dataesr/scientific-paragraphs-categorization huggingface dataset:
La documentation disponible depuis la découverte constitue un autre outil indispensable au suivi conservatoire des oeuvres et fait l'objet d'une mission d'archivage, de numérisation et de dépouillement. Cet historique événementiel relatif à la conservation du lieu depuis sa découverte constitue une base de données sous forme de chronogramme alimenté régulièrement. L'étape suivante consistera à reporter l'ensemble des informations dans les couches conservatoires du SIG de l'équipe de recherche, et à les adosser au relevé numérique 3D.
Cette carte constitue le coeur de l'ouvrage. Pour aider à sa lecture, sa sémiologie est présentée très en détail. La mise en place d'une base de données est devenue incontournable pour impulser une dynamique d'analyse spatiale et de recoupement des données : le chapitre 3 retrace la genèse du système d'information géographique (SIG) qui a accompagné la conception et la réalisation de cet ouvrage. La plupart des cartes thématiques et analytiques présentées dans l'Atlas ont été produites à partir de ce premier SIG.
Pour pallier ce défaut, un fond topographique ombré des sols, précis au centimètre, a été réalisé par Julien Monney au moyen du logiciel ArcGIS à partir des nuages de points 3D Perazio de 2010, complétés par les contours topographiques au format raster provenant des levées topographiques Le Guillou-Maksud. Ces compléments concernent la Salle Morel, la Galerie du Bénitier, la Galerie Perdue, la Galerie de la Bretelle, la Galerie Rouzaud, le fond de la Galerie de l'Apodémus et la Galerie du Belvédère. Une nouvelle étape de relevé géomorphologique en grotte a été menée par Jean-Jacques Delannoy, Stéphane Jaillet et Benjamin Sadier sur la base de ce fond topographique de grande précision. Elle a permis de valider et de repositionner dans la géométrie de la grotte les informations initiales (carte de 2005) mais également de compléter le relevé cartographique, et parfois de modifier certaines attributions à des générations de concrétionnement ou à des processus morphogéniques, voire à des actions anthropiques.
3. 2. Un outil informatique pour gérer des données spatiales Un SIG est un outil informatique spécifiquement conçu pour gérer et analyser des données spatiales. En plus de présenter une grande souplesse pour l'édition de plans et de cartes, sa spécificité majeure tient au fait qu'il comporte une base de données permettant d'associer de multiples informations à chaque élément représenté sur une carte. Un SIG offre ainsi la possibilité de créer, d'organiser, d'archiver et de présenter des données alphanumériques à la fois complexes et spatialement référencées (ou encore « géoréférencées »), mais aussi d'effectuer des requêtes spatiales et/ou attributaires et des croisements de données (par exemple : analyse de distance, de contiguïté, d'intersection, de voisinage)[FIG. 24].
étude de la grotte 3. 4. Inventaire, acquisition et intégration des données Une fois ce socle acquis, l'une des premières étapes a été d'inventorier les données existantes à intégrer dans le SIG. Trois grands types d'informations ont été identifiés : des cartographies non liées à des bases de données, des bases de données non spatialisées et, enfin, des données restant entièrement à synthétiser à partir des observations de terrain (Boche et al. 2012). Plusieurs protocoles d'intégration ont été définis selon la nature et le type de données[FIG. 26]. 185. 75 185. 76 186. 11 186. 12 186. 21 186. 21 186. 38 186. 41 186. 41 186. 41 186. 44 186. 46 186. 46 186. 86 186. 86 186. 76 186. 76 186. 80 186. 80 186. 75 186. 75 186. 71 186. 72 186. 75 186. 75 186. 74186. 74 186. 72 186. 71 186. 72 186. 72 186.
