dataesr/scientific-paragraphs-categorization huggingface dataset:
2. 7  [34]. Two independent runs were performed for 10,000,000 generations and sampled every 500th generation. The burn-in was set for the first 25% of the sampled trees. Bayesian analyses were executed online on NGPhylogeny. fr  [52]. Two analyses of molecular variance were carried out on Cryptocotyle lingua samples to assess the presence of different populations. The first analysis was based on the Cryptocotyle spp. populations from the different geographical areas, the second on the different fish species. Pairwise genetic differentiation of C. lingua was estimated with the fixation index (F st ), using ARLEQUIN 3. 5 software  [25]. This parameter ranges between 0 and 1, in which F st = 0 indicates no differentiation between the populations, and F st = 1 means complete differentiation among the sequences of the different populations.
Pairwise comparisons of F st (assuming that p < 0. 05 indicates a significant difference) were based on 1,000 permutations of the data matrix. Then, Tajima's D neutrality test  [82]  and Fu's Fs  [26]  were calculated to verify the null hypothesis of selective neutrality, using DnaSP 6. 12. 03 software  [71]. Estimation of the population genetic diversity of C. lingua among sampling areas and among fish species was inferred from mtDNA cox1 gene and ITS region rDNA sequence data sets with the following parameters: number of haplotypes (Nh), nucleotide diversity (p), haplotype diversity (Hd), average number of differences (K), number of polymorphic sites (S). All parameters were estimated using DnaSP 6. 12. 03 software  [71]. Haplotype network constructions were carried out using PopART 1. 7 software  [51]  based on cox1 sequences gene (269 bp).
Molecular identification Sequence analysis of the mtDNA cox1 gene locus (320 bp) was successfully obtained on 1,034 metacercariae out of the 1,909 analyzed, allowing the identification of the parasite species. Likewise, PCR of the ITS region of rDNA from 255 parasites (95 identified parasites) resulted in a product of approximately 1,500 bp long. Sequences of the cox1 gene and ITS region were deposited in GenBank under accession numbers MZ731829-MZ731932 and MZ595783-MZ595830, respectively. BLAST search (Supplementary data 2 and Table  5 ) of the cox1 fragments (performed in February to May 2021) led to an average of 99. 83% similarity with 4 GenBank sequences corresponding to C. lingua samples from Denmark (928 sequences), 99. 41% similarity with 13 GenBank sequences corresponding to C. lingua from Europe (Ireland, UK, Norway, Denmark, France, and Sweden), Canada and the USA (72 sequences), and 98.
67% similarity with a GenBank sequence of C. lingua from Russia (14 sequences). Four sequences were identified as Cryptocotyle concava with 99. 5% similarity with GenBank accession Nos. MT422312 (C. concava. Russia: White Sea), and MT422306 (C. concava, Varangerfjord, Norway). Four sequences showed only a low similarity value (79%) with sequences of other Heterophyidae (KT883857, Pholeter gastrophilus and LC422949, Metagonimus sp. ). Likewise, three sequences had a low similarity value (74. 94%) with AY504855 and AY504859 (Larval bucephalid sp. ). BLAST analysis (Supplementary data 2 and Table  5 ) of the ITS fragments (carried out from April to May 2021) led to an average of 99. 8% similarity with 7 GenBank sequences corresponding to C. lingua from Danish seas and the English Channel, France (76 sequences).
99. 81% similarity was found with 1 GenBank sequence corresponding to C. lingua from the White sea. 92. 80% similarity was obtained for 1 sequence with a GenBank sequence corresponding to Bucephalus margaritae and an average of 88. 46% similarity was found for 14 sequences with a GenBank sequence of Bucephalus polymorphus. Cryptocotyle lingua identifications were confirmed with both markers for 71 individuals. The ML, NJ, ME and Bayesian methods produced phylogenetic trees with similar topologies. Only the ML tree is presented in this manuscript. The cox1 (Fig. 5A ) and ITS (Fig. 5B ) trees had the highest log likelihoods of À2466. 53 and À5763. 65 (Fig. 5 ), respectively. Phylogenetic trees based on nucleotide sequences of the cox1 gene (Fig. 5A ) and ITS region (Fig. 5B ) showed that all the sequences identified as C.
