dataesr/scientific-paragraphs-categorization huggingface dataset:
The DMs were dried at room temperature and stored at -80 °C until used for the experiment. Peptides were extracted from the tissue samples in 25-50 μL of 0. 1% trifluoroacetic acid (TFA), stored at -80 °C, and analyzed by LC-MS/MS (timsTOF Pro; Bruker, Billerica, MA) with nanoElute (Bruker). Mass spectra obtained by LC-MS/MS were analyzed by ProteinScape (Bruker), and the peptides and proteins were identified. Samples ID C1, C2, F1, and F2 (Table  1 ) were used for preliminary experiments to confirm that shotgun proteomics is feasible in flat-mounted DMs. Enrichment analyses. The Database for Annotation, Visualization, and Integrated Discovery (DAVID; http:// david. ncifc rf. gov) was utilized to conduct functional enrichment analyses  43. Gene Ontology (GO) analysis was performed to investigate the functions of the proteins identified by shotgun proteomics.
The samples were incubated for 60 min at 37 °C in each solution. Nuclei were counterstained with 2 µg/mL DAPI (D1306, Invitrogen) in PBS at room temperature for 10 min. The samples were given 3 rinses with PBS between all steps, except between the saturation step for non-specific protein binding sites and incubation with primary antibody. The flat mounts were covered with fluorescence mounting medium (NB-23-00158-2, Neo Biotech, Nanterre, France) and a glass coverslip. Images were acquired using an epifluorescence inverted microscope IX81 (Olympus, Tokyo, Japan) equipped with cellSens imaging software (cellSens Dimension, Olympus, Germany). The specificity of the markers was confirmed using non-specific rabbit and/or mouse IgG (Zymed, Carlsbad, CA) as primary antibodies for negative controls.
Acknowledgements This work was supported by  JSPS KAKENHI  Grant Numbers  21K09731 ,  AMED  under Grant Number  JP22ek0109590 , and the  Region Auvergne Rhône Alpes ,  Pack Ambitiuon  internationale  2020-P010O003. This research was also supported by  Japan - France Integrated Action Program (SAKURA)  from  Japan Society for the Promotion of Science  and by the  Hubert-Curien Partnership (PHC) ,  SAKURA 41024TE, Ministère des Affaires Etrangères et du Développement International, Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche.
The propagation and diversification of signals downstream of the T cell receptor (TCR) involve several adaptor proteins that control the assembly of multimolecular signaling complexes (signalosomes). The global characterization of changes in protein-protein interactions (PPI) following genetic perturbations is critical to understand the resulting phenotypes. Here, by combining genome editing techniques in T cells and interactomics studies based on affinity purification coupled to mass spectrometry (AP-MS) analysis, we determined and quantified the molecular reorganization of the SLP76 interactome resulting from the ablation of each of the three GRB2-family adaptors. Our data showed that the absence of GADS or GRB2 induces a major remodeling of the PPI network associated with SLP76 following TCR engagement.
Primary T cells from GADS-deficient mice showed impaired T cell development in the thymus which could explain stronger signaling abnormalities in the periphery. In Jurkat cells, the addition of CD6, which is weakly expressed in the parental cell line, could partially rescue the defect in calcium release that has been observed under suboptimal TCR stimulation conditions. While taking these considerations into account, these data suggest that ITK-dependent SLP76-mediated signaling on PLCg1 can occur in LAT-independent manner and can eventually precede the LAT-PLCg1 interaction. The interaction stoichiometry analysis revealed an unexpected molecular reorganization of the SLP76 signalosome in GRB2 deficient cells. We observed a displacement of SLP76 toward the CD6 signaling module characterized by the presence of UBASH3 molecules  (18) , with a parallel reduction of interactions with LAT and PLCg1.
Flow cytometry Stained cells were analyzed using an LSRII system (BD Biosciences). Data were analyzed with the Diva software (BD Biosciences). Cell viability was evaluated using SYTOX Blue (Life Technologies). The following antibodies were used: anti-CD3e (OKT3), anti-CD28 (CD28. 2), anti-CD6(M-T605) and anti-CD69 (FN50); all from BD Biosciences.
1% formic acid for 100 min and 22-32% acetonitrile/H20; 0. 1% formic acid for 20 min). For peptides ionization in the EASYSpray source, spray voltage was set at 1. 9 kV and the capillary temperature at 250°C. All samples were measured in a data dependent acquisition mode. Each run was preceded by a blank MS run in order to monitor system background. The peptide masses were measured in a survey full scan (scan range 375-1500 m/z, with 70 K FWHM resolution at m/ z=400, target AGC value of 3. 00×106 and maximum injection time of 100 ms). Following the high-resolution full scan in the Orbitrap, the 10 most intense data-dependent precursor ions were successively fragmented in HCD cell and measured in Orbitrap (normalized collision energy of 25%, activation time of 10 ms, target AGC value of 1. 00×105, intensity threshold 1.
