dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments This study was funded by the  University of Arizona ,  TRIF BIO5  Seed Grant number  5833210  (to JG and CG, multiple principal investigators). We gratefully acknowledge the contributions of  Yessenya Barraza ,  Chelsey Bergmann ,  Chloe Dillingham ,  Jacob Rafko ,  Lauren Taylor , and  Jialiang Zhang , without whom this project would not have been successful.
Immunofluorescence Placental tissues were incubated with mouse podocalyxin (10 µg/mL) (R &D system, France) primary antibody. Incubation was performed overnight at 4 • C in PBS with 2% goat serum, 1% bovine serum albumin. Slides were then washed and incubated with a secondary antibody (Goat-antimouse Cy3, Abcam) for 1 hour at room temperature and counterstained with Hoechst 33342. Images were taken by Zeiss AxioVision microscope, and processed using AxioVision SE64 Rel. 4. 9. 1 software  [28]. Negative controls were treated in an identical manner, except that podocalyxin antibody was replaced by PBS.
Wound-Healing Assay RCHO-1 cells were seeded and grown to confluency in 12 well plates. Differentiated confluent RCHO-1 cultured cells (i. e. , giant cells) in a dish were scratched with a sterile tip to create an artificial wound which was allowed to heal for the next 12 h. The cells were treated at T0 with the antagonists alone or in combination at 1 µM. in the presence of mytomicin (1 µM) to inhibit proliferation during the wound closure. The treatment lasted for 12 h. The size of the wound was measured and quantified using the photomicrographic images captured from three separate experiments. The closing of the wound was analyzed using Scion Image software (version 4. 0. 2). The results are presented as percentage of wound closure following 12 h of treatment.
Statistical Analysis All statistical analyses were performed using SigmaStat (Jandel Scientific Software, SanRafael, CA, USA). Data were analyzed using one-way ANOVA. All data were verified for normality and equal variance. When normality failed, a nonparametric test followed by Dunn's was used. (SigmaPlot and SigmaStat, Jandel Scientific Software). All data are expressed as means ± SEM (p < 0. 001, 0. 01, and 0. 05).
Conceptualization, N. A. and M. B. ; methodology, G. B. , Q. -Y. Z. , D. R. and F. S. ; validation, C. C. and R. A. N. ; formal analysis, W. T. ; investigation, P. H. and N. A. ; writing-original draft preparation, D. R. and P. M. and C. M. ; and editing, N. A. and P. M. ; supervision, N. A. and M. B. ; funding acquisition, M. B. and N. A. All authors have read and agreed to the published version of the manuscript. Financial support: We acknowledge the following sources of fundings: Institut National de la Santé et de la Recherche Médicale (INSERM), University Grenoble-Alpes, VALO-GRAL CBH-EUR-GS (ANR-17-EURE-0003), Région Auvergne-Rhône-Alpes through Cancéropôle Lyon Auvergne Rhône-Alpes, Ligues Départementales (Isère & Savoie) contre le Cancer and Fondation pour la Recherche Médicale (FRM) SPF20150934074.
Author Contributions:Funding: Conceptualization, N. A. and M. B. ; methodology, G. B. , Q. -Y. Z. , D. R. and F. S. ; validation, C. C. and R. A. N. ; formal analysis, W. T. ; investigation, P. H. and N. A. ; writing-original draft preparation, D. R. and P. M. and C. M. ; and editing, N. A. and P. M. ; supervision, N. A. and M. B. ; funding acquisition, M. B. and N. A. All authors have read and agreed to the published version of the manuscript. Financial support: We acknowledge the following sources of fundings: Institut National de la Santé et de la Recherche Médicale (INSERM), University Grenoble-Alpes, VALO-GRAL CBH-EUR-GS (ANR-17-EURE-0003), Région Auvergne-Rhône-Alpes through Cancéropôle Lyon Auvergne Rhône-Alpes, Ligues Départementales (Isère & Savoie) contre le Cancer and Fondation pour la Recherche Médicale (FRM) SPF20150934074.
Selection of anti-prion drug candidates ROCS shape-based virtual screening: The latest release of DrugBank (version 5. 1. 0, released 2018-04-02) was downloaded directly from https://www. drugbank. ca and filtered to only conserve FDA-approved or withdrawn drugs. Multiconformer files were generated by OMEGA v2. 5. 1. 4 from OpenEye Scientific Software (http://www. eyesopen. com/), leading to 1887 approved or withdrawn drugs saved in oeb. gz format. These generated multiconformational files were used as the input database for performing similarity search with Rapid Overlay of Chemical Structures (vROCS 3. 2. 2. 2 from OpenEye Scientific Software (http://www. eyesopen. com/)). ROCS is designed to carry out large-scale 3D database searches. It performs similarity searches by using a shape-and/or pharmacophore-based superposition method that finds the similar but non-intuitive compounds.
