dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS This study was supported by  INRAe, University of Bordeaux  " Investissements d'avenir Initiative d'excellence" (Idex ,  ANR-10-IDEX-03-02 ), internal support to the  International Associated Laboratory (LIA OptiNutriBrain) , the  Canadian Institutes of Health Research  ( MOP 102532 ), the  Quebec Network for Research on Aging , the  Alzheimer Society of Canada  (# 1502 ), and the  Canadian Foundation for Innovation  (# 34480 ). M. T. was funded by a doctoral scholarship from the  Alzheimer Society of Canada. F. C. is a  Fonds de Recherche du Québec -Santé  ( FRQ-S) scholar  (# 253895 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors' disclosures available online (https:// www. j-alz. com/manuscript-disclosures/20-0637r1).
Bernabé Linares-Barranco  (This work was supported in part by the  International Consortium of Nanotechnologies (ICON)  under Grant  G0086 ; in part by  EU  ( European Union )  H2020  grants  824164  (HERMES), 871371 (MeM-Scales), 871501 (NeurONN), 899559 (SpinAge),  PCI2019-111826-2 (APPROVIS3D ); in part by the  Spanish Ministry of Science and Innovation  under Grant  PID2019-105556GB-C31  ( NANOMIND ) and Grant  PID2019-103876RB-I00  (CORDION) (with support from the  European Regional Development Fund ); and in part by the  Junta de Andalucía  under Grant  US-1260118  ( Neuro-Radio ). The work of L. A. Camuñas-Mesa was supported by the  VI PPIT  through the  Universidad de Sevilla.
RNA isolation, qRT-PCR and RNAseq analyses Total RNA from cultured cortical neurons was isolated using the Nucleospin RNA (Macherey-Nagel). RNA concentration and purity were assessed with NanoDrop™. RNA quality was determined by the RNA Integrity Number (RIN) algorithm using the Agilent® 2100 Bionalyzer Instrument; only samples with RIN>9 matched our standard. For qRT-PCR experiments, first-strand cDNA was synthesized from 1 μg of total RNA using the Invitrogen SuperScript IV First-Strand cDNA Synthesis System (ThermoFisher). Quantitative real-time PCR (qPCR) was performed using the Applied Biosystems QuantStudio 3 Real-Time PCR system and analyzed with the QuantStudio 3 Design and Analysis software (v1. 5. 1,ThermoFisher). Briefly, real-time qPCR was assayed in a total volume of 20 μl reaction mixture containing the ready-to-use PyroTaq EvaGreen qPCR Mix Plus ROX (Cmb), 5pmol of forward and reverse (rv) primers (detailed in Table  S1 ) and cDNA.
PCR thermal conditions included an initial hold stage with 5 min at 50ºC and 15 min at 95 °C followed by 40 cycles of denaturation for 30 s at 95 °C, annealing for 32 s at 60 ºC and primer elongation for 32 s at 72 °C. All qPCR reactions were run in triplicates. Mean cycle threshold (Ct) values for each reaction were recorded and the relative RNA expression levels were calculated referring to Gapdh, encoding glyceraldehyde 3-phsophate dehydrogenase: ∆ = 〖〗_ -〖〗_( ). The gene expression fold change normalized to GAPDH and relative to control sample was calculated as 2^∆Ct. For RNAseq experiments, we performed bulk mRNA sequencing single-end with a length of 50bp using the RNAseq Illumina Hiseq2500. The preparation of the polyA sequencing library, library's quality control and quantification, sequencing run and base calling data were carried out by the Genomics Core Facility of the Centre for Genomic Regulation (CRG, Barcelona).
For the analysis, adapters were trimmed using trim_galore v0. 6. 4_dev and reads with longer length than 40 bp were selected. Trimmed reads were aligned using star c2. 6. 1b to the mouse genome (mm10). Reads with mapq >30 were selected using Samtools v1. 9. Mapped reads were quantified using R scripts (R version 4. 0. 3, 2020), Rsubread v2. 4. 3 and the Mus_musculus. GRCm38. 99. gtf annotation data. Differential expression analysis was performed using DESeq2 1. 31. 1 and limma 3. 46. 0; genes were annotated using biomaRt v2. 46. 3 and Volcano plots were performed with EnhancedVolcano 1. 6. 0. The tracks from the samples were performed with DeepTools v3. 5. 0, normalized with RPKM and visualization was done in IGV v2. 6. 3.
