm from somatic border were defined as proximal whereas those that were more than 20 µm away were distal.
Two-color images except for Fig. 3d  were spectrally unmixed with ImageJ software (NIH) Plugin Spectral unmixing in order to separate spine morphology signals (e. g. , YFP, Citrine) and astrocytic morphology/Ca 2+ signals (e. g. , ZsGreen, GCaMP6s). A contact was defined by the presence of at least one pixel overlap between spines and astrocytic components (nodes or shaft). Spine heads were also manually identified and morphological parameters of spines and nodes (perimeter and area) were measured using ImageJ. Coverage fraction was calculated for all planes that includes a given spine and was subsequently averaged to acquire a representative value. Spines without full 3D information were excluded from the analysis. Coverage fraction for spines was calculated by dividing node-contacting spine head perimeter by total spine head perimeter.
For automatic and unbiased detection and analysis of spontaneous Ca 2+ events the ImageJ plugin LC_Pro 52 was used. Detected events were manually verified using Igor Pro (Wavemetrics)  12. The spatial spread was defined as the maximum best-fit ellipse area above 95% confidence of signal threshold during the event interval. The frequency was calculated by the number of detected Ca 2+ events in the field of view (12. 5 × 25 µm 2 ) per minute. To determine the initiation site of the Ca 2+ signals in the spongiform domain (Fig. 7 , Supplementary Fig. 5d-g ), Ca 2+ events detected by the software were matched with the STED image to identify their location. Ca 2+ events that were located at nodes were categorized as confined (node) or non-confined (node + shaft). There were no events detected only at the shaft.
We plotted the Ca 2+ trace using the ImageJ plugin Time Series Analyzer V3. We used the software NeuroMatic  53  to determine the onset times of the Ca 2+ transients: after binominal smoothing of the trace, a sigmoid (Boltzmann) function was fitted to the data (achieving a goodness of fit (R 2 ) of >0. 95) to compute the point of maximum curvature, which was defined as the onset time. If the software detected less than 1 frame onset difference between the node and the shaft, it was categorized as Node and/or shaft initiating event. If the onset of node was equal or greater than 1 frame earlier than shaft, then it was categorized as Node initiating event. LC_Pro never detected any events that were initiated on shafts, and we also confirmed this by measuring onset times in the different compartments.
Acknowledgements The study was supported by research grants from the  Agence Nationale de la Recherche  ( ANR-12-BSV4-0014  and  ANR-17-CE16-0002  to UVN and  SHRO ;  ANR-16-CE16-0001-0  to A. P. ) and  Fondation pour la Recherche Médicale  ( DEQ20160334901 ) and  LabEx BRAIN. M. A. was supported by postdoctoral fellowships from  RIKEN  and  JSPS (Japan). We thank  D. Gonzales ,  S. Laumond ,  J. Tessaire ,  L. Dupuy  and the  Neurocentre Magendie mouse facility  staff for mouse care and genotyping,  J. Tønnesen  for technical support and  M. Sherwood  and  S. K. Kim  for comments on the paper.
Measurements and samples collected in the outdoor system The outdoor behavior of the pigs was studied twice, near the middle (d7) and the end of the experiment (d19). During 24 continuous hours and every five minutes, the physical activity, feeding behavior and position of each pig in the field area were recorded. Data collected were used to estimate the covered distance in 24 hours by each pig. In the second trial, blood samples were collected before the adaptation (d-4), one day after adaptation (d1), in the middle of the experiment (d11) and toward the end (d22). Blood samples were used to determine hematological characteristics of pigs. Twenty samples of 0. 02 cm 3 of soil were collected to detect the macrofauna (10 before the arrival of the pigs and 10 after their departure). The soil was sampled using a frame (25 x 25 x 30 cm) and a spade, then the macrofauna was separated from the soil.
Calculations and statistical analyses A thermal humidity index (THI) was calculated for each day based on the following formula from the US National Oceanic and Atmospheric Administration (1976, cited by  Zumbach et al. [2008] ): THI (°C) = T -(0. 55 -0. 0055 x RH) x (T -14. 5) where T is the average daily ambient temperature (°C) and RH the average daily relative humidity (%). The average daily weight gain between the beginning and the end of the experiment was computed. Data on production traits (average daily gain, initial and final body weights, final back-fat thickness) were analyzed using a linear model (GLM procedure, SAS version 9. 4, Cary, NC, USA) with the fixed effects of the system (n = 3, CSC, CSP and OSP), the breed (n = 2, CR vs LW) and their interactions as main effects. The same models were used to analyze outdoor pigs' behavior (time spent in physical or feeding activities), without taking into account the system as fixed effect.