Identification of new approved anti-prion drugs based on flunarizine structure In order to broaden the range of new anti-prion drugs that could potentially be used to treat patients with prion diseases, and considering that flunarizine might not be the most optimized anti-prion drug, we performed an in silico screening, ranking the 1887 FDA-approved or withdrawn drugs present in the Drugbank database (https://www. drugbank. ca/) for their structural similarities with flunarizine. In terms of pharmacophoric pattern, flunarizine is composed of three aromatic moieties, as well as two protonable nitrogen atoms, which can interact with specific biological targets through electrostatic or H-bond acceptor interactions (Fig. 2a ). We chose to use the ROCS method from OpenEye Scientific, using a shape-and/or pharmacophore-based superposition method that finds similar but non-intuitive compounds.
However, at this concentration, flunarizine and ebastine showed toxicity. These two drugs were thus further used at 1. 5 mM, concentration at which both drugs shown no toxicity (Fig. S7b ). Drugs were administered to adult flies orally in the food at the indicated concentrations from day 2 to day 5, and fresh food with drug was provided every day. Wing posture defects were recorded from day 3 to day 6 of adulthood. The effect of drugs was quantified by recording the number of PABPN1-17ala-expressing flies with abnormal wing posture. Flunarizine, metixene and ebastine showed a beneficial effect with a significant decrease in the number of flies with abnormal wing posture compared to DMSO alone (Fig. 5b ), without affecting Drosophila survival (Fig. S7b ). Altogether, these data demonstrate that these new anti-PFAR drugs are active in alleviating defects in OPMD cell and Drosophila models.
Acknowledgments We thank  G. Butler-Browne  for careful review of the manuscript,  A. Nasir  for critical reading of the manuscript,  Séverine Loisel ,  Marie-Françoise Scoazec  and  Manuel Feillant  for expert animal care,  Hélène Simon  and  Johanna Mazé  for their excellent technical assistance,  Laetitia Guedeville ,  Laetitia Herzog ,  Fabienne Reine ,  Emilie Jaumain  for expert animal care and excellent technical assistance, and  Fanny Roth  for technical assistance. This work was supported by  Institut de France -Fondation NRJ (CV) ,  MESR (AB, PHN) ,  Inserm  (CV and CT),  UBO (CV) ,  CNRS  and  University of Montpellier (MSg) ,  AFM-Téléthon  eOPMD project  17110  (CT and MSg),  Sorbonne Université  and  Association Institut de Myologie (CT) ,  DIM MALINF ,  INRAE  and  Fondation pour la Recherche Médicale  (Equipe FRM  DEQ20150331689 ) (VB and SH),  Association Défi Organisation (CV).
Electrochemical data Electrochemical polymerizations were performed using a potentiostat (Metrohm Autolab) equipped with a three-electrode system fitted with a gold plate (2 cm 2 ) as the working electrode, a carbon-rod as the counter electrode and a saturated calomel electrode (SCE) as the reference electrode. The electrochemical cell was first filled with 10 mL of anhydrous acetonitrile containing 0. 1 mol L -1 of tetrabutylammonium perchlorate (Bu4NClO4) as the electrolyte as well as 0. 01 M of monomer. After determination of the oxidation potential (E ox = 1. 48 V vs SCE) for each synthesized monomer, electropolymerizations were performed under potentiodynamic conditions via cyclic voltammetry at a scan rate of 20 mV s -1. The total number of scans was varied  (1, 3 and 5)  in order to study polymer growth.
Surface characterization Surface hydrophobicity was characterized by goniometry using a DSA30 goniometer (Bruker) and the "Drop Shape Analysis System" software. Water droplets (2 L) were deposited onto surfaces and the apparent contact angles (w) were determined. Each data point presented reflects a mean of five measurements (n = 5). For dynamic contact angles, after deposition of a water droplet, the substrate was inclined until the droplet moved. The maximum inclination angle is named sliding angle (). The advancing and receding contact angles are taken just before the droplet moves. In case the droplets do not move, even with an inclination of 90°, the substrates are considered sticky and can be described as parahydrophobic. Surface morphology was investigated via scanning electron microscopy (SEM) using a JEOL 6700F microscope.
