dataesr/scientific-paragraphs-categorization huggingface dataset:
Cell Imaging Immunofluorescence microphotographs were processed and analyzed with ImageJ 1. 48p software (https://imagej. nih. gov/ij/ index. html), measuring integrated pixel intensity. COUP-TFI signal quantification was performed on three biological replicas per group and on ten different randomly chosen fields for each sample. Analysis of COUP-TFI expression was performed by first applying an appropriate threshold for each channel in order to remove background signal, then normalizing COUP-TFI pixel intensity on the nuclear staining (DAPI). EGFP reporter activity in HEK293T and neuralized ESCs was evaluated as EGFP/DAPI pixel intensity ratio. For HEK293T analysis, three independent cultures were imaged (n = 9 random fields per treatment). For neuralized ESCs, ten different randomly chosen fields of two biological replicas per group were analyzed.
ACKNOWLEDGMENTS We thank  Dr. Marco Groth  from the core facility DNA sequencing of the  Leibniz Institute on Aging -Fritz Lipmann Institute in Jena  for his help with miRNA sequencing and  Greta Ghiloni  for tech-nical assistance in molecular cloning. This work was supported by  University and Research  grant  PRIN-2102  to F. C. , by an  ERA-NET-ANR Neuron  grant  ANR-15-NEUR-0002-04  to M. S, by '' Investments for the Future'' LabEx SIGNALIFE  (grant  ANR-11-LABX-0028-01 ) to M. S. and by a postdoctoral fellowship from the  Ville de Nice, France (''Aide Individuelle aux Jeunes Chercheurs'')  to  M. Bertacchi.
Clinical evaluation Medical records were reviewed by a clinician (BSA) and data were collected on demographics (age at death, gender, and race/ethnicity). Disease onset was defined as the time at which the first persistent and consistent symptom of prion disease was observed. Data on family history of dementia as well as past medical and surgical history were also collected. The mean incubation period in iCJD was measured from the mid-point of GH therapy or date of receipt of the DM graft to the clinical onset of the disease.
Acknowledgements We thank all the clinicians and administrative personnel for referring patients to the partecipating National Prion Diseases Surveillance Centers. We gratefully acknowledge  Dr. Marta Couce ,  Alison Boyd ,  Dr. Christiane Stehmann ,  Dr. Colin L. Masters ,  Dr. Anna Ladogana ,  Yvonne Cohen ,  Dr. Laura Cracco ,  Dr. Wenquan Zou ,  Dr. Lan Zhou ,  James Metcalf ,  Miriam Warren ,  Katie Eppic , and  Janis Blevins  for their assistance and advices.
Funding This work was supported by:  CDC 000309CK14  to  J. G. Safar ;  NIH P01AI106705 ,  NIH   5R01NS083687  and  Charles S. Britton Fund. to  P. Gambetti ; The  Réseau National de Référence de maladies de Creutzfeldt-Jakob  and the  "Centre National de Référence des agents transmissibles non conventionnels" (Paris, France ) are supported by  Santé Publique France ;  Inserm 1127 has received funding from the program  " Investissements 276 d'avenir "  ANR-10-IAIHU-06 ;.
ACKNOWLEDGMENTS and authors' note The expert meeting and the Delphi panel were supported by the Edmond & Lily Safra Foundation, Institute Claude Pompidou, University Côte d'Azur, and by the IA association. Thanks for the ISTCM and ISTAART contribution, and a special acknowledgment to all clinicians and researchers working for so many years on the topic. The apathy diagnostic is part of the MNC3 program University Cote d'Azur Valentine Mantua: The opinions expressed in this presentation are the personal views of the Author and may not be understood or quoted as being made on behalf of or reflecting the position of the Italian (AIFA) or European (EMA) Medicines Agency or any of their Committees. The mention of commercial products, their sources, or their use in connection with material reported herein is not to be constructed as either an actual or implied endorsement of such products by any Public Department or Health and/or Payer Services.
