dataesr/scientific-paragraphs-categorization huggingface dataset:
Structure solution and refinement The structure of VdPelB was solved by molecular replacement using Phaser  [42]. The data were phased using pectate lyase BsPelA (PDB: 3VMV, Uniprot D0VP31), as a search model. Model was build using Autobuild and refined using Refine from PHENIX suite  [44]. The model was iteratively improved with Coot  [45]  and Refine. The final structure for VdPelB has been deposited in the Protein Data Bank (PDB) as entry 7BBV.
Digestions were performed overnight. Non-digested pectins were pelleted by centrifugation and the supernatant dried in a speed vacuum concentrator (Concentrator plus, Eppendorf, Hamburg, Germany). Separation of OGs was done as previously described using an ACQUITY UPLC Protein BEH SEC column (125 Å, 1. 7 μm, 4. 6 mm × 300 mm) at a flow rate of 0. 4 mL min -1. MS detection was performed using an ACQUITY UPLC H-Class system coupled to a SYNAPT G2-Si-Q-TOF hybrid quadrupole time-of-flight instrument (Waters) equipped with an electrospray ionization (ESI) source (Z-spray) and an additional sprayer for the reference compound (lock spray). Samples were analysed by ESI-high-resolution MS (HRMS) and MS/MS in negative ionization mode. Data acquisition and processing were performed with MASSLYNX software (v.
Simulations were replicated 7 times for a total production run time of 1. 05 μs per complex. Replicates differed with respect to the random particle velocity sets computed under the NVT ensemble. For analysis, the first 50 ns of each production run were discarded as equilibration time. In-house Python 3 scripts implemented using Jupyter notebooks  [53]  were used to carry out analyses. Figures were created and rendered with Matplotlib  [54]  and VMD (Visual Molecular Dynamics)  [55].
VdPelB has a right-handed parallel β-helix fold Pectate lyase VdPelB was crystallized and its 3D structure was determined using X-ray diffraction. VdPelB crystallized in monoclinic P 1 2 1 1 asymmetric unit. Four data sets, collected from the same crystal at 1. 2 Å resolution, were integrated, scaled and merged. There are two - cillium [VDAG_00740 (G2WQU8), VDAG_02904 (G2WXC5), VDAG_05344 (G2X628), VDAG_07242 (G2XBA4), VDAG_07759 (G2XC77), VDAG_02709 (G2WWT0), VDAG_02843 (G2WX64), VDAG_02886 (G2WXA7), VDAG_03656 (G2X1P5), VDAG_05402 (G2X597), VDAG_07144 (G2X9U9), VDAG_07238 (G2XBA0), VDAG_07566 (G2XBY8), VDAG_08067 (G2XD35), VDAG_08154 (G2XDC2), VDAG_08734 (G2XF02), VDAG_10475 (G2XJZ3), VDAG_03354 (G2WZB2), VDAG_03551 (G2WZV9), VDAG_07267 (G2XBC9), VDAG_07768 (G2XC86), VDAG_08236 (G2XDK4), VDAG_06155 (G2X8L4), VDAG_06523 (G2X7R5), VDAG_08685 (G2XEV0), VDAG_09523 (G2XH91), VDAG_09536 (G2XHA4), VDAG_00063 (G2WR80), VDAG_07350 (G2XGG7)], Arabi- dopsis thaliana [AtPLL15 (At5g63180), AtPLL18 (At3g27400), AtPLL21 (At5g48900)], Dickeya dadanti [DdPelA (P0C1A2), DdPelC (P11073), DdPelE (P04960), DdPelI (O50325)], Bacillus subtilis [BsPel (P39116)], Bacillus Sp.
