dataesr/scientific-paragraphs-categorization huggingface dataset:
MATerIAls AnD MeTHODs study design and population We investigated the gut microbiome, faecal, blood and urinary metabolomic profiles in 82 overweight/obese subjects in response to an 8-week isocaloric dietary intervention with an MD or a control diet. Each participant provided written informed consent and received no financial compensation. The trial was registered at ClinicalTrials. gov (number NCT03071718 The study design, selection criteria and participant flow throughout the study are reported in the online supplementary materials (online supplementary figure  1 ). Plasma lipids (including plasma cholesterol and triglycerides) and faecal levels of short-chain fatty acids (SCFAs) were registered as primary outcomes of the study, while changes in gut microbiota and some intermediate markers of metabolic disease, such as blood pressure, fasting blood glucose, serum high sensitivity C reactive protein (hs-CRP), urinary and plasma trimethylamine oxide (TMAO), plasma gastrointestinal peptides and urinary polyphenols, were secondary outcomes (detection methods described in the online supplementary material).
Metagenomics A full description of the sampling, sequencing and data analysis procedures is reported in the online supplementary material. DNA libraries were sequenced using the Ion Proton Sequencer (ThermoFisher Scientific, Waltham, USA), with a minimum of 20 million 150 bp high-quality reads generated per library. Metagenomic species pangenome (MSP)  24  was used to identify and quantify species associated with the 9. 9-million-gene integrated reference catalogue. The functional potentials of the intestinal gut microbiota were determined by using the in-house FAnToMet pipeline as described in the online supplementary material.
Gut microbiota During the run-in period, some subjects (12 in the MedD group and 6 in the ConD group) undesirably increased their intake of fruit and vegetables above three servings/day compared with their consumption at the time of enrolment. We decided to strictly focus on the population who maintained a baseline dietary intake of fruits and vegetables <3 servings/day. In addition, two subjects were not considered because not all the faecal samples were available. Therefore, the subsequent data analyses were carried out with a subgroup of 62 subjects, 32 in the ConD group and 30 in the MedD group. High compliance with the intervention was confirmed in both groups. Changes in dietary intake of nutrients from several food categories are shown in online supplementary figure  3. The effect of MedD on plasma cholesterol was confirmed in this subgroup.
Several GMMs (n=19) were enriched in the MedD group, mainly including pathways related to amino acid and carbohydrate degradation. The pathways also included triglyceride and glycoprotein degradation and conversion of acetyl-CoA and glutamate degradation, both leading to crotonyl-CoA, a possible precursor of butyrate metabolism (online supplementary table  7 ). Although only 6% variation was observed after 8 weeks, enrichment in glutamate degradation to crotonyl-CoA was maintained in the MedD group. This pathway was significantly linked to the levels of F. prausnitzii msp_0388 (Spearman's rho=0. 73, p<10e-6, online supplementary figure  30 ). Altogether, by integrating the three meta-omics datasets,  34  we observed a separation of the ConD and MedD groups on the basis of microbiome diversity, functional modules and metabolomic profiles (Hotelling T 2 =40.
Acknowledgements We would like to thank agria spa, Fiammante icab spa, Olio Dante spa and  Pastificio Di Martino  spa for kindly providing foods to be included in the food boxes for our participants. The authors would also like to thank cecilie Fryland appeldorff, sofie skov Frost and sarah  Fleischer Ben soltane  ( University of copenhagen ) for excellent technical assistance on ultra-high-performance liquid chromatography mass spectrometry (UhPlc-Ms) analyses; sébastien Fromentin,  Magali Berland ,  Kévin Da  silva and  Florence Thirion (MgP Metagenopolis)  for their distinguished bioinformatical guidance; and  Dr Maria  assunta gallo and centro  Diagnostico san ciro (Portici, italy)  for their support with the clinical visits.
data, and Ml, VM, FDF, eP and nP analysed the microbiome data and performed the statistical analyses. all authors participated in the data interpretation; De wrote Data are available in a public, open access repository. Metagenomic reads generated in this study are available (without conditions of reuse) under the accession number PrJeB33500 at the european nucleotide archive (ena) in eBi (https://www. ebi. ac. uk/ ena/ data/ view/ PrJeB33500).