Par conséquent, les éléments situés dans ces secteurs ne peuvent être géoréférencés directement sur ordinateur par le biais du modèle numérique 3D. Leur localisation, de même que la visualisation de leur topographie dépendent de documents réalisés par d'autres moyens, au premier rang desquels la topographie Le Guillou-Maksud et le fond géomorphologique. Données extraites du SIG Atlas Chauvet, logiciel ArcGIS Esri France (date de l'interrogation du SIG : déc. 2014). FIG.
3. 5. La constitution du SIG Atlas Chauvet 3. 5. 1. La plateforme logiciel Tel qu'il se présente aujourd'hui, le SIG Atlas Chauvet est un SIG en mode vecteur -mode qui correspond le mieux aux données à saisir (à savoir des données individualisées) et aux objectifs d'analyse spatiale envisagés. Il est opérable au moyen du logiciel ArcGIS qui, complété des modules Spatial Analyst et 3D Analyst, permet de gérer des bases de données complexes et importantes tout en offrant de nombreuses fonctionnalités de traitement, dont celle, non négligeable, consistant à travailler avec des données réellement 3D au lieu de simples modèles numériques de terrain en pseudo 3D (dites « 2,5D »).
model with centimeter-level accuracy. (State of the database in March 2017). sélection d'une entité désignation de la couche d'information type de données, vecteurs (points, lignes, surfaces) ou raster nombre de champs nombre d'éléments (entités) géoréférencés précision centimétrique (3D ou tachéomètre) total désignation de la couche d'information type de données, vecteurs (points, lignes, surfaces) ou raster nombre de champs nombre d'éléments (entités) géoréférencés précision centimétrique (3D ou tachéomètre) total ÉCHANTILLONS, LIEUX DE MESURE AMÉNAGEMENTS ACTUELS ÉCHANTILLONS échantillons 36 Cl échantillons charbons échantillons palynologie échantillons colorants échantillons os (+ os tachéo) point point point point point 14 40 10 37 51 (+ 11) ----99 21 227 6 30 275 aménagements (interphone, raccordement électr.
Subjects The participants in this study belonged to a cross-sectional analysis at age 7 years of the AVCnn database (Accident Vasculaire Cérébral du nouveau-né, i. e. , neonatal stroke; PHRC régional n°03-08052 and PHRC interrégional n°10-08026; Eudract number 2010-A00329-30). This cohort was described in detail elsewhere. 6, 8 In a few words, 100 term newborns with an arterial cerebral infarct, confirmed by early brain imaging (CT and/or MRI before 28 days of life), who were symptomatic during the neonatal period (thus matching the 2007 definition of NAIS 6 ) were consecutively enrolled between November 2003 and October 2006 from 39 French centers. Seventy-two children took part in a clinical, neuropsychological, and language assessment at 7 years (AVCnn 7ans ). During this assessment, an MRI was proposed to the families.
Fifty-two children participated in this MRI study (AVCnn signal ; PHRC 2010-07; Eudract number 2010-A00976-33). Among them, 38 had a unilateral lesion in the median cerebral arterial (MCA) territory. However, after further examination six patients were excluded due to poor segmentation results (for more details please refer to (Dinomais et al. , 2015a)), leaving 32 patients. They constituted the patient population of this study. Based on a previous study that indicates different outcomes following the side of the lesion,  31  Patients were divided into two groups: patients with lesions in the left hemisphere (LLP) and patients with lesions in the right hemisphere (RLP). In addition to the LLP and RLP patients, we recruited 30 healthy controls (HC). These controls were matched in age and gender with the patients.
Lesion masks For each patient, the boundaries of the lesion were manually delineated on a slice by slice basis by two of the authors (MD, SG) that were blinded to the clinical information, especially motor function. This delineation was performed on the individual 3D T1 images to create a binary lesion mask using the MRIcron software (http://www. mccauslandcenter. sc. edu/mricro). 35 In case of a main branch MCA stroke, the lateral border of the lesion mask was drawn along the inner border of the skull, comprising the whole porencephaly. 36.
