dataesr/scientific-paragraphs-categorization huggingface dataset:
brassicicola interaction at this early stage of the plant life cycle. Plants 2022, 11, x FOR PEER REVIEW yses. Contrariwise to the higher susceptibility phenotype of the coi1 in A. brassici fected rosette leaves  [27] , the coi1 and jar1 mutant exhibited a total resistance to A sicicola infection at the very early post-germinative stage (Figure  5 ). Interestingly at 3 DAS, a high enrichment index in the DEGs assigned to the c response to hypoxia was observed. The contribution of this pathway in plant pa interaction is increasingly documented  [59] [60] [61] [62]. Hypoxia or pathogen respon through ERF-VII (ethylene response factor VII) and WRKYs (WRKY transcription f involved in oxygen sensing and signaling. Nearly three quarters of these genes des to be related to both hypoxia and pathogen response in Arabidopsis  [61]  was fou regulated in our RNA-seq dataset and particularly in germinating seeds (Supplem Table  S1 ).
To minimize observation bias, the notation of each condition was validated when the same score was determined by three different observers. The data were subjected to statistical analyses. For each condition, seeds and seed-lings were scored according to their growth and infestation stage. Data were converted into three sets of binomial data: germination (0 for non-germinated seeds, 1 for germinated seeds), fungal colonization (0 for seeds/plantlets devoid of fungus, 1 for seed plantlets with fungal mycelium) and fungal necrosis (0 when absent, 1 when present). Each set of binomial data were fitted in logistic models. 95% confidence intervals was then calculated for each log odds ratio. Log odds ratios were then converted into probabilities. The confidence interval was not calculated when obtained probabilities were 0 or 1.
RNA Sequencing Bioinformatic Analyses After quality control  [78, 79] , plant high-quality reads were mapped on reference genome/transcriptome of Arabidopsis Araport 11  [80, 81]  using quasi-mapping alignment of SALMON, version 0. 14. 1  [82]. Differentially expressed genes (DEGs) between healthy and infected seeds were determined using DESeq2 algorithms  [83]. Genes with log2FC > 1 or < -1 and Benjamini-Hochberg adjusted p-values < 0. 05 were considered as differentially expressed. Gene Ontology Analysis using GO enrichment terms was performed with Cluster-profiler 4. 0 package  [42]  in RStudio version 4. 2. 0. To detect significantly enriched GO terms related to different biological processes, an adjusted p-value cut-off of <0. 05 after Benjamini-Hochberg multiple testing procedure was applied.
Acknowledgments: We would like to thank  Helen North ,  Francoise Corbineau ,  Celine Masclaux  and  Barbara Anne Halkier  for providing defective mutants in mucilage, E. T. , autophagy and G. S. L. respectively. Thanks to  Adriana Tofiño ,  Aida Vasco , and  Luz Marina Melgarejo  for productive discussion about this project; to  Chrystian Camilo Sosa  for his advice during the bio-informatic analyses and the  FUNGISEM team  for their support. This research was conducted in the framework of the  GERMRESIST  project funded by the  regional programme "Objectif Végétal, Research, Education and Innovation in Pays de la Loire ", supported by the  French Region Pays de la Loire ,  Angers Loire Métropole  and the  European Regional Development Fund.
Acknowledgments: This work was supported by the  FCT-Foundation for Science and Technology , I. P. , within the scope of the project Refª  UIDB/00681/2020. Furthermore, we would like to thank the  CERNAS Research Centre  and the  Polytechnic Institute of Viseu , for their support. Thanks also to PDR2020 Program through project  ValorCast  ( PDR2020-101-032035 ). Finally, the authors thank the students from the  Course on Food Engineering at Agrarian School of Viseu , for the involvement in this work, in the ambit the classes of the curricular unit IDAPA (academic year  2021/2022 ).
8-11. 7 ka ago)  (Stojak et al. , 2016). Recently, an ancient DNA investigation of the common vole remains from the Western Carpathians has shown the presence of the Eastern lineage from the early Holocene onwards. However, it also showed that from at least 18 ka ago the Central lineage was present in this region suggesting a population replacement around the Pleistocene/Holocene transition  (Baca et al. , 2020). This challenged the simple model of post-glacial recolonisation of the Eastern lineage from the Carpathian refugium and suggested that the analyses based solely on extant genetic diversity may not recover the full complexity of the Late Pleistocene population dynamics. To refine the evolutionary history of common vole populations in Europe and to compare it with the past histories of coeval cold-adapted species such as the collared lemming, we generated and analysed a new mitochondrial dataset consisting of nearly 200 sequences from Late Pleistocene and extant individuals.
