dataesr/scientific-paragraphs-categorization huggingface dataset:
Nous avons réalisé une étude rétrospective incluant des patientes prises en charge pour une ECR de janvier 2005 à mars 2020 par un chirurgien gynécologue (H. R. ), avec ou sans la présence d'un chirurgien colorectal, et enregistrées dans la base de données du gynécologue. L'inclusion des patientes a commencé lorsque le chirurgien est devenu chef de clinique au CHU de Rouen (janvier 2005) et s'est terminée en mars 2020, au moment du confinement dû à l'épidémie COVID-19. Les patientes incluses ont bénéficié d'une prise en charge chirurgicale de l'ECR infiltrant au moins la couche musculaire du rectum ou celle du côlon sigmoïde. Toutes les techniques chirurgicales ont été incluses : le shaving, l'exérèse discoïde, la résection segmentaire colorectale ou l'association des deux dernières (exérèse discoïde du rectum associée à la résection segmentaire du côlon sigmoïde).
L'inclusion dans l'étude a été étendue sur une durée de 15 ans, divisée en 4 périodes successives, en fonction du nombre de patients avec ECR prises en charge par le chirurgien : • la 1 re période (P1, 2005-2006 et 2008-2009), avec moins d'un cas d'ECR/semaine ; • la 2 e période (P2, 2010-2014) avec plus d'un cas d'ECR/semaine ; • la 3 e période (P3, 2015-juin 2018) avec > 3 cas d'ECR/semaine ; • la 4 e période (P4, septembre 2018-mars 2020) avec > 4 cas d'ECR/semaine (Fig. 1). De 2005 à juin 2009, les patients ont accepté d'être enregistrées dans la base de données personnelle du chirurgien, concernant un nombre limité d'items, principalement liés aux caractéristiques et aux localisations de l'endométriose, aux principaux gestes chirurgicaux effectués sur le tube digestif et aux complications majeures.
De juin 2009 à mars 2020, les données préopératoires et peropératoires, les principales techniques chirurgicales, les suites postopératoires et les données liées au suivi à long terme ont été enregistrées de manière prospective dans la base de données de la cohorte inter-régionale de Nord-Ouest des patients opérées pour une endométriose (CIRENDO) (NCT02294825) par un technicien de recherche clinique dédié. L'enregistrement prospectif des données a été approuvé par l'autorité francaise CCTIRS (Comité consultatif sur le traitement de l'information dans la recherche en santé). La cohorte CIRENDO a évolué pendant 10 ans, avec l'ajout successif de nouveaux items. Comme tous les items n'étaient pas disponibles pour toutes les patientes prises en charge sur la période de 15 ans, notre étude a utilisé seulement les données enregistrées chez toutes les patientes.
De novembre 2006 à octobre 2007, aucune patiente n'a été enregistrée dans la base de données pendant 12 mois consécutifs au cours desquels le chirurgien a accompli un stage de recherche à l'université médicale de Charleston, Caroline du Sud (USA). La limite séparant la P3 et la P4 a été fixée à juillet 2018, correspondant au passage du chirurgien du CHU de Rouen au centre d'endométriose de la clinique Tivoli-Ducos, Bordeaux.
Données peropératoires et gestes chirurgicaux stratifiés selon la survenue d'une fistule digestive (analyse univariée). La création de la base de données CIRENDO en 2009 a permis d'enregistrer prospectivement un nombre élevé d'items, grâce au travail d'un technicien de recherche clinique dédié, avec un faible taux de données manquantes ou de perte de vue des patientes. Seules les patients francophones ou anglophones qui acceptaient d'enregistrer leurs données ont été inscrites dans la base de données, néanmoins le nombre de patientes éligibles qui ont refusé l'inclusion dans la base de données est probablement inférieur à 20 au cours des 10 ans. Le principal point faible de cette étude est d'ailleurs commun à toutes les séries rétrospectives recouvrant une longue période de temps, et est lié au nombre relativement limité d'items qui sont disponibles pour l'ensemble de la population.