Protein extraction and western blotting Cultured neurons were collected in lysis buffer containing 50 mM Tris-HCl pH 6. 8, 10% glycerol, 2% SDS, 0. 1 M (D,L)-Dithiothreitol, 0. 04% bromophenol blue and supplemented with protease (cOmplete Protease Inhibitor Cocktail) and phosphatase (PhosSTOP) inhibitors. Lysates were incubated for 10 min at 65 ºC, briefly centrifuged at maximum speed, separated by SDS-PAGE and immunoblotted as described  (Fiuza et al. , 2013)  using the antibodies indicated in the Table  S2. Specific bands were quantified using the ImageQuant 5. 2 software. For in vivo studies on mouse tissue, hippocampi and somatosensory cortex were dissected on ice, snapped frozen in liquid nitrogen and stored at -80ºC until processing. Tissues were homogenized in 15 (w/v) volumes of modified ice-cold RIPA buffer (50 mM Tris-HCl pH 7.
Statistical Analysis Statistical analyses were conducted with GraphPad Prism software. Comparison of quantitative variables between two groups was performed using Student's t-test. One-way or two-way analysis of variance (ANOVA) followed by a post-hoc comparison test were used when more than two groups were compared, as indicated in the corresponding figure legend. Results are presented as mean ± standard error of the mean (s. e. m. ). Statistical methods used for behavioral studies are indicated in the corresponding figure legends.
Data availability RNAseq data have been deposited at GEO-NCBI under the access code GSE175920. Raw Western blots for each figure are presented in source-data-files. Zhang, H. , Webb, D. J. ,  Asmussen, H. , and Horwitz, A. F. (2003). Synapse formation is regulated by the signaling adaptor GIT1. The Journal of cell biology 161, 131-142. Zhu, P. J. , Chen, C. J. , Mays, J. ,  Stoica, L. , and Costa-Mattioli, M. (2018). mTORC2, but not mTORC1, is required for hippocampal mGluR-LTD and associated behaviors. Nat Neurosci 21, 799-802. Cortical neurons infected with lentivirus expressing a shRNA against GIT1 (GFP-shGIT1) or a control lentivirus (GFP) were stimulated with BDNF (100 ng/ml, 1 h) with or without pre-incubation with rapamycin (100 nM, 1h). (A) BDNF induction of phosphorylated S6K and S6 normalized to total protein levels (n=8-10 samples from 4-5 independent cultures; # pS6K: p=0.
ACKNOWLEDGEMENTS We thank  Stuart Lipton  and  Nobuki Nakanishi  for providing the Grin3a knockout mice,  Beverly Davidson  for the AAV-caRheb,  Jose Esteban  for help with behavioral and biochemical experiments, and  Noelia Campillo ,  Rebeca Martínez-Turrillas  and  Ana Navarro  for expert technical help. Work was funded by the  UTE  project  CIMA ; fellowships from the  Fundación Tatiana Pérez de Guzmán el Bueno, FEBS  and  IBRO  (to M. J. C. D. ),  Generalitat Valenciana  (to O. E-Z. ),  Juan de la Cierva  (to L. G. R),  FPI-MINECO  (to E. R. V. , to S. N. ) and  Intertalentum postdoctoral program  (to V. B. );  ANR  ( GluBrain3A ) and  ERC Advanced Grants  (# 693021 ) (to P. P. );  Ramón y Cajal program   RYC2014-15784 ,  RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077  FEDER funds (to R.
Participants A total of 52 wine experts (35 men and 17 women) with an average age of 49 years old were recruited via an internal database and the LinkedIn social network. Wine experts were separated into three panels based on their main professional activity. The first panel, named Makers, was composed of people who make, supervise, or advise on all the stages and operations of winemaking in the Beaujolais vineyard. This panel was composed of eleven winemakers and five consultants in oenology. The second panel, named Sellers, was composed of people who participate in the direct trade of wine bottles with consumers in stores or restaurants in the Beaujolais region. This panel was composed of eight sommeliers and ten wine merchants. The third panel, named Critics, was composed of seventeen professionals who taste wines to write articles, books, or blogs.
Data analysis As the drawings obtained in the drawing elicitation task were used as a support for participants to express their thoughts, the analysis was carried out only on the explanations of the drawing. Nevertheless, we looked at the styles (e. g. , the use of words, symbols, numbers, hierarchies, or maps) and the level of details of each drawing. The drawings produced were very heterogeneous from one expert to another within a same panel, but this heterogeneity remained similar between the three expert panels. As an illustration, four different drawings of the Maker panel are shown in Fig. 1. Thus, fifty-two interviews were transcribed and separated into three corpuses, one for each panel: Makers, Sellers, and Critics. These corpuses were separated into two sub-corpuses: a first sub-corpus including the verbalization of the drawing about the diversity of Beaujolais wines and a second one, the verbalization of the knowledge on wine from Pierres Dorées.
