dataesr/scientific-paragraphs-categorization huggingface dataset:
Thus, the behavior of DS rats contrasts the phenotype of the control rats, which spend 2/3 of their total exploration time interacting with the available social target (Fig. 11 ). These behavioral defects of the DS model correlate well with a significantly suppressed discrimination between the novel and familiar conspecifics compared to controls, scoring below the chance level in the retention   At the end of the study, upon animal euthanasia, trunk blood was collected and processed with VetScan® Analyzer for analysis of circulating markers of organ function. Each dot represents one animal per experimental condition. The mean ± SEM per experimental condition was additionally calculated and plotted as bar graphs and lines in subfigures (A) and (B), respectively. Weight data (n =11 per experimental group) were analyzed by two-way ANOVA at each time point and hematological data (n=8 per experimental group) were processed with three-way ANOVA analysis followed by post-hoc analysis with Bonferroni correction.
A DMOD 405 laser was used for DAPI excitation. A pulsed Supercontinuum White Light Laser was used for excitation of Alexa 488 or Alexa568. Proprietary Acousto-Optical Beam Splitter (AOBS) enabled the use of simultaneous independent laser lines. Fluorescence of DAPI was acquired by excitation at Ex 405 nm and recording the emission at Em 415-470 nm, Alexa Fluor™ 488 dye was acquired at Ex 488 nm, Em 498-555 nm and Alexa Fluor™ 568 fluorescence was acquired at Ex 553 nm, Em 570-630 nm. Scanning format used for confocal acquisition was as followed: 1240 x 1240 pixels, scan speed 200 Hz, pinhole diameter 1AU, Z-step interval 0. 42-μm. For image  reconstruction and morphometric analyses, Imaris 9. 7. 1® software (Bitplane, AG, Switzerland) was used. For automatic neuron tracing and analysis of neuronal branching, the "Filament Tracer" software package was used.
For volume and fluorescence intensity determination "Cell" software package and "Surface" software package of the Imaris software were used as described  [91]. The same parameters and algorithm settings were applied for comparison between WT and DS group. Determination of CBS-mediated H 2 S generation in various brain regions ex vivo. In a pilot experiment, animals of both genotypes were euthanized by isoflurane overdose, followed by decapitation. The brains were rapidly removed from the skull and dissected into coronal sections of 1 mm. From the sections, we subsequently isolated the prefrontal cortex (PFC), hippocampus (HIP), entorhinal cortex (ETC), and basal forebrain (BF). Two-to-three sections per brain area of interest per rat were placed into a well of a 24-well tissue plate that contained 1 ml of pre-warmed artificial cerebrospinal fluid (aCSF; 120 mM NaCl, 3.
Signals were acquired at 25 kHz, and the data were stored on a PC for offline analysis. LFPs were downsampled to 1 kHz and were partitioned into 1 s epochs. Epochs containing artifacts were rejected by generating a histogram of peak-to-peak amplitude for each epoch and rejecting epochs during which this value exceeded the median plus1 SD; generally, 10% of the epochs were rejected using this criterion. Artifactfree LFPs were used for all further analyses. Power spectra were calculated as described  [29, 54]  for each epoch by fast Fourier transform. Gamma (γ) power was calculated by taking the mean value of the power spectrum between 30 and 80 Hz. Delta (δ) band, theta (θ) band, and beta (β) band ranges were defined as (1-5 Hz), (6-10 Hz) and  (12) (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) (27) (28) (29) (30) , respectively  [29, 93].
During the retention trial, each rat had similarly 5 min to explore the apparatus, with the previously blocking guillotine door now lifted, rendering free access to all choice arms. Animal activity was recorded by the overhead Logitech HD Webcam C270 at all times. At the end of each session, the apparatus was thoroughly cleaned with 70% ethyl alcohol to eliminate residual olfactory cues. Footages were then processed with the tracking/analyzer software ANY-Maze (Stoelting Co. , Dublin, Ireland). Each generated track was analyzed for the time spent in the novel and familiar arm of the apparatus within the first minute during the retention trial. The acquired data were further utilized for the calculation of the Success Rate that describes the percent ratio of the time allotted to the novel arm over the total time engaged in both arms.
