dataesr/scientific-paragraphs-categorization huggingface dataset:
2. 1. 1  [53] ). This step resulted in two species-specific transcriptome on which we further selected transcripts containing an open reading frame (hereafter referred as genes) with TransDeCoder (Galaxy Version 3. 0. 1  [54] ). Then, for each transcriptome, genes were clustered based on similarity (threshold put at 96% for S. haematobium and S. bovis, i. e. , which allowed to keep redundancy percentage measured on Busco (Galaxy Version 4. 0. 4  [55] ) under 10%) to retain only non-redundant protein coding genes. This resulted in a final transcriptome composed of respectively 11 161 genes and 10 768 genes for S. haematobium and S. bovis From these two references we built one single reference, where S. haematobium genes, S. bovis genes and orthologous genes were indicated. To do so, we identified strict orthologous genes using a reciprocal blast hit approach.
Quantification of gene expression and differential expression analysis The reference transcriptome we assembled was composed of both S. haematobium and S. bovis transcripts. For this reason, we used de novo transcriptome assembly tools to estimate gene expression levels of both parental lines and hybrids. We relied on the two Trinity tools, namely "Align reads and estimate abundance" and "Build expression matrix" to estimate gene raw counts  [54]. The raw counts matrix resulted in a set of 17,191 quantified transcripts and was processed in R (version 4. 0. 0  [59] ) using the package DESeq2 (version 1. 28. 1  [60] ). Transcripts with less than 10 counts across all samples were excluded from further analysis hence resulting in a set of 16,613 analyzed transcripts. We relied on the R package DESeq2, that internally corrects for library size, to calculate differential gene expression and hence to determine gene expression profiles.
Transcriptome annotation and functional analysis Annotation was conducted with PLAST (version 2. 3. 3  [61] ) on the non-redundant protein database of NCBI (released of the 2022-01-07  [62] ). Blast2GO (which compare within each GO the number of gene from a define gene set and to the number of genes from the reference to test whether this GO contains significantly more genes from the gene set compare to genes from the reference) followed by a False Discovery Rate (FDR) analysis to correct for multiple comparisons. To ease result interpretation, we further selected non-redundant GO terms falling into biological processes and displayed Tree Map graphical representations using Revigo with list size set to small  [65]. Analyses were conducted on gene sets of each hybrid expression profile categories (under-and over-expressed, intermediate, S.
Materials and Methods We have interrogated the WormBase ParaSite (WBPS) database  [12]  over the last two years, because this is the reference database for helminth, and we present the data from the session WS282 (last accession 31 March 2023), searching, within the genome of Schistosoma mansoni, for the terms "Micro-Exon Gene", "MEG", "antigen 10. 3", "GRAIL", and "ESP". For each gene, WBPS presents its structure, the possibility to retrieve the sequence, the position on the chromosome, and a translation identified with (at least) one associated UniProt ID. On the UniProt website  [17] , each entry is associated with both its WBPS and GenBank ® identifiers, when available. An example of the WBPS entry for MEG 3. 2 isoform 1 is given in Figure  1. One class of genes, in particular, has attracted the attention of researchers, the socalled micro-exon genes (MEG).
Materials and Methods We have interrogated the WormBase ParaSite (WBPS) database  [12]  over the last two years, because this is the reference database for helminth, and we present the data from the session WS282 (last accession 31 March 2023), searching, within the genome of Schistosoma mansoni, for the terms "Micro-Exon Gene", "MEG", "antigen 10. 3", "GRAIL", and "ESP". For each gene, WBPS presents its structure, the possibility to retrieve the sequence, the position on the chromosome, and a translation identified with (at least) one associated UniProt ID. On the UniProt website  [17] , each entry is associated with both its WBPS and GenBank ® identifiers, when available. An example of the WBPS entry for MEG 3. 2 isoform 1 is given in Figure  1. Figure  1. Screenshot of the entry for MEG-3.