15 ) with the commercial antibody we had used and that was previously used by others  38. This has prevented us from concluding if NUFIP is present in Bif, and the data has been removed from the current manuscript. In addition, a recent study has questioned the role of NUFIP as a ribophagy receptor  39. We next assessed if these structures could result from enhanced autophagy. Using siRNA we managed to partially deplete the autophagy-initiation protein Beclin1 (Supplementary Fig. 16 ), which is essential for initiating autophagy. We quantified the number of Bif in wild-type infected cells at 48 h post-infection, using NVL as a marker. We found a clear reduction in the number of NVL-positive Bif in the absence of Beclin1 (Fig. 6a ), consistent with an autophagy-derived process. To determine if Bif could correspond to autophagosomes, we labelled with either lysosomal-associated membrane protein 1 (LAMP1) to detect lysosomes or the microtubule-associated protein light chain 3 (LC3), a commonly used marker for autophagosomes.
abortus or c 48 h. Mock-infected cells are included as controls. Data are represented as means ± 95% confidence intervals from four independent experiments. Each experiment is colour coded and all events counted are shown. Data were analysed using one-way ANOVA by including all comparisons with Tukey's correction. Not all comparisons are shown. d Representative images of NVL cytoplasmic punctate accumulation (white) in HeLa cells treated with control siRNA (top) or depleted for SENP3 (bottom) followed by infection for 48 h with B. abortus expressing DSRed. Scale bars correspond to 5 μm. e Quantification of the number of NVL-positive Bif in HeLa cells pre-treated with control siRNA or an alternative siSENP3(b) mix, siBeclin or siPIAS3 and infected for an additional 24 h with wild-type B. abortus.
Data correspond to means ± 95% confidence intervals from five independent experiments. Data were analysed using one-way ANOVA by including all comparisons with Tukey's correction. f HeLa cells depleted for Beclin or PIAS3 or treated with the control siRNA for 48 h were infected with wild-type B. abortus expressing DSRed and the percentages of cells with either 1-5, 6-10 or more than 10 bacteria per cell were quantified by microscopy at 48 h post-infection. Data correspond to means ± 95% confidence intervals from five independent experiments. A two-way ANOVA with Bonferroni correction was used to compare each condition to the siControl-treated cells. The p values are indicated in the graphs (a-f), and not significant (ns) corresponds to p > 0. 05. g NyxA/B are translocated into host cells, being detected on the vacuolar membrane, in the vicinity of replicating bacteria and in the nucleus.
Lastly, they were mounted on a slide with ProLongGold (Life Technologies). The coverslips were visualised with a Confocal Zeiss inverted laser-scanning microscope LSM800 and analysed using ImageJ 54 software and final figures were assembled with FigureJ  55. Note that neither blocking nor antibody solutions did not contain Triton (only the permeabilisation step). It is important to point out that occasional intravacuolar labelling was observed in weak DSRed bacteria, perhaps indicative of fragile BCVs. The same protocol was done for NUFIP1. For all other antibodies, when used in the absence of 4HA or 3Flag for translocated effectors, cells were permeabilised with a solution of PBS containing 0. 5% triton for 20 min followed by blocking for 20 min in a solution of PBS containing 2% bovine serum albumin (BSA), 10% horse serum, and 0.
Legionella infection Legionella pneumophila strain Paris was cultured in N-(2-acetamido)-2aminoethanesulfonic acid (ACES)-buffered yeast extract broth or on ACES-buffered charcoal-yeast (BCYE) extract agar  56. The human monocyte cell line (THP-1) was cultured and infected as previously described  57. For immunofluorescence analyses, cells were fixed in 4% paraformaldehyde, permeabilised with PBS-triton 0. 5% and stained with 4-6diamidino-2-phenylindole (DAPI), Phalloidin and primary anti-NVL antibody (16970-1-AP). Immunosignals were analysed with a Leica SP8 microscope at ×63. Images were processed using ImageJ software.
Quantification of SENP3 localisation Colocalisation analysis for the transfected HeLa cells was performed with a custom ImageJ/Fiji 59 -based macro (http://c2bp. ibcp. fr/CL_ ArthurL_coloc_2-corr. ijm), that segmented the nuclei and the nucleoli of the cells in each image, classified the cells in two classes according to the intensity of HA-NyxA/NyxB, and then measured in the areas of each nucleus the Pearson correlation coefficients (by calling the plugin Coloc2-https://github. com/fiji/Colocalisation_Analysis) between the signal of SENP3 and the nucleolin as well as between the signals of SENP3 and HA-NyxA/NyxB. For each nucleus, the ratio between the mean intensity of the SENP3 signal in the nucleoli and the mean intensity of the SENP3 signal outside the nucleoli is also calculated. The details can be found in the source code and the comments of the macro.
Crystallisation and data collection The screening was conducted using a Mosquito workstation (TTP Labtech) on commercial crystallisation solutions with the sitting-drop vapour diffusion technique, against a protein solution. All crystallisation trials were performed at 19 °C and visualised on RockImager 182 (Formulatrix). Crystals of native NyxB were obtained with 21 mg/ml NyxB in 25% PEG4000, 0. 2 M CaCl 2 , 100 mM Tris pH 8. Crystals were frozen in a reservoir solution supplemented with 15% Gly. Diffraction data were collected at the European Synchrotron Radiation Facility (ESRF) Beamline line ID23EH1 and crystals diffracted up to 2. 5 Å resolution in space group P6 1 22, with 12 molecules per asymmetric unit. Crystals of Se-Met NyxB were obtained using a reservoir solution containing 2.