Modern specimens DNA of modern specimens from various locations across Europe was extracted previously (Table  S2 ). A target 4. 2 kb region of mtDNA spanning positions 12,000 to 16,247 according to the reference sequence (NC_038176;  Folkertsma et al. , 2018)  was generated using various approaches. It was either PCR amplified, sonicated, transformed into sequencing libraries and sequenced or the genomic DNA was sonicated and transformed into sequencing libraries. It was then either enriched for target fragment using in-solution hybridization and sequenced or the target region was extracted from deep shotgun sequencing data (see Appendix A1. 1 and Table  S2  for more details).
Phylogenetic analyses and molecular dating of specimens We used a Bayesian approach, implemented in BEAST 1. 10. 4 (Suchard et al. , 2018) , to estimate divergence times of common vole lineages and the age of specimens which were not directly dated. For the phylogenetic inference we used only ancient and modern sequences with at least 70% and 90% of the target mtDNA fragment (4. 2 kb) recovered, respectively. Sequences were aligned with MAFFT v. 7. 407  (Katoh & Standley, 2013). The best substitution model selected by jModelTest2  (Darriba, Taboada, Doallo, & Posada, 2012) , TIM2+F+I+G4, was not easily available in BEAST we therefore used the closest available one: GTR +I+G. First, we used Bayesian evaluation of temporal signal (BETS)  (Duchene et al. , 2020)  to check whether there is sufficient temporal resolution within our dataset to calibrate the molecular clock.
We used all directly radiocarbon dated (n = 20) and modern (n = 51) specimens and tested four alternative models. In two of them, we assigned real sampling times to the sequences (heterochronous analysis) and used either strict clock or uncorrelated relaxed lognormal clock. In the two other models, we used the same sampling time for all sequences (isochronous analysis) and applied either strict clock or uncorrelated relaxed lognormal clock (see Appendix A1. 7 for more details). Then, we performed the leave-one-out analysis on the directly radiocarbon dated specimens to check the accuracy of the age estimates produced using the available calibration dataset. In this analysis we estimated the age of each directly radiocarbon dated specimen using all the remaining radiocarbon dated and modern specimens to calibrate the molecular clock.
Results We generated a dataset of 4. 2 kb long mtDNA sequences from 199 ancient and modern common vole specimens (148 ancient and 51 modern). Sequences of 82 ancient specimens are reported for the first time and either 4. 2 kb or 1kb fragments of mtDNA of the remaining 66 specimens were reported previously  (Baca et al. , 2020; Baca et al. , 2021; Lemanik et al. , 2020)  (Table  S1 ). All 82 newly reported specimens yielded short inserts and elevated level of cytosine deamination at the terminal nucleotides characteristic for ancient DNA (Table  S1 ). Ancient specimens which yielded mtDNA sequences came from 40 sites scattered across Europe and covered the period of the last ca. 60 thousand years (Table  S1 , Figure  1a ). MtDNA cytochrome b sequences of most modern specimens were reported previously  (García et al.
All other direct dates are regarded as reliable based on their chemical indicators (collagen yield, stable isotopic and elemental values; Table  S3 ). As a result, we used sequences of 20 directly radiocarbon dated and 51 extant specimens to calibrate the molecular clock. The analysis of temporal signal (BETS) showed that the dated specimens included in our dataset are suitable for calibration of the molecular clock. The heterochronous model, with a strict clock and correct sampling times assigned to specimens, was strongly supported over all other models (2lnBF > 9) (Table  S4 ). The leave-one-out analysis revealed that the dated dataset enables relatively accurate estimation of specimen ages, although in the case of three specimens (MI074, MI1337 and MI1355) the 95% highest posterior density intervals (95% HPD) of estimated ages did not overlap within 2-sigma ranges of the radiocarbon dates (Figure  S1 ; Appendix A).
The divergence of the main common vole mtDNA lineages estimated in this study was also older than previously suggested. All mtDNA lineages present in extant European populations (WS, WN, ITA, B, CEN, E) diverged prior to 40 ka ago, and the earliest specimens belonging to each of those lineages in our dataset pre-date 25 ka ago. This suggests, contrary to previous hypotheses  (García et al. , 2020; Heckel et al. , 2005; Stojak et al. , 2015) , that climate deterioration during the LGM did not play the major role in the initial divergence of the main extant mtDNA lineages. However, the population decline and increased isolation during the period of the most inhospitable climatic conditions may have reinforced the previously existing divergence. Most of the observed divergence events occurred between ca.
