dataesr/scientific-paragraphs-categorization huggingface dataset:
Dealing with sequencing depths Due to different sampling times and sequencing runs, the choice of bioinformatic techniques for data analysis was very important. Thus, we considered and compared several methods to cluster sequences and to normalize the considered dataset. During the last decade, two ways have been used to cluster sequencing reads: the Operational Taxonomic Units (OTUs) or the ASVs. OTUs cluster sequences which are identical up to a fixed similarity threshold (usually 97%) while ASVs regroup identical sequences after a sequencing error correction step  (Callahan et al. , 2016). Comparing the 2 methods, it appears that biological conclusions are very similar  (Allali et al. , 2017; Glassman & Martiny, 2018). However, ASVs are advised for improved reproducibility, comparison across studies, meta-analysis and nucleotide-level resolution  (Callahan, McMurdie & Holmes, 2017; Porter & Hajibabaei, 2020).
As the samples considered in our study had been collected during 3 different experiments and were sequenced separately, we chose to analyze sequencing data using the ASV method implemented in the DADA2 package under RStudio  (Callahan et al. , 2016)  in order to enable comparison among samples. After sequencing data analysis, library sizes among samples varied from 15399 to 554056 reads because of different sequencing depths. As a consequence, hierarchical clustering based on Bray-Curtis dissimilarity of non-normalized data showed a clear sequencing depth effect as samples sequenced together gathered together (Fig. S3 ). In order to compare samples, data needed to be normalized. The rarefaction method has been extensively used to normalize metabarcoding data but it leads to non-reproducible tables and randomly suppresses OTUs or ASVs  (McMurdie & Holmes, 2014).
The edgeR and DESeq methods have been advised but involve the use of logarithms and do not handle well null values   (Weiss et al. , 2017)  which were quite abundant in our dataset. A recent study showed that simpler methods lead to satisfying normalizations  (Bushel et al. , 2020). Thus, we chose the Count Per Million (CPM) method which enabled hierarchical clustering of the samples according to their bacterial compositions rather than their sequencing runs.
ACKNOWLEDGEMENTS We are grateful to the SASV teams for their help throughout all the experiments: zootechny and laboratory support. We especially thank  Jean-Sébastien Lam  and  Julien Le Rohellec  for their precious help in the hatchery;  Florence Antypas  and  Etienne Lopez  for their contribution; as well as  Valentine Ballan  and  Gwenola Plougoulen  for their valuable biomolecular work.
Further description about the functioning of the instrument is given in Sect. 2. 1. According to EBAS database  (Tørseth et al. , 2012) , in the last 10 years (2011-2020) a total of 57 European stations or sites have reported data from particle light absorption measurements using filter-based photometers, including Aethalometers. These measurements contribute to networks and projects such as ACTRIS (41 sites) and EMEP (European Monitoring and Evaluation Programme, five sites) among others, and some stations may contribute to more than one network at the time. Data from stations using FBAP in 29 non-European countries are also available in EBAS. The COST Action CA16109 Chemical On-Line cOmpoSition and Source Apportionment of fine aerosoL COLOS-SAL, reports in its catalogue the cooperation with 49 sites using FBAP in Europe.
Data processing and analysis Equivalent black carbon concentrations were measured every minute. Subsequent to the workshops, the data from the Aethalometers were cleaned based on the instrument status codes. The AE33 reports a series of status codes representing the operational state, internal procedures in progress, and warning alerts or errors in the instrument, e. g. , 0 for normal measurements, 1 for filter tape advance, 8 to check flow status history, and 384 for tape error (tape not moving, end of tape) (Magee  Scientific, 2018). As more than one condition may occur at the same time, these statuses are built under a binary system; therefore they may be numerically combined, e. g. , 9 to check flow status history (warning) + tape advance (procedure) and 387 for tape error (tape not moving, end of tape) + stopped.
This value needs to be checked and confirmed each time the filter tape is changed. Both the filter type and the correction parameter C should be reported alongside the measurement data when submitting the measurements to databases like EBAS. The change in tape from one (T60A20, also referred to as M8020) type to the current one (M8060) requires the user to change the multiple-scattering parameter C and the leakage factor Zeta. In our experience, this is the most important systematic error in the measurements that the user can make in a field or laboratory measurement campaign. The operators must perform maintenance following the frequencies and instructions given in the user manual. Flow verification, a leakage test, and a check of the spot shape are good starting points to verify the instrument performance.
