dataesr/scientific-paragraphs-categorization huggingface dataset:
The differential was calculated using the Diff function of Matlab after smoothing the intensity curve (10 time points averaging window) and aligning the curve on the time of disappearance (end of extrusion) of the first cell. Note that the analysis of caspase reversion was restricted to neighbours having a positive slope before the elimination of the first cell (in order to see caspase shutdown). To cross-correlate GC3Ai and ERK dynamics, local projections centered on nuclear miniCic were used (with GC3Ai plane of interest shifted apically). miniCic nuclear intensity and GC3Ai cytoplasmic intensity were measured by manually tracking small circular ROI (20px) in the center of the cells (Fiji home-made macro). The cross-correlation between GC3Ai differential and miniCic nuclear signal was calculated on Matlab with the "xcorr" function with the 'coef' option (normalised cross-correlation).
Analysis of death distribution For the analysis of death distribution we selected movies lasting 16 to 20 hours in the posterior region of the pupal notum. Cell extrusion events were clicked by hand and checked twice. Extrusion localisations were corrected for global drift (translation) of the tissue (Matlab procedure). Spatio-temporal distribution of death was first checked by xy-t histogram. According to that distribution, for each movie, an area of interest (in time and space) was selected by hand to obtain an area where distribution was as homogeneous as possible (double checked by x-y-t histograms). These data sets were then the basis of three statistical analyses (see below).
Distribution of distances Distances in time and space between all couples of extrusions were computed. For each data set we plotted the maps of densities of death at a given distance (number of deaths divided by the area of the disc considered) as a function of spatial and temporal distances from each dying cell. From each data set we estimated the effective death rate, i. e. the intensity of the random spatio-temporal process, and used it to simulate the corresponding Poisson process 200 times. For each simulation we performed the same analysis as for the experimental data set, namely calculating maps of death densities, and eventually averaged the 200 maps. Finally, for each movie we calculated the difference between the averaged simulated map and the corresponding experimental map. We show in the main figures the average of the "difference map" for every experiment (5 for WT, 4 for EGFR-RNAi).
2D simulations of death rate To evaluate the effect of the duration of the feedback as a function of the intrinsic rate of death we made Python routine as follows: We use a hexagonal grid as an approximation of the cell arrangement in the tissue. Each node in the grid represents a cell, with the intrinsic rate of death. Number of cells per side is , so in total we have  2 cells. The cells can be in 2 different states: "regular" (sensitive to death), or "inhibited for death" (probability to die is 0). When one cell dies it inhibits itself, and its 6 neighbours to die during some time  (in minutes). Each death,  = (  ,   ,   ), is described with the time of death,   , and its coordinates in the grid (  ,   ). We simulate the times of death for the Poisson process with rate  =  ⋅   2. For each simulated time,   , we assign a random position (  ,   ) in the grid.
Acknowledgements We thank members of  RL lab  for critical reading of the manuscript, especially  Alexis Matamoro-Vidal  for suggestions on the manuscript organisation. We would like to thank  Jakub Voznica  for initiating observations of miniCic in the pupal abdomen during his internship. We also thank  Virgile Andreani  for help in improving simulations, statistical analysis of the data, and some mathematical expressions. We are also grateful to  Magalie Suzanne , the  Bloomington Drosophila Stock Center , the  Drosophila Genetic Resource Center , the  Vienna Drosophila Resource Center  for sharing stocks and reagents. We also thank  B Aigouy  for the Packing Analyser software and  J. Ellenberg  group for MyPic autofocus macro. LV is supported by a  Post-doctoral grant  " Aide au Retour en France " from the  FRM (Fondation pour la Recherche Médicale ,  ARF20170938651 ) and a  Marie Sklodowska-Curie postdoctoral fellowship  (MechDeath,  789573 ), work in RL lab is supported by the  Institut Pasteur  ( G5  starting package), the  ERC starting grant CoSpaDD (Competition for Space in Development and Disease , grant number  758457 ), the  Cercle FSER  and the  CNRS  ( UMR 3738 ).
Analyses statistiques Les résultats des variables quantitatives sont présentés sous la forme moyenne ± écart-type. Ceux des variables qualitatives sont exprimés en fréquences et pourcentages. Une analyse univariée a été suivie par une analyse multivariée. Pour entrer dans le premier modèle multivarié, les variables devaient présenter en analyse univariée un degré de significativité ≤ 0,25. Le modèle multivarié a été simplifié en utilisant la méthode pas à pas descendante pour aboutir au modèle final. Les interactions pertinentes entre variables présentes dans le modèle final ont été recherchées. Le seuil de significativité choisi pour l'ensemble des analyses statistiques est de 0,05. Le logiciel utilisé est SAS 9. 4 (SAS Institute, Cary, USA).