While no N-glycosylation sites could be revealed on the VdPelB structure, six O-glycosylation sites carrying mannose are visible for each molecule: T22, T44, T45, T46, S48 and T54, in accordance with the shift in size previously observed (Fig. S2A ). During data acquisition no heating of the crystal was observed, as shown by low B factors and good occupancies (Fig. S3A  and B ). The final models' geometry, processing and refinement statistics are summarized (Table  1 ). The VdPelB's structure has been deposited in the Protein Data Bank as entry 7BBV. The VdPelB has a right-handed parallel β-helix fold which is common in pectinases  [59]. The β-helix is formed by three parallel β-sheets -PB1, PB2 and PB3 which contain 7, 10 and 8 β-strands, respectively. Turns connecting the PB1-PB2, PB2-PB3 and PB3-PB1 β-sheets are named T1turns, T2-turns and T3-turns, respectively, according to Yoder and Jurnak (Fig.
2A , Fig. S4A  and B )  [60]. T1-turns consist of 2-14 amino acids and builds the loop around the active site on the C-terminus. T2 turns mostly consist of 2 amino acids with Asn being one of the predominant amino acid, forming an N-ladder with the exception of an N245T mutation in VdPelB  [15, 20]. Pectate lyase VdPelB has a α-helix on N-terminus end that shields the hydrophobic core and is commonly conserved in PLs and PGs  [15, 61] , while the C-terminus end is also protected by tail-like structure carrying one α-helix. Interestingly N-and C-terminus tails pack against PB2 (Fig. 2A ). There are only two Cys (C25 and C137) that do not form a disulphide bridge. Sequence and structural alignments show that VdPelB belong to the PL1 family. The VdPelB shares the highest structural similarity with BsPelA (PDB: 3VMV), with 30.
06 % sequence identity and Cα rmsd of 1. 202 Å. The second-best structural alignment was with DdPelC (PDB: 1AIR) with 24. 20 % identity and Cα rmsd of 1. 453 Å  [43, 62]. Both of these structures lack the long T3 loop described in A. niger pectate lyase (AnPelA, PDB: 1IDJ, Figs. S2B  and S5 )  [15]. The putative active site is positioned between the T3 and T2 loops (Fig. 2A  and B ).
" Samples in this panel were selected based on field maps and plant labels to have a representation of the assumed genetic diversity of the INERA Coffee Collection in Yangambi. The Discovery Panel was additionally used to selected a minimal set of loci that could discriminate all the unique genetic fingerprints in the Discovery panel to design a HiPlex screening assay. Validation of the HiPlex screening assay was performed on a subset of 105 samples of the Discovery panel, namely the "Validation Panel. " Because validation of genotype calls per sequencing technique requires good quality data of both, the selection of samples for the Validation Panel was based on data completeness for both GBS and HiPlex data. Only samples with GBS data for >80% of the 86 highquality HiPlex loci were retained in this panel.
(2023)  Overview of the data analysis workflow. Step I, primary screen: a set of diverse genotypes ("Discovery Panel," n = 218) was compiled based on the field maps and plant labels and genotyped using genome-wide molecular markers (Genotyping-by-Sequencing) to identify unique genetic fingerprints. Step II, HiPlex amplicon design: a high-throughput screening assay based on multiplex amplicon sequencing (HiPlex) was created with sufficient genetic resolution to discriminate the unique genetic fingerprints. Step III, validation of the HiPlex assay: 105 samples with high locus completeness for both GBS and HiPlex data ("Validation Panel") were compared on the level of high-quality loci, SNPs and haplotypes, Jaccard Inversed Distances (JID) and unique genetic fingerprints. Step IV, genetic composition of the Yangambi coffee collection: the HiPlex assay was then used to comprehensively screen the Yangambi coffee collection ("Screening Panel," n = 730) and to identify all unique genetic fingerprints.
6x MagNA magnetic beads (GE Healthcare Europe, Machelen, BE) and eluted in 30 μL TE. Of the purified DNA eluate, 3 μL was used for amplification with Taq 2x Master Mix (NEB) using an 18 cycles PCR protocol. PCR products were bead-purified with 1. 6x MagNA, and their DNA concentrations were quantified using a Quantus Fluorometer. The library quality and fragment size distributions were assessed using a QIAxcel system (Qiagen, Venlo, NL). Finally, equimolar amounts of the GBS libraries were pooled, bead-purified, and 150 bp paired-end sequenced on an Illumina HiSeq-X instrument by Admera Health (South Plainfield, United States). Reads were processed with a customized script available on Gitlab. 1  First, the quality of sequence data was validated with FastQC v0. 11  (Andrews, 2010)  and reads were demultiplexed using Cutadapt v2.