KNN To predict the presence or not of CP, a K-Nearest Neighbor KNN classification model was employed using Matlab 2015a. 51 Two nearest neighbors, corresponding to either no CP (0) or CP (1), were set for the classifier. For each group of patients (LLP and RLP), motor connectivity values were used as features in order to train the KNN model. The accuracy of the prediction was evaluated using also the leave-one-participant-out cross-validation technique. The accuracy was then computed as the percentage of correctly classified patients (that were not a part of the training set) between CP or no CP.
Funding Information The research was supported by the  University Hospital of Angers  (eudract number  2010-A00976-33 ), the  Ministère de la solidarité et de la santé  (eudract number  2010-A00329-30 ), and the  Fondation de l'Avenir  ( ET0-571 ). M. Al Harrach , was supported by grants obtained from the  Fondation pour la Recherche Médicale  ( FRM-DIC20161236453 ). Sponsors of the study had no role in the study design data collection, data analysis, data interpretation, writing of the report, or decision to submit for publication.
SAXS Solution scattering data were collected at ESRF BM29 using a sec-1 frame rate on Pilatus 1 M detector located at a fixed distance of 2. 87 m from the sample, allowing a global q range of 0. 03-4. 5 nm with a wavelength of 0. 01 nm. SEC-SAXS experiments were carried out using Nexera High Pressure Liquid/Chromatography (HPLC; Shimadzu and 3D models from structural models was performed using CRYSOL. A summary of SAXS data collection and analysis results is shown in Table  1. ). The data were subjected to a non-linear regression analysis using four-parameter sigmoidal equation using Sigmaplot software (version 13). SKOV-3 cell migration assays. Agonist-induced cell migration was measured by seeding 50,000 SKOV-3 cells resuspended in serumfree RPMI supplemented with 0. 1% BSA (BioFroxx) in each of the upper wells of a 96-well Boyden chamber (AC96, Neuro Probe).
Crystals were taken for X-ray diffraction experiments using a microfocus beam at the ESRF in Grenoble, France, and resulted in the collection of complete datasets and determination of the molecular structures at 1. 6 Å resolution (Figure  1B ) and 1. 8 Å for K1K1 and K1K1H6 respectively. Both proteins crystallized in space group P 1 21 1 with K1K1 having two molecules per asymmetric unit and K1K1H6 only one. In addition, in K1K1H6 both kringle domains had a HEPES molecule bound to a groove which is analogous to the lysine binding pockets found in proteins such as plasminogen (Figure  1C ). This HEPES molecule originates from the crystallization condition and was also found in crystal structures of NK1 obtained in our lab and in several obtained by others  25, 36, 43, 44. Structurally, K1K1 with and without poly-histidine tag are very similar, having a backbone root mean square deviation (RMSD) of 0.
Acknowledgments We thank  SATT Nord (France)  for financing the proof of concept experiments,  Thierry Chassat  from the  PLETHA animal Facility in Lille Pasteur Institute  for helpful advises and kind availability. We would also like to thank  Dr Dimitri Y. Chirgadze  at  the department of Biochemistry, University of Cambridge, UK , for his help in solving the structure of  K1K1  and  K1K1H6  and are grateful for his support and contributions to our work over the many years we collaborated. Figure Legends:.
The emitted signal intensity was measured using standard Alpha settings on an EnSpire® Multimode Plate Reader (PerkinElmer). Measurements are expressed as technical duplicates (mean+/-SD, n=2). The data corresponding to the 3 nM MET condition was subjected to a non-linear regression analysis using four-parameter sigmoidal equation using Sigmaplot software (version 13). treated for subsequent experiments. SKOV-3 cells were cultured in RPMI 1640 medium supplemented with 10% FBS and Penicillin-Streptomycin all purchased from Gibco/ThermoFisher Scientific. Western BlotsThe assay was performed according to Simonneau et al. , 201534. Hela cells were collected by scraping and lysed on ice with a lysis buffer (20 mM HEPES pH 7. 4, 142 mM KCl, 5 mM MgCl2, 1 mM EDTA, 5% glycerol, 1% NP40 and 0. 1% SDS) supplemented with freshly added protease inhibitor (1/200 dilution, #P8340, Sigma Aldrich) and phosphatase inhibitor (1/400 dilution, #P5726, Sigma Aldrich).