Introduction > La transfusion de concentrés plaquettaires en fin de vie en onco-hématologie ne fait pas l'objet de recommandations et dépend des représentations partagées par les patients, les infirmiers et les hématologues. L'objectif de cette étude est de décrire ces représentations de la transfusion plaquettaire dans un contexte d'hémopathie grave et avancée à travers les représentations sociales de ses protagonistes. Méthodes > Une étude qualitative, utilisant la méthode du réseau d'association et incluant trois groupes de 15 participants (patients en phase avancée d'une hémopathie maligne, régulièrement transfusés en plaquettes, infirmiers et médecins) issus de quatre centres d'hématologie a été conduite entre février et avril 2019. L'analyse a été réalisée avec le logiciel IraMuTeQ. Résultats > Les patients attendent de la transfusion plaquettaire un impact bénéfique direct sur leur santé et mettent en avant l'importance de la relation humaine.
Methods > A qualitative study, using the associative network method and including three groups of 15 participants (patients with an advanced hematologic malignancy, regularly transfused in platelet concentrates; nurses and hematologic oncologists) from four hematology centers was conducted between February and April 2019. Analysis was carried out using IraMuTeQ software. Results > Patients expect platelet transfusion to have a direct beneficial impact on their health and highlight human relations. Nurses aim at the patient's well-being, in his or her individuality, and at respecting the transfusion protocol. Physicians seek to relieve symptoms by taking into account a multitude of decision-making factors. The textual clustering method, nuances those previous results and individualizes four different orientations, independent of groups: dependency, singularity, subjectivity and neutrality.
Analyse Le corpus brut, constitué des évocations produites par les participants, a été transcrit dans une feuille de calcul Excel. Le calcul des indices a été effectué manuellement. Les autres analyses ont été effectuées avec le logiciel libre et gratuit IraMuTeQ (interface de R pour les analyses multidimensionnelles de textes et de questionnaires) après lemmatisation (ramener à l'infinitif du verbe, au masculin singulier) puis nettoyage (étape triangulée) pour n'obtenir que des formes actives (adjectifs, noms ou verbes). Polarité, neutralité et stéréotypie L'indice de polarité (P), mesurant l'attitude implicite et reflétant l'opinion des participants, a été calculé selon la formule suivante : fP ¼ ðnombre mots positifs À nombre mots négatifsÞ= nombre total de mots L'indice de neutralité (N), reflétant la prise de position des participants, a été calculé selon la formule suivante : N ¼ nombredemotsneutres À ðnombredemotspositifs þ nombredemotsnégatifsÞ=nombretotaldemots L'analyse de stéréotypie (Y), utilisée comme une mesure différenciative du dictionnaire (pour donner une idée du répertoire lexical de chaque groupe) a été calculée selon la formule suivante : Y ¼ ðnombre de mots différents associés par chaque groupe de sujet=nombre total de mots associés par chaque groupeÞ Â 100 Analyse importance-fréquence L'analyse importance-fréquence a été réalisée en croisant le rang d'importance (étape 4) avec la fréquence d'apparition  [15, 19]  et en sélectionnant une occurrence de deux pour chacun des groupes.
La survenue d'un collapsus de la tête et la reprise par prothèse totale de hanche (PTH) a été évaluée par l'intermédiaire de courbes de Kaplan-Meier. La recherche de facteurs de risques de collapsus de la tête (PTH) à 2 ans post-chirurgie a été réalisée grâce à des modèles de Cox à risques proportionnels. Le seuil de significativité a été fixé à 0,05. Les analyses ont été réalisées à l'aide du logiciel SAS version 9. 4 (SAS Institute, Cary NC, États-Unis).
Remerciements Remerciements aux membres de la SOFCOT qui ont inclus des patients :  Pierre Martinot  (Lille),  Philippe Chiron  (Toulouse),  Arthur Justo  (Toulouse),  Zainoul Jaffarbandjee  (Réunion),  Hicham Riouach  ( Clermont Ferrand ),  Jean Marc Puch  ((Nice),  Thierry Fabre (Bordeaux), Charles Dacheux (Bobigny), Erwan Pansard (Boulogne) ,  Henri Migaud (Lille) ,  Antoine Desseaux  (Brest),  Charles De Lam-.