Automatic analysis The automatic analysis was carried out with the IRaMuTeQ textual analysis software version 0. 7 alpha 2  (Ratinaud, 2009)  based on the R statistical software version 4. 0. 3 for Windows (R Core Team, 2020) and Python language. Following Souza et al. (  2018 ), all corpuses were preprocessed using the following steps: 1) lemmatization (singular/plural, masculine/feminine, infinitive/conjugation); 2) binding of certain inseparable words (e. g. , Beaujolais_Villages, Beaujolais_Nouveaux, Pierres_Dorées); 3) simplification of the corpus by removing verbs, adverbs, and prepositive phrases (only nouns and adjectives were kept in the analysis). The rational to remove verbs was that most of the verbs used were common French verbs (e. g. , to be, to have, to do, to go) which did not bring useful information; and 4) suppression of the words with a frequency lower than five (only words occurring more than five times in each corpus were kept for the analyses).
Acknowledgments This research was supported by  CIFRE  convention no. 2018/0716  and  Inter Beaujolais. The authors express their thanks to  Bertrand Chatelet  for his helpful advice in the elaboration of the study and to both  Véronique Boulanger  and  Francine Griffon  for their help in the transcription of the interview. The authors also thank  Catalina Onofrei  for her proofreading and corrections of the article.
| fMRI data acquisition fMRI data were acquired on a Siemens 3 Tesla Skyra MRI scanner (Siemens Medical system, Erlangen, Germany) using a 32-channel coil. S1 ). Significant associations with the predictor variables and outcome variables are included in the main text. Paired-sample t test was performed to test the difference in reaction times between rewarded and non-rewarded trials and thus verifies whether the reward task manipulation resulted in the expected behavioural effects. Finally, a hierarchical linear regression analysis was performed to assess the relationship between reaction times (RTs) and current ETS exposure and monthly smoking. Pubertal development, smoking of mother during pregnancy, familial risk, gender, alcohol and cannabis were entred as covariates in the first step.
| fMRI data preprocessing Preprocessing steps were conducted in SPM12 (www. fil. ion. ucl. ac. uk/ spm). Preprocessing of the functional data included conversion of the MRI data info NIFTI format, followed by realignment to the first image of the time series. Subsequently, 30 volumes, acquired before the start of the actual experiment, were used to estimate weights for a BOLD contrast-to-noise ratio map for each echo. Weighted summation was used to combine all echoes into a single dataset (PAID F I G U R E 1 Monetary incentive delay task. A blue or yellow square (counter-balanced across participants) was presented for 500 ms as a cue announcing a rewarding trial or non-rewarding trial. Cue presentation was followed by a delay during which a fixation cross was presented (jittered between 2,500 and 8,500 ms).
ACKNOWLEDGMENTS The study was funded by the  Dutch Cancer Society (KWF Kankerbestrijding :  TI 2014-6984 ). ML was supported by a  VENI grant  ( Nederlandse Organisatie voor Wetenschappelijk Onderzoek , nr. 451-15-029 ) from the  Netherlands Organisation for Scientific Research (NWO). The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. Furthermore, we would like to thank  Vivian Heuvelmans ,  Esther Rijnders ,  Anna Boormans ,  Kelly van Egmond ,  Rozemarijn Erdbrink ,  Tamara te Winkel ,  Milagros Rubio ,  Dennis Trommelen  and  Vera van 't Hoff  for their assistance with data collection and participant recruitment.
| Apparatus Computational routines were generated in MATLAB (The MathWorks) and stimuli were presented using "Psychtoolbox"  (Brainard, 1997). A PROpixx projector (VPixx Technologies, Saint-Bruno, QC Canada) was used to project the visual stimuli on the screen, with a resolution of 1920 Â 1080 and a refresh rate of 120 Hz, and the audio stimuli were presented through MEG-compatible ear tubes. Behavioural responses were collected via a MEG-compatible response box. MEG was recorded from a whole-head MEG system with 275 axial gradiometers (VSM/CTF Systems, Coquitlam, BC, Canada) in a magnetically shielded room and digitized at 1200 Hz. Eye position data was recorded during the experiment using an Eyelink 1000 eye tracker  (EyeLink, SR Research Ltd. , Mississauga, Ontario, Canada)  for further eye blink and saccade artefact rejection.
During the session, head position was recorded and monitored online  (Stolk et al. , 2013)  by coils placed at the nasion, left and right ear. At the end of each block, participants were asked to reposition the head in case they moved more than 5 mm away from the initial position. MEG analyses were performed using FieldTrip software  (Oostenveld et al. , 2011)  and repeated measures ANOVA were performed in JASP, Version 0. 9. 0 (JASP Team, 2018).