In silico analysis of TcGPXs A GPX cDNA was identified in a library of T. cacao meristem (genotype TSH1188) infected by M. perniciosa  [10]. A search in the CocoaGenDB database  [11]  through local alignment with BLASTn and BLASTp  [33]  using the GPX cDNA  [10]  allowed the identification of five homologous sequences named TcPHGPX, TcGPX2, TcGPX4, TcGPX6 and TcGPX8 according to the nomenclature and numeration of the cocoa genome (Supplementary material 1). The complete sequences of the genes and corresponding proteins were obtained from the CocoaGenDB database. The proteins were analyzed using InterProScan  [34]  and their classification validated by the presence of the GPX domain codes. The MCScanX tool  [35]  was used to identify possible duplications of the TcGPX genes in the cacao genome.
The prediction of theoretical isoelectric point (pI) and molecular weight (MW) was obtained using the Expasy Molecular Biology Server (www. expasy. org). The conserved domain and family protein were analyzed using the Pfam program  [36]. Post-translational events were predicted using the NetPhos 2. 0 Server to identify putative sites of phosphorylation (Ser/Thr/Tyr)  [37]  and NetNGlyc 1. 0 Server  [38]  to identify putative sites of N-glycosylation. Predictions of subcellular localization were conducted with the programs TargetP  [39]  and PSORT  [40]. Signal peptide presence was analyzed using the SignalP 4. 0 Server  [41]. Homologous sequences to TcGPXs were searched using BLAST  [33]  on the National Center for Biotechnology Information (NCBI) and plants and mammals sequences showing the highest homology levels (> 79%) were selected.
Multiple sequence alignment of these sequences was performed with the ClustalW2 software  [42] , and an unrooted phylogenetic tree was built using the neighbour joining method with the ClustalW2, with 1000 bootstraps  [42]  and MEGA 6  [43]  programs. The search for regulatory sequences of the TcGPXs gene was performed in the CocoaGenDB database  [11]. A region of 1500 bp upstream the UTR was identified and selected for cis-element analysis. The presence of the cis-regulatory elements in the promoter regions of the TcGPX genes was analyzed using the plantCARE (sphinx. rug. ac. be:8080/PlantCARE/cgi/index. html) software  [44].
Molecular modeling and docking analysis The prediction of the three-dimensional (3-D) models of the TcGPXs proteins was obtained using the Swiss-Model server and the Automated Protein Homology-modeling, which relies on the high similarity of target-template  [45]. The crystal structure of poplar (Populus trichocarpa) glutathione peroxidase (PtGPX5; Protein Data Bank code: 2p5q) was used as the template to build the 3-D models of TcGPXs, because of its high identity with TcGPXs (>79%), high coverage of protein sequences and high resolution (2. 0 Å). The stereochemical quality of the models was evaluated using the Procheck  [46]  and Anolea programs  [47]. The 3-D model visualization was obtained using the PyMol (The PyMOL Molecular Graphics System, Version 1. 5. 0. 4 Schrödinger, LLC. ) and Discovery Studio 4.
0. The docking analysis between TcGPXs and SeMet was performed using the AutoDockTools 1. 5. 6  [48]. SeMet 2D structure was found in PubChem databases (http://pubchem. ncbi. nlm. nih. gov). The 2D structure of this compound was copied into Similies and saved in PDB format using the Marvin program. The ligand and receiver structures were saved in pqbqt format to be used in docking calculations. AutoDock Vina was used to perform Docking Scoring for the complex formed by the receptor -ligand  [49]. The reports of each calculation were analyzed for the energy (Kcal / Mol) values of affinity for each binder conformation in its respective complex. The Discovery Studio program was used to verify the ideal complex.
Specific primers and amplified regions containing different size, melting temperature, GC content and GC/AT ratio were defined to avoid cross-reaction between genes from cacao GPX family (Supplementary material 2). The expression analysis of TcPHGPx and TcGPx2 was performed using standard settings of the ABI PRISM 7500 and Sequence Detection System (SDS) software, version 1. 6. 3 (Applied Biosystems). The qPCR reaction consisted of 10 ng/μl of cDNA, 1 μM of each primer from reference or targets genes (Supplementary material 2) and 11 μl of Power SYBR Green Master Mix (Applied Biosystems) in a total volume of 22 μl. Cycling conditions were: 50°C for 2 min then 95°C for 10 min, followed by 40 cycles at 95°C for 15 s, 60°C for 1 min and 72°C for 30 s. To verify that each primer pair produced only a single PCR product, a dissociation analysis was carried out from 60°C to 95°C and analyzed with the Dissociation Curve 1.