In parallel, we have performed exactly the same search on UniProt KnowledgeBase  [17]  and cross-verified the results. All the protein sequences downloaded from UniProt were passed into psi-BLAST from NCBI [18], restricting the search to S. mansoni in order to collect the maximum number of protein sequences annotated as MEG. Afterward, we performed a trimming, eliminating the duplicated entries, which displayed the same sequence with two different protein accession numbers, one from NCBI and one from UniProt. Whenever this was the case, we arbitrarily kept the UniProt ID only for consistency with the cross-annotation of WBPS. While we were writing this manuscript, on 13 April 2023, a new release of WPBS was published, which included more transcriptomic data and increased the number of putative megs, without the associated protein data; therefore, we did not change our verified workflow.
Emboss on the EBI server  [22]  was used to put in evidence conserved linear motifs, which were displayed with Weblogo  [26]. Primary sequence analysis was performed by the ProtParam tool [27] on the Expasy website  [28]  (last access on 31 March 2023); the results on calculated molecular weights, isoelectric point, aliphatic index, and GRAVY index are presented in the supplementary Table  S1. In this table both the WBPS gene name and the corresponding code from GenBank ® (when available) are listed (last access on 18 August 2023).
MEG Filiation In S. mansoni, 35 megs code for at least 87 verified MEG proteins with a unique Uni-Prot ID, mainly originating from alternatively splicing the central exons. In the past, the gene sequences have been annotated and clustered into 23 families, numbered from 1 to 16 and from 26 to 32. MEG proteins have been found prior to the genome sequencing in the secretions from eggs and adult worms, in both transcriptomics and proteomics studies. At the beginning, they were named "antigen 10. 3", "Egg secreted protein no 15 (ESP15)", and "Grail", before their peculiar gene structure was discovered  [5, 10, 11, 13, 14, 30]. We have aligned the 87 verified proteins, whose sequences are given in the supplementary Table  S1 , and we found that, among the three most used software offered on the EBI tools webpage  [22] , MUSCLE  [21]  was the one that reflected the splicing constraints the most.
MEG Filiation In S. mansoni, 35 megs code for at least 87 verified MEG proteins with a unique UniProt ID, mainly originating from alternatively splicing the central exons. In the past, the gene sequences have been annotated and clustered into 23 families, numbered from 1 to 16 and from 26 to 32. MEG proteins have been found prior to the genome sequencing in the secretions from eggs and adult worms, in both transcriptomics and proteomics studies. At the beginning, they were named "antigen 10. 3", "Egg secreted protein no 15 (ESP15)", and "Grail", before their peculiar gene structure was discovered  [5, 10, 11, 13, 14, 30]. We have aligned the 87 verified proteins, whose sequences are given in the supplementary Table  S1 , and we found that, among the three most used software offered on the EBI tools webpage  [22] , MUSCLE  [21]  was the one that reflected the splicing constraints the most.
Statistical Analyses Data were subjected to ANOVA using the MIXED procedure of SAS (SAS Inst. Inc. , Cary, NC, USA). The statistical model applied included the fixed effect of diet, breed, sampling time, and corresponding interactions. Time of sampling within the pig was considered as a repeated measure. Concentration at time zero of the AA was included as a covariate in the statistical analysis. The differences were considered significant when p < 0. 05.
HIV serology results were was negative. The patient was transferred to Cayenne Hospital on day 3 of empirical treatment, with a treatment course of intravenous ceftriaxone (1 g/d). Because of ongoing fever, antimicrobial therapy was switched to piperacillin/ tazobactam. Computed tomography of the chest, abdomen, and pelvis showed isolated hepatomegaly (19 cm) and splenomegaly (13 cm). Gram-negative bacilli were identified in blood cultures on day 9, after 68 hours of incubation. Mass spectrometry (MALDI Biotyper [Bruker, https://www. bruker. com/en. html]; security-relevant database; score 2. 4) and VITEK 2GN ID card (bioMerieux, https://www. biomerieux. fr) (score 98%) identified the presence of B. melitensis. No serodiagnosis could be performed. After establishing a diagnosis of brucellosis (September 15, 2020), we switched the patient's antibiotic regimen to a combination of rifampin (900 mg 1×/d) plus oral doxycycline (100 mg 2×/d) and a dose of gentamicin (250 mg).