Twelve monomers were positioned and the resulting electron density map was then subjected to the AutoBuild programme, part of the Phenix programme suite. Model building was completed with sessions of the manual model building using Coot combined with model refinement using Phenix  65. The final model was refined to a final R work /R free of 0. 21/0. 24 with excellent geometry (Supplementary Table  2 ). The coordinates and structure factors of NyxB have been deposited in the protein DataBank with code 8AF9. Figures were generated with Pymol, Molecular Graphics System, Version 2. 0 Schrödinger, LLC.
, Santa Barbara, CA). Small-angle X-ray scattering SAXS data were collected for NyxA and NyxB on BioSAXS beamline BM29, ESRF using an online size-exclusion chromatography setup. 50 µl of protein (10 mg ml -1 ) were injected into a size-exclusion column (Agilent BioSec-3) equilibrated in 50 mM Tris, pH 8. 0, 200 mM NaCl. Images were acquired every second for the duration of the sizeexclusion run. Buffer subtraction was performed by averaging 20 frames on either side of the peak. Data reduction and analysis were performed using the BsxCuBE data collection software and the ATSAS package  66. The programme AutoGNOM was used to generate the pair distribution function (P(r)) and to determine D max and R g from the scattering curves (I(q) versus q) in an automatic, unbiased manner. Theoretical curves from the models were generated by FoXS  67.
Graphs, statistics and reproducibility For microscopy counts of individual cells, super plots were used  72. All data sets were tested for normality using the Shapiro-Wilkinson test. When a normal distribution was confirmed we used a One-Way ANOVA test with a Tukey's correction for multiple comparisons. For two independent variables, a Two-Way ANOVA test was used. For data sets that did not show normality, a Kruskal-Wallis test was applied, with Dunn's correction. All analyses were done using Prism Graph Pad 7. For all microscopy, data were obtained from at least three independent experiments, and for all western blots data was reproduced in two independent experiments. and Myc antibodies developed by Bishop, J. M. were obtained from the Developmental Studies Hybridoma Bank, created by the NICHD of the NIH and maintained at the University of Iowa.
GFP-SENP3 was a gift from Mary Dasso (Addgene plasmid #34554; RRI-D:Addgene_34554). CB lab was funded by the Institut Pasteur and ANR-10-LABX-62-IBEID for the Legionella experiments. We acknowledge the contribution of the SFR Biosciences (UAR3444/CNRS, US8/ Inserm, ENS de Lyon, UCBL) facilities: Protein Science Facility for mass spectrometry and crystallography experiments and the Plateau Technique Imagerie/Microcopie (PLATIM) for all microscopy studies.
Acknowledgements We would like to thank  Rémi Lagorce  for help with the purification of the N-terminus of  SENP3 ,  Inès Bordin  for the optimisation of the expression conditions of NyxB,  Marie-Pierre Candusso  and  Mégane Guinot  from the  Protein Science Facility  of  SFR Biosciences  for help with protein purification of NyxB and crystallography experiments. We are grateful to  Gunnar Schroeder  ( Queen's University of Belfast ) for the pMMB 207c,  Renée Tsolis  ( University of California, Davis ) for the pFlagTem,  Matthias Faure  ( CIRI, France ) for the LC3-GFP expression vector,  Xavier de Bolle  ( University of Namur ) for the pNPTS138 and  Jean Celli  ( Washington State University ) for the pUCTminiTn7T_Km. We are also thankful for the HEK NUFIP KO cells gently provided by  Heeseon An  and  Wade Harper  ( Harvard University, USA ) and for the iBMDM by  Thomas Henry (CIRI, France).
The LAMP1 We thank staff scientists from beamlines Proxima-2 (synchrotron SOLEIL), ID23EH1 (ESRF), and  BM29  ( ESRF ) for assistance with data collection. These effectors were discovered under the  ERA-Net Pathogenomics grant  and the remaining work funded by  ANR-15-CE15-0011-01  attributed to  Suzana Salcedo. The work was completed with the  ANR  SNAPshot  ANR-21-CE15-0024  attributed to  Suzana Salcedo. We also thank  Steve Garvis  and  Stéphane Méresse  for critically reading the manuscript. Jean-Paul Borg  is a scholar of the  Institut Universitaire de France.