Success Rates exceeding the chance level (50%) indicate spontaneous spatial alternation. The tracks were also analyzed for the latency time to the first successful entry to the novel arm along with the number of successful entries to the novel arm. Video processing and data handling were performed by an experimenter blinded to the genotype and treatment of the animals. Open field test (OFT). Relative anxiety levels and general motor function were assessed in the open field test  [95]. The testing apparatus consisted of a black-colored square plastic arena (60 × 60 cm) with a metal grid floor and surrounded by a continuous wall 40-cm-high wall. Light intensity of 15 ± 5 lux was reaching the apparatus. Each rat was gently placed into the center of the arena and allowed to freely explore the apparatus for 10 min, with the experimenter out of the animal's sight.
White noise at 60 dB was produced over the open-field course to cover any background noise and the activity of the animal in the arena was video-recorded with the HD ultra-wide Genius WideCam F100 mounted above the arena. At the end of each trial, any fecal deposits were removed, and the apparatus was thoroughly cleaned with 70% ethanol to eliminate any residual olfactory cues. Footages were subsequently processed with the automated tracking/analyzer software ANY-maze. Within the software, the testing arena was divided into 25 squares (12 × 12 cm each). The four squares located in the central area covering an area of 24 × 24 cm were designated as the central zone, and the four squares located at each corner defined the thigmotactic corners. Each generated track represented the total distance traveled per minute and analyzed for the percentage of time spent in the corners to quantify the percentage of thigmotaxis per minute.
Each rat was allowed to freely explore the objects for 3 min. Ten minutes later, a retention trial followed, during which each rat was assigned to reexplore the familiar arena that at that time contained one object at the same location as in the acquisition trial and the second object positioned diagonally opposite to the first one (novel location). The retention trial lasted for 3 min and aimed to assess the animal's place recognition memory. Over both trials, light and noise conditions remained identical to the ones during the OFT. We recorded the activity of each rat over sample and choice sessions using the overhead Genius WideCam F100. At the end of each session, the apparatus and the objects were thoroughly cleaned with 70% ethyl alcohol to eliminate any residual olfactory cues. Footages were subsequently processed with the automated tracking/analyzer software ANY-maze to quantify the exploration time allotted in each object during acquisition and retention trials.
A rat is considered to explore an object when its nose is within a distance of 2 cm from the object. Acquired data were then processed for the calculation of the Recognition Index that describes the percent ratio of the time spent in the object in the familiar or novel location over the total time spent in object exploration during the retention trial. A Recognition Index for the novel location exceeding the chance level (50%) indicated the formation of spontaneous place recognition memory. We also recorded and compared the total exploration time allotted to the objects during the acquisition trial, along with the velocity and total path length of each animal in the retention trial to ascertain that no lack of motivation or emotional defects had interfered with the task acquisition and memory testing.
Acquired data were further processed for the calculation of the Preference Index that describes the percent ratio of the time allotted to the novel or familiar social target over the total time engaged in interacting with either cage during the retention trial. Preference Index exceeding the chance level (50%) indicated a preference for social novelty. Behavioral scoring and data analysis were performed by an experimenter blind to the genotype and assigned treatment groups of the rats. Collection and processing of blood and brain tissue. Upon completion of the neurobehavioral assessment, rats were terminally anesthetized by isoflurane inhalation and euthanized by decapitation. Trunk blood was collected into micro sample tubes with heparin (Sarstedt, Sevelen, Switzerland) and processed for VetScan® analysis (Abaxis Europe GmbH, Griesheim, Germany).
Rac1 activation assay Pull-down assay We performed Rac1-GTP pull-down assay using the Rac1 activation kit (# BK035-S, Cytoskeleton) according to the manufacturer's instructions. After centrinone or doxycycline treatment (and corresponding controls), adherent cells were scrapped and collected in lysis buffer. Then, protein extracts were incubated with PAK-PDB affinity beads. All the experiments were done at 4°C. Next, beads were washed and resuspended in Laemmli buffer for western blotting analysis. Western blotting: Proteins were separated on 4-20% SDS electrophoresis gel and transferred onto PVDF membranes using  Trans-Blot Turbo Transfer System (#1704156, Biorad). Images were acquired using Chemidoc Imaging system (Biorad) and band intensities were quantified using Image Lab 6. 0. 1 software (Biorad).
Immunofluorescence microscopy For tissue sections Confocal microscopy LSM Nikon A1r was used to obtain optical sections along the Z axis (60×, Z-distance of 0. 5 lm, NIS Element software) of ten random fields from the entire tissue section. Centrosomes were identified through the co-localization of two centrosomes markers. Super resolution microscopy Images were acquired on a spinning disk microscope (Gataca Systems, France), through a 100× 1. 4NA Plan-Apo objective with a sCMOS camera (Prime95B, Photometrics, USA), z distance of 0. 2 lm. Multi-dimensional acquisitions were performed using Metamorph 7. 10. 1 software (Molecular Devices, USA). Super resolution was achieved on the CSU-W1 spinning disk equipped with a super-resolution module (Live-SR, Gataca systems). Images are presented as maximum intensity projections generated with ImageJ software.