Nous avons utilisé les données prospectivement enregistrées dans la base de données CIRENDO chez 95 % de la population incluse dans l'étude, et les dossiers personnels du chirurgien chez les autres 53 patientes prises en charge de 2005 à 2006 et de 2007 à 2009. CIRENDO étant une base de données évolutive, de nombreux items ont été successivement ajoutés à partir de 2009 jusqu'au 2020, qui n'étaient par conséquent pas disponibles chez toutes les patientes. Facteurs associés à la fistule digestive (modèle de régression logistique, après ajustement sur le nombre et la taille des nodules digestifs).
Remerciements Les auteurs remercient  Mlle Amélie Breant et Sophie Marinette pour leur précieux travail de gestion de la base de données CIRENDO. Les auteurs remercient Mme Helene Braund  d'avoir corrigé le manuscrit. Les auteurs remercient les  Professeurs Valérie Bridoux ,  Francis Michot  et  Michel Scotté ,  Dr Haitham Khalil ,  Rachid Chati ,  Julien Coget ,  Basil Tasivilis ,  Jean Remy Legros ,  Baabak Kianifard ,  Sabrina Kermich ,  Marlène Antor ,  Marie Dazza ,  Eglantine Voitellier du CHU de Rouen  et  Dr Myriam Noailles ,  Damien Forestier  et  Éric Magne de la Clinique Tivoli-Ducos à Bordeaux , qui étaient les chirurgiens colorectaux impliqués dans nos équipes chirurgicales multidisciplinaires.
Le temps opératoire a progressivement diminué de plus de 50 % de la P1 à la P4. Des informations précises sur la hauteur des nodules rectaux n'étaient disponibles que chez 783 femmes (73,9 %) opérées à partir de 2016, lorsqu'un item spécifique « Hauteur du nodule colorectal le plus bas » a été introduit dans la base de données CIRENDO. La hauteur des nodules était occasionnellement notée de 2009 à 2015, lorsque la taille et la hauteur pouvaient être mentionnées dans une question ouverte « Notes chirurgicales ». Les informations disponibles sur la hauteur des nodules montrent que plus d'un tiers des patientes traitées pendant la P3 et la P4 présentaient une endométriose profonde infiltrant le moyen ou le bas rectum (à moins de 7 cm au-dessus de la limite anale). La proportion de patientes prises en charge par exérèse discoïde a été multipliée par deux de la P2 à la P4, alors que cette technique n'était qu'exceptionnellement employée pendant la P1.
Nous avons utilisé les données prospectivement enregistrées dans la base de données CIRENDO chez 95 % de la population incluse dans l'étude, et les dossiers personnels du chirurgien chez les autres 53 patientes prises en charge de 2005 à 2006 et de 2007 à 2009. CIRENDO étant une base de données évolutive, de nombreux items ont été successivement ajoutés à partir de 2009 jusqu'au 2020, qui n'étaient par conséquent pas disponibles chez toutes les patientes. Facteurs associés à la fistule digestive (modèle de régression logistique, après ajustement sur le nombre et la taille des nodules digestifs). Patientes sans Patientes avec p fistule digestive fistule digestive n = 1019 (96,1 %) n = 41 (3,9 %).
Implementation of ECTM and WCCTM Cheddar is a GPL framework that provides a scheduling simulator, schedulability tests and various features related to the design and the scheduling analysis of real-time systems. To model the system to analyze, Cheddar provides a specific architecture design language, called CheddarADL  [24]. CheddarADL allows users to describe both the software and the hardware parts of the system they expect to analyze. Fig. 11  is an overview of the software architecture of our prototype and a subset of Cheddar framework libraries. As shown in Fig. 12 , the evaluation process consists of two stages: generation of an architectural model and its scheduling simulation 1.