Acknowledgment The group thanks  Christelle Boscagli  from the  Centre Commun de Microscopie Appliquée (CCMA, Université Côte d'Azur ) for the preparation of the substrates necessary for the SEM analyses. This work has been supported by  CNRS   GDR 2088  « BIOMIM ». This project was supported by  JSPS [KAKENHI ,  Grant-in-Aid for Scientific Research  (B), No. 19H02504 ,  Fostering Joint International Research (A) , No. 15KK0221 ,  Grant-in-Aid for Challenging Research  (Exploratory), No. 17K19002 ], and  Leading Research Organizations (RCUK [ through  EPSRC EP/I018301/1 ],  ANR  [ 13-G8ME-0003 ]) under the  G8 Research Councils Initiative for Multilateral Research Funding-G8-2012. The authors acknowledge  Shared Facility Center for Science and Technology, Hirosaki University (SFCST)  for 1 H-NMR and FT-IR spectra measurements and elemental analysis.
After washing, membranes were incubated with horseradish peroxidase-linked antibody (1:2000, Cell Signaling Technology, 7074, 7076, 7077). The detection of specific signals was performed using the ECL Chemiluminescent Kit (Bio-Rad, 170-5070) on a LAS 4000 device (Fuji). Densitometry analysis with ImageJ software (National Institutes of Health) was used for quantification. Blood pressure measurements and physiological assessments Systolic blood pressure of mice was recorded using the tail-cuff method (Visitech Systems Inc. , BP-2000). Ten measurements from each mouse were taken, and then a mean value was determined. Systolic blood pressure was measured at baseline (12 weeks of age) and then weekly until the end of the treatment period. All mice were placed in metabolic cages with free access to water for 6-hour urine collection.
After TBS-T rinses, fluorophore-conjugated secondary antibodies donkey anti-guinea pig IgG AF594-conjugated antibody (Jackson ImmunoResearch, 706-585-148) and donkey anti-rabbit IgG AF488conjugated antibody (Invitrogen, A21206) were applied. Images were taken using a Zeiss 2 fluorescent microscope, an AxioCam HRc camera, and Axiovision 4. 3 software. For formalin-fixed paraffin-embedded (FFPE) kidneys, sections  (3.
Quantitative polymerase chain reaction array Freshly isolated glomeruli were frozen in QIAzol Lysis reagent (Qiagen) at À80 C. Total RNA extraction using the phenol-based method was processed according to the manufacturer's recommendations. cDNAs were synthesized using the RT 2 First Strand Kit (Qiagen, 330401), and real-time polymerase chain reaction (PCR) was performed using a Custom RT  2  Profiler PCR Array (Qiagen, CLAM36771C) with RT 2 SYBR Green qPCR Mastermix (Qiagen, 330502). The quantitative PCR plates were run on an Applied Biosystems StepOnePlus cycler. Each array contains quality control for reverse transcription efficiency and genomic DNA contamination. Quantitative PCR analysis was performed using the 2-DDCT method with the help of the GeneGlobe Data Analysis Center (www. qiagen.
In silico prediction of the calpain cleavage site in podocyte proteins We used several in silico tools to predict potential calpain targets in podocytes (Supplementary Tables  S1  and S2 ). Three online databases were compared: GPS-CCD,  54  CaMPDB,  55  and DeepCalpain. 56 In silico analysis identified several podocyte proteins, nephrin and podocin among them, that could be cleaved by calpains. Thus, calpastatin-mediated glomerular protection could be linked to a reduction of calpain enzymatic activity, leading to reduced degradation of some podocyte proteins. Furthermore, at least 3 autophagy-related proteins are direct targets of calpains. ATG5 is cleaved by calpains, leading to a disturbance in the ATG12-ATG5 complex formation. 57, 58 dministration of calpain inhibitors in vivo also prevented cleavage of the autophagy protein Beclin-1.