ACKNOWLEDGEMENTS We thank  Mike Cates ,  Suraj Shankar  and  M. Cristina Marchetti  for illuminating discussions. LPD thanks the  Department of Physics, Indian Institute of Science , for hospitality and support. SR was supported by a  J C Bose Fellowship of the SERB (India)  and the  Tata Education and Development Trust. 1 ) unlike in active scalar models (model A or B). This is to be expected on symmetry grounds.
"This study was supported by the  Institut d' Études Cognitives  ( ANR-10-LABX-0087 IEC  and  ANR-10-IDEX-0001-02 PSL* ). We are also grateful to  Dr. Bahador Bahrami  for providing us the stimuli. " should read: "This study was supported by  Frontiers in Cognition (FrontCog ,  ANR-17-EURE-0017 ). We are also grateful to  Dr. Bahador Bahrami  for providing us the stimuli and to  Raphael Delage  for his valuable help in data collection. ".
Database for cross-correlation analysis. From the 307 analyzed behavioral sessions, we selected 92 sessions (46 in each task) including 224 neurons recorded from two monkeys based on the following criterion. We excluded the neuron pairs in which both neurons were recorded from the same electrode to avoid the possibility of contamination. We also excluded neuron pairs recorded less than 50 trials in one of the two tasks. Finally, we excluded neuron pairs with a neuron with a null firing rate during the fixation period in at least one task. The remaining neuronal sample consisted of 439 neuron pairs, 335 from monkey 1 and 104 from monkey 2. During the recording sessions, the action potentials from single units were isolated with quartz-insulated platinium-iridium electrodes (80 µm outer diameter; impedance, 0.
For the latter, we resorted neuronal waveforms with Offline Sorter (Plexon). NIMH CORTEX software (https://www. nimh. nih. gov/ labs-at-nimh/research-areas/clinics-and-labs/ln/shn/software-projects. shtml) controlled behavior and collect data. Data Analysis. We used the Matlab (http://www. mathworks. com) and the Fieldtrip Matlab toolbox  60  (http:// www. ru. nl/neuroimaging/fieldtrip) to analyze the data. For subsequent analysis, we selected neurons that were recorded in both tasks for at least 50 trials in each task. We applied the Joint Peri Event Time Histogram (JPETH) analysis to the pairs of simultaneously recorded neurons (Aertsen et al. 36  ). The JPETH analysis was performed on each selected neuron pairs by building the two-dimensional cross-correlograms with time versus lag on both abscissa and ordinate axis and the correlation strength on the color axis.
Acknowledgements We thank  Mr. Alex Cummings  for the histological material,  Dr. Andrew Mitz  and  Dr. Steve Wise  for their numerous contributions. This research was supported by the  Intramural Research Program  of the  National Institutes of Health, National Institute of Mental Health (NIMH ;  Z01MH01092-28 ) and partially supported by the Italian FIRB 2010 grant ( RBFR10G5W9_001 ).
Ethical approval The experimental protocol was approved by the Institutional Review Boards for Human Investigation at the University of San Andres, La Paz, Bolivia (CNB #52/04), University of Lausanne, Lasusanne, Switzerland (#89/06, #94/10), and University of Glamorgan, Pontypridd, UK (#4/07), and subsequently registered (clinicaltrials. gov; Identifier: NCT01182792). All participants were informed of the purpose/risks of the experiment and signed an informed consent form, with all procedures adhering to guidelines set forth in the Declaration of Helsinki.
S-Nitrosothiols (RSNO): Plasma (400 µL) was mixed with 5% acidified sulphanilamide and left to incubate in the dark at 21º C for 15 min to remove nitrite (NO  2 ) prior to injection into triiodide reagent for direct measurement of RSNO. calculated by subtracting the concentration of RSNO. We performed all calculations using Origin/Peak Analysis software.