Méthodes statistiques Toutes les analyses statistiques ont été réalisées avec le logiciel Stata v15 (StataCorp, College Station, Texas, USA). Tous les tests étaient bilatéraux et une p-value < 5% a été considérée comme statistiquement significative. Les paramètres de nature quantitative sont présentés en termes de moyenne ± écart-type associé et minimum et maximum ; Les paramètres de nature binaire / catégorielle sont décrits par des effectifs et pourcentages associés. Le taux d'échec ou de complication, traité comme une donnée censurée, a été estimé par des méthodes de survie, prenant en compte comme point de départ la date de l'intervention, comme évènement l'échec ou la complication et considérant le délai de l'intervention jusqu'à la date de l'évènement ou jusqu'à la date des dernières nouvelles.
Analyses statistiques Toutes les analyses statistiques ont été effectuées avec le logiciel Statistica (v. 13,0, DELL, TIBCO Software Inc. ). Le seuil de significativité a été fixé à p <. 05. Dans le cadre de cette étude nous avions à comparer des distributions de scores en début de la modalité d'exposition en réalité virtuelle au cours d'une prise en charge en soins courant avec des distributions de scores en fin de la modalité d'exposition en réalité virtuelle par les mêmes sujets. Les distributions sont normales, et l'effectif étant inférieur à 30, le test statistique indiqué est le test de Wilcoxon.
Image analysis The image analysis of 2D micrographs was performed using the image processing software ImageJ  [39]. The Fast Fourier Transform (FFT) analysis was applied to the image after Hanning windowing. The image in the Fourier space was then radially averaged to obtain the spectrum I(q). The wave vector q represents a spatial frequency, it is a function of the distance from the centre in the Fourier space and of the image size, and is expressed in µm -1. The image is multiplied by a Hanning window of the same size before the Fast Fourier Transform is calculated. The spectrum I(q) is obtained using the plugin Radial Profile to perform a radial average of the Fourier transform. The decrease of the spectrum I(q) is then fitted by a power law, linear in double logarithmic scale. Its intersection with the plateau defines the critical spatial frequency q c.
Lower panel: residues of RcsF were replaced by DiZPK to map the zone of interaction with OmpA. In this cartoon of the NMR structure of RcsF (PDB: 2L8Y), the truncated N-terminal portion of the protein is shown as a dashed line and the residues that were found to interact with OmpA appear in magenta. The side chains of the residues that were selected for further experiments are shown as spheres, and other side chains are represented as sticks. The online version of this article includes the following figure supplement(s) for figure  1 :     (Singh et al. , 2003; Stathopoulos, 1996). The C-terminal region of OmpA is necessary and sufficient for binding RcsF The results above indicated that RcsF interacts with the C-terminal region of OmpA, raising the question of whether the N-terminal region also participates in this interaction.
RcsF interacts with the periplasmic domain of OmpA in vitro We next sought to validate our in vivo observations by probing the formation of a complex between RcsF and the soluble, periplasmic domain of OmpA (OmpA 186-325 ) in vitro using purified proteins. However, attempts to pull-down OmpA 186-325 with a soluble, His-tagged version of RcsF failed (data not shown), suggesting that the interaction between these two proteins was weak. Because NMR is a highly effective tool to investigate weak protein-protein interactions  (Vaynberg and Qin, 2006) , we employed NMR titration experiments of 15 N-labeled OmpA 186-325 by RcsF. In this approach, the 15 N-1 H 2D NMR spectra of OmpA were recorded upon addition of increasing amounts of RcsF (2 and 10 molar equivalents); when OmpA and RcsF interact, concentration-dependent perturbations in the NMR spectra appear.
