dataesr/scientific-paragraphs-categorization huggingface dataset:
Protein identification by MaxQuant analysis The raw files were analyzed using the MaxQuant software (version 1. 6. 7) and the Uniprot human database (2020/03/21, 75,777 entries). The settings used for the MaxQuant analysis were: 2 miscleavages were allowed; fixed modification was carbamidomethylation on cysteine; enzyme was Trypsin (K/R not before P); variable modifications included in the analysis were methionine oxidation, protein N-terminal acetylation and carbamylation (K and N-terminal, only for pulse-SILAC experiments). We used a mass tolerance of 7 ppm for precursor ions and a tolerance of 20 ppm for fragment ions and the following parameters were used: multiplicity of 2 SILAC media (R0K0, and R10K8), identification values "PSM FDR", "Protein FDR," and "Site decoy fraction" of 0. 05, minimum ratio count of 1 and the "Re-quantify" option was selected.
To be considered a DCAF interactor, proteins should have a SAINT score over 0. 7. We conducted the experiments in biological duplicates. Results of pulse-chase SILAC experiments are presented as volcano plot with Prostar (see below) and the differential analysis of L intensities after myc-BirA*-DDB2 and ERCC8 expression was performed using four independent biological replicates for each condition (and 2 replicates for the rest of the DCAFbase). Proteins with a log2 fold change (FC) ≤ -1 (between DCAF-expressing cells and control cells) and which passed the FDR significancy threshold in Prostar (see below) were considered to be less abundant and to be potential substrates. Statistical analysis were performed using Prostar software tools  [30, 31]  and we retained them as differentially abundant (i.
Interaction of DDB1-CUL4 associated factors with DDB1 Cullin Ring ligase complex To identify which DCAFs could interact with the CRL4 complex (Figure  2A  Moreover, DDA1, DCAF6 and ERCC8 were identified as DDB1 partners in BioGRID and OpenCell databases, while PHIP VprBP and GRWD1 were only reported in the BioGRID database.
Accessing the data for all the DCAFs through DCAFbase Given the massive amount of data generated by the experiments described in this article, which can be tedious to navigate in extensive supplementary tables, we found it necessary to create a simple interface to visualize the data for each DCAF. The online resource, called DCAFbase, allows accessing and visualizing the data for each of the 58 DCAFs in a relational database in a web interface at https://labofmb. github. io/DCAF-web/. The R package is also available at https://github. com/laboFMB/DCAF-web. The interface shows validation for expression and localization (immunoblotting and immunofluorescence microscopy), along with the interactome and degradome data (Figure  6 ). These can then be filtered with different score and p-Value thresholds, with downloadable generated tables.
To experimentally identify and validate these proteins as associated factors, we first performed extensive proximity labelling assays and DDB1 co-immunoprecipitations, followed by proteins identification by mass spectrometry. Surprisingly, only 14 DCAFs (23%) were enriched in these assays, suggesting that perhaps fewer of these proteins are actually interacting with either DDB1 or Cul4, and that some of them may not be substrate receptors for this complex. This observation is consistent with other large-scale interactomics experiments (BioPlex, BioGRID and Opencell), which also identified 13 of these 14 proteins. The BioPlex 3. 0 includes two additional DCAFs interacting with DDB1 (DCAF4 and DET1), and more than ten additional DCAFs were found enriched in the BioGRID database, while no additional DCAFs were found in the DDB1 interactome reported in the Open cell database  [37].
The BioPlex interactome is an approach similar to ours (large-scale AP-MS) and is very consistent with the DCAFs found associated with DDB1 using our AP-MS or BioID approach. In contrast, the BioGrid database is a compilation of data from a comprehensive curated effort, which also includes data such as co-fractionation, two hybrid, co-purification, co-crystal structures and more. Interestingly, BioPlex 3. 0 uses two cell lines (HCT116 and 293T), which could explain the different DCAFs found associated with DDB1 as compared to our study. Some interactions between DDB1 and some DCAFs might be cell-specific or occur under specific conditions, which is particularly important considering that the expression of the DCAFs is very different in the tissues we examined (Figure  1A ). Accordingly, we decided to perform the reciprocal experiment by cloning and expressing all the proposed DCAFs, of which we managed to express and validate 58 of the 59 possible DCAFs initially reported.