Keratinocyte Culture and treatment with Vichy Thermal Spring Water To avoid possible bias due to single donor intrinsic variability, pooled foreskin Normal Human Epidermal Keratinocytes (NHEK) were obtained from Lonza (Amboise, France, CC-2507) and cultured in MCDB153 reconstituted growth medium (US Biological â , Salem, MA, USA, powder K0200) solubilized either in normal water or in water containing 50% of VTSW -, supplemented with Human Keratinocyte Growth Supplement (HKGS, S-001-5, Invitrogen/Thermo Fisher Scientific, Villebon-sur-Yvette, France,), gentamicin (Invitrogen, 15710-049), and 0. 03 mM calcium chloride (CaCl 2 ). Keratinocytes were grown for 18 h before RNA extraction. These culture conditions were treated in triplicate.
Microarrays hybridization and data acquisition For each sample, 50 ng of RNA was treated with the Ovation Pico WTA System V2 (NuGEN, 3302-12, NuGEN, Leeks, The Netherlands). Then, 5 lg was fragmented and labelled with biotin (NuGEN Encore Biotin Module, 4200-12) and hybridized on Human Gene 2. 0 ST DNA chips (Affymetrix/Thermo Fisher Scientific, Villebonsur-Yvette, France, Affymetrix, 902112). The hybridization, washing and fixing were carried out according to Affymetrix protocol. Revelation step was performed with GeneChip Fluidics Station 450 (Affymetrix, 00-0079) and signal measurement with the GeneChip Scanner 3000 (Affymetrix).
Microarrays statistical analyses and selection of differentially expressed genes Treatment of raw signals was performed through the 'R' software (v3. 1. 1) [31]  and 'oligo' package (v1. 30. 0) from BioConductor project (v3. 0)  [32]. Data normalization was carried out through the RMA algorithm  [33, 34]. The statistical analysis was performed gene by gene and significantly differentially expressed genes between treated and untreated samples were identified using contrasts based on moderated t-statistics, performed with the R package 'Limma 3. 33. 1' [35]. Only genes presenting a fold change value |FC| ≥ 1. 5 and a P Value < 0. 05 were selected, as differentially expressed. In addition to the univariate comparisons between VTSW and Control's conditions, an unsupervised multivariate analysis (sPCA) based on all genes was performed to compare the conditions in a more global approach  [36].
Thematic analysis of over-represented groups of genes Functional analysis of differentially expressed genes was carried out by Laboratoires StratiCELL S. A. (Isnes, Belgium) using the 'Strati-CELL Skin Knowledge Database'  [37] , Straticell's proprietary database in which the genes are annotated in a context of cutaneous biology, based on public databases knowledge. The enrichment or over-representation of functional groups was carried out with the hypergeometric test method.
Immunofluorescence NHEK were isolated from foreskin leftovers and cultured in Epilife TM medium at 37 °C for 3 days, then transferred into a powdered MCDB153 medium (Calcium free) solubilized in either pure water (with and w/o CaCl 2 at 1. 8 mM or 200 mg L À1 ) or VTSW at 25% and 50% for 24 h. NHEK's were fixed and incubated with primary antibodies directed against TGM-1 (Harbor Bio Products 5003), CK-10 (Abcam ab76318) and FLG (Abcam ab81468) followed by appropriate fluorescent secondary antibodies (Molecular Probes A11001 or A11008). In addition, a fluorescent molecule, DAPI (4,6-diamino -2-phenylindole) allowed the detection of the nuclei of keratinocytes. The various fluorescent images, obtained from a Leica camera (DFC420C, obj. 940), were analysed by dedicated software (QWin/Leica/6 images per culture).
Transcriptomic study Unsupervised sparse Principal Component Analysis (sPCA) A majority of genes bring more noise than information and make the estimates of multivariate analyses unstable. In order to reduce the size of the matrix to a limited number of unsupervised selected genes, with minimal loss of information (low-rank reconstruction), a sPCA with a Lasso constraint has been performed using the normalized expression data for all the genes measured on the microarray. This powerful and robust approach allowed to reduce the dataset to 2862 genes. A representation of the samples in the first factorial plane shows a clear separation between the samples associated with the thermal water and the control growth medium on the first factorial axis (Fig. 1 ). This robust unsupervised approach demonstrates clearly that the samples from the untreated and TVSW treated conditions present clear differences in their gene expression patterns.