Western Europe and Iberian Peninsula In Western Europe, we documented two consecutive mtDNA lineage turnovers at the end of MIS 3 (WNIII/WNII and WNII/WN). The first one took place around 45 ka ago (Figure  3 ). In our dataset there are few specimens of similar age from other parts of Europe; however, the divergent position of three specimens from the Western Carpathians (MI299, MI300, and MI1701; Figure  2 ) dated to 53 and 45 ka ago suggests that synchronous lineage turnovers may also have taken place in other parts of Europe. The second one occurred around 32 ka ago and appears to have been restricted to Western Europe (Figure  3 ). The oxygen isotope record from Greenland ice cores shows that the period between 45 and 29 ka ago was characterised by multiple short-term climatic oscillations  (Rasmussen et al.
4C-seq mapping, trim, capture and profiling The pipeline for the analysis of the 4C data was modified from the pipe4C pipeline  (45)  and is available on github (https://github. com/Mathias-Boulanger/pipe4C). The steps are the following: Reads filtering (trim-capture), mapping to reference genome, assignment of reads to their restriction fragment and creation of normalized score per fragment. Only reads containing the amplification sequence (CGTGACGCACGGAAACGTC) were kept for further analysis. Then, sequences downstream of the restriction enzyme cutting site of each selected reads were mapped to GRCH37p13 human reference genome with Bowtie2 aligner. Restriction fragment map was extrapolated from the reference genome using the cutting sequence of restriction enzymes. The interaction peak calling has been performed with peakC and the differential profiling analysis with DESeq2  (44, 46).
4. 0. 3, www. maxquant. org). All resulting MS/MS spectra were searched against the human Uniprot database (www. uniprot. org) by the Andromeda search engine using the reversed database strategy applying a false discovery rate of 0. 01 at both peptide and protein levels. Overrepresentation of Gene Ontologies of the identified proteins were analyzed using Fisher's exact test from InnateDB (50).
Acknowledgments We thank the members of the " Ubiquitin Family in Hematological Malignancies " group at the IGMM for fruitful discussions. Funding was provided by the  CNRS, Ligue Nationale contre le Cancer (Equipe Labellisée  to MP and PhD fellowships to MB),  Fondation de France  ( 2011-00025575 ),  FRM  (contract  FDT20140930973  to MR and  FDM201906008566  to LG). The HEMODIAG_2020 collection of clinical data and patient samples was funded by the  Montpellier University Hospital , the Montpellier SIRIC and the  Languedoc-Roussillon Region. MGX acknowledges financial support from the  France Génomique National  infrastructure, funded as part of " Investissements d'Avenir" program  managed by the  Agence Nationale pour la Recherche  (contract  ANR-10-INBS-09 ). Work at  Novo Nordisk Foundation Center for Protein Research (CPR)  is funded in part by a generous donation from the  Novo Nordisk Foundation  (Grant number  NNF14CC0001 ) and the  Danish Cancer Society KBVU  project grant ( R90-A5844 ).
Hallmark gene set analyses To evaluate the potential role played by specific ensembles of gene sets, hallmark gene sets from the Molecular Signatures Database (MSigDB,  [13, 14] ) were obtained for Mus musculus using the msigdbr package (version 7. 2. 1). Among the 50 available gene sets, we focused our attention on a subset of 14 hallmark gene sets related to PrP recognized physiological functions (see below). Comparisons of interest for the hallmark gene set analysis were defined for four different experimental groups as compared to WT mice: (1) Prnp 0/0 Sprn 0/0 ; (2) Prnp 0/0 Sprn 0/0 Sprn KD ; (3) Prnp 0/0 Sprn 0/0 Prnp KD ; and (4) Prnp 0/0 Sprn KD. To minimize possible off-target effects, contrasts for comparisons with groups (2)-(4) were constructed by averaging over the two lentiviruses for each gene knockdown.
Most of the differentially expressed genes were reported to be transcribed in the embryo ectoderm and mesenchyme, and only a few in the endoderm or in the extraembryonic component (Table  2 ,  [20] ). Finally, we focused our attention on the three genes expressed in the extraembryonic component (Spint1, Cds2, Ada); in particular, Ada exhibited strong differential expression (log fold-change = -2. 1, Table  2 , Figure  2 ). Differential expression of these three genes was further assessed by RT-qPCR analysis. The results validated those obtained from the microarray data for Ada and Cds2; a similar but insignificant trend was observed for Spint1 (Table  2 ).