Holistic approach The holistic approach has been introduced by Tindell and Clark  [26]. The authors describe how to assess the feasibility of real-time distributed systems considering fixed priority tasks and a TDMA (Time Division Multiple Access) network. Later, in  [27] , Tindell and Burns have extended the analysis to systems with real-time and token communication protocols. In the holistic approach, feasibility is assessed by computing how timing behavior of the messages affects the response time of the tasks and respectively. In the seminal Tindell proposal, jitter of a task i models lateness introduced by tasks run before task i or messages sending data to task i. The key aspect of the holistic approach is the ability to compute worst case response times for both tasks and messages by a step by step approach.
Acknowledgements This work and Cheddar 2 are supported by  Brest Métropole ,  Ellidiss Technologies ,  CR de Bretagne, CD du Finistère ,  H2020 MOSAR  and  Campus France PESSOA  programs  27380SA  and  37932TF. The authors would like to thank all the supporting staff and partners of the  MOSAR  Project:  Space Applications Services N. V. (Belgium) ,  Deutsches Zentrum Fuer Luft -Und Raumfahrt Ev (DLR) ,  GMV Aerospace And Defence Sa (GMV) ,  Thales Alenia Space UK Ltd (TAS-UK) ,  Sitael Spa  (SITAEL),  MAG SOAR S. L. (MAG SOAR S. L. ) , the  University of Strathclyde (UK) ,  Thales Alenia Space S. p. A (France)  and  Ellidiss Technologies  (ELLIDISS). MOSAR is part of the  PERASPERA  project  on Space Robotics Technologies , and has received funding from the  European Unions   Horizon 2020 research and innovation programme  under grant agreement No  821996.
4A  and B ). The full dataset is reported in Appendix 3. All measurements were made on the well-exposed skarn body on the west side of the mineralized fault. Pyroxene crystals were selected based on available measurement surfaces, and measurements were grouped into domains based on their position on the outcrop (near the upper contact, at center, near the lower contact: Fig. 4C ). Most measurements were made on coarse-grained pyroxene (more than 2 cm in length) and spaced apart by 3-5 cm. For each domain, every individual crystal that could be measured meeting the above criteria was recorded, with accepted biases of grain size and geometric constraints of the outcrop. Because the massive texture of the skarn body, no preference was given to crystal orientation relative to the skarn front, as was done in the previous study  (Vezzoni et al.
Bulk Rock analyses Whole-rock measurements were performed by wavelength dispersive X-ray fluorescence (XRF) spectrometer PANalytical Axios mAX fitted with a 4,0 KW Rh X-ray tubeon glass pellets at the University of Lausanne, Switzerland for major element compositions. Trace element compositions were determined on the same glass pellets by using an Inductively Coupled Plasma -Mass Spectrometer (ICP-MS) coupled to an excimer laser system at ETH Zürich. In situ measurements were also made using Thermo Fischer Niton XL3t portable XRF with an 8 mm spot size. Whole-rock methodology is reported in Appendices 1. 3 and 1. 4, and data tables can be found in Appendix 4.
In-situ Mineral analyses Major element compositions of pyroxene and epidote were measured using a JEOL 8200 Superprobe at the University of Geneva, Switzerland. Measurement conditions used an accelerating voltage of 15 kV with a current of 20 nA, and a beam diameter of 1 μm. Detailed methods and data treatment are reported in Appendix 1. 5. Trace-element compositions of pyroxene and epidote were determined using a RESOlution excimer ArF (193 nm) laser ablation system with a spot size of 19 μm coupled to an Element XR sector-field ICP-MS. Detailed methodology can be found in Appendix 1. 6. All in-situ geochemical results are reported in Appendices 6 and 7.
Trace element geochemistry Epidote trace element analyses (n=301, Fig. 10 ) show that epidote 1 is characterized by higher contents of Mg, Ti, and Zn and lower contents of Mn, Sr, and Pb than epidote 2. Rather, the shift in Mn/Mg ratio is a definitive feature of the two epidote crystallization events, correlating with base metal (Pb and Zn) and Sr content (Fig. 10B ). The average of ΣREE (+ Y) is about two times higher than that of pyroxene, but still fails to meet the hundreds of ppm ΣREE (+ Y) present in the whole rock, which is principally hosted in metamorphic apatite and other accessory phases. The REE patterns, separated by sample and epidote generation (Fig. 10D ), are characterized by relatively flat slopes (La N /Yb N = 1. 15) and moderately positive Eu anomalies (Eu/Eu* = 2). The full dataset of epidote geochemical results can be found in Appendix 7.
