dataesr/scientific-paragraphs-categorization huggingface dataset:
Spatial Heterogeneity Indices The spatial heterogeneity of the fields was assessed through pixel-based and objectbased indices. Each index is defined in Table  2. All spatial heterogeneity indices were computed using eCognition Developer software. The pixel-based spatial heterogeneity was calculated by considering the value of all individual pixels in a given field and corresponds to the standard deviation of the pixel values by field and to various Haralick textural parameters  [64] [65] [66]  derived from the Gray-Level Co-occurrence Matrix (GLCM) and the Gray-Level Difference Vector (GLDV). The GLCM is a frequency tabulation of how often different combinations of two neighbor pixel gray levels occur in an image. A different co-occurrence matrix exists for each direction (vertical, oblique, horizontal) chosen to establish the neighborhood spatial relationship between pixels.
The ROC-AUC does not reflect the magnitude of the difference between the two groups. The ROC-AUC presents two main advantages. First, ROC-AUC is insensitive to the number of observations (fields) compared. This property enables use of it to compare classifier performance over situations presenting significantly different number of observations. Secondly, ROC-AUC is insensitive to changes in the class distribution  [68, 72] , i. e. , changes in the relative number of observations in each of the two classes. This property enables use of it to assess the separability among differently imbalanced datasets (i. e. , presenting different number of observations in the two groups), as those encountered in this study presenting imbalances varying between 48%/52% (rather balanced) up to 38%/63% (rather imbalanced).
The ROC-AUC was computed in R software with the ROCR package  [73, 74]  via the prediction and performance functions. The statistical significance of the difference between organic and conventional fields achieved with the computed indices was assessed through the p-value of the Mann-Whitney-Wilcoxon (MWW) non-parametric statistical hypothesis test  [75, 76]. This test was selected because this study deals with comparisons of independent samples from two populations of which the normality of distribution was not always met. As a rank test  [77, 78] , this is less affected by extreme values than tests based on observed numerical values. For a given dataset with a given number of observations, the MWW test statistic W is equivalent to the ROC-AUC  [79] [80] [81] ; however, this relation breaks when considering datasets of different sizes as the MWW W statistic depends on the sample size while ROC-AUC does not.
These results are very encouraging and suggest, for the first time, that satellite images could effectively support the organic maize certification process. However, given the limited representativeness of the dataset used in this study (approximately 30 maize fields located in a relatively small area) compared to the variety of situations in which this technique might potentially be applied, and in the view of developing an operational system, the next step is to test the robustness of the method at a larger scale in a more diverse context (larger dataset and another region and climate) and also for other crops. The method itself could also be enhanced with the use of multivariate-multitemporal discrimination techniques and with the use of more recent satellite sensors, such as Sentinel-1, Sentinel-2, and SkySat, and PlanetScope very high spatial resolution constellations.
Acknowledgments: For having supported this research, thanks to  Yves CORNET ,  Antoine STEVENS ,  Bakary DJABY ,  Robert OGER ,  Jos VAN ORSHOVEN ,  Christian BARBIER ,  Christophe Mackels ,  Michel NOEL ,  Moussa EL JARROUDI ,  Catherine TIMMERMANS , the  Centre de Recherche Public-Gabriel Lippmann (CRP-GL-Luxembourg ). Field surveys benefited from full access to the fields and manpower and machinery support of the local farmer. Landsat-5 images courtesy of the  U. S. Geological Survey.
Data Availability Statement: The in situ datasets generated and/or analyzed during the current study and the satellite derived database are available from the corresponding author upon reasonable request. The geographical boundaries of the fields analyzed during the current study are not publicly available due to privacy protection. The satellite images analyzed during the current study are not publicly available due to restrictions from the commercial license, except for the Landsat-5 satellite image, which is freely available at https://earthexplorer. usgs. gov/.
[34] They also reported that the reduction of the CNC suspension concentration from 1. 0 to 0. 05 wt% before freezedrying could result in the formation of ultra-fine cellulose fibers rather than the flake by minimizing their parallel selfassembly. Thus, the combination of micron-sized flakes and ribbon-like fibers obtained in this study after freeze-drying of CNC demonstrates the formation of self-assembled CNCs along with their longitudinal and parallel directions. The microstructural characterization of the ND and FD CNC suspensions were also investigated via SAXS. The change in morphology is evident from the SAXS patterns (Figure  3 ). Indeed, the SAXS data obtained for ND CNCs in water were fitted using a rigid elliptical cylinder model with a fixed length of 140 nm (derived from TEM measurements) and minor and major radius of 2.