The aim of this study was to identify the genetic variation p. Ile112Thr as a predictive factor for an increased risk of bleeding in mHB patients. All haemophilia B patients with the p. Ile112Thr variation and follow-up in a French Hemophilia Treatment Center were identified in haemophilia referent genetic laboratories. All F9 gene exons and flanking introns were sequenced for every first symptomatic patient in each family. If the mutation was reported in the family and X-linked transmission of the disease was respected, a patient was considered as presenting the mutation. Female patients were excluded from the study. Given the retrospective nature of this study, informed consent was not required; however, patient information notes were sent and the study was registered under Clinical Trial Registration number NCT03946384.
In total, 23 males with mHB and the p. Ile112Thr variation were included. Median age at last data collection was 19 years (range 6-67 years), and seven patients (30. 4%) were aged under 12. No signs of connective tissue disorder were mentioned in the clinical files. The median baseline residual plasma FIX activity levels FIX:C, measured by one-stage clotting assay, was 36 IU/dL (range 26-47 IU/ dL). The median activated partial thromboplastin time (aPTT) ratio was 1. 20s (range 1. 07-1. 50s), and for 10 patients (43. 5%) this ratio was not prolonged. FIX:C was measured by two-stage clotting assay in 3 patients, and the levels seemed similar. Other bleeding disorders, such as fibrinogen anomalies, anomalies in prothrombin time, low factor VIII (FVIII) and XI (FXI), anti-FIX inhibitor, von Willebrand disease, and platelet disorders, were excluded in patients who underwent those tests.
2 In addition, some significant BE may have been underestimated. Our clinical data were mostly collected from patient treatment diaries, but some BE may not be traced in this type of diary; we therefore described only the minimum number of BE. Moreover, bleeding severity was underestimated because some patients had joint procedures without any joint bleeds recorded. This abnormal bleeding phenotype could justify earlier prophylaxis in these patients. Patients should not be treated on the basis of the initial severity classification based on FIX levels, but rather on the severity of the BE. If the symptoms are similar to those of a severe HB patient, the same therapeutic plan should be chosen because a delay in treatment may be damaging. This genetic variation may thus be deleterious. Out of the 725 HB patients followed in the French national mHB cohort, only 8 have prophylactic treatment, 3 of whom have the genetic variation p.
Ile112Thr (FranceCoag, data updated on 05. 18. 2019). No discordance between FIX one-stage and two-stage clotting assays was described in our patients in whom those tests were performed. A difference between those assays is well described in FVIII dosage and is associated with certain genetic variations in the F8 gene. 3 In haemophilia A, clinical symptoms seem best correlated to FVIII levels measured by two-stage clotting assay. Discrepancies between FIX clotting assays have been described in HB patients and could be linked to a genetic mutation, but in those studies two-stage clotting assays gave higher levels than one-stage clotting assays. 4 wever, no other articles seem to describe a discrepancy between FIX levels and clinical severity. This missense variation switches an isoleucine for a threonine amino acid (AA) in the first epidermal growth factor (EGF-1) module, but the implication of such a domain in interaction with factor VIII within the tenase complex has not been fully elucidated.
b Joint procedures include arthrodesis and arthroplasties (total joint replacement, hip, knee, elbow) and other joint procedures such as synoviorthesis, meniscectomies and joint infiltrations. c ABR, annual bleeding ratio or median annual number of bleeds. of this AA. To predict the impact of point mutation on protein stability, we used CUPSAT software (Cologne University Protein Stability Analysis Tool). 9 The p. Ile112Thr change confers unfavourable torsion, destabilizing the protein. To predict the overall protein impact, we used Poly-Phen-2 (Polymorphism Phenotyping version 2),  10  which considers the variation of interest only as a genetic polymorphism. In all, variation p. Ile112Thr does not seem to have a severe impact on protein activity. However, in these prediction models, FIX was rarely considered as a whole, and intra-molecular interactions and interactions within the tenase complex were often not analysed.
Ajustement lineaire du nombre de coup/s determinepar gamma camera en fonction de l'activitedu fantome determinepar l'activimetre, la pente correspond au facteur de calibration (H). Absorbed renal doses measured for each patient by operators with the reference method (A), 1 sVOI (B) and 3 sVOI methods (C). Bland-Altman analysis comparing the absorbed renal dose of each alternative dosimetry strategy with the reference method based on data measured by Operator 3 (D-G) (the solid line corresponds to the average bias; the dotted lines correspond to the concordance limits, 95 % confidence interval or 2 standard deviations). Linear adjustment of the number of count/s determined by the gamma camera as a function of the phantom activity determined by the activimeter; the slope corresponds to the calibration factor (H).