Acknowledgements. ACTRIS ( Aerosols, Clouds and Trace gases Research Infrastructure ) and COLOSSAL ( COST Action   CA16109   Chemical On-Line cOmpoSition and Source Apportionment of fine aerosoL ) are thanked for their logistical support in the preparation and execution of the workshops. The WCCAP is thanked for hosting the experiments in their laboratories. Aerosol d. o. o. , Slovenia, the manufacturer of the Aethalometer  AE33 , is thanked for troubleshooting support during the workshops. María Fernández-Amado  acknowledges the  Ministerio de Ciencia e Innovación  ( PTA2017-13607-I ). Financial support. ACTRIS and COLOSSAL provided financial support for the execution of the experiments. Instrument  S04-00387  is operated and maintained thanks to the  Spanish Ministry of Science and Innovation  (project nos.
CGL2016-81092-R ,  CGL2017-42 90884REDT , and  RTI2018. 101154. A. I00 ). Gloria Titos is funded by the  Juan de la Cierva-Incorporación postdoctoral program  (grant no. IJCI-2016-29838 ). IMT  Lille Douai  ( Joel Ferreira De Brito ,  Veronique Riffault ) received financial support from the  Labex CaPPA project , which is funded by the  French National Research Agency (ANR)  through the  PIA (Programme d'Investissement d'Avenir ) (contract no. ANR-11-LABX-0005-01 ), and the  CLIMIBIO  project; both projects are financed by the  Regional Council "Hauts-de-France " and the  European Regional Development Fund (ERDF). The operation of instruments  S00-00055  and  S02-00156  is funded by the projects  CRISOL (MINECO/AEI/FEDER ,  UE ; grant no. CGL2017-85344-R ) and  TIGAS-CM  (grant no. Y2018/EMT-5177 ).
Data availability. Experiment data will be available at the Public data repository for experimental aerosol physics from the Leibniz Institute for Tropospheric Research TROPOS, https://exp-aerosol-physics. tropos. de/public/publications/2021/ Cuesta_et_al_amt (last access: 31 March 2021, TROPOS, 2021). Supplement. The supplement related to this article is available online at: https://doi. org/10. 5194/amt-14-3195-2021-supplement. Author contributions. LD, ACM, TM, GM, SP, and AW planned and designed the study. All co-authors participated in the experiments. ACM processed the data and prepared the paper with inputs from LD, TM, GM, and AW.
In red, locations where F. hirta is pollinated by Valisia javana sp1, in blue locations where it is pollinated by V. javana sp2. Locations Ding and Wan are pollinated by a distinct population of V. javana sp1. Map drawn with the package 'rworldmap' using the public domain Natural Earth map dataset https://naturalearthdata. com. Note: The designations employed and the presentation of the material on this map do not imply the expression of any opinion whatsoever on the part of Research Square concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. This map has been provided by the authors.
Adult Plant Phenotypic Measurements One month after the young seedlings were exposed to shade (2 July 2018), adult plants were measured to test for the effect of shade on phenotypic measurements. Phenotypic measurements included height in cm, number of branches, presence or absence of floral buds, number of internodes, and stem diameter in mm. Internode length was calculated as the average stem length in cm per internode (plant height/number of internodes). Five fully developed leaves were collected, scanned, dried (3 days at 45 • C), and weighed. The area of leaves was measured using the ImageJ software  [29]  and the specific leaf area (SLA) was calculated as leaves surface (m 2 )/leaves mass (kg).
Bioinformatics We used a bioinformatics pipeline integrated in the snake-make workflow called epiGBS2  [32]  to remove PCR duplicates and demultiplex samples. The pipeline is available at: https://github. com/nioo-knaw/epiGBS2. The filtered and demultiplexed reads from epiGBS2 pipeline were used in another pipeline adapted from previous work  [33] , using the Galaxy project server as applied in  [34]. Adapter removing was done using TrimGalore! V06. 5  [35]. Single-end reads were aligned to the snapdragon plant genome version 3. 0  [36]  with BSMAP Mapper  [37]. Mapped reads were merged and used as input in BSMAP Methylation Caller to get a tabular file with cytosine and thymine counts that were used as input to calculate coverage and Frequency of C and T for subsequent analysis. CpG methylated sites with coverage of at least eight reads per position found in all samples were filtered with the package Methylkit  [38].