0 program (Applied Biosystems). The expression analysis of TcGPXs in meristems of cacao plantlets inoculated or not with M. perniciosa, was obtained by RT-qPCR using 3 experimental replicates. The relative expression was obtained using the comparative Ct method (2 -ΔΔCt ) that considered: i) MDH and ACT as endogenous reference genes (average of expression values from both genes); and ii) non-inoculated (control) plants (average of expression values of each TcGPX gene in 5 control samples harvested as described above) as calibrator -for this reason the relative expression value of the control (= non-inoculated plants) is always 1. 0. Statistical analysis was made using the SASM-Agri software  [56]  which tested the experiments as a completely randomized design. t-test and F-test (ANOVA) were applied with a critical value of 0.
1C ). The alignment of TcGPXs sequence using the BLASTP tool revealed high identity with GPXs from other organisms (plant and mammals) and allowed the identification of the conserved region containing a conserved cysteine residue in plants and SeCys is mammals (Supplementary material 3). The full-length amino acid sequences of plants and mammalian of GPXs available in the databases were used to build an unrooted phylogenetic tree (Supplementary material 4). Plant and mammalian GPXs were separated and formed two distinct branches in the tree (Fig. 2 ). The five TcGPXs have close phylogenetic relationship with members of the same classification in other plant species (Fig. 2 ). In silico analysis of the TcGPXs promoter region revealed the presence of several conserved cis-elements characteristic of different plant species (Table.
Acknowledgements The work of AMMA was supported by the  Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB). The work of SPMR was supported by the  Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). KPG and FM received o Productivity grant from the  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq). This research was supported by the  FAPESB  project ( DTE0038/2013 ) coordinated by FM. The authors thank  Francisca Feitosa Jucá  ( UESC/Ceplac ) and  Louise Araújo Sousa (Ceplac)  for technical help in plant inoculation experiments. The authors thank  Raner José Santana Silva  ( UESC ) for advising in modeling, and  Dr. Janisete Gomes da Silva Miller  ( UESC ) for correcting English language. This work was developed in the frame of the  International Consortium in Advanced Biology  (CIBA; https://www.
2013; Weigand and Leese 2018). Thanks to high-throughput sequencing technologies, these methods can now be used to perform Genome-Wide Scans for Selection (GWSS) using single nucleotide polymorphism (SNP) datasets  (Ahrens et al. 2018; Haasl and Payseur 2016; Oleksyk et al. 2010). Although GWSS have identified cohorts of genes associated with past or ongoing selective processes, they are not designed to identify gene coadaptation, resulting from epistatic selection on interacting genes  (Otto and Whitlock 2009). Few studies have examined the impact of epistatic selection models in population samples using DNA polymorphisms. Simulations of two-locus epistatic models with different degrees of recombination (i. e. , 0 < c < 0. 5) in a panmictic population have shown that the efficiency of epistatic selection and its statistical detection are improved if standing genetic variation already exists, rather than if selection operates on de novo mutations  (Takahasi 2009; Takahasi and Tajima 2005).
2012 ), population structure and relatedness among individuals generate nonindependence between individuals and tend to bias upwardly the LD values. This is particularly the case in highly inbred or predominantly selfing species  (Glémin et al. 2006). At a given locus, Mangin and collaborators proposed to weight the observations by multiplying the vector of genotypes by V À 1 2 , where V is the kinship (or relatedness) matrix among individuals. V is built with the V ij covariance for all pairs (i,j) of individuals. V ij is the average number of identical genotypes between individuals i and j over all SNPs, in a genomewide SNP dataset. This measure of Identity In State is a good proxy of Identity By Descent as SNP markers are likely to be accurately modeled by an infinite site mutation model.
Simulation and LD-based detection of epistatic selection in structured population Simulations of neutral evolution at two independent biallelic loci were carried out in order to evaluate the distribution of T r , T corPC1 , T r v , and T corPC1 v statistics under the null hypothesis and their fit to a Student distribution τ (n-2). In addition, two-locus epistatic selection was simulated in the same framework to evaluate the statistical power (1-β) of these measures to detect two-locus epistatic selection given a type I error (α) for the null hypothesis. Details of our simulation procedure are provided in the Supplementary Method File 1, along with the python code used to run the simulations. Briefly, genome-wide (four chromosomes) SNP data (~15,000 SNPs per chromosome) in a twopopulation split model with 250 diploid individuals per population during 300 generations (the ancestral population before the split was generated by coalescent simulations) were replicated 1000 times for all combinations of the following parameter settings: (i) selection regimes as neutrality, coadapted (COAD) and compensatory (COMP) twolocus epistatic selection, or additive (ADD) two-locus selection (all selection models starting 100 generations after the split time), (ii) random or self-mating (95% selfing rate) since the initial generation, and (iii) complete recessivity, codominance or dominance of the mutations under selection.