CSB was not identied as a target in our study as our cells were not treated with UV. Therefore, we clearly missed CSB which is a substrates of ERCC8 in a specific context. Moreover, CSB was not detected in our dataset. Interestingly, none of the proteins modulated in myc-BirA*ERCC8 and DDB2 expressing cells were identified as interactors in proximity labelling assay. Indeed in such assay, it is possible to miss potential targets because they are degraded after DCAF recruitment and most of the biotinylated targets could be rapidly degraded. Another possibility is that DCAFs could harbor a scaffolding role  [58] , which could also explain why most of the interactors found in proximity labelling assay were not identified as potential targets in pulse-SILAC experiments. In such a model for example, PHIP brings the CRL4 complex to specific DNA marks and switches with RBBP7 leading to degradation of specific substrates such as  CDT1 and BUB3 [58, 59].
Taking together, those informations indicate that DDA1 can display a scaffolding role with or without swithing with them and especially with DCAF6. In conclusion, our work significantly expands our understanding of DDB1-CUL4-DCAF complex associations, and the reciprocal interaction analyses narrowed down the possible substrate receptors for the DDB1/CUL4 complex. The seven substrate receptors of DDB1-CUL4A/B complex we identified as DCAFs with a high confidence level were also found able to interact with DDB1 in three other databases (BioGRID, BioPLEX and OpenCell). Moreover, with pulse-SILAC experiments, we defined the degradomes of each DCAF and highlighted potential new targets for the CRL4 complex. We were also able to confirm that RAB34 and UBTF are affected by ERCC8, confirming that we could identify potential protein substrates of DCAFs.
Fourteen of the 59 annotated DCAFs were enriched in myc-BirA* -DDB1 or GFP-DDB1 expressing cells compared to control, with a H/L ratio over 2 (Figure2D-E). Moreover, five DCAFs were enriched in both experiments (DDB2, VprBP, DDA1, DCAF6, WDTC1). Otherwise, four were only enriched in myc-BirA*-DDB1 proximity labelling experiments only (DTL, PHIP, TRPC4AC, DCAF15) and five were only enriched in GFP-DDB1 pulldown only (SNRNP40, DCAF8, DCAF11, ERCC8, GRWD1) (Figure2F). Interestingly, all of them except SNRNP40 were also found as DDB1 interactors in BioPlex[35], BioGRID [36], and OpenCell [37] protein interaction databases (Figure1G). DTL, DDB2, DCAF15, DCAF8, WDTC1, DCAF11 and TRPCA4P were found in DDB1 interactomes of the BioPlex, BioGRID and OpenCell.
We defined a threshold of 2 to consider a protein as enriched in cells overexpressing DDB1 fused proteins (N=3). DCAFs appear in red, CUL4A and DDB1 in green F, Venn diagram representing DCAFs found enriched in the myc-BirA*-DDB1 proximity labelling assay and the GFP-DDB1 AP-MS. G, Venn diagram showing DCAFs identified as DDB1 interactor in both BioID and AP-MS experiment compared to BioPlex, BioGRID and OpenCell databases.
In order to clarify the viable cell number, decreased in the treated conditions, overnight EdU incorporation was measured. Quantification of EdU-positive cells by immunofluorescence showed that EdU incorporation was significantly reduced in etoposide and IL-1β conditions at day 1 and day 8 compared with the control at day 1, indicating a reduced cell proliferation (Figure  2E , Supplementary Figure  2A ). The apparent contradiction between the high number of viable IL-1β-treated cells at D8 and the proliferation arrest observed with EdU at the same time may result from contact inhibition when chondrocytes reach maximum confluence. These data suggest that treatment with 20 μM etoposide for 24 h sustainably impaired cell-cycle progression. Conversely, chronic IL-1β treatment only transiently impacts cell proliferation.
The cells were then washed once with PBS 1X, 3% BSA. Subsequently, for phosphorylated histone H2AX on serine 139 (γH2AX) staining, cells were incubated with 5% normal goat serum and 0. 3% triton in PBS for 1 h at RT. The blockage solution was then removed and HACs were incubated with γH2AX antibody (Cell Signalling Technology, 9718, 1/400) at 4°C overnight. The next day, cells were washed 3 times in PBS and incubated with Alexa Fluor 647 goat anti-rabbit IgG (Thermo Fisher Scientific, A21244, 1/500) for 1 h at RT and with Hoechst 2 ug/mL for 20 min. Coverslips were mounted with ProLong ™ Gold Antifade Mountant (Invitrogen ™ , P36930). Images were acquired with a confocal microscope (Nikon A1R-s Confocal Microscope) and quantifications were performed using the Image J software, to measure number of γH2AX foci and EdU positivity; at least 100 cells per condition were analyzed.