Statistical Analysis We summarized the epiGBS data on DNA methylation changes by using PCA for each methylation protocol and line. PCA was conducted with the package factoextra, FactoMineR, emmeans, and missMDA (scripts available at the end of the supplementary materials). We retrieved PCA coordinates per individual, the relative and absolute contributions of the components (also named dimensions) to the global variance, and the contribution of variables (cytosines positions) to the components (also named dimensions) by DNA methylation context (CpG, CHG, and CHH) and by tissue (apex and leaves) for the subsequent analyses. We assessed the effect of the light versus shade treatment on (1) the phenotypic traits (plant height, internodes length, stem diameter, number of flowers, number of ramifications, and SLA), and (2) methylation patterns summarised by PCA dimensions with Mann-Whitney U-tests for each line, tissue, and methylation protocol.
Funding: This project has received funding from the  European Research Council (ERC)  under the European Union's  horizon 2020 research and innovation program  (grant agreement No  ERC-CoG-2015-681484-ANGI ) awarded to BP. This work was supported by funding from the  French "Agence Nationale de la Recherche " ( ANR-13-JSV7-0002 "CAPA" ) to BP.
Data Availability Statement: Data will be made available upon request. Acknowledgments: This study is set within the framework of the "Laboratoires d'Excellences (LABEX)" TULIP (ANR-10-LABX-41). With the support of LabEx CeMEB, an ANR "Investissements d'avenir" program (ANR-10-LABX-04-01) through the Environmental Epigenomics Platform. We thank the editors and anonymous reviewers for their comments and suggestions, which significantly contributed to improving the quality of this article.
Hydrometric monitoring Rainfall depth was measured continuously using a Davis Instruments Tipping Bucket Rain Collector. Groundwater levels were monitored every 6 min using capacitance probes (Odyssey Capacitance Water Level recorder). Short periods of missing data due to battery failure were recorded. Probes were calibrated before and after deployment, with typical accuracy under field conditions of ±20 mm. To monitor infiltrated stormwater and its interaction with the shallow water table, a network of monitoring bores was established in and around the basin (figure  1 ). A well within the infiltration basin (Basin) allowed water level measurement and water sampling. Downslope monitoring bores formed a transect 0 m (DS0), 7 m (DS7), 17 m (DS17) and 24 m (DS24) downslope (DS) from the edge of the basin.
Sapwood was then weighed fresh, dried in an oven at 80 • C for three days and weighed dry. To correct for potential probe misalignment, climate data from a nearby Bureau of Meteorology climate station (Scoresby Station ID:086104) were filtered to identify conditions where sap flux density should equal zero  [25]  and data were linearly offset accordingly. Due to failure of sensors installed on the north side of several trees, we used data from sensors installed on the south side of trees only. Periods of less than four hours with missing data were gapfilled using a linear interpolation. Days where at least one sensor had more than four hours of missing data were excluded. Two periods of missing sap flux data (August-September 2018 and April-May 2019) were due to failure of power supply to the sensor network.
Data and statistical analyses All statistical tests were conducted in MINITAB 17. To assess the effect of season and location on tree δ 18 O isotopes, sap flux, or normalized sap flux, both single and two-factor analyses of variance (ANOVA) were performed. Assumptions of normality were evaluated and determined to be satisfied after natural log transformation was applied to sap flux. To evaluate the nature of the differences between season and location for tree isotopes, statistically significant ANOVA was followed-up with Fisher's least significant difference (LSD) post-hoc tests at the 95% confidence interval. Despite a slight skew in the standardized residual plot for tree δ 18 O isotopes, Fisher's LSD results on raw data and square-root-transformed data were near-identical; we thus report only results based on the raw data.
Acknowledgments This project was funded by the  Australian Research Council Discovery Program  ( DP170102870 ). In a previous role, Fletcher received payment for his contribution to the engineering design of the Wicks Reserve Infiltration System. We benefited from the early advice and ongoing support of  Jeffrey J McDonnell  ( University of Saskatchewan ). The authors would also like to sincerely thank our late colleague,  Justin Costelloe , for his contributions to the early stages of this project. This paper benefited substantially from the suggestions from three anonymous reviewers and the Editor.