To probe this directly, we determined the affinity constants of the periplasmic domains of OmpA and IgaA for RcsF. Note that the periplasmic domain of IgaA interacts with RcsF in vivo and in vitro  (Cho et al. , 2014; Hussein et al. , 2018). First, from the NMR shift data, we calculated the equilibrium dissociation constant (K D ) of OmpA 186-325 for RcsF as being 125 ± 85 mM (Figure  5C ). Second, using biolayer interferometry, we measured that the periplasmic domain of IgaA has a K D of 1. 6 ± 0. 3 nM for RcsF (Figure  5D , see Figure  5 -source data 2 for statistics). Thus, these values confirm that IgaA has substantially more affinity for RcsF than OmpA (see Discussion). Interestingly, we noted that the BamA-RcsF complex was not modified by the increased expression of IgaA (lanes 7-10 in Figure  5B ), which is consistent with the fact that BamA has a much higher affinity for RcsF (K D ~400 nM; Rodrı ´guez-Alonso et al.
Weak complex formation was also observed with OmpA R242X and OmpA Y248X. The expression levels of the OmpA variants were verified by immunoblotting (lower panel). The online version of this article includes the following source data for figure  4    OmpA functions as a buffer for RcsF Finally, if OmpA does not allow RcsF to reach the surface, what could be the function of the OmpA-RcsF complex? On the basis of our results, we propose that the role of OmpA in Rcs is to modulate the activity of this system. Consider the equilibrium dissociation constants of the IgaA-RcsF and OmpA-RcsF complexes: K OmpAÀRcsF d ¼ OmpA ½ RcsF ½ OmpA À RcsF ½ (1) K IgaAÀRcsF d ¼ IgaA ½ RcsF ½ IgaA À RcsF ½ (2) We estimate that OmpA's C-terminal domain is present in the periplasm at ~1 mM, RcsF at ~15 mM, and IgaA at ~1 mM (Materials and methods).
Immunoblotting and antibodies Protein bands were transferred from the gels onto nitrocellulose membranes (Millipore) using a semi-dry electroblotting system. The membranes were blocked with 5% skim milk. The rest of the immunoblot steps were performed using standard protocols. Signal from antibody binding was visualized by detecting chemiluminescence from the reaction of horseradish peroxidase with luminol. Polyclonal RcsF antibodies were purified against the carboxy-terminal domain of RcsF as previously described  (Cho et al. , 2014 ) and used at a dilution of 1:20,000 in 1% skim milk in 50 mM Tris-HCl [pH 7. 6], 0. 15 M NaCl and 0. 1% Tween 20 (TBST). Since we found that the anti-OmpA antibody only recognizes the periplasmic domain (data not shown), we used an antibody directed against loop 4 of the ß-barrel of OmpA to detect OmpA 1-170.
Figure4continued colored in blue. Cartoon (C) and surface (D) view of OmpA 186-325 (PDB: 2MQE): top view (on the left) and bottom view (on the right). The residues in OmpA that undergo a CSP larger than two standard deviation (as in panel B) appear as dark blue and are labeled. Most of these residues are located between b-strand 2 and a-helix 3. The residues R242 and Y248 that do not interact well with RcsF in (E) are colored in light blue. (E) To confirm the importance of the loop between b-strand 2 and a-helix 3 of OmpA for the interaction with RcsF, we used site-specific photo-crosslinking. DompA rcsF + cells expressing wild-type (WT) OmpA or three DiZPK-containing OmpA variants (OmpA R242X , OmpA D246X , and OmpA Y248X ) from pPR21 were irradiated with UV light (+) or not (-), and protein samples were immunoblotted with an anti-RcsF antibody.
A strong 55 kDa band, corresponding to the size of the OmpA-RcsF complex, was observed with the OmpA D246X variant, confirming the NMR data. Weak complex formation was also observed with OmpA R242X and OmpA Y248X. The expression levels of the OmpA variants were verified by immunoblotting (lower panel). The online version of this article includes the following source data for figure4:.
