dataesr/scientific-paragraphs-categorization huggingface dataset:
Identification of Collagen Type X Genes in the Genomes and Transcriptomes of Chondrichthyans Collagen 10a1 (Col10a1), Collagen 8a1 (Col8a1), and Collagen 8a2 (Col8a2) sequences for human, mouse, and zebrafish were collected from GenBank. Elephant shark whole genome assembly GCA_000165045. 2 Callorhinchus_milii-6. 1. 3 (Venkatesh et al. 2014 ) was downloaded and screened for Col10a1, Col8a1, and Col8a2 sequences using BLAST. Scaffolds with best matching alignments were downloaded and genes were predicted with Genscan  (Burge and Karlin 1997)  and Augustus  (Stanke and Morgenstern 2005). Predicted Col10a1, Col8a1, and Col8a2 protein sequences from elephant shark were used as TBLASTN queries in little skate (L. erinacea) Transcriptomic Contigs-Build 2 of Skatebase  (Wyffels et al. 2014 ) and against the locally assembled lesser spotted catshark and thornback ray jaw and vertebrae transcriptomes on the Montpellier Bioinformatics Biodiversity (MBB) platform (http://mbb.
univ-montp2. fr/ MBB//index. php). Nucleotide sequence data reported are available in the Third Party Annotation Section of the DDBJ/ENA/GenBank databases under the accession numbers TPA: BK010855-BK010872. Catshark Col10a1 cDNA sequences were used to search for similar sequences in a whale shark genome (R. typus) using BLASTN (GCA_001642345. 2 ASM164234v2  [Read et al. 2017] ). Thornback ray and little skate cDNA sequences were used to map synteny on the Thorny skate A. radiata draft genome using BLAST (data accessed with permission from Vertebrate Genome Project https://vgp. github. io/genomeark/Amblyraja_radiata/).
Acknowledgments We thank the  Genoscope-Centre National de S equencage (Evry, France)  for access to the catshark draft genome and  H elene Mayeur  ( Observatoire Oc eanologique, Banyuls sur Mer, France ) and  Jean-Marc Aury (Genoscope)  for assembling genomic data. We thank the national infrastructure  France-BioImaging  and  RIO Imaging platform (Montpellier, France ,  ANR-10-INBS-04 ,  ANR-10-LABX-0020 ) for nanozoomer acquisitions. We thank the MBB and GenSeq platforms for help with the transcriptome analyses; the  RHEM at the Institute of Cancer Research of Montpellier  ( IRCM-U1194 ) for histology data acquisition. We thank  SciLifeLab  and  Genome Engineering Zebrafish Facility (Uppsala, Sweden)  for providing zebrafish embryos,  Marlene Schmidt  for the help with zebrafish in situ hybridization,  A ˚sa Mackenzie  and  Maria Papathanou  for nanozoomer acquisitions.
We thank  Prof Per E. Ahlberg  for valuable discussion about the evolutionary significance of the findings. M. D. -T. was supported by  Centre national de la recherche scientifique Peps-Exomod  and  Centre M editerran een de l'Environnement et de la Biodiversit e  ( ANR-10-LABX-0004   Skel ' Estro  project); S. M. was supported by  Fondo Nacional de Desarrollo Cient ıfico y Tecnol ogico  (the research grant  1151196 ); T. H. was supported by  Vetenskapsra  ˚det (Starting grant  621-2012-4673 ).
Membranes were then washed three times in TBS-0,1% Tween ® 20 and incubated with the appropriate second antibody conjugated to horseradish peroxidase (HRP) two hours at Room Temperature (RT). Membranes were incubated with mouse anti-actin HRP-conjugate (Sigma-Aldrich) in 5% Blotting-Grade Blocker in TBS-0,1% Tween ® 20 for 2 hours at RT. Detection was performed with ECL Western-blotting Detection Reagent (GE Healthcare). The intensity of bands revealed was quantified by mean of densitometry with Multi-application gel imaging system PXi software (Syngene).
Immunostaining on Cytospin. Cytospin preparations without MGG staining were fixed in paraformaldehyde 4% (Sigma-Aldrich). After 3 lavages in TBS, Cytospins were incubated 10 min in TBS-0. 3% Triton X-100. Then, Cytospins were washed 3 times in TBS, blocked in TBS-1% BSA-10% SVF during 45 min and incubated with primary anti-histone H3-citrulline (Abcam, ab5103) or control isotype antibodies over night at 4 °C. After 3 lavages in TBS, Cytospins were incubated 1 hour at room temperature with anti-Rabbit IgG conjugated to Alexa 488. Cytospins were counterstained using 4′,6-diamidino-2-phenylindole (DAPI) for 10 min, rinsed and coverslip were mount with Mowiol (Sigma-Aldrich). Cells were observed using a Nikon eclipse 80i microscope and images were treated using ImageJ software.