ACKNOWLEDGMENTS This work was supported by the  Institut National de la Santé Et de la Recherche Médicale (Inserm)  and  Université de Paris. IB was supported by a graduate fellowship from the  Ministère de l'Education Nationale, de la Recherche et de la Technologie. OL was funded through a  European Foundation for the Study of Diabetes (EFSD)  award supported by  EFSD/Novo Nordisk Programme for Diabetes Research in Europe  and a grant from the  Société Francophone du Diabète (SFD). BR and CH were funded by Starting Grant 107037 from  European Research Council  and the  European Union  (P-LT). YS was supported by a graduate fellowship from the  Fondation de France. We thank  Elizabeth Huc ,  Nicolas Perez ,  Corina Suldac , and the  ERI   U970  team ( Université de Paris, PARCC, Inserm, Paris, France ) for assistance in animal care and handling,  Nicolas Sorhaindo  for biochemical measurements ( ICB-IFR2 ,  Laboratoire de Biochimie, Hôpital Bichat, Paris, France ), and  Alain Schmitt  and  Jean-Marc Masse  for transmission electron microscopy ( Institut Cochin, Paris, France ).
Data collection The data analysed were extracted from the databases of the BCSP-structure. These databases were regularly enriched with sociodemographic, diagnostic, and follow-up data provided by radiologists, pathologists, oncologists, surgeons, gynecologists, general practitioners, health insurance plan, or medico-administrative databases. The study distinguished the follow-up of the left breast from that of the right breast. The end date of follow-up (end-date) was the date of the last mammogram. Women aged <73 years were considered "lost to follow-up" whenever the date of the last mammogram was before 2015 because they could have had another mammogram before age 74. The end of follow-up criterion was the diagnosis of a B-cancer lesion. Regarding B-cancer diagnosis, the study adopted the C50 code of the 10 th version of the WHO International Classi cation of Diseases (ICD-10)  [27]  : i) ductal carcinoma in situ, lobular carcinoma in situ, and nipple Paget's disease were classi ed as "adenocarcinoma in situ" (TIS); ii) in ltrating/invasive ductal or lobular carcinomas were classi ed as "in ltrating adenocarcinoma" (ADK-I); and, iii) all other malignant tumors (papillary, tubular, mucinous, medullary, etc.
The B-cancer risk analysis according to the age at nding of each mammographic abnormality was carried out by estimating the adjusted relative risk (RRa) using a multivariate Cox model. Only women who had at least one of the ve mammographic abnormalities, were included in this analysis. The cox-model included all covariates regardless of their p-values in univariate analysis. Because of their multiple collinearities, the ve variables relative to the presence of an abnormality in the contralateral breast were introduced into the nal model in three modalities (Absent, Present ("Anterior"+"Same_date"+"Posterior") and NA). The parameters of the model were estimated by the maximum likelihood method. All analyses were performed using STATA software version 13 (College Station, Texas, USA). The threshold of statistical signi cance was 5%.
Limitations The incidence rates found here may be underestimated because of incomplete data due to censoring before age of 74 for loss to follow-up or relocation while the results of last mammograms were classi ed ACR 3, 4 or 5. Based on mammographic reading reports, this study cannot establish, with certainty, the link between a radiological abnormality seen during a mammogram and a similar abnormality seen during a subsequent mammogram. The lack of interconnection between departmental databases does not make it possible to know the antecedents of women who have relocated one or more times between the age of 50-74 years. Women excluded because having only one participation in BCSP probably have a history of BCSP campaigns participation in other departments.
The physics program and reach of the multipurpose CASTOR calorimeter are broad and unique, because no comparable instrumentation exists in this η range at any other interaction point (IP) of the LHC. The installation of a calorimeter at the forward rapidities covered by CASTOR involves significant challenges. The beam pipe is just ≈1 cm away from the detector and must be carefully protected. The calorimeter is immersed in the forward shielding of CMS, which channels the strong magnetic field from the central region of the apparatus. Small gaps in the shielding produce strong local variations in the magnetic field structure. The field has a magnitude of about B = 0. 2 T in the vicinity of the detector and has an impact on the shower development inside the calorimeter and also, more importantly, on the gain of the photomultiplier tubes (PMTs) used to record the signals.
6. The left panel illustrates the impact of the field on the PMT response measured with pp data in 2010, and the right plot is the result from LED data taken in 2016. Some general features, as the insensitivity in the range of the modules 6-9, are visible in both years, but there are also important differences clearly asking for a careful time-dependent calibration. There were major modifications to CMS between 2010 and 2018, e. g. , the installation of an additional 125-ton yoke endcap shielding disc. Details of the shieldings directly around CASTOR (rotating and collar shields) were also changed, and finally the exact positioning and geometry of CASTOR is slightly different in each installation period. For data taking with the nominal CMS magnetic field, the recordings by most channels in modules 7 and 8 are significantly less useful, and modules 6, 9 and 10 are also compromised.