We fit the model to the binned velocity-traction relationship in the thawed and frozen regions of each catchment (number of bins is 20, logarithmically spaced) using a nonlinear least-squares regression implemented in MATLAB. Fitting the binned data gives equal weights to high-and lowvelocity regions of each catchment regardless of the number of grid cells of each. We do not fit models to the FS tractions which we limit to velocities above 100 m yr -1 and do not reflect the full velocity range. We note that velocity and traction magnitudes are dampened due to grid cell averaging; thus the binned relationships and model fits will reflect this range rather than the full range possible in each catchment.
Acknowledgements. We would like to thank the anonymous reviewer and  Bradley Lipovsky  for detailed comments which significantly improved the quality of the manuscript. The Elmer/Ice computations presented in this paper were performed using the GRI-CAD infrastructure (https://gricad. univ-grenoble-alpes. fr), which is supported by Grenoble research communities. This work also benefited from many fruitful discussions with colleagues at  IGE. Financial support. This research has been supported by the  French National Research Agency  (grant no. ANR-17-CE01-0008 ). Review statement. This paper was edited by  Joseph MacGregor  and reviewed by  Bradley Lipovsky  and one anonymous referee.
Code and data availability. All data used to generate this paper are currently archived and publicly available for download: MEaSUREs Multi-year Greenland Ice Sheet Velocity Mosaic v1  (Joughin et al. , 2016 ; https://doi. org/10. 5067/QUA5Q9SVMSJG), MEaSUREs Greenland Ice Mapping Project (GIMP) Digital Elevation Model from GeoEye and WorldView Imagery v1,  (Howat et al. , 2017 ; https://doi. org/10. 5067/H0KUYVF53Q8M), IceBridge BedMachine Greenland v3  (Morlighem, 2018;    https://doi. org/10. 5067/2CIX82HUV88Y), Likely Basal Thermal State of the Greenland Ice Sheet v1 (McGregor et al. , 2017;   https://doi. org/10. 5067/R4MWDWWUWQF9), and Firn Area Delineation (multi-year averaged snowline) (Vandecrux et al. ,  2019;  https://doi. org/10. 18739/A2V40JZ6C). Elmer/Ice code and output is available upon request.
, 2013; Selmer et al. , 2006). Through its cycle of association, ATPase hydrolysis, and subsequent dissociation from pre-40S particles, RIO1 might thus act as a conformational and functional probe that assesses the tRNA translocation capacities of the small subunit and couples triggering of the last maturation step to functional proofreading of the ribosome. Cell culture and treatment with siRNA duplexes HEK293 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1 mM sodium pyruvate. HEK293 FlpIn TRex cell lines (Invitrogen, RRID:CVCL_ U427) and expressing HASt-DIM2, HASt-LTV1, RIO1(wt)-StHA, and RIO1(D324A)-StHA have been described previously  (Wyler et al. , 2011). Cell lines used in this study were not further authenticated after obtaining them from the indicated source.
Bioinformatic MS data analysis Mascot (Mascot server v2. 6. 1; http://www. matrixscience. com) database search engine was used for peptide and protein identification using automatic decoy database search to calculate a false discovery rate (FDR). MS/MS spectra were compared to the SwissProt H. sapiens database (supplemented with the sequence of the D324A RIO1 mutant). MS mass tolerance was set at 5 ppm and MS/MS mass tolerance was set at 0. 8 Da and 0. 02 Da for data acquired on LTQ-Orbitrap Velos and Orbitrap Fusion Tribrid mass spectrometers, respectively. The enzyme selectivity was set to full trypsin with two missed cleavages allowed. Protein modifications were fixed carbamidomethylation of cysteines, variable phosphorylation of serine, threonine and tyrosine, variable oxidation of methionine, variable acetylation of protein N-terminus.