Supervised analysis: differentially expressed genes When keratinocytes were grown in the presence of 50% VTSW for 18 h, the expression of 1745 probesets (including 1356 annotated probesets) was found modulated, with a threshold of significance set for a P-value P < 0. 05 and a fold change |FC| ≥ 1. 5. The thematic analysis of these selected genes exhibiting a |FC| ≥ 1. 5 through Straticell proprietary skin database revealed that 34 modulated genes were representative of functional groups particularly relevant of skin biology, namely structure of DEJ, epidermal renewal, cell-ECM and cell-cell interactions, and desquamation (Fig. 2 , Table  S1 ), 14 modulated genes were linked to the response to oxidative stress (Fig. 3 , Table  S2 ), and 12 modulated genes were involved in the response to stress-induced DNA damage and DNA repair (Fig.
3), HBEGF and SFN. Induction of AQP3 was confirmed by QRT/PCR (FC = 4. 3, P < 0. 001). Of note, AQP3 is expressed in the basal and spinous epidermal cells, and is the most abundant skin aquaglyceroporin. Recent data suggest that glycerol transport by AQP3 is involved in the metabolism of lipids in skin as well as in the regulation of proliferation and differentiation of keratinocytes  [40, 41]. CD44 is involved in the regulation of keratinocyte proliferation in response to extracellular stimuli  [42]. HBEGF is a keratinocyte autocrine factor which plays a major role in the skin healing process by accelerating the migration of keratinocytes during re-epithelialization phase and contributing to a faster closing of the wound  [43]. Stratifin, or 14-3-3r protein, is involved in the epidermal proliferation-differentiation switch  [44].
Sor Juana Inés et le programme Phoebus : tester sur le gongorisme un logiciel d'exploration de l'intertextualité Mercedes Blanco 1 Malgré de nombreuses publications, qui se sont multipliées ces dernières années, on est loin d'être venu à bout de l'exploration du gongorisme, un phénomène dont l'importance a été reconnue depuis qu'il existe une histoire de la littérature espagnole. C'est une tâche d'une ampleur dissuasive que d'arpenter l'ensemble des textes qui pourraient porter les traces de l'influence de don Luis de Góngora (1561-1627), même si on se borne au XVII e siècle, période où elles sont plus directes et plus abondantes. Il est moins trivial encore de dire à quoi ces traces devraient ressembler. Or c'est à ce prix qu'on ramènerait le gongorisme à quelque chose de scientifiquement solide : un inventaire complet ou du moins une évaluation quantitative précise de relations hypertextuelles entre les écrits de Góngora et ceux qu'il a marqués de son empreinte.
Cet encodage lui-même peut être automatisé, totalement ou en partie. Les humanités numériques seraient donc le moyen idéal pour obtenir les données permettant de décrire de manière précise et globale un phénomène tel que le gongorisme 2. On se heurte cependant à des difficultés énormes dont on ne cachera pas qu'elles sont, en l'état actuel de nos moyens, insurmontables. Mais la tentative elle-même est instructive, dès lors qu'elle engage à mieux définir ce qu'il y aurait à trouver 3. 3 La présente étude est un premier pas vers un tel programme de recherches. Elle ne prétend pas résoudre le problème, ni même nous mettre sur une voie sûre pour le résoudre. Il nous suffira de montrer que même un outil qui est pour l'heure peu propre à la tâche qu'il est censé effectuer, en l'occurrence le logiciel Phoebus, développé, dans le cadre de l'OBVIL ou dans son voisinage, par Jean-Gabriel Ganascia et son équipe  4  , permet de réaliser une comparaison automatisée entre les poésies de don Luis de Góngora (Cordoue 1561-Cordoue 1627) et une oeuvre qui se situe dans le champ de leur influence ; celle de la célèbre religieuse mexicaine, Sor Juana Inés de la Cruz (San Miguel Nepantla, 1648-México, 1698).
L'application du logiciel Phoebus à la comparaison de ces deux ensembles de poésies nous est apparue comme un test ou une mise à l'épreuve méthodologique. Sor Juana étant tenue aujourd'hui pour le plus grand poète de l'Amérique coloniale -qu'il s'agisse d'une femme rend plus remarquable cette reconnaissance -, on dispose de plusieurs bonnes éditions de ses oeuvres et d'une bibliographie exponentiellement croissante. Bon nombre de réminiscences de Góngora dans ses vers ont été signalées dans l'édition de référence de l'oeuvre complète, parue dans la décennie de 1950 5 ; la question, objet d'une poignée de contributions critiques, est souvent touchée en passant dans les autres travaux dédiés à cette femme hors du commun.