For cell lines Fluorescence microscopy Images were acquired on an upright widefield microscope (DM6B, Leica Systems, Germany) equipped with a motorized XY and a 100× objective (HCX PL APO 100×/1,40-0,70 Oil from Leica). For each condition, optical sections of images were acquired with a Z-distance of 0. 3 lm (Metamorph software) from at least 10 random fields. Images are presented as maximum intensity projections generated with ImageJ software. Live imaging Images were acquired every 30 min over 12 h using a spinning disk microscope (20× objective, 2. 5 lm of z sections, Gataca Systems, France). Images were presented as maximum intensity projections generated with ImageJ software.
Tumors For each sample, 10 randomly chosen fields were considered. Using ImageJ software, we visually counted the number of nuclei and the number of centrosomes in a blind manner without taking into account tumor identity. Quantification of the frequency of centrosome amplification events and the frequency of nuclei without centrosomes Any group of more than two centrosomes including isolated centrosomes, clusters, and super-clusters was considered as one centrosome amplification event. In regions of dense centrosomes and dense nuclei, where it was not possible to ascertain one centrosome or a group of centrosomes to a given nuclei and so to consider if it corresponds to centrosome amplification, were discarded for quantification. Considering nuclei without centrosomes, we only took into account, areas of the tissue containing nuclei that were separated enough from other nuclei to be able to distinguish nuclei without centrosomes.
Acknowledgements The authors are grateful to the patients who consented to participate in this research and to the medical teams involved in their care. The authors thank  S. Godinho ,  F. Gergely ,  S. McClelland ,  S. Taylor  for sharing unpublished results, discussions, and/or comments on the manuscript. We thank  V. Marthiens ,  F. Edwards ,  S. Gemble ,  A. Goupil ,  D. Vargas  for discussions and comments on the manuscript. We thank  A. Holland  for the gift of the PLK4 expressing plasmid. The authors thank the  Tissue Imaging (PICT-IBiSA ) and  Nikon Imaging Centre at Institut Curie , member of the  French National Research Infrastructure France-BioImaging  ( ANR10-INBS-04 ). We thank  A. Vieillefon ,  A. Rapinat , and  D. Gentien  from the  Genomics Platform of the translational research department at Institut Curie  for cell line authentification.
The project was supported by a  PIC  project grant from the  Labex CelTisphybio  ( 2013 ,  Institut Curie ),  INCA PL-BIO  grant ( 2015-PLBIO15-237 ), WWC research grant ( 21-0042 ),  Institut Curie  and the  CNRS. The  Basto lab  is a member of the CelTisphybio labex.
Additionally, endoA -/-animals that express EndoA D265A or EndoA D265R are extremely uncoordinated and the animals die much earlier than endoA -/-mutants that express wild type EndoA (Figure  2G ). Hence, these data suggest that mutations within EndoA flexible region fundamentally affect EndoA function. EndoA -/-null mutants show a severe defect in synaptic vesicle endocytosis  (Dickman et al. , 2005; Guichet et al. , 2002; Verstreken et al. , 2002). To assess whether EndoA D265A and EndoA D265R affect synaptic vesicle cycling, we performed a FM 1-43 dye uptake assay. Larval fillets were incubated with the lipophilic dye FM 1-43, which is internalized into newly formed synaptic vesicles upon nerve stimulation  (Ramaswami et al. , 1994). EndoA -/-animals expressing EndoA D265A or EndoA D265R show efficient FM 1-43 dye uptake that is similar to that measured in endoA -/-mutants that express wild type EndoA (Figure  2C-C' ).
, 2016; Soukup et al. , 2016; Wang and Montell, 2007). While the amplitude of depolarization in 3-day-old and 7-day-old control and EndoA D265A mutant flies is similar, EndoA D265R already show a clear age-dependent reduction in ERG amplitude when kept in dark conditions (Figure  5A, A', C, C', E, E', G, G', I ). We also placed the flies in constant light to cause light-induced stress and repeated this experiment. While control and endoA -/-flies expressing EndoA WT are fine, now both endoA -/-flies expressing EndoA D265A and EndoA D265R show strongly reduced ERG depolarization amplitudes (Figure  5A '',C'',E'',G'',I), a hallmark of neurodegeneration. To further corroborate these findings we also evaluated neuronal morphology in toluidine blue-stained retinal sections. Quantification of the number of intact ommatidia with 7 visible photoreceptors validated the ERG data and also shows age-dependent degeneration in 7-day old dark-reared EndoA D265R -expressing flies and in EndoA D265R -and EndoA D265A -expressing flies kept for 7 days in constant light (Figure  5B-H'', J ).