Thus, the FD CNCs showed very little increase in their scattering intensity with increasing concentration in the probed q-range, as can be seen in Figure  3b. Therefore, in this case, due to their various sizes, the SAXS fitting would not be truly representative for the actual FD CNC microstructure obtained after freeze-drying (thus, fitting was avoided for the FD CNC suspension). SAXS analysis of ND and FD CNC films was also performed on an Anton-Paar SAXSpoint 2. 0 covering the q range of about 0. 07-1. 8 Å -1. The scattering data from the ND CNC film was also fitted using a rigid elliptical cylinder model considering the same fitting parameters (except for the scaling factor, see Table  1 ) used for the scattering of ND CNC suspension. This suggests that the individual CNC particles remained as discrete scattering objects on the SAXS length scale even after drying into a film, which is also evidenced by the 2D AFM image of the ND CNC film, shown later in Figure  4d.
The XRD patterns of both ND CNC an FD CNC films demonstrated the characteristic major peak at 22. 8°, with additional double peaks at 14. 9° and 16. 5° at room temperature (25 °C), as presented in Figure  9a ,b, which is consistent with the diffraction pattern of reference cellulose (ICDD patent PDF-2 database, File no. 00-050-2241). [57] However, with increasing temperature, the crystalline peak at 22. 8° associated with the (200) crystal lattice plane of both FD and ND CNC films shifts to the lower diffraction angle. The peak intensity also decreases with increasing temperature (after normalizing the baseline, see inset in Figure  9a, b ), suggesting the thermal degradation of the crystalline phase. The crystallinity index (CI) is found around 89% at 25 °C for both films (Figure  9c ). A slight decrease in crystallinity to ≈84% is observed at 150 and 200 °C due to the initial thermal degradation, which correlates well with the TGA profile discussed above.
5 mm, Capillary Tube Supplies Ltd, Bodmin, UK) and sealed. The scattering pattern from an empty capillary and a capillary containing DI water were also recorded for solvent background subtraction. [40] The probed q-range was 0. 005-0. 2 Å -1. Data are provided in absolute scaling. The intensity I(q) can be written as follows I q P q S q ( ) ( ) ( ) ∝ (1) with P(q) the form factor of the objects studied, giving information about their shape and S(q) the structure factor associated with the interactions between the objects probed. SAXS measurements of the film samples were performed on an Anton-Paar SAXSpoint 2. 0 provided by the Material and Chemical Characterisation Facility (MC²)  [62]  equipped with a copper source (Cu K-α, λ = 1. 542 Å) and a 2D EIGER R series Hybrid Photon Counting (HPC) detector.
The distance between the film sample holder (containing ND and FD CNC films) and the detector was 556. 9 mm and the data were collected at 25 °C in one frame, with 900 s exposure covering the q range of about 0. 07-1. 8 Å -1. SASView software (version 4. 1. 2) was used to fit the SAXS data using a rigid elliptical cylindrical and mass fractal models. [40] haracterization-Surface Charge: A dilute CNC suspension (0. 1 wt% in DI water) was used to measure the ζ-potential utilizing a Malvern Zeta-sizer Nano ZSP (Malvern, UK). Samples were placed in a folded capillary electrode cell and equilibrated at 25 °C for 120 s prior to testing. The data were taken from an average of 5 measurements from 100 scans each. Characterization-Atomic Force Microscopy (AFM) Analysis: The ND CNC and FD CNC films were fixed onto microscope glass slides using double-sided polyimide Kapton tape to maintain them flat.
Characterization-Fourier Transform Infrared Spectroscopy (FTIR): The principal chemical groups present in ND CNC and FD CNC films were identified using an FTIR spectroscopy (PerkinElmer, Spectrum 100, USA) equipped with a standard attenuated total reflectance (ATR) cell. The films were scanned in transmittance mode over the wavenumber range from 4000 to 650 cm -1, and the obtained spectra were analyzed using OPUS software (version 5. 5). Characterization-Thermogravimetric Analysis (TGA): TGA was performed on a TGA Q500 (TA Instruments) from 25 to 500 °C with a heating rate of 10 °C min -1 under airflow. TA Universal Analysis 2000 software was used to calculate the weight loss (%) and the derivative weight loss of the films with temperature from the TGA scans. Characterization-Differential Scanning Calorimetry (DSC): DSC analysis was conducted utilizing a DSC Q20 (V24.