Statistical analyses Statistical analyses and plotting were performed using GraphPad 8 Prism Software. For all experiments, outliers were identified using the Grubbs test with α = 0. 05 and were excluded from subsequent analysis. The data were analyzed by Two-way ANOVA with Tukey's multiple comparisons or Mann-Whitney and Kruskal-Wallis tests for non-parametric values. P values equal to or less than 0. 05 were considered significant, * p ≤ 0. 05; ** p < 0. 01; *** p < 0. 001; **** p < 0. 0001.
FUNDING The authors are grateful to the  Agence Nationale de la Recherche (ANR)  for funding the projects  JCJC KLOTHOA  ( ANR-18-CE14-0024-01 ; CV), the  Foundation for Research in Rheumatology  for funding the project  FOREUM-EULAR SEN -OA  (CV, JG, MG), the region of the  Pays de la Loire RFI BIOREGATE  for funding the projects  GENOA (CV, AD) , and  INSERM  for funding the cross- disciplinary program   AGEMED 2. 0  (JG, CV) for their financial support.
e. , during subsequent surges) is still limited  [6, 10]. A decline in the rate of invasive mechanical ventilation use, as well as a rise in in-hospital mortality, was reported in USA between March 2020 and January 2021  [6]. Further studies are still needed to describe trends in ICU care and mortality related to COVID-19. Using the large French administrative health care database, we aimed to describe the characteristics and the outcomes over time of COVID-19 related critically ill patients. Our primary goal was to compare the characteristics, management, and outcome of patients in French ICUs between the different surges of the pandemic. In addition, we evaluated whether a surge was associated with invasive ventilation and mortality in this population. Finally, we sought to evaluate to what extent vaccination against SARS-CoV-2 could be linked to a decrease in invasive mechanical ventilation and mortality rate.
Study design and participants This retrospective cohort study used information from the French administrative health care database (Système National des Données de Santé  [SNDS] ). The SNDS contains data on outpatient care (medical consultation, paramedical interventions, and reimbursed drug dispensation) as well as data from the French hospital discharge database [programme de médicalisation des systems d'informations (PMSI)] collected during hospital stay (admission date, duration, ICD-10 codes for main and associated diagnosis, and medical interventions)  [11]. All these data are linked through a unique personal identification number. We included all adult patients (≥ 18 years old) hospitalized in French ICUs from March 1, 2020 to June 30, 2021, for whom a complete hospital course was available and who had at least one ICD-10 diagnosis code for COVID-19.
Ethics consideration The SNDS database was created by French law no. 2016-41 dated 26 January 2016  [16]. The purpose of the database is researched through the reuse of claim data gathered after names and social security numbers have been removed. Condition of use and security applying to the database is defined by French government regulation dated 22 March 2017  [17]. As part of its public statistics missions, the Department for Research, Studies, Assessment, and Statistics (DREES) of the French Ministry of Health has permanent access to the SNDS database. An Internet page informs the public about the reuse of the database and their rights according to the European General Data Protection Regulation no. UE 2016/679 dated 27 April 2016  [18].
Indeed, between the first surge and the others, expert recommendations were published advocating the use of corticosteroids and anticoagulants in critically ill patients with COVID-19  [25]. Unfortunately, the information was not available in our study and we therefore cannot assess the impact of these treatments on the prognosis of patients. Fourth, information about the variant of concern identified for each COVID case was not routinely recorded at the time of the pandemic. Finally, if the peak of ICU hospitalization was available, these data are too limited to be approach as a reliable proxy of excess of strain in ICU for two major reasons. First, COVID-19 pandemic has particularly involved medical and paramedical staff, accompanied by an excess of professional burnout and a possible decrease in the medical and nursing professional workforce  [35].
Neurophysiology testing Pelvic neurophysiology studies (Sierra® Summit TM , MedEvolve, Little Rock, AR) were performed by a single trained scientist (P. M. ) to evaluate the integrity of the sacral somatic sensory (pudendal, and S2 and S3 dermatomal sensory evoked potentials [SEPs]) and motor innervation (EAS electromyography [EMG]; Figure  1 ). Data were collected directly on the machine, and the position of the markers was checked if the values were outside the limits. Technical aspects have been described in a previous study  [17]  and are reported in Figure  1  and Data S1. Abnormal findings were defined as follows: EAS EMG was abnormal only if it satisfied the criteria for 'probable' or 'definite' abnormality, that is, if no less than two or three of the studied parameters were abnormal  [18].