Acknowledgements This research was supported by the  Swiss National Science Foundation  (SNF grant  200021_165752 ) and student research grants from the  Society of Economic Geologists Canada Foundation (SEGCF)  and from the  Society of Physics and Natural History of Geneva  ( Augustin Lombard Grant ) for ALH. Logistic support and assistance in the field was provided by  GORUBSO Madan  and by  Zlatko Kasabov  (chief geologist at Petrovitsa mine). Ianko Gerdjikov  ( Sofia University ) is greatly acknowledged for discussions on local geology, field work, and providing unpublished geological reports. We also thank  Jean-Marie Boccard  for high-quality thin section preparation and  Antoine de Haller  for assistance with XRF analyses. Partial support for field work for GM and RV by  BNSF   KP-06-N34/4  grant is also acknowledged.
Les variables peu participatives ont été supprimées de manière itérative des analyses jusqu'à n'avoir plus qu'un lot de variables significativement reliées au critère de fréquence du travail en groupe. L'ensemble des analyses a été réalisé sous le logiciel R version 3. 5. 3 avec le package PLS  (Mevik, Wehrens et Hoyde Liland, 2019). Ces variables prédictrices étaient issues de six catégories (voir tableau 1).
à leurs collègues enseignants en cycles 3 et 4 uniquement. L'envoi par la voie hiérarchique avait pour objectif de garantir une diffusion efficace de l'enquête et espérer un bon taux de complétude. Bien qu'ayant transité par cette voie interne à l'institution, cette diffusion en ligne, anonyme et rendue neutre vis-à-vis de l'enquêteur, vise à limiter les biais de désirabilité sociale (Butori et Parguel, 2010). 8 Source : site Open Data du ministère de l'Éducation nationale et de la jeunesse. Accès : https://data. education. gouv. fr/explore/dataset/fr-eneffectifs-des-personnels-des-ecoles-et-etablissements-du-2nd-degre/export/?refine. annee_scolaire=2018-2019&refine. academie=NANCY-METZ&refine. code_departement=057 (consulté le 10/06/2020). Dans un premier temps, les questions à choix multiples ayant n énoncés (ex.
Here, we determined the structure of an unexpected ternary NEO1-NET1-RGM complex that forms a defined and stable ''trimer-of-trimers'' assembly. We show that formation of the ternary NEO1-NET1-RGM complex inhibits both RGMA-NEO1-mediated growth cone collapse and RGMA-NEO1-and NET1-NEO1-mediated neuron migration. Our data demonstrate that NET1 and RGMs can bind simultaneously to NEO1 rather than competing for binding, thereby unveiling an intriguing mode of receptor regulation. The ternary structure acts as a silencing complex, preventing the formation of the signalingcompatible RGM-NEO1 complex as well as NET1-induced NEO1 ectodomain clustering, both required for signal transduction. Thus, our work reveals how two ligands with distinct and opposing cellular functions can control their receptor by reciprocal silencing of downstream signaling pathways.
Scale bar, 10 mm. (G) Quantification of growth cone collapse. Growth cones were treated with control or RGMA alone and in combination with different NET1 variants. Proportions of collapsed growth cones relative to control are displayed. n = 3 experiments, one-way ANOVA followed by Tukey's multiple comparison test. *p < 0. 05. Data are shown as means ± SEM. (H-J) Comparison of binary NEO1-RGM (PDB ID 4BQ6  [Bell et al. , 2013] ) and the ternary NEO1-NET1-RGMB complexes shown as ribbons. The ternary NEO1-NET1-RGMB protomer complex architecture (I) clashes with the NEO1-RGM dimer-of-dimers signaling conformation (H) when superimposed on NEO1 (marked with an asterisk) (J). See also Figures  S3, S4,  and S5. This can be inhibited by NET1 interface-1 and -2 mutants that both result in a reduction of the apparent molecular weight (F), corresponding to a 1:1 NET1-NEO1 complex stoichiometry.