Data analysis Raw MS files were processed with MaxQuant software (v. 1. 6. 3. 4) for database search with the Andromeda search engine and quantitative analysis. Data were searched against the Homo sapiens entries of the UniProtKB protein database (release Swiss-Prot reviewed 2019_01, 20,412 entries), and the set of common contaminants provided by MaxQuant. Carbamidomethylation of cysteines was set as a fixed modification, whereas oxidation of methionine, protein N-terminal acetylation were set as variable modifications. Specificity of trypsin digestion was set for cleavage after K or R residues, and two missed trypsin cleavage sites were allowed. The precursor mass tolerance was set to 20 ppm for the first search and 4. 5 ppm for the main Andromeda database search. The mass tolerance in tandem MS mode was set to 0.
5 Da. Minimum peptide length was set to seven amino acids, and minimum number of unique or razor peptides was set to 1 for validation. The I = L option of MaxQuant was enabled to avoid erroneous assignation of undistinguishable peptides belonging to very homologous proteins. Andromeda results were validated by the target decoy approach using a reverse database, with a FDR value set at 1% at both peptide sequence match and protein level. For label-free relative quantification of the samples, the match between runs option of MaxQuant was enabled with a match time window of 1 min, to allow cross-assignment of MS features detected in the different runs, after alignment of the runs with a time window of 20 min. Protein quantification was based on unique and razor peptides. The minimum ratio count was set to 1 for label-free quantification calculation, and computation of the iBAQ metric was also enabled.
1% formic acid), peptides were eluted from the analytical column by a two-step linear gradient (4-22% acetonitrile/H2O; 0. 1% formic acid for 130 min and 22-32% acetonitrile/H2O; 0. 1% formic acid for 15 min). For peptide ionization in the EASY-Spray nanosource, the spray voltage was set at 2. 2kV and the capillary temperature at 275°C. The Advanced Peak Determination (APD) algorithm was used for real time determination of charges states and monoisotopic peaks in complex MS spectra. The mass spectrometer was used in data dependent mode to switch consistently between MS and MS/MS. Time between Masters Scans was set to 3 s. MS spectra were acquired in the 400-1600 m/z range at a FWHM resolution of 120 000 measured at 200 m/z. AGC target was set at 4. 0. 105 with a 50 ms maximum injection time.
Data analysis of Jurkat cell proteome Raw MS files were processed as previously described with MaxQuant software (v. 1. 6. 3. 4). Data were searched against the Homo sapiens entries of the UniProtKB protein database (release Swiss-Prot reviewed 2020_01, 20,367 entries). Protein entries from the MaxQuant 'proteinGroups. txt' output were first filtered to eliminate entries from reverse and contaminant databases. Cellular protein abundances were determined from raw intensities using the protein ruler methodology, using the following relationship: protein copies per cell = (protein MS signal × NA × DNA mass)/(M × histone MS signal), where NA is Avogadro's constant, M is the molar mass of the protein and the DNA mass of a diploid human cell is estimated to be 6. 5 pg. Cellular protein abundances were log transformed and averaged sequentially over technical and biological replicates.
Funding This work was supported by  CNRS ,  INSERM , the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement  n°787300  (BASILIC) to BM),  Agence Nationale de la Recherche  ( LYMPHOSCAN  project to RR and SUPERBASILIC project to BM), and by fellowships from  DC Biol Labex  ( ANR-11-LABEX-0043 , grant  ANR-10-IDEX-0001-02  PSL; NJ. and JCG. ),  La Ligue  (KR). The Marseille Proteomics facility is supported by  IBISA (Infrastructures Biologie Sante ́et Agronomie) ,  Plan Cancer ,  Canceropo ̂le PACA, Re ́gion Sud Provence-Alpes-Co ̂te d'Azur, Institut Paoli-Calmettes, Centre de Recherche en Cance ́rologie de Marseille ,  Plateforme Technologie Aix-Marseille  and  Fonds Europe ́en de De ́veloppement Re ́gional.