Furthermore, in 2016 there appears to be a general larger impact on the first towers (numbers 1 to 5), which are located in the top part of the calorimeter, where displacements of the PMTs caused by the ramp-up of the CMS magnet are the largest. These observations clearly show the importance of properly calibrating the CASTOR channels during physics data taking with a stable magnetic field. The insensitivity in the central parts of CASTOR, induced by the magnetic field channeling through the massive radiation shielding of CMS, was discovered after the first data taking in 2009, and could not be mitigated without a major redesign of the shielding and/or the detector. However, the impact on almost all typical physics applications remains limited: the front modules 1 to 5 are sufficient to detect ≈100% of the electromagnetic showers, as well as ≈75% of the hadronic showers in the calorimeter.
At very small signals, one can see additional quantization effects from the nonlinear behavior of the QIE digitizers. further studies are still ongoing or planned in the future with the collected data  [27, 28]. The CASTOR electronics chain provides four simultaneous hardware trigger outputs using the standard CMS hadron calorimeter trigger readout (HTR) boards. There are eight HTR boards; each analyzing the data of one octant (two towers) of the calorimeter. Since one HTR board can handle 24 front-end channels, the last two modules per tower are not included in the trigger system. The output of all octants is further processed in the "trigger timing control" (TTC) board to form four trigger output signals for the whole CASTOR calorimeter. These are sent to the CMS L1 global trigger system.
The spread of the model predictions in the CASTOR acceptance provides an estimate of the model dependence of this extrapolation. The extrapolated average energy deposit in the CASTOR acceptance found by this procedure is E pp (7 TeV) ≡ dE/dη CASTOR = 665 GeV with an RMS of 60 GeV (10%) for the 7 TeV minimumbias proton-proton data. The uncertainties in the absolute calibration of the HF as well as in the HF generator-level correction are 10%, and the total uncertainty in the energy estimate in CAS-TOR is thus ∆(E pp (7 TeV)) = (10%) 2 + (10%) 2 ≈ 14%. The average charge signal recorded in the five frontmost modules for this minimum-bias data is S pp (7 TeV) = 21 000 fC. Since only these front modules of the calorimeter are used, about 75% of the energy of hadronic showers are contained. Furthermore, two channels of these front modules (module 1 in towers 5 and 6) are not included in the measurement due to stringent quality criteria on noise.
23 , the measured response of one infrared sensor in the 2D scan is shown. The surface of the beam pipe mockup is shown as dashed line. The uncertainties propagated to the position found with the minimization procedure are lower when the infrared sensors are pointing perpendicular to the beam pipe. Figure  24  shows the result of this procedure for the position of CASTOR after a magnet cycle in April 2015. A position with an uncertainty in x and y of about 2 mm is found. At the same time, other independent methods to determine the position of the calorimeter with LHC collision data have been implemented and cross-checked with the above procedure. Firstly, during 2013 a special trigger was developed to record single electrons in CASTOR during the pPb data taking. The trigger made use of the TOTEM T2 tracking station  [82]  in front of CASTOR (see Fig.
Electron candidates Figure  25 : Left: Noise distribution of e. m. clusters in data used for the alignment of CASTOR with TOTEM T2 tracks, measured with a random trigger in pPb events with no collisions  [66]. The RMS of the distribution is <1 GeV; the uncertainties are statistical only. Right: Projected (x,y) coordinates of single isolated T2 tracks onto the CASTOR front surface  [66]. Only tracks (electron candidates) that coincide with a single isolated e. m. cluster in CASTOR are plotted. The points are colored alternatively depending on which calorimeter tower has registered the deposited energy. The black contours indicate the optimal positions of the two halves of CAS-TOR as derived from the analysis of these data. The empty ring at a radius of about 110 mm is caused by the shadow of a conical beam pipe section.
data yielded a very accurate picture of the alignment relative to the T2 detector. The measured geometric correlation of T2 tracks with electromagnetic energy clusters in CASTOR is shown in Fig. 25  (right). The ring with reduced track density corresponds to the shadowing induced by the conical beam pipe in front of T2 and CASTOR. The number of background events in this plot becomes visually enhanced since the background is uniformly distributed, whereas the signal is highly clustered on top of each of the CASTOR towers. The main source of this background is calorimeter noise, since the energy threshold to select these electron events is 10 GeV per tower, whereas the calorimeter noise tails contribute at the level of <10 -4 per event (Fig. 25 , left). It can also be seen that the acceptance of T2 is slightly smaller than that of CAS-TOR.