GWESS with SNP data in M. truncatula and human GWESS was performed in M. truncatula using a raw dataset of 22,079,533 SNP markers identified on the eight chromosomes of the species by the Medicago HapMap Project on a collection of 262 accessions (see http://www. located in or near SLC24A5 and EDAR genes (chromosome 15 and 2, respectively), against each of the remaining SNPs of the genome. Functional genetic validation of the relationship between MtCLE02 and MtSUNN in M. truncatula The M. truncatula sunn mutant, the MtCLE02 cloning strategy for overexpression, the root transformation protocol, and the conditions for phenotyping the nodulation are described in the Supplementary Method File 2.
Detection of two-locus coadaptation in the M. truncatula plant To illustrate the statistical testing of the correlation coefficient between two loci using T corPCI or T corPC1 v , a onedimension GWESS was performed using a bait approach with the MtSUNN gene, which is a key regulator of nodulation in legumes, against the 48,339 other genes of the M. truncatula genome. Two scans were implemented, including SNP data from either the whole M. truncatula collection-n = 262 individuals-or from the FW subpopulation-n = 80 individuals-(Fig. 3a-d ; respectively). A clear inflation towards small p values could be observed for scans based on T corPCI (Fig. 3a, b ) compared with scans based on T corPC1 v (Fig. 3c, d ), and this inflation was higher with data from the whole collection that showed a higher degree of population structure.
However, the LD measured with T r v was still highly significant between SLC24A5 and EDAR, indicating that epistatic selection may have occurred between both genes at the level of geographic sub-regions. In order to localize the geographic origin of such selection signature, GWESSs were performed within six geographic regions of the world-wide sample: Central South Asia, East Asia, Sub-Saharan Africa, Middle East, Europe, and America (Supplementary Figs. S5-S10 ). Only the GWESS performed in Central South Asia indicated a significant LD between SNPs at the SLC24A5 and EDAR genes (Supplementary Fig. S5C , T r v -based p value = 6. 7 × 10 -6 at SNP 2_108973688; Supplementary Fig. S5D , T r v -based p value = 2. 8 × 10 -6 at SNP 15_46174380). Human population samples from the HGDP-CEPH dataset in Central South Asia are composed of eight different ethnic groups from Pakistan.
A natural extension of the one-dimension use of T r v -or T corPC1 v -based tests is the implementation of two-dimensional GWESS in which the correlation of each polymorphic locus (SNP, gene or genomic region) in the genome would be tested against all remaining polymorphic loci, thanks to parallel computations on bioinformatics platforms. We anticipate that such an approach will open the way towards exploring evolutionary coadapted gene networks. ftp://ftp. cephb. fr/hgdp_supp1 (http://www. cephb. fr/hgdp/). R scripts to implement the statistical test based on T r , T r v , T corPC1 , or T corPC1 v , along with an example dataset, are available at https://github. com/leaboyrie/LD_corpc1.
Acknowledgements This work was supported by the " DeCoD " project funded by the  French Agence Nationale de la Recherche  (grant number  ANR-16-CE20-0017-01 ). The PhD position of LB was funded by the  "DeCoD" project. We thank the bioinformatics platform Toulouse Midi-Pyrenees (Genotoul). This work was performed in the LRSV (Toulouse, France), part of the  "Laboratoire d'Excellence" (LABEX)  entitled  TULIP  (grant number  ANR-10-LABX-41 ). We thank  Carole Laffont  ( IPS2 ,  CNRS, Gif-sur-Yvette, France ) for providing results about MtCLE13 expression. Work in the  Florian Frugier laboratory  has benefited from a  French State grant  (Saclay Plant Sciences, grant number  ANR-17-EUR-0007 ,  EUR SPS-GSR)  and an  ANR grant  (" PSYCHE ", grant number  ANR-16-CE20-0009-01 ). We thank  Thomas Bataillon , two other anonymous reviewers, and  Pierre-Marc Delaux  for useful criticisms and comments to improve the manuscript.