Concerning flowering assay and chlorophyll content, 10-day-old Arabidopsis plants were sprayed with 500 µL of 10 µM of peptide, three times a week until bolting. Chlorophyll content was measured with a SPAD chlorophyll meter (Konica Minolta). The leaf surface was measured using ImageJ software. Concerning Arabidopsis root development, Col-0 seeds were grown in vitro as described above. Three days after sowing, seedlings were treated with 100 µM of the corresponding cPEP or its scramble every 2 days for 2 weeks. Seedlings were harvested 24 h after the last treatment and scanned to quantify the primary root length using the NeuronJ plugin of ImageJ. For growth experiments, B. vulgaris, A. hypochondriacus, A. thaliana, and G. max seedlings were treated just after sowing and three times a week with 500 µL of a mix of 20 µM of each peptide.
The excitation of the FITC donor at 470 nm was carried out by a picosecond pulsed diode laser at a repetition rate of 40 MHz, through an oil immersion objective (63×, N. A. 1. 4). The emitted light was detected by a Leica HyD detector in the 500-550 nm emission range. Images were acquired with acquisition photons of up to 1500 per pixel. From the fluorescence intensity images, the decay curves were calculated per pixel and fitted (by Poissonian maximum likelihood estimation) with either a mono-or double-exponential decay model using the SymphoTime 64 software (PicoQuant, Germany). The monoexponential model function was applied for donor samples with only FITC present. The double-exponential model function was used for samples containing FITC and Sytox. Experiments were repeated at least three times to get statistically valid data.
The HCD collision energy was set to 25% Normalized Collision Energy and the polydimethylcyclosiloxane background ion at 445. 120025 Da was used for internal calibration (lock mass). Data analysis was performed with MaxQuant (version 1. 6. 3. 4) using the Andromeda search engine with default search settings, including a false-discovery rate set at 1% on both the peptide and protein levels. Spectra were searched against the annotated sequences of the A. thaliana Col-0 genome (Araport11_TAIR11 containing 48,359 protein sequences), supplemented with peptide sequences (cPEPcpk3-HA and scrambled cPEPcpk3-HA). The mass tolerance for precursor and fragment ions was set to 4. 5 and 20 ppm, respectively, during the main search. Enzyme specificity was set as C-terminal to arginine and lysine, also allowing cleavage at proline bonds with a maximum of two missed cleavages.
Variable modifications were set to oxidation of methionine residues and acetylation of protein N-termini. Matching between runs was enabled with a matching time window of 1. 5 min and an alignment time window of 20 min. Only proteins with at least one unique or razor peptide identified were retained, leading to the identification of 712 proteins. Proteins were quantified by the MaxLFQ algorithm integrated into the MaxQuant software. A minimum ratio count of two unique or razor peptides was required for quantification. Further data analysis was performed with the Perseus software (version 1. 6. 2. 1) after loading the protein groups file from MaxQuant. Reverse database hits were removed and replicate samples were grouped. Proteins with less than three valid values in at least one group were removed and missing values were imputed from a normal distribution around the detection limit leading to a list of 463 quantified proteins that was used for further data analysis.
On these quantified proteins, a t-test was performed for a pairwise comparison of both conditions. The results of this t-test are shown in the volcano plot (Supplementary Fig. 4b ). For each protein, the log 2 (HA-tagged peptide/HA-tagged scrambled peptide) fold change value is indicated on the X-axis, while the statistical significance (-log p value) is indicated on the Y-axis. Proteins outside the curved lines, set by an FDR value of 0. 05 and an S0 value of 1 in the Perseus software, represent specific HA-tagged peptide interaction partners. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD017404 (ProteomeXchange Dataset PXD017404).
One microliter of each sample were loaded on an analytical C18 column (PEPMAP C18 2 µm 75 µm × 500 mm Thermo Fisher Electron) equilibrated in 95% of solvent A (5% acetonitrile + 0. 2% formic acid in water) and 5% of solvent B (80% acetonitrile + 0. 2% formic acid in water). Peptides were eluted using a 5-50% gradient of B for 130 min at a 300 nL/min flow rate. The Orbitrap Exploris 480 was operated in FAIMS mode (two compensation voltages used: -45 and -60 v) and data-dependent acquisition mode with the Xcalibur software. Survey scan MS spectra were acquired in the Orbitrap on the 375-1200 m/z range with the resolution set to a value of 60,000. The ten most intense ions per survey scan were selected for HCD fragmentation, and the resulting fragments were analysed in the Orbitrap with the resolution set to a value of 15,000.