Plusieurs equipes ont proposede personnaliser l'administration du 177 Lu-Dotatate en se basant sur la dosimetrie renale, selon le principe ''As High As Safety Achievable'' (AHASA)  [26]. Garske-Roman et al. ont ainsi repetel'administration de cycles de 7,4 GBq de 177 Lu-Dotatate jusqu'aatteindre une dose renale cumulee de 23 Gy  [23]. Ils ont montreune amelioration significative de la survie globale chez les 123 patients ayant atteint cet objectif (en 3 a 9 cycles ; mediane 54 mois IC 95 % 44-NA contre 25 mois IC 95 % 18-30 ; p < 0,0001) sur les 200 patients inclus. Les resultats preliminaires de l'etude ILLUMINETS (NCT01456078) qui propose de repeter l'administration de 7,4 GBq de 177 Lu-Dotatate jusqu'a àtteindre une dose equivalente biologique renale cumulee de 27 AE 2 Gy ou de 40 AE 2 Gy (en l'absence de toxicite) ont toutefois montreune toxicitehematologique potentiellement limitante (7/41 patients ont arreteles administrations pour cette raison)  [27].
Cell cycle analysis by flow cytometry For cell cycle analyses, control and TbRRP44 knockdown cells were collected 48, 72 and 96 hours after RNAi induction. The cells were centrifuged at 300 g for 10 min, washed with PBS and fixed with cold ethanol 70% (5 x 10 6 /mL) at -20 ºC. The cells were harvested by centrifugation, washed with PBS and suspended in 200 µL PBS plus 200 µL of the propidium iodide staining solution (3. 4 mM Tris. HCl pH 7. 4, 0. 1% NP40 (v/v), 10 mg/mL RNase A, 10 mM NaCl, 30 µg/mL propidium iodide). Data from 10,000 events per sample were acquired using a FACS Canto II (BD Biosciences). The propidium iodide fluorochrome was excited with a blue laser (488 nm) and the emitted fluorescence was collected with a 585/42 band pass filter. Single cells were gated based on PI-A vs.
Analysis of cell death using annexin V-Alexa 488 and propidium iodide staining A total of 2x10 6 cells from control and TbRRP44 knockdown cells from 48, 72 and 96 hours after RNAi induction were centrifuged at 300 g for 10 min, washed once with PBS and stained with Alexa Fluor 488 annexin V/Dead Cell Apoptosis Kit (Invitrogen -V13245) according to the manufacturer's instructions. The analyses (20. 000 events/sample) were performed on a FACS Canto II (BD Biosciences). Alexa Fluor 488-annexin V and propidium iodide fluorochromes were excited with a blue laser (488 nm) and the emitted light was collected with 530/30 and 585/42 band pass filters, respectively. Color compensation was used to minimize spectral overlap. The cell samples were stained and analyzed in triplicate. Data analysis was performed using the FlowJo software version 10.
Nucleus and kinetoplast quantification Control and TbRrp44 knockdown cells were collected at 48 and 72 hours after RNAi induction and fixed with 4% (v/v) PFA (~3 x 10 6 cells/mL) as described above. The cells were adhered to CellCarrier-96 Ultra Microplates (PerkinElmer) precoated with poly-L-lysine and stained with 2µg/mL of DAPI (4',6-Diamidino-2-Phenylindole). The images were acquired on an Operetta CLS High-Content Analysis System (PerkinElmer) using the confocal model, z-stack function (four planes at intervals of 0. 5 µm) and a 63x water objective lens (NA 1. 15 and WD 0. 6). The DAPI signal was collected using 355-385 nm excitation and 430-500 nm emission filters. Maximum projection images from Z-planes were analyzed with Harmony 4. 6 software. Cells were detected using the "find cell" algorithm (method A) in digital phase contrast (high detail) image.
The cells were incubated for further 30 min, washed with PBS and fixed with 4% (v/v) PFA as described above. Images of MitoTracker-stained cells were acquired on a Nikon Eclipse 80i microscope using a Planfluor 100x/1. 30 objective, Evolution MP Color camera (Media Cybernetics) and QCapture Pro 6. 0 software. The acquisition time of MitoTracker fluorescence images was 4 seconds using a 528-553 nm bandpass filter for excitation and a 590-650 nm filter for emission. Images were rescaled using the Analyze Menu tools of Fiji  [71]  to convert image size from pixels to m. Definition of cell contour, subtraction of background and fluorescence and area quantitation were performed as described above.