Proline software  (Bouyssieet al. , 2020)  was used for the validation and the label-free quantification of identified proteins in each sample. Mascot identification results were imported into Proline. Search results were validated with a peptide rank = 1 and at 1% FDR both at PSM level (on adjusted e-value criterion) and protein set level (on modified Mudpit score criterion). Label-free quantification was performed for all proteins identified: peptides were quantified by extraction of MS signals in the corresponding raw files, and post-processing steps were applied to filter, normalize, and compute protein intensities. For analysis of RIO1(kd)-StHA pre-40S particles composition, protein abundances were summarized in iBAQ values by dividing the protein intensities by the number of observable peptides  (Schwanha ¨usser et al.
Two of the five 3D classes yielded reconstructions with clear features. The first one, hereafter named state A, contained 104,844 particles and was further auto-refined to 3. 1 A ˚resolution according to gold-standard FSC procedure; the second one (state B) comprised 276,012 particles and was auto-refined to 2. 9 A ˚resolution. Subsequently, particles corresponding to the states A and B 'platform only' classes were retrieved from the dataset without signal subtraction and submitted to auto-refinement, yielding maps of 'full' states A and B particles solved to 3. 22 and 2. 96 A ˚, respectively (Figure  2 -figure supplement 1b, c). Because significant motion of the head and platform regions compared to the body was observed, multi-body refinement  (Nakane et al. , 2018)  was performed for both states by dividing pre-40S particles in three main domains: body, head, and platform.
Acknowledgements This work was funded by the  Agence Nationale de la Recherche  ( ANR 16-CE11-0029 ), the  CNRS , the  University of Toulouse-Paul Sabatier , the  Region Occitanie , the  European Union  ( Fonds Europeens de Developpement Regional, FEDER) , and  Toulouse Me  ´tropole. UK received funding from the  Swiss National Science Foundation  (grant  31003A_166565  and the  NCCR 'RNA  and disease'). Cryo-EM image acquisition was performed on the  METI facility  ( CBI, Toulouse ) and at the EMBL in Heidelberg with financial support from the iNext European initiative. Cryo-EM image analysis was performed using HPC resources from  CALMIP  (Grant 2018). We would like to thank the engineers and staff working on these facilities for their great help, as well as  Marion Aguirrebengoa  for her help on statistical analysis and  Odile Burlet-Schiltz  for her support.
Data availability Mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD019270. Cryo-EM maps have been deposited in the Electron Microscopy Data Bank (EMDB), under the accession codes : EMD-11440 (State A multi-body composite map); EMD-11441 (State B multi-body composite map); EMD-11446 (State A, head); EMD-11445 (State A, body); EMD-11447 (State A, platform); EMD-11443 (State B,.
Background. Poor transition planning contributes to discontinuity of care at the child-adult mental health service boundary (SB), adversely affecting mental health outcomes in young people (YP). The aim of the study was to determine whether managed transition (MT) improves mental health outcomes of YP reaching the child/adolescent mental health service (CAMHS) boundary compared with usual care (UC). Methods. A two-arm cluster-randomised trial (ISRCTN83240263 and NCT03013595) with clusters allocated 1:2 between MT and UC. Recruitment took place in 40 CAMHS (eight European countries) between October 2015 and December 2016. Eligible participants were CAMHS service users who were receiving treatment or had a diagnosed mental disorder, had an IQ ⩾ 70 and were within 1 year of reaching the SB. MT was a multi-component intervention that included CAMHS training, systematic identification of YP approaching SB, a structured assessment (Transition Readiness and Appropriateness Measure) and sharing of information between CAMHS and adult mental health services.
Design We conducted an eight-country, two-arm, parallel design, superiority, cluster-randomised controlled trial (cRCT) to assess whether MT improves mental health outcomes in YP approaching the CAMHS SB, compared to UC. The cRCT with economic evaluation was embedded within the MILESTONE longitudinal study (ISRCTN83240263 and NCT03013595), described elsewhere and funded by the European Union  (Singh et al. , 2017). Participating countries were Belgium, Croatia, France, Germany, Ireland, Italy, Netherlands and the UK. The authors assert that all procedures contributing to this study comply with the ethical standards of the relevant national and institutional committees on human experimentation and with the Helsinki Declaration of 1975, as revised in 2008. All procedures involving human subjects were approved in the UK by the National Research Ethics Service Committee West Midlands -South Birmingham (15/WM/0052) and equivalent ethics boards in the participating countries.