Only 22 patients underwent urodynamic studies, thereby limiting the evaluation of LUT dysfunction, and could have influenced the reported pattern of urodynamic findings in this cohort. Furthermore, normative data on detrusor contractility in women are lacking and therefore the extent of detrusor underactivity in this cohort could not be objectively assessed. Pelvic neurophysiology techniques to assess the sacral innervation are well established, but sacral dermatomal SEP studies are relatively new and are just being validated  [43]. Nevertheless, this assessment is routinely being performed at our centre by a trained scientist, effectively ensuring that technical issues were excluded. Some patients had abnormal pudendal SEPs with normal S2 and S3 dermatomal SEPs. Such a finding may occur with S4 root involvement.
In-mission Critical markers: For the ISS, there already exists a standard human behavior and performance competency framework for crewmembers  10. There have also been efforts to standardize the psychological/psychosocial and behavioral data collected during space agency sponsored research activities  [11] [12] [13]. This research has been used in ground-based studies in analogue environments, such as NASA-HERA, VaPER, AGBRESA, SIRIUS 19 & 20, as well as Antarctica. Standard measures have been used on the International Space Station in multiple expeditions  14. These standard measures have included cognition batteries, personality surveys, and neuroscience assessments of sensorimotor measures, together with biomarkers, immune markers, and actigraphy. All these data will help create useful benchmarks for LDSE missions.
g. , effects of autonomy during simulation studies)  16, 17. Their impact on cognition, affective experiences, behavior and performance, team dynamics, mental health, and performance should be carefully assessed. Some of these stressors can be studied in analog environments (e. g. , autonomy), others require spaceflight experiments during upcoming missions to the Moon (e. g. , hypogravity) and still others might be only investigated during actual LDSE missions (e. g. , Earth-outof-view effects). Moreover, the relationship among stress biomarker dynamics (e. g. , heart rate variability, cortisol), related biological processes, and individual and team function within these settings will have to be clearly unfolded. Individual and team characteristics: While there have been many studies on individual differences in relation to human spaceflight, data that exist remains relatively limited in a predictive sense  1.
After washing, we incubated the cells for 90 min at room temperature with the appropriate FITC-conjugated or Alexa 568-conjugated secondary antibody diluted in PBS containing 3% BSA and 0. 02% azide. Cells were washed with PBS containing DAPI (Molecular Probes). For each sample, images were acquired using an Axio observer Zeiss microscope (Zeiss, Germany) and Zen software (Zeiss, Germany) and were taken from three randomly chosen fields. Images were quantified using the ImageJ software. Data are presented as mean ± SEM of n = 4 culture wells from 4 independent rat embryos.
Analysis of confocal images For visualization of synaptic clusters stained by synapsin-1 and PSD95, images were acquired with x60, numerical aperture (NA) 1. 4 oil immersion objective using a scanning confocal microscope (NIKON A1 RSi, Nikon, Tokyo, Japan) driven by NIS-Elements software. High resolution 3D confocal images were done accordingly to the Nyquist sampling rate (0. 1 µm XY and 0. 15 µm Z step) and processed with the Lucy Richardson deconvolution algorithm (NIS-Elements Software). In each sample, the two fluorophores (FITC or Cy5) were recorded separately using sequential scanning to eliminate the possibility of overlapping emission.
Morphological analysis of transfected neurons Transfected neurons were analyzed by microscopy (Axio Observer Zeiss, Germany; Objectif X20). The transfection rate was calculated by counting the number of mGFP + neurons in a 48-well culture plate, normalized by the number of Hu + cells in the same well. We counted cells using the multi-point tool in the ImageJ software. The morphological classification of transfected neurons was based on the number and length of axons arising from the cell body as well as the diameter of the cell body. In addition, the dendritic morphology was scored as lamellar or filamentous according to previous studies  (Foong et al. , 2012). A total of 183 GFP-positive neurons have been analyzed from n = 6 culture wells from three independent rat embryos.
Dynamic experiments (30 fps) were performed using a resonant scanning confocal microscope (NIKON A1 RSi, Nikon, Tokyo, Japan) with an oil-immersion objective (×63, NA, 1. 40). Excitation and emission wavelengths were respectively set at 488 and 595 nm, accordingly to FM1-43 fluorescence spectrum. We analyzed images using the ImageJ software. The percentage of fluorescence after 60 s was calculated for each cluster using the formula: ((F 0s -F 60s )/F 0s )/×100 where F 0s is the fluorescence intensity at 0 s and F 60s at 60 s. Previous studies conducted in hippocampal neurons have described different populations of destaining events that might reflect different mode of exocytosis  (Richards et al. , 2005). We thus classified the FM1-43 synaptic clusters based on their percentage of remaining fluorescence at 1 min as compared to fluorescence intensity measured at t0.