Data and Code Availability Atomic coordinates and structure factors for ternary NEO1-NET1-RGMB and binary NET1-NEO1 complexes determined using X-ray crystallography have been deposited in the Protein Data Bank (PDB) with accession codes 7NE0 and 7NE1, respectively. Atomic coordinates for the ternary NEO1-NET1-RGMB complex determined by cryo-EM have been deposited in the Protein Data Bank with accession code 7NDG, and the cryo-EM density map has been deposited in the Electron Microscopy Data Bank with accession code EMD-12286. Raw movies of the dataset for the ternary NEO1-NET1-RGMB cryo-EM complex have been deposited in the Electron Microscopy Public Image Archive (https://www. ebi. ac. uk/pdbe/emdb/empiar/) with accession code EMPIAR-10637. The authors declare no competing financial interests.
Structure determination and refinement The binary NEO1 FN456 :NET1 DNTR complex was solved by molecular replacement in PHASER  (McCoy et al. , 2007)  using the structure of the fifth and sixth fibronectin type III domains of mouse NEO1 (PDB ID: 4BQ6  (Bell et al. , 2013) ), the fourth domain of human NEO1 (PDB ID: 1X5I) and chicken NET1 DNTR (PDB ID: 4PLM (Xu et al. , 2014)) as search models. The ternary NET1 DNTR -NEO1 FN456 -RGMB CORE complex was determined using coordinates from the binary NEO1 FN456 :NET1 DNTR complex from this study and human RGMB (PDB ID: 4BQ6  (Bell et al. , 2013) ) as molecular replacement search models in PHASER  (McCoy et al. , 2007). Structures were refined using initial rounds of refinement in REFMAC5  (Murshudov et al. , 2011)  and completed using autoBUSTER  (Bricogne et al.
Model analysis Stereochemical properties were assessed using MolProbity  (Davis et al. , 2007)  and are presented in Table  S1. PRIVATEER  (Agirre et al. , 2015b)  was used to validate carbohydrate structures. Superpositions were calculated using the program PyMOL  (Schrodinger, 2010) , which was also used for preparation of images for figures. Buried surface areas were calculated using the PDBsum (Laskowski, 2001) and PISA  (Krissinel and Henrick, 2007)  webservers with a probe radius of 1. 4 A ˚.
Grids were plunge frozen in liquid ethane. Cryo-EM data were collected on a Titan Krios G3i microscope (Thermo Fisher Scientific) operating at 300kV with a 50mm C2 aperture and Volta phase plate (Thermo Fisher Scientific), at the Division of Structural Biology, University of Oxford. Movies were recorded using a FEI Falcon III direct electron detector in electron counting mode using EPU software at a nominal magnification of 96000x, corresponding to a physical pixel size of 0. 85 A/pixel. A total dose of 40 e -/A ˚2 was used at a dose rate of 0. 77 e -/pix/sec. Detailed acquisition parameters are listed in supplemental information (Table  S2 ).
eNEO1 was injected for 400 s and NEO1 FN456 for 360 s at a flow rate of 30 ml/min, followed by a 60 s dissociation phase. Surfaces were regenerated using 3 M MgCl 2 , injected for 120 s. Experimental data were processed using program SCRUBBER2 (Biological). Non-linear regression curve fitting was used to fit data to a 'one-site specific binding' model (Y = B max 3 X /(K d + X); X, analyte concentration; B max , maximum analyte binding) using GraphPad Prism 7 (www. graphpad. com). NEO1/DCC:NET1 binding site analysis NET1 DNTR wild type, 'Interface-1' mutant and 'Interface-2' mutant were immobilized at a level of 1007, 1027 and 937 RU each. NEO1 FN456, NEO1 FN56 , DCC FN456 and NEO1 FN56 were purified by SEC and buffer exchanged into SPR running buffer as detailed above. Injection of 10 samples, prepared by a two-fold dilution series in running buffer from a highest concentration of 50 mM, was performed according to a series of: buffer blank, lowest-to-highest, highest-to-lowest, buffer blank.