Haplotype calling Per GBS or HiPlex locus, haplotypes were called using the SMAP haplotype-sites module within the SMAP package v4. 4. 0. Read-backed haplotyping was conducted based on the combined variation in SMAPs and SNPs in the GBS read data or based on SNPs in the HiPlex read data using the SMAP haplotype-sites module with mapping_ orientation ignore, partial exclude, no_indels, min_read_count 10, min_distinct_haplotypes 2, min_haplotype_frequency 5, discrete_calls dosage, frequency_interval_bounds 10 10 90 90, and dosage_filter 2.
Genetic similarity The genetic similarity between samples within the Discovery (n = 218), Validation (n = 105), Screening (n = 730), and Canephora Panel (n = 514) was quantified with the SMAP grm module within the SMAP package v4. 4. 0, using the Jaccard Inversed Distance  (Jaccard, 1912)  that was calculated based on the discrete dosage haplotype calls in polymorphic GBS or 86 high-quality HiPlex loci. SMAP grm was run with locus_completeness 0. 1, similarity_coefficient Jaccard, distance_method Euclidean, locus_information_content Shared, and 2 https://gitlab. ilvo. be/genomics/smap FIGURE 1 (Continued) genetic distance method (CC-X) were tested for the Yangambi coffee collection to propose complementary core collections. Step V, origin detection in the Yangambi coffee collection: in addition to the representatives of the unique genetic fingerprints in the Yangambi coffee collection, reference material for the rainforest in the Yangambi region and Luki coffee collection were genotyped using the HiPlex assay and reference material for Congolese subgroup A was genotyped using WGS ("Canephora Panel," n = 514).
Our GBS library preparation, which included a size selection step, displayed a strong bias toward short fragments (mostly <100 bp). Out of thousands of GBS loci that were used for genome-wide fingerprinting, only 483 loci had a length of 100-140 bp and two SMAPs and could be used for HiPlex amplicon design (target amplicon size range: 95-115 bp). To check for discriminative power across the 218 samples of the Discovery Panel, haplotypes were called for the loci with two SMAPs and length 100-140 bp and pairwise JID were calculated using the SMAP grm module. Next, HiPlex primer design was performed by running Primer3 v2. 4. 0  (Untergasser et al. , 2012)  implemented in the SMAP snp-seq utility tool on the 483 selected loci with parameter settings -d 300 -t 50 -u 20 -min 95 -max 115 -max_mis 12 -ex 10, taking all known GBS SNP positions into account.
Establishment of a core collection Core Hunter 3 v3. 2. 0 R package  (De Beukelaer et al. , 2018)  was used to test two core collection strategies for the 263 unique genetic fingerprints within the Yangambi coffee collection (Figure  1,  Step IV): the M strategy (hereafter referred to as CC-I), which focuses on selecting the most diverse loci to maximize the genetic diversity and; the genetic distance method (hereafter referred to as CC-X), which aims to select the most diverse plant material within a collection to maximize the genetic distance between the entries of the core collection. For both core types allele coverage (CV), diversity within and between alleles [He and Shannon's index (SH)], and average genetic Modified Roger's (MR) distance between entry-accession (AN) and entry-to-nearest-entry (EN) were calculated for nine different core sizes  (3, 5, 10, 25, 50, 100, 150, 200, and 263 accessions).
Discovery of the genetic diversity in the Yangambi coffee collection Based on available documentation (field maps and plant labels), a set of 218 samples (Discovery Panel) was selected from the INERA Coffee Collection in Yangambi and subjected to GBS (Figure  1 , Step I), yielding 7,627 high-quality GBS loci with read depth > 8 in more than 90% of the samples. These GBS loci had two types of polymorphic sites, namely 18,225 read mapping polymorphisms (SMAPs) identified by the SMAP delineate module and 11,488 SNPs called with GATK (referred to as GBS SNPs; Figure  2 ). The polymorphic sites (SNPs and SMAPs) were converted into 10,257 haplotypes using the SMAP haplotype-sites module (referred to as GBS haplotypes), yielding a genome-wide marker set of 3,177 polymorphic high-quality GBS loci.