, 2005; Orlowski and Grinstein, 2007; Deane et al. , 2013)  (Figure  1 ). In the human genome, the SLC9A6/NHE6 and SLC9A9/NHE9 genes localize at chromosomal positions Xq26. 3 and 3q24, respectively. In humans, several mRNA splice-variants of NHE6 have been documented in research databases (https://www. ncbi. nlm. nih. gov/gene/10479). Thus far, only two of these, NHE6v1 and NHE6v2 (originally called NHE6. 1 and NHE6. 0, respectively) have been examined at the protein level, with the former containing an additional 32 amino acid insertion within its second extracellular loop. This insert contains an additional glycosylation site, though its functional significance, if any, remains uncertain. As expected, overexpression of NHE6  (Ohgaki et al. , 2010; Xinhan et al. , 2011; Ilie et al. , 2016)  and NHE9  (Kondapalli et al.
In contrast, other mutations identified in CS patients have been demonstrated to exert only negligible effects on exchanger properties and cellular physiology. Specifically, two additional missense mutations, one in the extreme N-terminal cytoplasmic segment (pAla9Ser; A9S) and another in the regulatory C-terminal cytoplasmic domain (Arg568Gln; R568Q) appear to have comparable biochemical characteristics (i. e. , biochemical maturation, stability, and vesicular pH regulation) to that of WT NHE6 when expressed in AP-1 cells  (Ilie et al. , 2020). Engineering the equivalent A9S mutation in mice also revealed normal brain development and neuronal arborization and endosomal pH regulation  (Ouyang et al. , 2019). In addition, this NHE6 variant appears to be relatively common in healthy individuals (genome aggregation database, gnomAD; RRID:SCR_014964), confirming that this mutation alone does not likely lead to neurological impairments.
Statistical analysis All statistical analyses were performed using the two-sided t test function built in Excel 2010. Statistical tests and the number of biological replicates are indicated in figure legends. Biological replicates indicate samples that were collected from different batches of plants grown under the same conditions except biological replicates for transcript analysis and metabolite analysis were samples collected from different plants grown at the same time. Supplemental Figure  S4. The total amount and the rate of metabolites exported from mitochondria that were made via the NAD-ME pathway. The total amount of NAD-ME derived metabolites was calculated from time course experiments of either pyruvate and 13 C4-malate feeding (A, including unlabeled citrate, 2oxoglutarate, succinate, pyruvate) or pyruvate and 13 C4-malate feeding (B, including 13 C6-citrate, 13 C5-2oxoglutarate, 13 C4-succinate, 13 C3-pyruvate) to isolated mitochondria of Col-0, mpc1 and mpc1/gMPC1.
All experiments were performedin the presence of ADP at pH 6. 4 to initiate substrate uptake and consumption by both pathways. Metabolic reaction was stopped by centrifugation through a single silicon oil layer in which the mitochondrial pellet was separated from the extra-mitochondrial medium. Unused substrates and exported products in the extra-mitochondrial medium were quantified using LC-SRM-MS. Each data point represents averaged value from three or more biological replicates with error bars indicate standard error (n≥3). Significant differences between mpc1, Col-0 and mpc1/gMPC1 are denoted by asterisks based on Student's ttests (*, p < 0. 05). (C) Bar graphs show the calculated export rate of all metabolites combined which were made from ME-derived pyruvate after 5 minutes feeding the mitochondria with pyruvate and 13 C4-malate.
SDS-PAGE analysis Samples of UHT milk (Lactel) and Qishta were analysed by SDS-PAGE under reduced and non-reduced conditions according to the method described by  Anema (2000). The resolving and stacking gel contained 12e15% and 4% acrylamide, respectively. Electrophoresis was performed using a vertical electrophoretic unit type TV200YK twin-plate, associated with the source voltage EV202. SDS PAGE was performed at 30 V until the samples had completely left the stacking gel, then the voltage was increased to 90 V until the tracking dye reached 80% of the gel. Staining of gels was performed in 0. 23% solution of Coomassie Blue R-250, containing 3. 9% (w/v) TCA, 6% (v/v) acetic acid and 17% (v/v) methanol, for 90 min. The electropherogram obtained from SDS-PAGE was converted by image converter software and then analysed using the ImageJ 1:46 software.