Confocal Live Imaging and quantification Live imaging of dissected larvae was carried out on a Nikon A1R confocal microscope with a 60X (NA 1. 0) water-dipping lens. Dissected larvae were washed multiple times in HL3 prior to imaging. NIS Elements (Nikon) was used for data acquisition using the Resonant Scanning option, with a zoom factor of 3 and line averaging of 16. All images were acquired with a pinhole of one Airy unit and a resolution of 1024 × 1024. Z-stacks were used in data acquisition to capture fluorescence (puncta presence) across the whole NMJ. Low basal autophagy levels were always confirmed in control experiments. Quantification of the number of puncta within synaptic boutons was performed in ImageJ  (Soukup et al. , 2016). Atg8 3×mCherry puncta were manually counted and this was combined with the application of a threshold mask as to determine the area of the bouton.
Zeiss Airyscan Confocal Imaging and quantification A Zeiss LSM 880 (AiryScan detector enabled) with a 63X (NA 1. 4) was used to image the distribution of EndoA (WT, D264A and D264R) across the NMJ. Zen Black software (2012, Carl Zeiss) was used for image acquisition and processing. To quantify the distribution of EndoA within boutons, we selected boutons of similar size as previously described  (Kasprowicz et al. , 2014). These were then rescaled to a standard diameter and average the labelling intensities per position along the bouton diameter were defined. Boutons were resized to a width of 500 pixels, and integrated intensity was calculated for whole boutons fit into a 400 pixel diameter, while cytosol integrated intensity was calculated by 250 pixel diameter circle (in ImageJ). The average integrated intensity was calculated across all boutons of the same genotype.
1 molecules was carried out using a C-Apochromat 63X (NA 1. 2) water objective on the ELYRA PS. 1 microscope (Zeiss). Synaptic boutons were located using 488 nm laser illumination. A 405 nm laser was used for photoconversion, and the 561 nm laser was used during acquisition. To spatially visualize and temporally characterize individual photoconverted fluorophores, the 405 nm laser was used at 0. 00003-0. 03 % power, while the 561 nm laser was used at 20 % power. A sensitive electron-multiplying charge-coupled device (EMCCD) camera (Evolve, Photomertic) was used to collect single molecule fluorescence. Zen Black acquisition software (2012 version, Carl Zeiss) was utilized for movie acquisition. 15,000 frames images were captured per synaptic bouton at a frame capture rate of 20 Hz. Analysis of sptPALM movies is described in the Supplemental Experimental Procedure.
sptPALM Analysis NIH ImageJ was used to convert movies from Zen's CZI format to the format recognizable for the image analysis software -Tiff format. PALM-Tracer, a customized-written software plugin in Metamorph (Molecular Devices)  (Kechkar et al. , 2013; Nair et al. , 2013)  was used to localize single molecules and quantify their mobility. Mobility data was plotted as mean square displacement (µm 2 ) values (equation 1) as well as diffusion coefficient (µm 2 s -1 ) values (equation 2). The parameters were set to isolate and recognize trajectories of molecules undergoing free cytosolic diffusion, associated with organelles or bound to presynaptic plasma membrane. Only fluorescent molecules with sufficient threshold and with consecutive appearance across eight movie frames were tracked and used for data analysis.
The PALM-Tracer software generated trajectory maps, super-resolved average intensity as well as diffusion coefficient maps. The colour gradient in the trajectory maps indicate the time of detection of the tracks; the blue trajectories indicate molecules detected early during movie acquisition, while the white trajectories indicate later appearance and detection. (1) = + 4 (2) N is the number of data points in a trajectory, ∆t is the time interval of each frame, x and y are the coordinates of a particle, is the offset constant which incorporates the effects of localization error and finite camera exposure, and D is the diffusion coefficient. The MSD was calculated for the time interval τ = n∆t for the entire duration of each trajectory. The first eight points of the MSD were averaged over all trajectories and plotted against time.