Acknowledgments We would like to thank the  Institut National pour l'Étude et la Recherche Agronomiques (INERA)  for giving access to their collection;  Rachel Ndezu  and  CIFOR  (through the  FORETS  project, funded by the  EU 11th Development Fund)  for the logistic and administrative support during fieldwork in the Democratic Republic of the Congo. We would also like to express our sincere gratitude to the  Ministère de L'Environnement et Développement Durable (MEDD)  for their help with obtaining permits ( N°008/ANCCB-RDC/ SG-EDD/BTB/11/2020 ,  N°004/ANCCB-RDC/SG-EDD/BTB/2021 ,  N°014/ANCCB-RDC/SG-EDD/BTB/11/2021 , and  N°025/ ANCCB-RDC/SG-EDD/BTB/11/2022). 10. 3389/ fsufs. 2023. 1239442   Frontiers in Sustainable Food Systems   16  frontiersin. org.
Statistical Analysis The number of independent experiments, replicates and precision measures are reported in the Figure legends (n, mean ± SEM). Statistical analysis was performed using Prism 8. 2. 1 software (Graph Pad Prism Software). Unpaired t-test was used for comparing two different groups; one-way analysis of variance (one-way ANOVA) was used to analyze differences between more than two different group (i. e count of the mean of nuclei), while two-way analysis of variance (two-way ANOVA) was used for comparing different groups to examine the in uence of different independent variables on dependent variables (i. e Fusion index or Pax7 and Myod quanti cation). When data met the assumptions of the tests (e. g. , normal distribution) and the ANOVA was signi cant, post hoc testing of differences between groups were performed using Tukey's honestly signi cant difference (HSD).
ACKNOWLEDGMENT: We thank the  Biobank of Cells, Tissues  and DNA from patients with neuromuscular diseases, member of the  Telethon Network of Genetic Biobanks  (project no. GTB12001 ), funded by  Telethon Italy , and of the  EuroBioBank network , for providing us human myoblasts from skeletal muscle samples of DMD patients. This work contributes to the COST Action CA17116 International Network for Translating Research on Perinatal Derivatives into  Therapeutic Approaches  (SPRINT), supported by  COST (European Cooperation in Science and Technology).
7 kV (positive mode) or 2. 7 kV (negative mode), capillary temperature at 320 • C, a sheath gas rate at 60 units N 2 (ca. 200 mL/min), and an auxiliary gas rate at 15 units N 2 (ca. 50 mL/min). The m/z range for data-dependent acquisition was set between 100 and 1200 amu. The data were analyzed using Thermo Xcalibur software. Circular dichroism spectra were measured on a JASCO-J-810 polarimeter (JASCO Corporation, Tokyo, Japan). Optical rotations were recorded on an Anton Paar MCP 150 polarimeter (Anton Paar, Graz, Austria).
Fungal Material and Fermentation Stachybotrys chartarum MUT 3308 was isolated from the marine sponge Aplysina cavernicola sampled in the Mediterranean Sea at Villefranche-sur-Mer, France (Lat: 43 • 41 31. 48707839999 N, Lon: 7 • 19 12. 185658623999 E)  [31]. The fungus was isolated by direct plating of the sponge tissues on Corn Meal Agar Seawater (CMAS; corn meal 2 g, agar 15 g, sea salts mix 30 g, gentamicin sulfate 40 mg, piperacillin and tazobactam 11 mg, Sigma-Aldrich (Merck KGaA, Saint-Louis, MO, USA) up to 1 L DI H 2 O) after incubation at 15 • C. The fungus was identified based on its morphological features and by molecular analyses with the amplification of the Internal Transcribed Spacer-ITS. The sequence was deposited in GenBank (accession number MG980591), while the fungus was preserved at the Mycotheca Universitatis Taurinensis (MUT-http://www.