Calcium imaging We performed Ca 2+ imaging using Cal-520, AM dye (Abcam, Cambridge, UK) in Ibidi 8-well plates (µ-Slide 8 Well, #80826, Gräfelfing, Germany). Neurons were loaded into glia-conditioned medium supplemented with Cal-520 AM dye (5 µM) for 60 min at 37 • C in a cell culture incubator. High-frame-rate (60 fps) images were recorded using a resonant scanning NIKON A1 RSi confocal microscope (Nikon Instruments, Champigny sur Marne, France) with a dedicated oil immersion objective (×63, NA, 1. 40) and a temperature (37 • C)/CO 2 (5%) controller. The dye was excited by a laser source at 488 nm and the fluorescence signal was recorded at 520 nm. Video acquisition was performed using the Nikon imaging software NIS-Elements. We analyzed the images using the ImageJ software. The fluorescence intensity was measured in region of interest (ROI) delimitating neuronal cell bodies for spontaneous activity and upon pharmacological stimulations.
Voltage-sensitive dye imaging We perfomed voltage-Sensitive Dye (VSD) imaging using the FluoVolt TM membrane potential kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) in Ibidi 8-well plates (µ-Slide 8 Well, #80826, Gräfelfing, Germany). Neurons were loaded into glia-conditioned medium supplemented with the 1000X FluoVolt TM dye (1/1000) and the 100X Power Load Concentrate (1/100) for 15-20 min at 37 • C in an incubator. Similarly, for calcium imaging, the dye was excited at 488 nm, and the fluorescent signal recorded at 520 nm using a resonant scanning confocal microscope (NIKON A1 RSi) at 37 • C and 5% CO 2. We acquired images at 500 fps and analyzed them using the ImageJ software. Fluorescence intensity data were measured in an ROI of inter-cluster fibers. The fibers were classified according to their size with the following criteria: small-caliber fibers = width ≤1 µm and large-caliber fibers = width ≥ 1µm.
5 mM ATP, 10 mM HEPES, and 6 mM EGTA (pH adjusted to 7. 2 with KOH, and osmolarity was adjusted to 300 mosmol). We recorded data using a HEKA amplifier (EPC10 USB double) and the PATCHMASTER software (HEKA Instrument Inc. , New York, USA). The signals were digitized at 1 kHz. Whole-cell recordings were corrected for a junction potential of +18 mV. The series resistance was monitored throughout the experiment using a brief voltage step of -10 mV at the end of each recording. In total, 23 neurons were patched (from n = 5 cultures from 5 independent rat embryos) but only 15 neurons had an analyzable action potential (AP).
17. 8. 21078). We analyzed the data using a MultiChannel Analyzer (version 2. 18. 0. 21200). The recordings were digitized at 50 kHz. During offline analysis, a digital 2nd order high pass Bessel filter with a cutoff of 100 Hz was applied. The peak detection threshold was set with an average noise of five times the signal standard deviation on a perchannel basis (dead time of 3 ms, pre-trigger of 1 ms, and post-trigger of 2 ms). Bursts were analyzed using the following parameters: maximum interval of 50 ms to start/end the burst, minimum interval of 100 ms between bursts, minimum burst duration of 50 ms, and at least four spikes in a burst. Data are presented as mean ± SEM of n = 3 chips from 3 independent rat embryos.
Statistical analysis All data are expressed as mean ± SEM (Standard Error of the Mean). Normality and equal variance were verified using the Shapiro-Wilk and Brown-Forsythe tests, respectively. Data were then compared using a t-test or one-way analysis of variance (ANOVAs), followed by post-hoc Tukey's comparison test. All statistical analyses were performed using the GraphPad Prism statistical software (GraphPad Software, Inc. , La Jolla, CA, USA). Statistical significance was set at p < 0. 05.
Funding This work was supported by the  Entérautisme  project funded by  "la Région Pays de la Loire ", and the project  ANR Microbioautism  ( ANR-19-CE14-0024 ). This work was also supported by the  "Institut National de la Santé et de la Recherche Médicale " (INSERM) and by 3Brain with  Massimo Grattarola  Award  2021  obtained by MC.