25 % (v/v) NP40 in PBS buffer for 2 minutes and blocked with 4% bovine serum albumin in PBS buffer for 1 hour. Atg8. 2-YFP was localized by immunostaining with an anti-GFP nanobody (clone LAg16-G4S-2,  [77] ) conjugated with Alexa Fluor 488 and simultaneously stained with a 1:1500 dilution of a 1% Evans Blue (v/v) solution. Images were acquired on a Leica Microsystems DMI6000B microscope using the same objective and set of filters described above for the analysis of autofluorescence in the green range. The images were analyzed with Columbus Image Data Storage and Analysis System for Microscopy (PerkinElmer). Cells were detected using "find cell" algorithm (method A) from the Evans blue signal (red channel). Border objects were excluded to analyze only entire cells. Isolate cells were selected with the morphology (roundness and area) properties.
Acquisition of cryo soft X-ray tomography data sets and 3D volume reconstruction Cryo soft X-ray tomography data were collected at the MISTRAL beamline (Synchrotron ALBA, Barcelona Spain)  [79]. The vitrificated grids were transferred to the beamline under cryogenic and vacuum conditions. The data sets were acquired at 520 eV energy with 1 sec of exposure, in a tilt range from -70 to 70 degrees, rotating 1 degree between each image. Alignment of the tilted series was performed with IMOD  [80]  using the gold fiducial markers. Final reconstructions were performed using Tomo3D  [81]  and cell segmentation was performed using the Amira 3D Software for Life Sciences (ThermoFisher Scientific).
Cryo soft X-ray spectromicroscopy In order to analyze the calcium content in the cells, cryo spectromicroscopy was performed and XANES spectra of the Ca-containing vesicles were analyzed plotting the average intensity of the pixels of the vesicles area as a function of the energy (from calcium pre-edge to calcium post-edge). All vesicles spectra showed the Ca in solution form  [57]. Calcium localization in different controls and TbRrp44 knockdown cells was carried out by subtracting an image of the cell taken at pre-edge from the one taken at the L3-edge. The contrast in the difference image is dominated by areas containing substantial Ca content. Image subtractions were carried out using the Fiji software  [75]. The volumes of acidocalcisomes were calculated using the Microscopy Image Browser software platform  [82].
Nile red signals was collected using 460-490/500-550 (green) and 615-645/655-760 (red) excitation/emission filters. Maximum projection images from Z-planes were analyzed with Harmony 4. 6 software. Cells were detected using the "find cell" algorithm (method C) using the red images. Border cells were excluded and only entire cells were kept in the analysis. Isolated cells were selected based on morphology properties (width, length, area and roundness). The intensity average of the green fluorescence signal from the selected cells was used for comparisons.
Statistical analysis The data are presented as the mean ± standard error of the number of cells analyzed and measurements performed. Differences between two samples were assessed by t-test. Differences between four or more samples were assessed one-way analysis of variance (ANOVA) followed by Tukey's multiple comparison test using GraphPad Prism version 7. 01 software. *: 0. 01<p<0. 05; **: 0. 001<p<0. 01; ***: p<0. 001.
This indicates that at this time, the cells start to undergo DNA damage. (C) Quantification of cells according to nucleus/kinetoplast ratio configuration. There is a small but significant increase of the 1N/1K population, accompanied by a decrease of the 1N/2K population in TbRrp44 knockdown cells at 72 h of depletion. (D) Quantification of nuclei area showing higher area average for TbRrp44-depleted cells (E) Representative images used in the analysis of N/K ratio per cell. Nuclei and kinetoplasts were stained with DAPI and selected using Harmony 4. 6 software from PerkinElmer.
Acknowledgements The authors are grateful for the following institutions and people:  Synchrotron SOLEIL  for beam time awarded at DISCO beamline (proposal 20160888) and all the support they benefited as SOLEIL's users. Synchrotron ALBA  for beam time awarded at MISTRAL beamline (proposals 2017022087, 2018022705) and all the support they benefited as  ALBA's users. FIOCRUZ Network of Technological Platforms  for access to its facilities (Platforms  RPT07C -Confocal  and  Electron Microscopy  and  RPT08L -Flow Cytometry ). Dr. Bruna H. Marcon  for support with the analyses performed at Platform  RPT07C. Prof. Jeremy Mottram ,  Centre for Immunology and Infection, University of York ,  United Kingdom , for providing plasmids pGL2165 and pGL2166. Funding was provided by  CAPES-COFECUB program  ( CAPES 862/2015, -COFECUB Me862-15 ),  CNPq  ( NITZ: 312195/2015-0; BGG: 304027/2015-4 ),  FIOCRUZ Inova program  ( 3501948026 ).