(b) Timeline of the stimuli in the trials and the delay in the main analysis window. The yellow shadow represents the analysis window (delay from 1 to 2. 5 s). (c) Accuracy and reaction times (mean and standard error of the mean in bold) for the rhythmic task, as a function of SOA and attended modality. Individual participant data are shown in lighter grey performed 48 trials for each in-phase delays (1, 2, 3 s) and 24 trials for each antiphase SOAs (1. 5, 2. 5 s) in each sensory modality condition. The blocks were always presented in a pseudo-random order, where no more than 3 same type blocks could be presented in a row, and participants were instructed about the block-type before its beginning.
| Multivariate pattern analyses MVPA were performed using linear discriminant analysis (LDA) as implemented in MVPA-Light toolbox (https:// github. com/treder/MVPA-Light). Features consisted of activity in the MEG sensors (267 AE 3 sensors). Feature scaling was performed as preprocessing step in all analyses: data were normalized for each time point, across trials, using z-score transformation based only on the training set. Final scores were calculated based on the distances estimated by LDA from the six classes' centroids in multiclass classification or from the hyperplane in the two-class classification.
5 s, with no other stimulation after that. Additionally, 400 ms after the offset of the unattended stimulus (at 1 s), the modality signal reverses to the attended modality by staying largely positive and significant during the delay. This suggests that such modality signal during the delay reflects preparatory sensory activity rather than the previous stimulus evoked activity. An oscillatory modulation of the modality signal was clearly present in the grand-averaged data (Figure  4b ). We next assessed whether this rhythmicity was reliably present across participants, by fitting two models to the activity in the delay period (1 to 2. 5 s) for each participant. The first was a linear model with intercept and slope as free parameters. The second model was a combination of a linear function with a 1 Hz sine and 1 Hz cosine function (which is equivalent to a 1 Hz sinusoid with phase as a free parameter)  (Zoefel et al.
ACKNOWLEDGEMENTS This work was supported by  São Paulo Research Foundation  ( FAPESP , grants  2016/04258-0  and  2018/08844-7  awarded to LCB, and grant  2017/25161-8  awarded to AMC), by The  Netherlands Organisation for Scientific Research (NWO Veni  grant  016. Veni. 198. 065awarded to ES and Vidi grant  452-13-016  awarded to FPdL), and by the  European Research Council (ERC) , under the European Union's  Horizon 2020 Research and Innovation Programme  (grant agreement No. 678286  to FPdL). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
Funding: The authors' work has been financed by grants from the  European Union  ( H2020  project  SOLVE-RD , to G. S. ), the  Spastic Paraplegia Foundation  (to G. S. ) and the  ALS-HSP-France association  (to G. S. ). M. L. and L. T. were the recipients of PhD fellowships from the  PSL-Biogen program  and the  French Research Ministry  through the  EPHE-472 doctoral school , respectively.
Statistical Analysis Statistical analyses were conducted via SigmaPlot 12. 0 software, a scientific graphing and statistical analysis software package including normality and variance analyses. No statistical methods were used to predetermine the sample size. Normally distributed data were first tested for significance using Student's t test prior to be analyzed by one-or -two way analysis of variance (ANOVA) followed by Neuwman-Keuls post-hoc test, when requested, as in our previous studies  [5, 11, 12, 54]. The initial sample size was N = 5 per group and was sometimes reduced to 4 for technical or unexpected concerns. For each ZT, first the 'Group' effect between control and experimental animals, treated with either cocaine or sucrose, was evaluated and secondly the 'Time' effect in control rats injected with saline or exposed to oral water intake.
Transgenic Mice DMSXL transgenic mice (>99. 8% C57BL/6 background) carry 45 kb of human genomic DNA from a DM1 patient  (Seznec et al. , 2000; Gomes-Pereira et al. , 2007)  within the first intron of the Fbxl7 gene (data not shown). The breeding of hemizygous DMSXL mice generated DMSXL homozygotes and WT controls in the same litter. The DMSXL mice used in this study were homozygous for the human transgene, and carried more than 1,500 CTG repeats within the human DMPK gene. Transgenic DMSXL status was assessed by multiplex PCR using the oligonucleotide primers, which hybridize the DMPK transgene and the transgene integration site in the mouse Fbxl7 gene: FBF (forward, TCCTCAGAAGCACTCATCCG), FBFBR (reverse, AACCCTGTATTTGACCCCAG) and FBWDR (reverse, ACCTCCATCCTTTCAGCACC). FBF and FBFBR primers hybridize the mouse Fbxl7 gene, amplifying a sequence of 167 bp in WT mice.