Cardiopulmonary function We employed finger photoplethysmography (Finometer ® PRO, Finapres Medical Systems, Amsterdam, The Netherlands) to monitor beat-to-beat mean arterial pressure (MAP) using the Model Flow method that incorporates participant sex, age, stature and mass (BeatScope 1. 0 software; TNO; TPD Biomedical Instruments) to calculate stroke volume (SV) and cardiac output (Q). We corrected for vertical displacement of the finger cuff relative to heart level using a reference probe placed on the chest at the fourth intercostal space in the mid-clavicular line. We measured heart rate (HR) using a lead II electrocardiogram (Dual BioAmp; ADInstruments). We sampled end-tidal partial pressures of oxygen and carbon dioxide (PET O2/CO2 ) from a leakfree mask and analysed via capnography (ML 206, ADInstruments Ltd, Oxford, UK).
Data sampling: We sampled beat-by-beat data continuously at 1 kHz using an analog-to-digital converter (Powerlab/16SP ML795; ADInstruments, Colorado Springs, CO, USA) stored on a personal computer for off-line analysis (Chart version 7. 2. 2, ADInstruments, Colorado Springs, CO, USA). We gave chart files a coded number (not named) by an investigator blinded to the study. We "time-aligned" the MAP and TCD channels given the time-delay (1. 07 s) associated with MAP signal processing when using the Finometer ® PRO.
Dynamic cerebral autoregulatory capacity (dCA): We employed a combination of spontaneous (seated) and driven (repeated squat-stands) oscillations in blood pressure (BP) and MCAv in order to assess dCA via transfer function analysis (TFA). Following 10 min of rest in the seated position, we obtained a 5-min segment of BP and MCAv data for spectral analysis of spontaneous oscillations. In order to increase BP variability and improve the reliability and interpretation of the TFA metrics  (Katsogridakis et al. , 2013) , participants then performed 5-min periods of repeated squat-stand maneuvers at randomly assigned frequencies of 0. 05 Hz [10-sec squat, 10-sec standing) and 0. 10 Hz (5-sec squat, 5-sec standing) with 5 min of standing rest between frequencies  (Smirl et al. , 2015). During these maneuvers, we instructed participants to maintain normal breathing and to avoid Valsalva.
JP-R2 15 Power calculation: We analysed these data using G* Power 3. 1 software. Assuming comparable differences and corresponding effect sizes previously observed in plasma A •-(η² = 0. 54) and NO  2 (η² = 0. 67)  (Bailey et al. , 2013c)  our primary end-outcome variables for OXNOX stress, the present study required a (minimum) sample size ranging between 24-36 participants (8-12 per group) in order to achieve a power of 0. 80 at P < 0. 05. We chose to further inflate this during recruitment given the potential for incomplete data collection.
Inferential statistics: We analysed these data using using the Statistics Package for Social Scientists (IBM SPSS Statistics Version 24. 0). Shapiro-Wilk W tests (P > 0. 05) confirmed that all data sets were normally distributed. We analysed demographic (Table  1 ), metabolic (Table  2 ), haemodynamic (Table  3 ), cognition and depression (Table  5 ), CVR CO2 (Figure  2 ) and TFA (Figure  3 ) datasets using one-way analyses of variance (ANOVAs) and post-hoc Bonferonniadjusted independent samples t-tests if we observed a main effect. We analysed education data (Table  1 ) using Pearson Chi-square tests. We analysed responses to hyperoxia in the highlanders (Table  4 ) using two-way (subgroup × inspirate) ANOVAs and post-hoc Bonferonni-adjusted paired samples (within subgroups) or independent (between subgroups) samples t-tests if we observed an interaction effect.
S-nitrosothiols) nitric oxide metabolites (D-F) at rest in the systemic circulation of a lowlander and highlanders without (CMS-) and with chronic mountain sickness (CMS). A-C: Oxidation of the ascorbate monoanion (AH -) by any free radical (R • ) with a one electron reduction potential that exceeds +282 mV will yield A •-(schematic illustrated above). The unpaired electron is delocalised over a highly conjugated tri-carbonyl π-system rendering it resonance stabilized thereby facilitating direct detection by EPR spectroscopy. At the current settings, A •-appears as a (filtered) doublet with a hydrogen hyperfine coupling constant (a H  Values are mean ± SD; CMS-/CMS+, highlanders without/with chronic mountain sickness; *different vs. Lowlanders for respective challenge (P < 0. 05). Individual hypocapnia and hypercapnia datasets analysed using one-way analyses of variance and post-hoc Bonferonniadjusted independent samples t-tests.