Acknowledgements We thank  Pr François Erard  for helpful discussions. We also thank all people from the TAAM for mouse breeding. Support by  Centre National de la Recherche Scientifique , the  University of Orleans , The  Region Centre Val de Loire  ( 2003-00085470 ), the  ≪Conseil Général du Loiret≫ and European Regional Development Fund (FEDER  No. 2016-00110366  and  EX005756 ).
Image Analysis. Using the MIPAV (Medical Image Processing, Analysis, and Visualization) application (https:// mipav. cit. nih. gov/), MR images were visually inspected in search for areas in the corpus callosum exhibiting a normalization of the natively hyposignal (Figure  1(a) ) and for any edematous hypersignal encompassing the corpus callosum and adjacent areas (Figure  1(b) ). A region of interest (ROI) encompassing the abnormal area of the corpus callosum was manually drawn on MR slices and mirrored onto the contralateral corpus callosum. In addition, brain slices were screened to identify and measure the maximal width of the lateral ventricle along the mediolateral plane (Figure  1(c) ). Each of these two measurements was performed by two operators (blind to other data). MR images were then imported in the Inveon Research Workpackage (IRW, Siemens) and registered onto PET/CT images.
Image Analysis. Autoradiograms were visualized on Multigauge software (Fujifilm). ROIs were drawn manually on the targeted injection sites in the corpus callosum by a single operator, and lesion-to-contralateral uptake ratios were calculated. Corresponding ROIs were also drawn manually on histological images, and myelin content in ipsilateral and contralateral corpus callosum were semiquantitatively measured by an experienced observer blind to the autoradiography results, using Image-Pro Plus 6. 0 software (Media Cybernetics) and expressed as optical density per unit area. e lesion-to-contralateral ratios were then calculated for optical density per unit area. For each animal, quantification was performed on 4 brain sections encompassing the whole volume showing a decreased binding, hence resulting in 20 measurements.
01 level). Importantly, deviations were below the resolution of PET imaging. Raw data are provided as supplementary dataset S2, and mean of the two measurements is reported thereafter. Figure  2  summarizes the results of this optimization process in three experimental groups. In the first group, we adapted previously reported injection conditions (group 1: 4 injection sites in striatum and corpus callosum; total volume 10 μl). is led to detectable edematous hypersignals in half of the animals and a mean ventricle width of 1. 9 ± 0. 5 mm. In group 2, increasing the distance between the 4 injection points and the lateral distance from the bregma only slightly decreased the rate of edema (4 over 9 animals) and reduced ventricle width (1. 7 ± 0. 5 mm). As edematous foci were mainly observed in the striatum, we simplified the injection protocol and kept only two injection sites, at the lower and upper levels of the corpus callosum (group 3; total volume 5 μl); with this protocol, no animals showed focal edema, and ventricle width was further reduced (1.
Acknowledgments Dr. Min Zhang  was supported by the  National Natural Science Foundation of China  ( 81501499 ),  Shanghai Jiaotong University Med-X Interdisciplinary Research Funding  ( YG2017MS61 ), and  Shanghai Pujiang Program  ( 18PJD030 ). is work was performed at  CERMEP-Imagerie du Vivant  within the framework of the  Labex PRIMES  ( ANR-11-LABX-0063 ) of the  University of Lyon , under the " Investissements d'Avenir" program  ( ANR-11-IDEX-0007 ) operated by the  French National Research Agency (ANR).
It grows equally efficiently at medium and high temperature but less at low temperature, where it might experience physiological stress  [50]. In the Gulf of Naples, L. aporus has been found to bloom in summer but the species is present during other seasons as well  [6, 51]. Indications of a cold adapted population resulted from a worldwide high throughput sequencing (HTS) metabarcoding analysis on Leptocylindraceae, offering a possible explanation of the species occurrence through the year  [51]. In the current study, (i) we used RNA sequencing of multiple strains of L. aporus to explore expression differences in response to temperature changes, focusing on TEs. (ii) Intraspecific genetic diversity was assessed with a single-nucleotide polymorphism (SNP) analysis. In addition, in order to detect possible genetic changes in laboratory conditions for the oldest strain, an additional SNP analysis was conducted comparing present data to the already available transcriptome in the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)  [52].