Analytes were injected for 110 s at a flow rate of 10 ml/min, followed by a dissociation phase of 60 s. Surfaces were regenerated using 3 M MgCl 2 , injected for 120 s. Experimental data were processed using program SCRUBBER2 (Biological). Non-linear regression curve fitting was used to fit data to a 'one-site specific binding' model (Y = B max 3 X /(K d + X); X, analyte concentration; B max , maximum analyte binding) using GraphPad Prism 7 (www. graphpad. com) NET1:RGM interaction study NET1 DNTR was immobilized at a level of 900 RU. RGMB ECD and RGMA ECD were purified by SEC and buffer exchanged into SPR running buffer as detailed above. Injection of 12 samples, prepared by a two-fold dilution series in running buffer from a highest concentration of 40 mM (RGMB ECD ) or 25 mM (RGMA ECD ), was performed according to a series of: buffer blank, lowest-to-highest, highest-to-lowest, buffer blank.
RGM ECD analytes were injected for 110 s at a flow rate of 10 ml/min, followed by a dissociation phase of 60 s. Surfaces were regenerated using 3 M MgCl 2 , injected for 120 s. Experimental data were processed using program SCRUBBER2 (Biological). Non-linear regression curve fitting was used to fit data to a 'one-site specific binding' model (Y = B max 3 X /(K d + X); X, analyte concentration; B max , maximum analyte binding) using GraphPad Prism 7 (www. graphpad. com).
Analytical ultracentrifugation Sedimentation velocity (SV) experiments were performed at 20 C using a Beckman Optima XL-1 analytical ultracentrifuge (Beckman Instruments), utilising a scanning absorbance of 280 nm and interference optics. Samples were contained within 12 mm Epon sectorshaped two-channel centerpieces and spun at 400,000 rpm (An60Ti rotor, Beckman Coulter Inc. , CA), with 100 sample distribution scans taken in 6 minute intervals, alongside interference optics. Absorbance data for scans were analyzed using the program SedFit  (Brown and Schuck, 2006)  for size-and-shape distributions [c(s,fr), where fr is the frictional ratio and for a sphere fr = 1 and for other species fr > 1]  (Brown and Schuck, 2006). This enables the plotting of contour plots of c(s,M), where M is the weight of the protein.
0 mg/ml). At the lower concentrations, ternary complex disassembly led to contamination of the overall dataset by non-3:3:3 complexes. For modelling of the NET1 DNTR solution structure, missing residues were first added to the crystal structure using Modeller  (Eswar et al. , 2003). Then, 50 independent all-atom ensembles of 100 models were generated using Allosmod  (Weinkam et al. , 2012)  and calculation and fitting of theoretical scattering curves was performed using FoXS  (Schneidman-Duhovny et al. , 2016). This entire procedure was automated via the use of Allosmod-FoXS  (Guttman et al. , 2013). The best-scoring model was used as input for MultiFoXS  (Schneidman-Duhovny et al. , 2016)  to model flexibility at inter-domain hinge points. This process produced 10000 conformations, followed by scoring of multi-state models fit to experimental scattering data as described above using FoXS.
For both assays three biological replicates were performed (n = 3), each technical replicate contained 2 coverslips. To test the differences between conditions one-way ANOVA was performed in GraphPad Prism (version 9. 0. 0) Analysis of single-cell RNA-seq data of adult SVZ cells Raw single-cell expression data from ventricular-subventricular zone (V-SVZ) cells from 8-10 week old mice was downloaded (GSE109447)  (Mizrak et al. , 2019). Data was processed using SCANPY version (1. 4. 6)  (Wolf et al. , 2018). The dataset contained 13005 cells and 48529 genes. First, cells were normalized and log-transformed. Second, highly variable genes (HVGs) (minimal mean expression = 0. 0125, maximal mean expression = 3, minimal dispersion = 0. 5) were selected. Third, principal component analysis (PCA) was performed based on the HVGs.