Acknowledgements We thank  Mrs Catherine Romero  and staff of the  Instituto Boliviano de Biologia de Altura (La Paz, Bolivia)  for technical support. ADInstruments provided exceptional technical input/support during the period of data logging. Finally, we appreciate the participants and patients' enthusiasm and commitment to this study. Our study is dedicated to the memory of the late  Dr Christopher K Willie  ( University of British Columbia Okanagan, Kelowna, Canada ) whose memory remains a constant source of inspiration.
Congitive abilities were measured by using the Ymaze (short term memory) and the Moorris Water maze (long term memory) tests. Mice were sacrificed at the end of week 12 and blood, liver and brain samples were collected for protein (synaptic proteins in brain) and lipid analyses. promoting obesity  (Cheng et al. , 2015). However, there is still a debate the ARA influence on obesity-associated inflammation  (Suitor et al. , 2017). The role of intestinal microbiota should be considered to reconcile the various data on dietary ARA effects on systemic chronic sub-inflammation in obesity, Bowel disease or chronic pathologies proinflammatory. For example,  Zhuang et al. (2017)  recently showed that dietary ARA favour obesity and by acting on the hypothalamus-liver-adipocytes axis but the effect is modulated by sex and intestinal microbiota, female mice being less pejoratively affected.
Colchicine was also from Sigma-Aldrich (C9754). At least 12 different fields were identified via a micro-ruled coverslip (Cellattice CLS5-25D, Nexcelom Bioscience) and pictures were taken before treatments. Cells were then treated with either dopamine 4 mM, colchicine 0. 5 µM or without treatment (control). After incubating for 1 h at 37 • C with 5% CO 2 pressure, pictures of the exact same fields located via the micro-ruled coverslip were taken again. Only neuronal-like cells with at least one primary neurite longer than two times the soma size before treatment were traced. Only the longest primary and the longest secondary neurite for each cell traced were included in the analysis. Cells were traced manually using a semi-automated software called FIJI which is a plugin for ImageJ an open source image processing program.
Antibodies were diluted in PBS containing 0. 1% saponin and 0. 3% BSA. Actin was stained with rhodamine phalloidin (1/200, Molecular Probes, Invitrogen, R415). Images were visualized under a wide-field microscope (Leica DMI 6000) equipped with a Micro MAX-1300YHS camera using an HCX PL APO 60X oil objective (Princeton Instruments). Images were acquired using Metamorph Software (Version 7. 1. 3; Molecular Devices).
Single Cell RNA-Sequencing and Primary Data Processing We utilized microfluidic single cell capture and single cell mRNA sequencing technologies to explore genome wide gene expression in 17 cells exposed to our transdifferentiation protocol. Fluidigm's C1 TM Single-Cell Autoprep System (C1) allows fully automated capture of up to 96 single cells and subsequent cDNA synthesis to then perform qPCR or RNAsequencing. The cell suspension was loaded on the C1 by using an integrated fluidic circuit (IFC) chip which allows capturing a single cell per well. After optical confirmation of cell number at each capture site on the chip, the cells were processed for in-line cell lysis, reverse transcription and cDNA amplification steps. The resulting cDNA was subjected to a sequencing library using Illumina's Nextera XT library preparation kit.
Quantitative PCR were performed with an ABI 7900HT PCR system (Applied Biosystems, Foster City, CA, USA), or a LC480 light cycler (Roche, Basel, Switzerland). Ct numbers were calculated for both reference gene GAPDH and target genes with auto-baseline and auto-threshold. 2 -∆∆Ct was used to determine the fold increase. Data were collected and analyzed using the ExpressionSuite v1. 1 software (ThermoFisher, Waltham, MA, USA) or LightCycler 480 (Roche, Basel, Switzerland).