Acknowledgements The authors would like to thank  EPSRC  for funding this project (Grant  EP/N033310/1 ). V. C. thanks the  University of Bath  for supporting his Ph. D. studies. Prof. Nick Terril ,  Dr. Andy Smith , and  Dr. Tim Snow  are thanked for their assistance with SAXS experiment (Experiment no. SM20409-1 ) at I22 beamline,  Diamond Light Source, Didcot, UK. This work benefited from the use of the SasView software (developed under  NSF  Award  DMR-0520547 ) containing code developed under the  EU Horizon 2020 programme  (the  SINE2020  project Grant  654000 ). Data supporting this work is freely accessible in the Bath research data archive system at https://doi. org/10. 15125/BATH-00930.
Bioinformatic and statistical analyses Identi cation of Operational Taxonomic Units (OTUs) was performed by using the FROGS pipeline  [27]. FastQC program to control quality and the Cutadapt program to nd and remove adapter sequences from sequencing reads, and R1 and R2 reads were merged and ltered (at Phred >= Q20) by using the Flash program  [28]. OTUs were identi ed using the Swarm program  [29]. Chimera OTUs were removed using the VSEARCH program  [30] , taxa ltering was performed with a minimum abundance threshold of 0. 005% as proposed by  [31]. Finally, phylogenetic a liations were identi ed using the Silva database by using the blastn+ program  [32]. OTUs representing less than 0. 5% of global reads and samples with less than 10,000 reads were removed. The phyloseq (1. 24. 2) and vegan (2.
5-3) packages were used with R to perform the diversity analysis on normalized data. Alpha diversity was measured using the Shannon index and beta diversity using the Whittaker index. Analyses of variance (Anova) were performed to test the signi cance of differences of alpha and beta diversity between conditions (line, sex, experiment or isolator). We evaluated the Bray-Curtis distances using the env_ t method that we plotted in an NMDS (Non-Metric Multidimensional Scaling) representation. Permutational Multivariate Analyses of Variance (Permanova) were used to test for the signi cance of differences of diversity according to variations in lines, experiments, isolators and sex. The R package metagenomeSeq (1. 24. 1) was used for the identi cation of differentially abundant (DA) OTUs between lines N and 6 1 and between high and low carriers within line 6 1.
The OTU table was rst normalised, and the model was tted using the tZIG method by including experiment, isolator and sex as cofactors. Heatmaps were built using the function plotMRheatmap on signi cant DA OTUs. Then, OTUs were aggregated by family and genus with the command aggregateByTaxonomy to identify DA families and genera. Functional gene families and MetaCyc pathway were predicted using the PICRUST2 package. DA KEGG ortholog (KO) and DA MetaCyc pathway were identi ed with the R package DESeq2 (1. 26. 0). DA MetaCyc pathways were aggregated at the super-pathway level using MetaCyc database  [33]. Metadata table, unrare ed OTU table, and corresponding taxonomic classi cations have been included as Additional les 2, 3 and 4, respectively.
Cell Culture Fibroblasts from patients were obtained from the INSERM UMR1052 COPERNIC cell collection  (16). This collection was approved by the regional Ethical Committee (CPP Sud-Est, Lyon, France) and cell lines were declared under the numbers DC2008-585 and DC2011-1437 to the Ministry of Research. The database derived from the COPERNIC collection is protected under the reference IDDN. FR. 001. 510017. 000. D. P. 2014. 000. 10300. All the anonymous patients were informed and signed consent according to the ethics recommendations. This collection is composed of cancer patients presenting with overreactions in normal tissues after radiotherapy. Severity of side-effects was graded for each patient according to the Common Terminology Criteria for Adverse Events scale, version 4. 03  (17). Sampling was performed in non-irradiated, non-photo-exposed anatomical region after local anesthesia.
Transcriptome Analysis Total RNA was isolated from fibroblasts at confluency with the NucleoSpin RNA plus kit (Macherey-Nagel, Hoerdt, France) or RNeasy Plus Minikit (Qiagen, Courtaboeuf, France) according to the manufacturer's instructions. For next-generation RNA sequencing at CNRGH (CEA, Evry, France), RNA sequences were captured using a TruSeq RNA Library Prep Kit v2 (Illumina, Evry, France) with input of 1 μg. Paired-end RNA sequencing was performed on HiSeq4000 with 100 bp paired-end reads. Sequencing data quality control was performed using FastQC 0. 11. 7 before and after adapter trimming by Cutadapt 1. 13 (parameters: -q 15 -a 5'-AGA TCG GAA GAG CAC ACG TCT GAA CTC CAG TCA C-3' -5-AAG ATC GGA AGA GCG TCG TGT AGG GAA AGA GTG TAG ATC TCG GTG GTC GCC GTA TCA TT-3'). The reads were mapped to the human genome (GRCh37/hg19) using HISAT2 2.