Single-Molecule Localization Microscopy and Cluster Analysis EndoA ::mEos3. 1 expressing larvae were dissected in either HL3 with Nefiracetam and NAS with or without 1 mM CaCl2 and then fixed with 4 % para-formaldehyde. Single-molecule localization was carried out on an ELYRA PS. 1 microscope (Zeiss). Each dataset was acquired at a rate of 20 Hz for a duration of 20,000 frames by which point the mEOS3. 1-tagged molecule were fully photoconverted. Coordinates of individual localizations were retrieved from each time-lapse video using Zen software (Zeiss). The datasets were corrected for x,y drift using Zen's automated fiducial markers and affline transform algorithms. Localizations that appeared within 1 frame and 1 pixel of each other were consolidated to account for individual fluorophore blinking.
Density-based spatial clustering of applications with noise (DBSCAN) analyses, a spatial clustering algorithm based on density, was used to quantify the clustering of proteins  (Ester et al. , 1996). DBSCAN identifies clusters in large datasets of localization coordinates by a continuous and propagative method that links components of a common cluster based on two MSD(n´Dt) = i=1 N-n å x((i + n) ´Dt) -x(iDt) [ ] 2 + y((i + n) ´Dt) -y(iDt) [ ] 2 N -n parameters, r, and ε. Were r is the search radius and ε is the minimum number of neighbouring localizations within the search radius. Localizations outside the search radius and neighbouring points were classified as noise. The DBSCAN was implemented in Python.
Electrophysiology Current clamp experiments to record EJPs were performed as previously described  (Kasprowicz et al. , 2014; Slabbaert et al. , 2016). Third instar larvae were dissected in Ca 2+ free HL3 which was subsequently replaced with HL3 with 2 mM CaCl2 and nerves were cut below the ventral nerve cord. Motor nerves from muscle 6-7, segment A2 or A3 were stimulated at 10 Hz for 400s at least 50 % above the threshold, using a suction electrode. EJP sets were omitted when the recording did not hold its basal membrane potential throughout the 400 s stimulation paradigm. Signals were amplified using the Axoclamp900A amplifier (Molecular Devices), filtered using a 1 kHz Bessel filter and digitized at 10 kHz using a Digidata 1440A (Molecular Devices). Data storage, processing and analysis was done using Clampfit 10.
Proteins were concentrated to ~2 mg/ml, filtered through a 0. 22 μm filter (Millex) and loaded on a low binding 394-well black plate with transparent bottom (Costar). The autocorrelation of scattered light intensity was averaged over 5 recordings to obtain single data points. Wyatt Dynamics software (v7) was used to calculate the hydrodynamic radius. For Small angle X-ray Scattering (SAXS) purified Drosophila EndoA and human ENDOA1 proteins were run though a Superdex200 10/300 increase chromatographgy column (GE Healthcare) to isolate the peak corresponding to the dimeric protein. The column was buffered in 20 mM MOPS, 150 mM NaCl, 1 mM DTT, pH 7 or 20 mM MOPS, 150 mM NaCl, 1 mM DTT, 1 mM CaCl2, pH 7. Dimeric proteins were concentrated with an Amicon Ultra centrifugal filter to a concentration of at least 6 mg/ml.
Concentrations were determined by absorbance. SAXS data were collected according to Supplemental Table  1. The sample of Drosophila EndoA D265A mutant was measured at the BM29 beamline of the ESRF synchrotron (Grenoble, France)  (Pernot et al. , 2013) , while all other samples were measured at the SWING beamline of the SOLEIL synchrotron (Paris, France)  (Thureau et al. , 2021). Measurements were performed using the HPLC-SEC setup available at the beamlines by injecting 30-50 µl of 6-11 mg/ml of protein onto an Advanced BioSEC 300Å 2. 7/300 column. The column was preequilibrated with a buffer containing 20 mM MOPS (pH 7), 150 mM NaCl, 1 mM DTT, 5 % glycerol and either no calcium or 1 mM CaCl2. The flow rate was set at 0. 3 ml/min for the measurement performed at the BM29 beamline and at 0.
35 ml/min for the ones measured at the SWING beamline. The radial averaging was performed using BsxCuBE  (Pernot et al. , 2013)  for the data collected at the ESRF synchrotron and using FOXTROT  (Perez J. , Bizien T. , 2022)  for those collected at the SOLEIL synchrotron. Buffer subtractions were performed using CHROMIXS  (Panjkovich and Svergun, 2018)  and the averaged data, corresponding to the peak of interest, were further processed using the ATSAS software package  (Petoukhov et al. , 2012). The molecular weight estimations were taken from the Bayesian assessment method  (Hajizadeh et al. , 2018) , while the Kratky plots were generated using the ATSAS program PRIMUS  (Konarev et al. , 2003) ).