Quality Check, Assembly and Annotation The quality of the reads was checked using FastQC v0. 11. 3 (Babraham Bioinformatics) and the trimming of adapters was performed by Trimmomatic 0. 33  [57]  (Parameters: ILLUMINACLIP:TruSeq3-PE-2. fa:2:30:10:1:true, SLIDINGWINDOW:3:22, MINLEN:25). Paired-end reads were assembled with Trinity 2. 0. 6  [58]  (Parameters: -normalize_reads -inchworm_cpu 15 -bflyHeapSpaceInit 24G -bflyHeapSpaceMax 200G -bflyCalculateCPU -CPU 15 -jaccard_clip -min_kmer_cov 2). CD-HIT-EST  [59]  was used in order to reduce the redundancy of isoforms that belong to the same gene, clustering together all the transcripts having a high percentage of sequence similarity (CD-HIT threshold of 95% identity) (Parameters: -c 0. 95 -n 8). The reads were aligned to the transcripts generated by the assembler with Bowtie v.
1. 1. [60]  (Parameters: -p 20 -maxins 500 -chunkmbs 10240 -seedlen 20 -a -fr -tryhard) and SAMtools idxstats  [61]  were used to count the mapped reads. EdgeR  [62]  and an in-house R script (Annocript DEA)  [63, 64]  were used in order to calculate CPMs (count per million) and extract transcripts with a CPM greater than 1 for at least 2 samples, respectively. Annocript 1. 1. 2 [64]  was executed for the annotation of the transcripts using Swiss-Prot  [65] , UniRef90  [66] , the Conserved Domains Database (CDD)  [67] , Rfam  [68]  and the SILVA  [69]  database. The completeness of the assembly and annotation was quantified using the software BUSCO v. 2 using the "protists" set of lineage-specific single copy genes  [70]. The BUSCO results were compared to the corresponding ones produced from the L.
Differential Expression Analysis To assess the distance among samples, non-metric multidimensional scaling (NMDS) analysis was performed based on the expression values (CPMs) of all transcripts. Subsequently, we used EdgeR to evaluate the expression of the transcripts obtained and statistically distinguish the expression of the genes among the experiments. The following comparisons were performed: 13 vs. 19 • C, 19 vs. 26 • C, 13 vs. 26 • C. Different strains were used as replicates. Transcript counts were obtained using samtools idx. Raw counts were transformed in count per million (CPM) with the R library "edgeR", followed by a normalization step with the functions calcNormFactors, estimateCommonDisp and estimateTagwiseDisp. For each couple of sample CPMs, we executed a paired t-test to avoid the effect of the differences among strains using the R function exactTest.
Transcripts were considered differentially expressed when the FDR (false discovery rate) ≤ 0. 05 and the FC (fold change) > 2. A complementary analysis was performed between strain couples (1A1 vs. B651, 1A1 vs. 3A6, B651 vs. 3A6) using the temperature conditions as replicates. Significantly differentially expressed (DE) transcripts with no annotation were manually blasted in the National Center for Biotechnology Information (NCBI) and CDD databases. All significantly DE transcripts were also annotated for KEGG pathways using GhostKOALA  [71]. The KEGG pathway annotation results were further processed in a similar way as in Liang et al. 2019  [17]. KEGG pathways and Brite categories were selected from the following categories: metabolism, genetic information processing, environmental information processing, and cellular processes.
SNP Analysis For the intraspecific diversity assessment, the quality checked and trimmed reads of all strains at 19 • C were mapped on the transcriptome using STAR 2. 7. 0c  [73]  and further processed with samtools (sorted and indexed). The software Opossum 0. 2 was used in order to adjust the mapping of RNA-seq reads for variant calling  [74]. The SNPs were called using FreeBayes v1. 2. 0-4-gd15209e  [75]  and filtered with bcftools by samtools, removing reads not properly mapped and with mapping quality less than 30. Variants with allele frequency (AF) equal or less than 0. 2 were not considered (Figure  1 ). To address possible variations over the culturing time, the same workflow was also followed mapping B651 reads acquired from this study and public B651 reads already available in MMETSP on the B651 MMETSP transcriptome.