3, 290-300 mOsm/L). After a gigaohm seal and whole-cell access was achieved, electrical activity was recorded using an Axopatch 1D amplifier (Axon Instruments, Union City, CA, USA), digitized using a Digidata 1200 interface (Axon Instruments). Delivery of command voltages and other analyses were driven by the pClamp 6 software from Axon Instruments (Clampex 6. 0. 4 for evoked responses and Fetchex 6. 0. 4 for spontaneous activities). Recordings were performed at room temperature (20-25 • C). Cell input resistance and membrane capacitance transients were monitored during the entire recording.
Statistical Analysis Statistics were performed using medians and maximal and minimal values for small number of samples, mean and SEM for n > 30. A non-parametric Mann-Whitney test was used to make pairwise comparisons. ANOVA followed by Tukey's post-test was used to make multiple comparisons. The analysis was done using Graph Pad Prism Software version 6. 0f. P values lower than 0. 05 were considered significant.
ACKNOWLEDGMENTS We would like to thank  Professor Kent E. Vrana  for his thorough editorial comments,  Aude Marzo  for her kind advice and help on the manuscript. We also would like to thank the  Clinical Research Team  from the  Service Hospitalo-Universitaire-S14, Sainte-Anne Hospital (CERC ) as well as  Sara Shimko  from  Penn State Hershey Medical Center, Department of Pharmacology  and  Dylan Van Kampen  from  Penn State Hershey Medical Center, Neural & Behavioral Sciences  for their technical assistance.
FUNDING This work was financially supported by  Penn State College of Medicine ,  Penn State Hershey Medical Center, Université Paris Descartes Sorbonne Paris Cité ,  Institut National de la Sante et de la Recherche Medicale (INSERM) ,  CNRS, Foundation pour la Recharche Medicale (FRM ;  SPF20080511940  to AB;  FRM DPP 2015 1033966  to MOK, AH and AW), the  French Government 's  Investissement d'Avenir program ,  Laboratoires d'Excellence ''Integrative Biology of Emerging Infectious Diseases''  ( ANR-10-LABX-62-IBEID) ,  Consejo Nacional de Ciencia y Tecnologia  ( CONACYT 74641  to AB) and by the  Young Minds in Psychiatry Award  given by the  American Psychiatric Association  to AB.
Data analysis We first performed a sequence of analyses to separate periods of smooth pursuit, saccades and blinks. The identification of blinks led to the removal of about 1% of eye recordings. Eye position time series were then low-pass filtered with a Butterworth (4th order) using a cutoff frequency of 25 Hz. The resultant eye position signals were differentiated and were low-pass filtered with a cutoff frequency of 25 Hz to remove the noise from the numerical differentiation. The resultant eye velocity signals were also differentiated and low-pass filtered at 25 Hz to provide acceleration traces. A dedicated Matlab script identified the beginning and end of each saccade based on acceleration and deceleration peaks (>1500˚/s 2 ). Subsequent visual inspection allowed to detect saccades (<1˚) that could not be identified by our program.
Acknowledgments This work was part of  Innovative Training Network 'Perception and Action in Complex Environment' (PACE ) that has received funding from the  European Union 's  Horizon 2020 research and innovation program  under the  Marie Sklodowska-Curie grant  agreement  N6 42961. This paper reflects only the authors' view and that the  Research Executive Agency (REA)  of the  European Commission  is not responsible for any use that may be made of the information it contains. The authors would like to thank  Alexandre Eusebio  to ensure that none of the participants had contraindications to TMS.