Acknowledgements We are indebted to  Marie Renault  ( CNRS, Toulouse ) for discussion and to  Harris Bernstein (NIH, USA) ,  Eric Cascales  and  Roland Lloubes  ( CNRS, Marseille ) for sharing antibody with us. We are grateful to  Alexandra Gennaris  ( UCLouvain ),  Pauline Leverrier  ( UClouvain ) and  Camille Goemans  ( EMBL, Heidelberg ) for critically reading the manuscript and providing feedback. We thank the members of the lab for helpful discussions, and  A Boujtat  for assistance in experiments. This work used the platforms of the Grenoble Instruct-ERIC center (ISBG;  UMS 3518 CNRS-CEA-UGA-EMBL ) within the  Grenoble Partnership for Structural Biology  (PSB), supported by  FRISBI  ( ANR-10-INBS-05-02 ) and GRAL, financed within the  University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS  ( ANR-17-EURE-0003 ).
Materials and methods This retrospective observational cohort study included all women who gave birth to liveborn singletons from 34 to 36 weeks+6 days of gestation, in a French level III maternity hospital during the 5-year period 2013-2017. Multiple pregnancies, fetal deaths, and medical terminations of pregnancy were excluded. Neonates with one or more congenital and/or chromosomal abnormalities likely to aggravate the neonatal prognosis were also excluded. After identifying eligible women in the computerized database, we reviewed all original obstetric and pediatric records. The National Data Protection Authority (Commission National de l'Informatique et des Libertés, CNIL n°1755849) approved this study. Under French regulations, this study is exempt from IRB review because it is an observational study using anonymized data from medical records.
Probable neonatal infection was defined by clinical signs and a neonatal CRP ≥10 mg/L. Neonatal sepsis included both the cases of early-onset sepsis (defined as a neonatal infection within 72 hours after birth) and those that developed later. We collected data on maternal characteristics: age (years), obesity (BMI>30 kg/m2), geographical origin (Europe, Africa, and elsewhere), health insurance (patients with or without social health insurance), parity (nulliparous, parous patients), gestational diabetes (diagnosed between 24 and 28 weeks of gestation in patients with fasting blood glucose 0. 92 g/L and/or after induced oral hyperglycemia (75 g glucose), blood glucose 1. 80 g/L at 1 hour and/or 1. 53 g/L at 2 hours. ). The fetal characteristics collected were gestational age (weeks of gestation), birthweight (grams), and sex.
The principal obstetric characteristic was mode of delivery (spontaneous vaginal delivery, instrumental vaginal delivery, or cesarean). We also extracted from the files the use of antenatal corticosteroid therapy, defined by at least 2 intramuscular injections of 12 mg of betamethasone 24 hours apart. Our center's protocol does not advise corticosteroid injection after 33 weeks + 6 days. Categorical variables were compared with the Chi 2 test or Fisher's exact test, as appropriate. For continuous outcomes, data were analyzed with t tests for normally distributed variables and Kruskal-Wallis tests for nonnormally distributed variables, as appropriate. All analyses were performed with STATA software version 15. Preterm labor was used as the reference because it was expected to have the fewest complications  11, 12.
Another advantage of this classification is that by separating the population into mutually exclusive groups, it enables more relevant analyses. Finally, this classification makes it possible to assess neonatal prognosis before birth according to the disease identified by the obstetric team. The most frequent morbidity in each group was respiratory distress, a finding consistent with the studies assessing morbidity in late preterm births  6, 28, 29. Two studies reported a higher risk of neonatal morbidity or mortality for births due to PPROM than for those due to spontaneous preterm labor  11, 12. Nonetheless, these data were collected from birth registers that included very little medical information and did not take into account confounding variables such as antenatal corticosteroid therapy and gestational age at birth.