05. Alternative splicing analyses were performed using the open source FaRLine pipeline  (Benoit-Pilven et al. , 2018). Significant missplicing events were selected for further analysis if the percentage of splicing inclusion (PSI) between genotypes was > 10% with p-value (corrected for multiple comparisons) < 0. 05 (Fisher's test). PSI was calculated as: (inclusion of alternative exon)/[(inclusion of alternative exon) + (exclusion of alternative exon)]. The datasets generated for this study can be found in the Gene Expression Omnibus repository, https: //www. ncbi. nlm. nih. gov/geo/query/acc. cgi?&acc=GSE162093.
Reverse Transcription and PCR Assays For reverse transcription, 150-500 ng RNA was subjected to cDNA synthesis using the SuperScript II first-strand synthesis system (Thermo Fisher Scientific) with random hexamer primers in a total volume of 20 µL. In RT(-) control samples, water was added instead of reverse transcriptase. Primer sets for PCR were designed using MacVector and NCBI Primer-Blast software. Amplification products were resolved by agarose gels electrophoresis. Primer sequences are listed in Supplementary Table  1.
Two blanks were run between each sample to prevent sample carryover. Phosphopeptides eluting from the column were analyzed by data dependent MS/MS, using top-8 acquisition method. Phosphopeptides were fragmented using higher-energy collisional dissociation (HCD). Briefly, the instrument settings were as follows: resolution was set to 70,000 for MS scans and 17,500 for the data dependent MS/MS scans in order to increase speed. The MS AGC target was set to 1 × 10 6 counts with maximum injection time set to 200 ms, while MS/MS AGC target was set to 2 × 10 5 with maximum injection time set to 120 ms. The MS scan range was from 400 to 1,800 m/z. MS and MS/MS scans were recorded in profile mode. Dynamic exclusion was set to 30 s.
Data Processing Following NanoLC-MS/MS Acquisition The MS files were processed with the MaxQuant software version 1. 5. 8. 3 and searched with Andromeda search engine against the UniProtKB/Swiss-Prot Mus musculus database (release 27-07-2017, 16923 entries). To search parent mass and fragment ions, we set an initial mass deviation of 4. 5 ppm and 0. 5 Da, respectively. The minimum peptide length was set to seven amino acids and strict specificity for trypsin cleavage was required, allowing up to two missed cleavage sites. Carbamidomethylation (Cys) was set as fixed modification, whereas oxidation (Met), N-term acetylation and phosphorylation (Ser, Thr, Tyr) were set as variable modifications. The match between runs option was enabled with a match time window of 0. 7 min and an alignment time window of 20 min.
The false discovery rates (FDRs) at the protein and peptide level were set to 1%. Scores were calculated in MaxQuant as described previously  (Cox and Mann, 2008). The reverse and common contaminants hits were removed from MaxQuant output. The phosphopeptides output table and the corresponding logarithmic intensities were used for subsequent statistical analysis using the Perseus software platform. Significant phosphorylation changes were considered for further analysis if the phosphosite was detected only in all the samples of one of the genotypes (but in none of the other) or when fold change between genotypes > 1. 4 and p-value (corrected for multiple comparisons) < 0. 05. The datasets generated for this study can be found in the PRIDE repository: http://www. ebi. ac. uk/pride/archive/projects/PXD025011.
Then, after three washes in TBS-T, membranes were incubated with 1/5,000 dilution of the following secondary antibodies conjugated to horseradish peroxidase (HRP) for 1 h at room temperature: donkey anti-goat IgG (Jackson ImmunoResearch, 705-035-147) for CAPZB membrane and goat anti-rabbit IgG (Thermo Fisher Scientific, 31460) for PALM membrane. Membranes were washed three times, developed by Clarity Western ECL Substrate (Bio-Rad, 1705061) and imaged with the ChemiDoc MP Imaging System (Bio-Rad, 17001402). Band intensity was quantified using Image Lab Software (Bio-Rad).
Microscope Imaging and Image Analysis Images were acquired with a Zeiss ApoTome 2 fluorescent microscope or a Leica SP8 SMD confocal microscope (×63 and ×40 objectives). RNA foci were counted in 3D stacks using the Spot Detector plugin of the ICY bioimageanalysis opensource program 1. INF2 and NUMA nucleo-cytoplasmic ratio was quantified on Z projections (using maximal intensity) of Z-stack confocal images, by quantifying the ratio between mean gray intensity values in nucleus and cytoplasm. IF and FISH images were treated with Fiji-ImageJ software  (Schindelin et al. , 2012)  to create the figures.