01 DTPA (diethylenetriamine-pentaacetic acid), pH 7. 3. Treatments with the reducing agent DTE (dithioerythritol, 5 mM) were performed at room temperature during 15-20 min in a Barth solution. Recordings were performed at -60 mV and at room temperature. Currents were sampled at 100 Hz and low-pass filtered at 20 Hz using an Oocyte Clamp OC-725 amplifier and pClamp 10. 5 (Molecular devices). Data analysis was performed using Clampfit 10. 5 and Kaleidagraph4 (Synergy Software). Whole-cell patch-clamp recordings in HEK cells. HEK293 cells were used for heterologous expression of recombinant GluN1/GluN3 receptors studied using whole-cell patch-clamp. Cells were obtained from ECACC (European Collection of Authenticated Cell Culture, catalog number: 96121229) and cultured under standard cell culture conditions (95/5% O 2 /CO 2 mixture, 37 °C).
Whole-cell patch-clamp recordings in CA1 pyramidal cells. Ex-vivo electrophysiological experiments were performed on coronal slices from the brains of juvenile wild-type (WT) and GluN3A-KO mice originating from the same litters (8-12 days old). Slices were prepared as described previously  61. Briefly, mice were anesthetized with isofluorane before decapitation. After isolation, the portion of the brain containing the hippocampus was placed in bicarbonate-buffered saline (BBS) at 2-5 °C for a few minutes. Slices (300 μm) were then cut using a 7000 smz-2 vibratome (Campden). The slicing procedure was performed in an ice-cold solution containing (in mM): 130 K + -gluconate, 15 KCl, 0. 05 EGTA, 20 Hepes, 25 glucose, 1 CaCl 2 , and 6 MgCl 2 supplemented with DL-APV (50 µM). Slices were then transferred for a few minutes to a solution containing (in mM): Pharmacology and data analysis.
CGP-78608 dose-response curve (DRC) experiments were performed using 100 µM glycine. In these, and most other, experiments, CGP-78608 was systematically applied before agonist perfusion. CGP-78608 DRC was fitted using the following equation: I rel = 1 + ((a-1)/(1 + ([C]/EC 50 ) nH ) were [C] is the compound concentration, a is the maximal potentiation and n H the Hill coefficient. EC 50 , a and n H were set as free parameters. Agonist DRCs were fitted with the following Hill equation: I rel = 1/(1 + (EC 50 /[A]) nH ), were [A] is the agonist concentration, and EC 50 and n H set as free parameters. Desensitization and glycine or CGP-78608 washout kinetics were fitted using single exponentials with Clampfit 10. 5 analysis software. When comparing the effects of various GluN1 competitive antagonists on GluN1/GluN3A current responses, glycine was used at 1 mM.
Finally, Tetrodotoxin (TTX; 500 µM; Latoxan) was aliquoted in an acetic acid (2%) water solution. Statistical analysis. Data are presented as mean ± standard error of the mean (SEM). Sample number (n) refers either to the number of recorded oocytes or HEK293 cells (Figs. 1-4), or to the number of recorded CA1 cells (Fig. 5 ). Unless otherwise stated, two-sided statistical analysis of the data shown in Figs. 1 2 3 4 was conducted using either two sample Student's t-test or the Mann-Whitney test when Equal Variance test failed. Data obtained from different conditions in Fig. 5  were compared statistically either with Mann-Whitney or Wilcoxon signed-rank test, as indicated in the text. Tests were performed using either SigmaPlot (Systat Software) or house-built routines in Igor (Wavemetrics).
Acknowledgements This work was supported by the  French government  ( Investissements d'Avenir   ANR-10-LABX-54   MEMO LIFE  and  ANR-11-IDEX-0001-02 PSL* Research University ),  Agence Nationale de la Recherche  ( ANR  grant  GluBrain3A  to M. A. D. and P. P. ), and the  European Research Council  ( ERC Advanced Grant  # 693021  to P. P. ). We thank  Nobuki Nakanishi  and  Stuart Lipton  ( Scintillon Institute, San Diego, CA, USA ) for providing the GluN3A-KO mouse line. We also thank  Boris Barbour  and  Mariano Casado  for critical reading of the manuscript.