Feature-Based Molecular Networking Analysis The data were processed by using the FBMN method  [44]. The data files were converted from the raw data format to mzXML format using MSConvert software (Prote-oWizard package 3. 0). All mzxml values were processed using MZmine 2. 53  [45]. Mass detection was realized with an MS 1 noise level of 5 × 10 6 and an MS 2 noise level of 5 × 10 3. The ADAP chromatogram builder was employed with a minimum group size of scans of 5, a group intensity threshold of 5 × 10 6 , a minimum highest intensity of 1. 7 × 10 7 , and m/z tolerance of 0. 0 (or 10 ppm). Deconvolution was performed with the Baseline cut-off algorithm according to the following settings: minimum peak height of 2. 7 × 10 7 , peak duration range of 0. 1-2 min, baseline level of 3 × 10 6 , and an auto m/z center calculation.
MS/MS scans were paired using a m/z tolerance range of 0. 02 Da and RT tolerance range of 0. 1 min. Isotopologs were grouped using the isotopic peak grouper algorithm with a m/z tolerance of 0. 0 (or 10 ppm) and a RT tolerance of 0. 2 min. Peaks were filtered using a feature list row filter, keeping only peaks with MS/MS scans (GNPS). Peak alignment was performed using the join aligner with a m/z tolerance of 0. 0 (or 10 ppm), a weight for m/z at 75%, a RT tolerance of 0. 2 min and weight for RT at 25%. The MGF file and the metadata were generated using the export/submit to GNPS option  [51]. The molecular network was calculated and visualized using Cytoscape software  [52]. The parent mass tolerance was 0. 02 Da and the MS/MS fragment ion tolerance was 0. 02 Da. The edges were filtered to have a cosine score above 0.
Contributions: M. D. (Marie Dayras) and E. S. purified the compounds and contributed to spectroscopic analyses data collection and interpretation; M. D. (Marie Dayras) contributed to cytotoxicity activity assay data collection and manuscript writing; E. B. cultured the fungus and contributed to manuscript writing; O. R. and M. D. (Maeva Dufies) contributed to cytotoxicity activity assay data collection; F. F. -V. contributed to computational analysis; E. T. -d. -G. and T. L. contributed to manuscript review and editing; G. P. and G. C. V. contributed to manuscript writing, review, and editing; M. M. contributed to spectroscopic analyses data interpretation and manuscript writing, review, and editing. All authors have read and agreed to the published version of the manuscript. Funding: This work has been supported by the French government, through the UCAJEDI Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-15-IDEX-01 and the FINNOVER project (Strategie Innovative per lo Sviluppo di Filiere Verdi Transfrontaliere)-Interreg Alcotra Italy-France European cross-border program 2014-2020, grant number 1198.
We thank the Canceropôle Provence-Alpes-Côte d'Azur, and the Provence-Alpes-Côte d'Azur Region for the financial support provided to the MetaboCell and MetaboPure projects. This publication is based upon work from COST Action CA18238 (Ocean4Biotech) supported by the COST (European Cooperation in Science and Technology) program. E. S. and M. D. (Marie Dayras) are recipients of thesis grants from the "Conseil Regional Provence-Alpes-Côte d'Azur". Institutional Review Board Statement: Not applicable.
Author Contributions: M. D. (Marie Dayras) and E. S. purified the compounds and contributed to spectroscopic analyses data collection and interpretation; M. D. (Marie Dayras) contributed to cytotoxicity activity assay data collection and manuscript writing; E. B. cultured the fungus and contributed to manuscript writing; O. R. and M. D. (Maeva Dufies) contributed to cytotoxicity activity assay data collection; F. F. -V. contributed to computational analysis; E. T. -d. -G. and T. L. contributed to manuscript review and editing; G. P. and G. C. V. contributed to manuscript writing, review, and editing; M. M. contributed to spectroscopic analyses data interpretation and manuscript writing, review, and editing. All authors have read and agreed to the published version of the manuscript. Funding: This work has been supported by the French government, through the UCAJEDI Investments in the Future project managed by the National Research Agency (ANR) with the reference number ANR-15-IDEX-01 and the FINNOVER project (Strategie Innovative per lo Sviluppo di Filiere Verdi Transfrontaliere)-Interreg Alcotra Italy-France European cross-border program 2014-2020, grant number 1198.