qPCR Validation of Gene Expression Levels from RNA-Seq Following the investigation of the expression and function of all significantly DE genes, eight of them were selected as targets for validation and further experiments with qPCR (Genbank MN738467-MN738474). Five of the selected transcripts expressed TE-related genes and three expressed heat stress-related genes (Table  3 ). Tubulin A1 (TUBA1) and tubulin B6 (TUBB6) were tested for stable expression under the different experimental conditions using NormFinder software  [76]. The samples used for validation with qPCR had undergone the same acclimation conditions and time as in the RNA-Seq experiment. The RNA was extracted following the same protocols described above and then reverse transcribed into cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Venlo, Limburg, the Netherlands).
Phylogenetic Analysis of the Selected TEs The selected transcripts coding for transposable elements were screened for interspersed repeats and low complexity DNA sequences, like simple tandem repeats, polypurine and AT-rich regions, in the RepeatMasker (Search Engine: cross match, DNA source: diatom;  [78] ). The same screening was performed for the CoDi/GyDi sequences, which belong to groups of transposable elements mainly found in marine organisms with most of them being identified only in diatoms to date  [32]. The CoDi/GyDi sequences were derived from Genbank using the Genbank accession numbers mentioned in  [32]. The results of the two screenings were compared in order to identify whether the selected TEs represent known groups or new CoDis/GyDis. In addition, a phylogenetic analysis of the selected transcripts and the known CoDi/GyDi elements was performed.
Leptocylindrus aporus Transcriptome Preliminary growth experiments were performed on several L. aporus strains in order to identify the best candidates for investigating the species acclimation and adaptation using RNA-Seq (Supplementary File 1). Based on the V9 region included in the beginning of ITS marker, none of the strains belonged to the possible cold adapted population found in the worldwide HTS analysis  [51]. Ultimately, one L. aporus strain isolated in summer 2010 (B651) and two isolated in winter 2013-2014 (1A1 and 3A6) were chosen, due to their diversity in terms of the year of isolation, seasonality and physiological characteristics. The final transcriptome of L. aporus (ArrayExpress ID: E-MTAB-8596), obtained using all results from the three strains grown at the three different temperatures, consisted of 19,963 transcripts.
Further statistics are presented in Table  S1. The transcriptome obtained in the current study was compared to the previously available MMETSP transcriptome  [52] , obtained from the oldest strain B651, in order to test whether the set of 215 protist lineage-specific single-copy genes were present in the assemblies (BUSCO analysis). This analysis gave an indication on the completeness of the assemblies as well as their redundancy. While the two assemblies contained a similar number of complete genes from the dataset (100 for the current and 103 for the older assembly), the older assembly had a higher proportion of potentially erroneous assembled transcripts and therefore were classified as duplicated by BUSCO (7 for the current and 34 for the old) (Table  S2 ).
aporus at low temperature (Table  6 ). The gene ontology (GO) enrichment analysis showed the GO terms enriched with respect to the overall transcriptome. The adjusted p-value cutoff to consider a class as significant was 0. 1, which means that 10% of significant classes might be false positives. The analysis indicated that three classes belonging to the biological process GO aspect were significantly enriched among the DE transcripts between high and low temperature, protein dephosphorylation, DNA integration and carbohydrate metabolic process. Interestingly, among them, the most represented was DNA integration (Figure  3 ), which refers to the incorporation of a segment of DNA, including a transposon, into another, usually larger, DNA molecule such as a chromosome. Manual inspection of annotations revealed 16 DE transcripts related to DNA integration, four of which had no further annotation and 12 had specific protein annotation by at least one of the databases used in Annocript (Table  6 ).
1, which means that 10% of significant classes might be false positives. The analysis indicated that three classes belonging to the biological process GO aspect were significantly enriched among the DE transcripts between high and low temperature, protein dephosphorylation, DNA integration and carbohydrate metabolic process. Interestingly, among them, the most represented was DNA integration (Figure  3 ), which refers to the incorporation of a segment of DNA, including a transposon, into another, usually larger, DNA molecule such as a chromosome. Manual inspection of annotations revealed 16 DE transcripts related to DNA integration, four of which had no further annotation and 12 had specific protein annotation by at least one of the databases used in Annocript (Table  6 ). These were annotated as (1) reverse transcriptase (RNA-dependent DNA polymerase), which is usually indicative of a mobile element such as a retrotransposon or retrovirus, (2) ribonuclease of_Ty1/Copia or Ty3/Gypsy family, an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid, which has been observed as adjunct domains to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing and non-LTR retrotransposons, (3) integrase, which mediates integration of a DNA copy into the host chromosome, or (4) a gag-pol polyprotein, encoding structural proteins and several enzymatic functions in LTR retrotransposons.