Dynamic exclusion was used within 45 s to prevent repetitive selection of the same peptide. Acquired MS and MS/MS data were searched with Mascot (version 2. 8. 0, http://matrixscience. com) against a custom-made database containing all Arabidopsis entries from the UniprotKB database, several interest protein sequences, and contaminants protein sequences. The search included methionine oxidation, and acetylation N terminal, as variable modifications, and carbamidomethylation of cysteine as a fixed modification. Trypsin P was chosen as the enzyme and two missed cleavages were allowed. The mass tolerance was set to 20 ppm for the precursor ion and 20 mmu for fragment ions. Raw MS signal extraction of identified peptides was performed across different samples. Validation of identifications was performed through a false-discovery rate set to 1% at protein and peptidesequence match level, determined by target-decoy search using the in-house-developed Proline software version 2.
Acknowledgements This work was funded by the  French ANR  project  BiomiPEP  ( ANR-16-CE12-0018-01 ). B. F. has been supported by the  Fondation ARC  pour la recherche sur le cancer. The work (proteomics) was funded in part by grants from the  Région Occitanie, European funds (Fonds Européens de Développement Régional, FEDER) ,  Toulouse Métropole , and the  French Ministry of Research  with the  Investissement d'Avenir Infrastructures Nationales en Biologie et Santé program  ( ProFI, Proteomics French Infrastructure  project,  ANR-10-INBS-08 ). We thank  Christian Mazars  ( LRSV, Auzeville-Tolosane, France ) for valuable advice about CPK3,  Marc Knight  ( Durham University, UK ) for Arabidopsis ABRE Luciferase lines, and  Camille Ribeyre  ( Micropep Technologies ) for Botrytis cinerea spores.
Data availability The 5 P sequencing data generated in this study have been deposited in the NCBI database under accession PRJNA605186. The MS data generated in this study have been deposited in the MassIVE database under accession MSV000090305 [https://massive. ucsd. edu/ ProteoSAFe/dataset. jsp?task=a7eb661040c74675abf409a0fbfc240a]. The IP MS data generated in this study have been deposited in the ProteomeXchange Consortium database under accession code PXD017404. Source data are provided with this paper.
We also completed 20 semi-structured interviews with elders, supplemented with participant observation of livestock husbandry practices and informal interviews. In three GRs in Kajiado (Olgulului-Ololorashi, Eselenkei, Imbirikani), we completed 132 interviews. Except for cases when permission was not granted, all interviews were recorded. To supplement the above social science mixedmethods, I used archival satellite records to create time series data sets of rainfall and primary productivity across sampling extents that could be compared to broad scale spatial and temporal patterns of access to land (Fig. 1 ). NDVI monthly composites Fig. 1  Locations of the study sites, sampling locations, and the observational scale of GIMMS NDVI data in Kenya of AVHRR imagery from the GIMMS NDVI3g. v1 dataset  (Pinzon and Tucker 2014)  were created for the time period of 1980-2015 using the gimms package in R software  (Detsch 2021).
Monthly rainfall estimates from the CHIRPS dataset  (Funk et al. 2015 ) (0. 05°, ~5 km) were resampled to match the spatial resolution of GIMMS rasters (1/12°, ~8 km resolution) using the bilinear method in R software. The observational scale of this imagery, though limited in its ability to account for important aspects of vegetation community heterogeneity, soils, and forage quality due to its coarse spatial grain (~ 8 km), provides the only comparable source of long term , high frequency (monthly), vegetation productivity data at a spatial and temporal extent that could be compared to the broad changes in pastoral mobility observed. Two sampling strategies were used to match the scale of analysis of changes in mobility over the past 40 years that were most important for livelihoods in each study site, applying an observational scale appropriate only for understanding broad scale patterns of mobility and dynamics of spatio-temporally variable rainfall and vegetation.
Acknowledgements I am indebted to the people of Koija, Imbirikani, Eselenkei, and  Olgulului-Ololorashi  group ranches for generously sharing their time and knowledge, teaching me about their lives and land, and for welcoming me into their homes. This work would not have been possible without the assistance in interviewing and translation, and the guidance of,  Naiputari Paul Wachira ,  Charles Ntimama Mutunkei ,  Richard Solonka ole Supeet , and  Sakimba Kennedy Kimiti. The research benefitted greatly from supervision and mentoring by  Elizabeth King ,  Laura German ,  Donald Nelson ,  Jeffrey Hepinstall-Cymerman ,  Forest Isbell ,  Mara Goldman ,  François Mialhe , and  Yanni Gunnell. The manuscript benefitted from the comments of two anonymous reviewers and  Anita Morzillo. This research was permitted by the  Republic of Kenya's National Commission for Science, Technology and Innovation  (permit nos:  NACOSTI/P/16/8312/1355 ,  NACOSTI/P/19/8312/30903 ).