Genome Sequencing and Analysis We sequenced genomic DNA by using an Illumina MiSeq (Illumina, https://www. illumina. com) platform. We used a Nextera DNA Flex Kit (Illumina) for the library preparation, using 500 ng of DNA as input. We assessed library molarity and quality on the Qubit and the tape station using a DNA high-sensitivity chip (Agilent Technologies, https://www. agilent. com). We used the MiSeq Reagent Kit v2 (Illumina) to load libraries. Paired-end reads of 150 bp were generated de novo and assembled by using Shovill 1. 1. 0, a GALAXY webtool  (7) , and the contigs were assembled via the CONTIGuator web server, using the B. ceti TE10759-12 genome (BioProject PRJNA224116) as a reference. We annotated consensus sequences by using the PATRIC genome annotation service (RASTtk)  (8).
We deposited the genome sequences in Gen-Bank under BioProject no. PRJNA728965 (accession nos. CP074683 for chromosome 1 and CP074684 for chromosome 2 of BRSO-2021-230 [BioSample SAMN19108195]; CP075601 for chromosome 1 and CP075602 for chromosome 2 of BRSO-2020-213 [Bio-Sample SAMN19107925]).
Microbiological Characterization We shipped bacterial isolates from both patients to the French Brucella National Reference Center in Nimes, France, for confirmation of identification; they were named BRSO-2020-213 (Cayenne) and BRSO-2021-230 (Kourou). Analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (Vitek MS with IVD database v3. 2. 0; bioMérieux) confirmed that both isolates belong to the Brucella genus. Slide agglutination using a polyclonal serum anti-Brucella (ANSES, https://www. anses. fr) also yielding positive results. Both isolates are gram-negative bacteria, forming nonhaemolytic, round, convex, smooth, greyish colonies with a diameter of ≈0. 5 mm after 48 hours of incubation on tryptic soy agar. Both isolates showed positive reactions for catalase (slide test), cytochrome-oxidase and urease (analytical profile index gallery tests) and a negative result for indole production (Table ).
Acknowledgments We thank the physicians that supported the patients and biologists that performed the blood tests. We are also grateful to  Elise Martin  for preparing the map of French Guiana (Figure 1). This work was supported by the  Institut National de la Sante et de la Recherche Medicale (INSERM) ,  Universite de Montpellier , and  Sante Publique France. Nimes University  hospital provided structural, human, and financial support through the award obtained by our team during the internal call for tenders "Thematiques phares. " J. P. L. , D. O. C. , and A. K. belong to the  FHU InCh  ( Federation Hospitalo Universitaire Infections Chroniques, Aviesan ). The protection of human subjects afforded in this study were in accordance with the International Committee of Medical Journal Editors guidelines.
The study was registered in the DPO processing of  Cayenne Hospital Center , from which 3 coastal hospital centers ( Saint Laurent du   Maroni , Kourou, and Cayenne) and 2 health centers in the interior (Maripasoula and Apatou) are all administratively dependent. Because this study involved retrospective data collected in the context of routine care, this research is not considered to involve human subjects and therefore follows the "méthodologie de référence MR-004" of the  French National Commission for Information Technology and Liberties. Every effort was made to contact the 2 patients to obtain their informed consent for the publication of these case reports, but this effort was unsuccessful. If the patients, at some time in the future, express their opposition, their data would be deleted from the database.
This work ow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all signi cantly involved in the development of the brain and the cranio-facial skull, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These ndings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
Materials And Methods We compiled a list of genes that show signals of selection in domesticated mammals, as compared to their non domesticated counterparts. Research on different species that we relied on includes: Guinea pig, pig, rat, dog, cat, cattle, domesticated fox, horse, rabbit, and sheep  (Womack 2005; Trut et   (Martens et al. , 2021). Results were then combined. Pathway enrichments were ranked according to their level of statistical signi cance across these 4 libraries. For enrichment analyses in TF targets, we queried the ChEA 2022 library of experimentally-demonstrated TF targets and binding sites, which is mostly based on ChIP-seq results. Finally, we used the Harmonizome website  (Rouillard et al. , 2016) , an Enrichr-connected integrated resource of OMICs datasets, to extract the lists of experimentally-demonstrated TF targets and to perform pathway enrichment analyses, following the same strategy described above.