All the significantly DE TE-related transcripts except one were highly expressed at low temperature in the recently isolated strains 1A1 and 3A6, while they were very low at all All the significantly DE TE-related transcripts except one were highly expressed at low temperature in the recently isolated strains 1A1 and 3A6, while they were very low at all temperatures for the old B651 strain. This expression pattern was also the one mostly seen in several of the other stress-related transcripts (HSFs, SYM1, AOX4, ALDH, RaiA), and in three transcripts, manually annotated by blasting in NCBI and CDD databases as likely homologs of the bacterial MAI genes related to biomineralization, which are known to undergo frequent transposition events  [81]. The observation of this expression pattern pointed towards a strain specific stress response.
Indeed, in an NMDS analysis using the global gene expression matrix, the oldest strain B651 clustered apart from the other two strains, for which samples from the medium and high temperature were interspersed (Figure  S4 ). All the above led to further investigation of the differences among strains. Considering couples of strains, significantly DE transcripts between 1A1 and 3A6 were 622; much less compared to the 3,015 between 1A1 and B651 and 2,418 between B651 and 3A6 (Figures  4  and 5 , Supplementary Files 4-7). Genes 2020, 11, 9 14 of 27 temperatures for the old B651 strain. This expression pattern was also the one mostly seen in several of the other stress-related transcripts (HSFs, SYM1, AOX4, ALDH, RaiA), and in three transcripts, manually annotated by blasting in NCBI and CDD databases as likely homologs of the bacterial MAI genes related to biomineralization, which are known to undergo frequent transposition events  [81].
The observation of this expression pattern pointed towards a strain specific stress response. Indeed, in an NMDS analysis using the global gene expression matrix, the oldest strain B651 clustered apart from the other two strains, for which samples from the medium and high temperature were interspersed (Figure  S4 ). All the above led to further investigation of the differences among strains. Considering couples of strains, significantly DE transcripts between 1A1 and 3A6 were 622; much less compared to the 3,015 between 1A1 and B651 and 2,418 between B651 and 3A6 (Figure  4  and 5, Supplementary Files 4-7). Genes 2020, 11, 9 14 of 29 temperatures for the old B651 strain. This expression pattern was also the one mostly seen in several of the other stress-related transcripts (HSFs, SYM1, AOX4, ALDH, RaiA), and in three transcripts, manually annotated by blasting in NCBI and CDD databases as likely homologs of the bacterial MAI genes related to biomineralization, which are known to undergo frequent transposition events  [81].
The strategy adopted to correct the observed v 2 for the fraction of prompt D mesons in the measured raw yields is the same as the one used in  [48] , and it is described in the following. The observed v 2 can be expressed as a linear combination of the prompt (D mesons coming directly from the hadronisation of a c-quark or from the decay of an excited open charm or charmonium state) and the feed-down contributions v obs 2 = f prompt v prompt 2 + (1 -f prompt )v feed-down 2 , (6) where f prompt is the fraction of promptly produced D mesons estimated as a function of p T with the same method used in  [32]. In particular, it is computed using (i) FONLL calculations  [85, 86]  for the production cross-section of beauty hadrons, (ii) the beauty-hadron decay kinematics from the EvtGen package  [87] , (iii) the product of efficiency and acceptance (Acc × ε) from Monte Carlo simulations and (iv) an hypothesis on the nuclear modification factor of feed-down D mesons.
Nevertheless, the comparison between D mesons and charged particles will be crucial for future larger data samples, to better asses the magnitude of the correlation between the D-meson and the soft-hadron v 2. To study a possible interplay between the azimuthal anisotropy of the event and the charm-quark radial flow (at low/intermediate p T ) and in-medium energy loss (at high p T ), the yields of prompt D 0 and D + mesons have been measured in six transverse momentum intervals in the range 2 < p T < 16 GeV/c, in the small-q TPC 2 and large-q TPC 2 samples. The D-meson raw yields integrated over ∆ϕ were extracted from the fits to the invariant-mass distributions in the ESE-selected and unbiased classes and normalised to the corresponding number of events in the considered sample. As described in Sec.