0. 5. For a single gene, sequences were aligned versus all known exons of all gene isoforms. The resulting BAM files were sorted by read pairs (using SAMtools 1. 3. 1) and counted using the HtSeq-count tool of HtSeq 0. 6. 1. For transcriptome analysis, filtering was applied to genes with low expression (mean number of reads in the training set <10). Principal component analysis and hierarchical clustering were performed using the R DEseq2 and stats packages. VennDiagram and plots were made using the VennDiagram and ggplot2 packages. Functional annotation of the gene list was performed using the WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) and the KEGG database 2019. Gene Ontology (GO) was performed using the clusterProfiler package in R software  (18). GO and KEGG enrichment analyses were based on a false discovery rate (FDR) threshold of <0.
Primers were designed with Methyl Primer Express Software v1. 0 (ThermoFisher Scientific) and were provided by Eurogentec. The following primers were used for methylation study: NFATC2mF: 5'-TTTAGATGAATAGTGTTTTGGG-3', NFATC2mR: 5'-ATTATCATTTCCTTCCTCTACTTC-3'.
All these functions might be involved in cellular radiation toxicity, but correspond to multiple intracellular pathways. We then searched for enriched pathways involving the 445 differentially expressed proteincoding genes using the WebGestalt and the KEGG database 2019. We found only one significantly enriched pathway (Supplementary Table  S2 ): Arrhythmogenic right ventricular cardiomyopathy (adjusted p-value 0. 0065733-10 genes out 72 modulated), a pathology of cardiac muscles with progressive loss of myocytes replaced by adipocytes. Systematic analysis of our gene list revealed that none of these genes was directly involved in any known genetic syndrome leading to increased radiosensitivity.
ACKNOWLEDGMENTS We thank  Dr Nicolas Foray  ( INSERM, Lyon ) for helpful support and discussion. We thank  CEA CNRGH (Evry, France ) for support. Christine Oger  ( PRABI, University of Lyon ),  Pascal Soularue  ( CEA, LGRK, Evry ), and  Olivier Alibert  ( CEA, CNRGH, Evry ) helped in the analysis of the RNAseq data. We also thank  Gisèle Froment ,  Didier Nègre , and  Caroline Costa  from the lentivectors production facility/ SFR Biosciences Gerland -Lyon Sud  ( UMS3444/US8 ). The study was supported by a grant from  La Ligue Contre le Cancer, Comited e Saone-et-Loire , and by  ANR-RSNR-INDIRA.
Analysis of sex specific variants based on a male reference genome Pool-seq data were mapped to the male A. ruthenus reference genome (Acipenser_ruthenus. ARUT1. 2. dna. toplevel. fa, which is nearly identical to the current reference genome at NCBI GCF_010645085. 1; electronic supplementary material, table  S1 ) by Minimap2 (with parameters -t 12 -x sr -a;  [39] ) and converted to sorted bam-files by samtools  [40]. Variants (SNPs, MNPs, INDELs) were called from both bam files using the Platypus variant caller  [41]  with integrated duplicate fragment reads removal (--filterDuplicates=1) and reassembly of reads (--assembleAll=1). The resulting vcf-file was screened for sex-specific variants using awk-scripting and different variant read coverage cutoffs (i. e. maximum reads in males (0, 1 …), minimum reads in females (10, 13 …) or vice versa).
Phylogenomic reconstruction To build a phylogenetic tree for sturgeons, we download transcriptome assemblies of Acipenser baerii, A. oxyrinchus, A. schrencki, A. sinensis and A. transmontanus from the Public Sturgeon Transcripts Database (http://publicsturgeon. sigenae. org/home. html) and of Acipenser gueldenstaedtii from NCBI (https://www. ncbi. nlm. nih. gov/Traces/wgs/?page=1&view=tsa&search=acipenser). The transcriptome of Huso huso was de novo assembled using Trinity  [44]  from mixed organs. Annotated genomes of A. ruthenus and Latimeria chalumnae were also downloaded from NCBI (electronic supplementary material, table  S2 ). To identify orthologs between two species, we used the "Reciprocal best hit (RBH)" method, and A. ruthenus as the hub to retrieve orthologous genes across all species.