Adipogenesis We then sought to identify a potential key regulatory TF among our short list of ve candidate TFs. To this aim, we rst surveyed the ChEA 2022 databank and extracted transcriptional regulatory links between our ve TFs (Fig. 1 ). In the identi ed regularity network linking these ve TFs, SOX2 exhibited the highest number of targets among candidate TFs. Additionally, we surveyed the proteomics databank "BioGrid" to know about potential interactions between these ve core candidates together with the list of 53 TFs subject to a positive selection process in domesticated mammals (Table  4 , central column) and the list of 66 TFs targeting a signi cant number of genes positively selected in domesticated mammals (Table  4 , right column) (Supplemental Data File 5; sheet 1 to 5). We found that SOX2 exhibits by far the highest number of partners among both lists (Table  4 , Fig.
Clinical data (age, sex and clinical symptoms) were collected using information communicated on the order form. Sterile swabs with liquid Amies culture medium were used to sample the affected animals, and were sent to the laboratory under cooled conditions. There, swabs were plated on solid culture media (Columbia agar additioned with 5 % sheep blood and colistine + nalidixic acid (CNA) under an extractor hood. Solid culture media were incubated at 35°C under 5% enriched CO2 atmosphere during 24 to 48h. Isolates belonging to the Corynebacteria of the diphtheriae complex form dry colonies of dark yellow color on the CNA culture medium. The identity of the suspected colonies was confirmed by Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS, Bruker Daltonics, Germany).
Antibiotic susceptibility testing was performed by disk diffusion on Mueller-Hinton culture medium supplemented with 5% blood following the instructions of the French AFNOR norm NFU-47. Diameters of the inhibition zone were read and interpreted using software tool SIRWeb (i2A, France   (Marosevic et al. , 2020a). Therefore, clindamycin was only tested for C. diphtheriae and C. rouxii. As there are no breakpoints for veterinary fluoroquinolones and cefovecin, these antibiotics were not tested. All Cdc isolates were sent to the National Reference Center for corynebacteria of the diphtheriae complex for confirmation of the identification and for the detection of the diphtheria toxin tox gene by real time PCR  (Badell et al. , 2019). This multiplex assay consists of amplifying a fragment of the rpoB gene with primer sets specific for either (i) the species C.
, 2010). Corynebacterium guidelines in humans recommend the use of beta-lactams or macrolides. Yet, while chronic human carriers can be treated with azithromycin or rifampicin, the use of the latter is forbidden in the veterinary field. Recent data suggest to use spiramycin in cases of animal infection by C. ulcerans. A 10-day course of the combination of spiramycin and metronidazole was successful to clear C. ulcerans from a dog, and a 6-day course of the same antibiotic combination was successful in cats  (Abbott et al. , 2020; UK Health Security Agency, 2022). As spiramycin only exists in a combination with metronidazole, and as metronidazole has side effects (neurotoxicity and effect on the microbiote), azithromycin seems to be a better choice for treatment. The efficiency of the antibiotic treatment should be verified ideally by 2 samples, taken 5 to 7 days following completion of the antibiotic course.
Funding This work was supported financially by the  French Government 's  Investissement d'Avenir program Laboratoire d' Excellence "Integrative Biology of Emerging Infectious Diseases"  ( ANR-10-LABX-62-IBEID ). This work used the computational and storage services provided by the  IT department at Institut Pasteur. The National Reference Center  for Corynebacteria of the diphtheriae complex is supported by  Institut Pasteur  and  Santé publique France (Public Health France). Initial microbiological analyses and logistics for referring isolates to the  National Reference Laboratory  were supported financially by  Cerba Vet. MH was supported financially by the PhD grant "Codes4strains" from the  European Joint Programme One Health , which has received funding from the  European Union 's  Horizon 2020 Research and Innovation Programme  under Grant Agreement No.
Criteria for Inclusion in the Study For inclusion in the study, patients had to present with a positive stool examination for S. stercoralis larvae, along with a complete set of data (demographic, epidemiological, clinical, and laboratory) that had been collected at their first visit to the clinic. According to these criteria, 69 file records were extracted from the department database. The covered period ranged from 1991 to 2013. Forty-eight patients attended the posttreatment followup consultation.