Results For isotropic behaviour of the homogeneous equivalent medium, a random distribution of grain orientations is needed ('isotropic texture'), composed of a large number of grains. For this purpose, 6000 randomly oriented grain orientations were generated by the ATEX software  [Beausir and Fundenberger, 2017]  for face-centered cubic (f. c. c. ), body-centered cubic (b. c. c. ), and hexagonal close-packed (h. c. p. ) cases. The grain shapes were taken spherical. As the plastic power and strain rate are non-incremental quantities, one-step simulations with zero time increment were carried out to obtain λ as a function of α. For the f. c. c. crystals, the 12 {111}<110> slip systems were used with equal reference shear stresses. In the b. c. c. case, the 12 {110}<111> and {112}<111> slip systems were employed with equal resistance to slip.
Acknowledgements L. S. T. : This research was partially conducted at the  University of Miskolc  as part of the " Developments aimed at increasing social benefits deriving from more efficient exploitation and utilization of domestic subsurface natural resources " project supported by the  Ministry of Innovation and Technology  from the  National Research, Development and Innovation Fund  according to the Grant Contract issued by the  National Research, Development and Innovation Office  (Grant Contract reg. nr. :  TKP-17-1/PALY-2020 ). S. K. S. and A. M. : This work was also supported by the  French State  through the program "Investment in the future" operated by the  National Research Agency (ANR)  and referenced by  ANR-11-LABX-0008-01  ( LabEx DAMAS ).
Acknowledgments The authors thank  Marjorie Cantener  for her assistance in proofreading the English language. They also thank  PICT-URCA platform  ( University of Reims Champagne-Ardenne ) for imaging core facilities. They also thank the  Plateforme Regionale de Biologie Innovante (PRBI)  ( Centre Hospitalier Universitaire, Reims, France ) for performing the DNA quantification assays.
Data collection Collection of routinely captured clinical and laboratory data was organized by the three endTB consortium partners and standardized across all sites. 11 Data were entered into a common Electronic Medical Record (EMR) system. 12, 13 gimen design and definitions Longer (18-21 months) individualized treatment regimens were constructed by the local treating physician according to NTP guidelines and WHO 2016 Guidelines,  14  and informed by the endTB clinical guide. 15 We defined treatment as consistent with 2022 WHO guidance  5  if the baseline regimen was all-oral and contained at least four likely effective drugs, and if it never included an injectable agent (i. e. , aminoglycosides, capreomycin, carbapenems). A drug was deemed likely effective based on existence of at least one of the following: confirmed susceptibility of the strain infecting the individual patient and/or no previous use of the medicine for.
Statistical analyses We report the number and frequency of end-oftreatment outcomes across groups defined by the baseline FQ resistance and number of WHO Group A, B and C drugs in the initial baseline regimen. We also report the distribution (median, 25 th and 75 th percentiles) of other key regimen characteristics, including the duration of the baseline regimen, the duration of each Group A drug included in the baseline regimen, and the number of drugs in the regimen likely and not likely to be effective. Analyses were conducted using SAS v9. 4 (SAS Institute, Cary, NC, USA) and RStudio, PBC v1. 4. 1106 (R Computing, Vienna, Austria).
5 hen large longitudinal datasets are available, application of the target trial framework, along with statistical methods (e. g. , inverse probability weighting, g-formula) that enable study of time-varying treatments, can address many of these challenges,  21, 23  and may facilitate the generation of evidence to inform treatment guidance with a higher degree of certainty. Table  4  Characteristics of all-oral regimens conforming to 2020 WHO guidance for rifampin-resistant or multidrug-resistant TB, stratified by number of Group A, B and C drugs in the baseline regimen and FQ resistance (n ¼ 572)* A).