2007) , where each missing base was imputed with the accession that shares the longest haplotype surrounding the base, on a window of 30 SNPs maximum (Bonhomme et al. 2014). For the calculation of T corPC1 v , the kinship matrix V of the 262 individuals was estimated based on 7,252,792 SNPs with a 5% Minor Allele Frequency (MAF). In human, GWESS was performed by using the dataset of 644,257 SNPs (431,951 SNPs with a 5% MAF) with no missing data from the HGDP-CEPH Human Genome Diversity Panel on a world-wide sample (America, Asia, Europe, Middle East, North Africa, Sub-Saharan Africa and Oceania) of 940 individuals belonging to 57 populations from 23 countries (Cann et al. 2002; Li et al. 2008 ). The genome version (i. e. , the gene positions) B36 was used for this analysis in order to fit with SNP positions in the HGDP-CEPH dataset, similarly to (Daub et al.
GRANTS For financial support of their projects on metabolic regulation and creatine kinase, the authors thank the French National Research Agency (Investissements d'Avenir program, ANR-15-IDEX-02) and the federal research structure (SFR) BEeSy at the University Grenoble Alpes. U. S. thanks the Institut Universitaire de France (IUF) for personal support. We thank Dr Shingo Kajimura, UCSF Diabetes Center, San Francisco, CA, for discussion. This shuttle is supported by specifically associated mitochondrial CK (black square) and cytosolic CK (gray squares) isoforms. At the mitochondrial site, CK functionally interacts with adenine nucleotide translocase and voltage-gated anion channel (small white circles) to exchange matrix ATP against ADP and cytosolic creatine (Cr) against PCr, respectively (14, 27).
Mapping, genotyping, and SEX-DETector analysis The SEX-DETector analysis requires mapping the reads of the individuals to a reference transcriptome and performing SNP-calling to genotype all individuals for all expressed genes. Ideally, the reference transcriptome is from a female individual so that the X and Y reads map to the same transcript and XY SNPs can be identified by SEX-DETector  (Muyle et al. 2016). We extracted the 30,074 transcripts from the annotation of the 2011 complete genome from a Purple Kush female individual  (van Bakel et al. 2011). The initial mapping analyses were done using BWA, allowing for five mismatches per read (version 0. 7. 15-r1140, bwa aln -n 5 and bwa samse) (see  Li and Durbin 2010). For comparison, an alternative mapping was performed with Bowtie 2 (version 2.
Circular representations of location of sex-linked genes in the C. sativa genome To map the sex-linked genes to the C. sativa genome, we used BLAST  (Altschul et al. 1990 ) to find the best hit of each C. sativa transcript in the  van Bakel et al. (2011)  transcriptome on one of the recent reference genomes (blastn -max_target_seqs 1 -max_hsps 1). For this mapping, we used the C. sativa reference genome with the best assembly statistics (size = 875 Mb, 10 pseudomolecules, 220 scaffolds, N50 = 91 Mb) (see https://www. ncbi. nlm. nih. gov/genome/genomes/11681 and  Grassa et al. 2018) , which was, however, unannotated. We then used Circos (version 0. 69-6)  (Krzywinski et al. 2009)  for visualizing the location of sex-linked genes. We split each chromosome in windows of 2 Mb using BEDTools makewindows (version v2.
Acknowledgments We thank the  BGI  for free sequencing, thanks to their call for RNAseq for medicinal plants. We thank  Aline Muyle  for advice with SEX-DETector and discussions. We thank  Dr. Tatyana Sukhorada , P. P. Lukyanenko Krasnodar Research and Development Institute of Agriculture  for providing seeds of the C. sativa cultivar "Zenitsa. "We thank three anonymous referees and the editor for their useful comments that helped improve this manuscript. This work was performed using the computing facilities of the  CC LBBE/ PRABI ; we thank  Bruno Spataro  and  Stéphane Delmotte  for cluster maintenance. This project was supported through  Agence Nationale de la Recherche (ANR)  grant  ANR-14-CE19-0021-01  to G. A. B. M. Author contributions: Conceptualization of the study: G. A. B. M. and G.
Immunocytochemistry APs were seeded on glass coverslips and treated as described in the text. Cells were rinsed with PBS and fixed with Roti-Histofix (Roth, Lauterbourg, France) for 20 min at room temperature. Fixed-cells were incubated in PBS with 3% goat serum, 0. 1% tween-20, and 0. 1% triton X-100 for 30 min at room temperature. Cells were incubated with the appropriate antibodies in the same buffer for 90 min at room temperature. After three washes in PBS, coverslips were incubated with the appropriate secondary antibody coupled to AlexaFluor (1:600) for 45 min at room temperature. Cells were mounted in mowiol. Images were taken on an Axio Observer microscope (Carl Zeiss, Le Pecq, France) with an EC Plan Neofluar 40X (NA 1. 3) oil objective using AxioVision 4. 8. 2 software.