Statistical Analysis Statistical analysis included descriptive statistics and the analysis of the variation in 4 parameters following anthelmintic treatment. These variables were the clinical score (see above), the level of blood eosinophilia and serum total IgE, and the result from immunodiagnosis, either by IFAT or ELISA. The statistical package Intercooled Stata™ (StataCorp LLC, College Station, TX, USA) was used for statistical analysis. A comparison of the studied parameters was made by the Wilcoxon signed-rank test or Cochran's Q test as appropriate. Since the Wilcoxon test is not parametric, only the median and the interquartile range [IQR] values, and not the mean and standard deviation values, of continuous variables were displayed in tables.
Animals Data collection took place in July-October 2020 (Study 1) and June-September 2021 (Study 2). Both studies were conducted in the same Danish conventional herd producing crossbred (Landrace & Yorkshire × Duroc) piglets. Prior to farrowing, the sows were kept loose in farrowing pens measuring 3. 1 × 2. 8 m, where they remained with their litter until weaning. In the first week post-farrowing, i. e. , during the experiments, the sows were crated. The piglets included in the studies were 3-4 day old on the day of testing (with day 0 defined as the day of birth of the last piglet in the litter), and weighed between 0. 94 and 2. 68 kg (1. 72 ± 0. 3 kg, mean ±SD). Piglets weighing less than 0. 8 kg or more than 2. 7 kg were not included in the study, to ensure that all piglets would properly fit in the castration bench.
Data collection 2. 6. 1. Social motivation test (Study 1 and 2) Indicators of social motivation were measured in a test situation involving the crossing of an open arena to reach siblings in a heated area, referred to as social motivation test. Immediately after (sham) castration, each piglet was transported to the test area (a corridor outside the farrowing room, adjacent to the area were piglets were castrated), using a plastic box layered with straw and placed on a cart. The test was performed in an arena (2. 4 × 0. 8 m) at one end of which three randomly chosen, non-experimental, littermates were placed in a heated, straw-bedded enclosure (0. 4 ×0. 8 m) delimited with a grid. Three obstacles (4 cm wide wooden laths with increasing heights: 5, 7, and 9 cm) were scattered along the arena (Fig.
Letters or numbers indicate significant differences in pairwise comparisons, as further explained in footnotes to tables and figures. Analyses were performed using SAS 9. 4 (SAS Institute Inc, Cary, NC, USA) with a significance level of 0. 05. Results are presented as overall F-(linear mixed effects models) or χ 2 -tests with corresponding P-values together with raw averages ± standard errors (SE). The dataset used for statistical analysis is available in supplementary materials. Trembling and/or quick and involuntary contraction of muscles under the skin (spasm). An event is defined as either one shivering/contraction or a set of contractions separated by less than 1 s Rump scratching Rubbing the rump against the floor or the pen walls Self-scratching Scratching of the rump or lower belly area with a hind-leg Tail wagging Up and down or side to side movement of the tail, with a range superior to body width.
Acknowledgement The study was commissioned and funded by the  Danish Veterinary and Food Administration (DVFA)  as part of the agreement with  Aarhus University  on research-based policy support, as well as by  Aarhus University. The authors thank the  Danish pig farmer Niels Aage Arve  and his staff for providing piglets and facilities for the study, as well as the technicians from  Aarhus University  involved in the project.
Statistical Analyses Inter-isolate differences in the life traits and fitness measures were compared across each of the environmental conditions, and their relative patterns of phenotypic expression were presented on radar graphs. Intra-isolate comparisons were also carried out to identify variations in the isolate's performance across different environmental conditions. Statistical analyses were based on a general linear model (GLM) with SPSS software Version 11. 5. Factors included the breed of sheep, isolate and climatic conditions. ANOVA was also performed on each of these factors. The FEC and fitness variables were log-transformed prior to analyses to normalize variance.
5  [9]  and BD1/28S1R  [77] , respectively. PCR products of the expected size were sequenced twice and from both sides (forward and reverse), using Sanger sequencing (Genoscreen, Lille, France) with the same primers. Each obtained consensus sequence was subjected to a BLAST search  [3] , after visualization in BioEdit 7. 0. 9. 0 software  [33] , clarification of ambiguous bases, and Clustal W alignment using MEGA 10. 1. 8  [45]. All sequences the diversity of were submitted to GenBank and assigned accession numbers.