Analyses of sterlet (A. ruthenus) female and male pool-sequencing Pool-sequencing resulted in 553,117,774 reads (83. 5 Gbp) and 486,762,084 reads (73. 5 Gb) for the female and the male A. ruthenus pools, respectively. Pool-sequencing Illumina reads are available in the Sequence Read Archive (SRA: SRX9341540; SRX9341541), under BioProject reference PRJNA670610. After mapping to the reference genomes, the peak of the unimodal coverage distribution was 42x for the female pool and 37x for the male pool. There was no significant difference in the percentage of mapped reads for both pools (96. 9% reads mapped). We initially used two bioinformatic strategies to uncover female-specific pool-seq data in A. ruthenus. We first analysed sex-specific variants based on a male reference genome. The number of female or male specific variants was low, but their ratio already hinted at a ZW sex determination system (details: electronic supplementary material, text S4).
The red block and arrow show the position of the AllWSex2-PCR-marker (CACTIG010000179. 1: 61246236 -61246344), which distinguishes sex in six sturgeon species. The green block and arrow mark the location of the only contig matching the region (CACTIG010000179. 1: 61261166 -61261703), when using the female-specific pool-seq read assembly approach. For final submissions, figures should be uploaded as separate, high resolution, figure files. The approximate position of A. sturio, for which reliable transcriptomic data were unavailable, was added according to www. timetree. org. The root of Acipenseridae was dated at ~180 Mya, according to  [33]. Red arrows mark those species, for we have obtained female-specific PCR-products, using primers AllWSex2_F/_R.
Acknowledgments This work was funded through  COFASP/ERANET (STURGEoNOMICS)  by the  German Federal Ministry of Food and Agriculture  through the  Federal Office for Agriculture and Food  (grant nos. 2816ERA04G ,  2816ERA05G ) to  M. Stöck , S. W. , J. G. and M. Schartl; by the  French National Research Agency  (grant nos. ANR-16-COFA-0002 ) to YG, CK and CR, and by the  Romanian Executive Agency for Higher Education, Research Development and Innovation Funding (UEFISCDI , contract  3/2017 ) to RS, MC and DH. This research was also in part supported by the  Russian Science Foundation (RSF)  to DP (grant number  18-44-04-007 ), by the  Deutsche Forschungsgemeinschaft to MSch  ( DFG SCHA 408/14-1 ), and by a  European Maritime and Fisheries Fund  to YG (EMFF/FEAMP project SIBERSEX). Research on A.
37 The test started in 1976 but was not conclusive: most of the chemists involved were not willing to abandon the traditional journal for composed abstracts  (Reese, 2002: p. 39 ). The introduction of a new communication regime (as in the case of the early GenBank, an abstract service from journals that housed sequence data that  Hilgartner (1995: p. 251 ) documented), was a missed opportunity. The 1970s were the years when the ACS was the most "endangered". Like other learned societies, it was under attack by the federal authorities. In 1976, the JACS was added to the list of journals that violated the United States Postal Service's rules regarding delivery via second-class mail. Insofar as the articles were paid for, the journal that compiled them was considered to be an advertising product, subject to higher mailing rates.
5 In his 1995 paper, Hilgartner sketches a rough outline of the scope of the journal regime (referenced above as publication regime) through five examples. In the regime of journals, there is a fairly sharp division between published and unpublished material (example 1). Articles that are later deemed to be incorrect remain part of the permanent record (example 2,). Scientists submit articles directly to journals (example 3). At the organizational and inter-organizational levels, the regime of journals has achieved a fairly orderly division of labor and a relatively stable economic structure (example 4). The assembly of information and knowledge from multiple publications is a task performed by readers (example 5, p. 248). The journal regime is mainly defined as the opposite to what it is intended to be replaced by (the new communication regimes based on biomolecular databases)  (Hilgartner, 1995: pp.
Notes 1 The journals and publishers appearing in this table are extracted from a database that I constituted for the needs of my research from a query (subject area = chemistry) in Ulrichsweb database, which has worldwide coverage. There are 2564 titles covering the discipline of chemistry, of which 2277 have been active since 2001. Among these journals, I have chosen a representative sample of about ten publishers to which I have added a few multidisciplinary journals (PLOS, Nature Research, BMC) in which chemists also publish. 2 OpenAPC initiative under the guidance of Bielefeld University. 3 In their quantitative study of the Research Excellence Framework in the UK (data collected during the five last cycles of REF), Paye and Renisio suggested that the rise of the article is a general trend of the considered period.