Bioinformatics identification and quantification Raw files from in-gel digestion were analysed using the Proteome Discoverer™ software (Thermo Scientific, version 2. 2). The SEQUEST algorithm was used for database searches with the UniProtKB/Swiss-Prot Bovine database (Bos taurus, January 2018, Sequences: 6014). For details, see Supplementary material A. Analysis of milk samples using LC-MS/MS from eFASP digestion data was performed using MaxQuant (version 1. 5. 3. 30). Cox and Mann (2008)  search was used for database searching against the UniProtKB/Swiss-Prot Bovine (Bos taurus, January 2018, Sequences: 6014). For details, see Supplementary material A.
Acknowledgements This research was supported by specific grants from ' Hallab 1881' Company ,  Tripoli Lebanon. The authors acknowledge the  IBiSA network  for financial support of the USR 3290 (MSAP) proteomics facility. The mass spectrometers were funded by the  University of Lille , the  CNRS , the  R egion Hauts-de-France  and the  European Regional Development Fund.
17 In mice, constitutive Bin1 knockout presented embryonic or perinatal lethality probably due to feeding defects. 18, 19   imilarly, such lethal phenotype was reproduced in a skeletal muscle specific knockout using the Cre recombinase under the control of the human skeletal actin (HSA) promoter. 18, 20   onversely, knockout of the musclespecific exon 11 led to viable mice that did not display CNM phenotypes. 20 Acute reduction of Bin1 with shRNA in adult mice however showed disruption of the triad structure linked to alterations of intracellular Ca 2+ release. 21 me potential therapies for centronuclear myopathies have been proposed. 22 Moreover, downregulation of Dnm2 with antisense oligonucleotides was shown to efficiently ameliorate the skeletal muscle phenotype in MTM1-and DNM2-CNM mouse models,  23, 24  an approach that is currently in clinical trials (NCT04033159).
12 In this line, DNM2 reduction via antisense oligonucleotides may represent a first translational approach to treat CNM related to BIN1 mutations. The existence of at least one founder BIN1 mutation in the Roma/Gypsy ethnic minority should foster further pre-clinical development. Noteworthy, as we previously showed that DNM2 downregulation rescues mouse models for myotubular myopathy (MTM1-CNM) and dominant DNM2-CNM, it becomes clear that DNM2 antisense oligonucleotides could represent a common therapy to treat these different CNM forms. 22 Noteworthy a 50% decrease in DNM2 in mice, either from embryogenesis in the Dnm2 +/-knockout or upon postnatal ASO treatment,  18, 24, 25, 27  does not lead to detectable toxic effects. DNM2 downregulation is on clinical trial for MTM1 and DNM2-CNM patients of more than 16 years old (NCT04033159) by Dynacure, and our present data on this novel BIN1-CNM model supports the inclusion of BIN1-CNM patients in such trial.
RNA extraction and RT-qPCR. RNA was extracted from TA of 8 weeks old mice using TRI Reagent (Molecular Research Center, Cincinnati, USA) and cDNA synthesis performed with SuperscriptTM IV Transcriptase (ThermoFischer Scientific, Whaltham, USA). For quantitative PCR, cDNAs were amplified with SYBR Green Master Mix I (Roche Diagnostics, Basel, Switzerland) using 0. 1 µM of forward and reverse primers in a Lightcycler® 480 (Roche Diagnostics, Basel, Switzerland). Primers specificity was validated by melting curve and sequencing of amplicons. Several primers were used in previous studies and are summarized in table  S1. 28, [46] [47] [48]  RT-qPCR was performed using technical triplicates and relative mRNA level was calculated with Rpl27 as a housekeeping gene. The data displayed in the figures are the average of the triplicates and the result of a single experiment.
50 For FDB from 8 weeks old mice and TA from 4 months and 12 months old mice, fiber segmentation was performed using HE images and Cellpose software for segmentation algorithm. 51 Fiber MinFere diameter and nuclei counting were calculated or counted using ImageJ. For fiber circularity distribution, the fibers were classified with a value from 0 to 1 where 0 corresponds to a line and 1 to a circle, and one transversal section of the whole muscle was quantified. For immunofluorescence, 8 µm TA cryosections were fixed with paraformaldehyde 4%, blocked with fetal calf serum and sequentially incubated with antiprohibitin (Rabbit, 1:500, ab28172),anti-LC3 (Rabbit, 1:1000, NB100-2220), anti-desmin (Rabbit, 1:200, ab15200) or anti-TOMM20 (Rabbit, 1:100, ab78547), and Alexa-Fluor 594-coupled goat anti-Rabbit (Goat, 1/250, A11012) and or Alexa-Fluor 488-coupled goat anti-Rabbit (Goat, 1/250, A11008) and Hoechst (Sigma-Aldrich, St Louis, USA).