MDS/CMML patients with TET2/IDH mutations display a distinct NK cell phenotype Blood NK cells from 33 MDS/CMML patients (myelodysplastic syndromes and chronic myelomonoytic leukaemia, respectively, Supplementary Data 1) and 23 HD were phenotyped by flow-cytometry. Surface expression of maturation markers (CD69, CD57, KLRG1), activating (NKp30, NKp46, DNAM-1, NKG2D) and inhibitory (CD96, KIR2D, CD85j) receptors was investigated (Supplementary Table  1 ). Small perturbations were observed on circulating NK cells of MDS/CMML individuals compared with HD in the expression of some activating (DNAM-1, NKp46) and inhibitory (CD96) receptors. Surprisingly, an almost 2-fold reduction of the killer immunoglobulin-like receptors (KIR) expression was found on MDS patients NK cells compared to HD (31. 2% and 54.
TET2 directly binds to and regulates KIR locus expression in NK cells To evaluate the role of TET2 in regulating KIR expression, we first analyzed the type and the positioning of the TET2 mutations found in MDS/CMML patients with a reduced percentage of KIR + NK cells (below 25 %) at diagnosis (Fig. 3A ). This analysis revealed that all but one patient showed either nonsense or frameshift mutations leading to a premature stop-codon and the absence of a functional TET2 protein, extending the observation made in KIR -NK cells (Supplementary Table  6 ). The only exception was the patient MUT30 who presented a missense mutation p. R1261H (c. G3782A substitution). This mutation has already been described in the catalogue of somatic mutations in cancer (COSMIC) database  18  with a functional consequence prediction (Functional Analysis through Hidden Markov Models FATHMM) score equal to 0.
05) (Fig. 4B , upper panel, Supplementary Data 2). Among the 97 genes found hypermethylated in TET2 MUT KIR LOW patients compared to KIR HIGH patients (Fig. 4B , lower panel, Supplementary Data 3), methylation of TYROBP (coding for DAP12) and TNF was predicted to significantly inhibit the NK cell mediated cytotoxicity pathway as defined by the KEGG database (p<0. 05, KEGG pathway hsa04650)  25. Reports suggested variations in methylation by TET2 of the CpG loci according to their position regarding the gene body and the respective regulatory elements  24, 26, 27. We analyzed the percentage of 5hmC in the gene bodies and 10kb upstream or downstream on the whole genome  26. Then, mean of methylation has been calculated for genes involved in pathways of interest for NK cell biology. Percentage of 5hmC trends up in TET2 MUT KIR LOW NK cells compared to KIR HIGH samples in coding and flanking regions of genes implicated in the cytokine-cytokine receptor interactions (KEGG pathway reference hsa04060), the JAK-STAT signalling pathway (hsa04630), the TNF signalling pathway (hsa04668) and the NK cell mediated cytotoxicity (hsa04650) (Fig.
8 ). To confirm in vivo our observations, NK cells from MDS patients recruited in the clinical trial NCT02985190 were analyzed for their capacity to produce IFN-γ and to restore their phenotype, before and after 3 or 6 cycles of treatment with AZA. NCT02985190 clinical trial is a phase II study of efficacy and tolerance of AZA in MDS patients with concomitant systemic auto-immune and inflammatory disorders (SAID), for which the primary outcome measure was the overall response rate of MDS and SAID  29. Functional experiments showed an increase in the production of INF-γ by NK cells stimulated in vitro by a mixture of PMA and ionomycin in patients after 3 cycles of treatment with AZA (n=6, Fig. 6B ). Moreover, KIR2D, perforin and granzyme B expressions, quantified by flow-cytometry, were significantly increased in this group of patients after 6 cycles of treatment (n=9, Fig.
Patient cohorts and Samples The first cohort was composed of 20 sternal bone marrow (BM) aspiration and 58 peripheral blood mononuclear cell (PBMC) samples that were collected from 63 MDS/CMML patients. Patients' samples were obtained with written informed consent in the Haematology Departments of the Saint Louis Hospital, Paris, France (Supplementary Data 1 and Table  7 ). MDS and CMML diseases were defined according to the World Health Organization 2016 criteria  39  , and classified according to the Revised International Prognostic Scoring System (IPSS-R)  40. Low-Risk (LR) disease was defined as IPSS-R verylow, low or intermediate whereas High-Risk (HR) disease designated as IPSS-R high and very-high. Disease evolution was assessed according to 2006 International Working Group criteria  41.