Code availability The pipeline code for image analysis of SENP3 in infected cells can be downloaded as a Cell Profiler project at http://c2bp. ibcp. fr/arthur2. cpproj. This file can be opened with the software CellProfiler 3. 0. 0 (available at https://cellprofiler. org/, following the instructions at https://cellprofiler. org/getting-started) and contains all the steps used to analyse the images. Colocalisation analysis for the transfected HeLa cells was performed with a custom ImageJ/Fiji macro (http://c2bp. ibcp. fr/CL_ ArthurL_coloc_2-corr. ijm) as described in the "Methods" section. All the information can be found in the macro.
Considerably higher prevalence was calculated for pens and farms, respectively, being positive for STEC-2e than for those being EDEC-positive since many samples only provided STEC-2e bacteria devoid of the fedA gene and whole DNA specimens that proved positive only for stx2e. These findings corroborate previous reports by our group and those of others  [15, 51]. In a paper from China even 96% of the investigated STEC-2e isolates did not encode for F18 fimbriae  [52]. In an earlier study, we confirmed by DNA-DNA hybridization that fedA was really missing in STEC-2e isolates that tested fedA-negative by PCR (data not published). We therefore assume for the present study that negative PCR results for F18 fimbrial genes were not caused by primer mismatches at the binding sites within target gene fedA although this assumption awaits direct experimental proof.
MALDI-TOF mass spectrometry All putative E. coli isolates that tested PCR-positive for stx2e were assessed for their species assignment by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) on a Microflex LT mass spectrometer system (V3. 3. 1. 0, Bruker Daltonics, Bremen, Germany). MALDI-TOF MS was performed according to manufacturer's instructions. The spectra obtained were compared against reference spectra of a commercial MALDI Biotyper database (MBT 7854 MSP library; Bruker Daltonics). A score value ≥ 2. 0 indicated species identification; a score value of 1. 7 up to 2. 0 indicated genus identification, and a score value < 1. 7 indicated no identification.
Farms were considered positive when at least one pen was classified as positive. The positive classification of samples, pens and farms was done assuming that the specificity of the test system (DNA detection using PCR) was 100%. A distinction was also made between (a) finding of STEC-2e or EDEC by bacterial culture, (b) finding of stx2e or stx2e/fedA by PCR in DNA extracts, and (c) a complete evaluation of all samples taken, and all laboratory techniques applied. Statistical prevalence was assessed using the software packages SPSS v25 and STATA v15. Frequencies with 95% confidence intervals were generated for all previously created sample classification variables.
Patients and Methods We conducted an open survey (single arm, observational survey) among 391 subjects from 4 countries (Italy, Poland, Slovenia, Croatia), either hairdressers or hairdresser-related professionals using hairdresser products: (i) We collected in an initiation visit information regarding (1) daily procedures, (2) the frequency, type and severity of hand issues associated with these procedures such as dryness, redness, irritations, cracks, and fissures, and (3) usage of gloves during the procedures to protect from alteration of the skin barrier function due to repeated contact with water, shampoos and other hairdresser products (National Clinical Trial NCT05471934). (ii) We also evaluated the satisfaction provided by a dermocosmetic containing niacinamide (soothing agent also reinforcing the skin barrier), glycerin (for hydration), shea butter (nourishing agent also reinforcing the skin barrier) and thermal spring water (soothing agent) after up to one month of application (evaluation visit).
Data Sharing Statement Individual data are anonymized. These data cannot be used alone. A subgroup analysis can be implemented according to pre-specified objectives. Demographic and evaluation data (efficacy and tolerance) are available from the corresponding author upon reasonable request. Other study documents including data base, protocol and conclusions will be made available. Data will be accessible on request and after request evaluation by the study sponsor. The sponsor reserves the right to refuse if the objective is not admissible. Upon provision, a secure link will be provided. Data will be made available for 10 years.
The procedure to select the variables for the final multivariable model is described in  [28]. In brief, univariable associations were tested and the variables with p<0:2 were retained to be included in the multivariable analysis. The least significant variables were then removed using a backward and forward stepwise procedure. Only variables with p<0:05 were retained in the final model. Concerning the occurrence of reproductive disorders, bovine brucellosis status of the farm and farm size were considered as risk factors and tested directly in a multivariable analysis. Statistical analysis were performed using the RStudio software version 1. 4. 1717 and the epiR, car, and MASS packages  [29]. The georeferenced maps were obtained in shape file format and scale 1 : 50,000 from the Geoportal of the Ecuadorian Military Geographic Institute (http://www.
Acknowledgments Data collection and fieldwork was undertaken by veterinary students from the  Universidad San Francisco de Quito, Ecuador  and local health technicians. Laboratory diagnosis was conducted by the  National and WOAH Animal Brucellosis Reference Laboratory, Anses, Maison Alfort, France. The authors are grateful for the support of  IICA-Ecuador , and the  Asociación de Ganaderos de Quinindé  that facilitated the contact with the participating farmers. We also thank the students Ñusty  Maldonado ,  Elsy Maigua , and  Camilo Gonzales  who collected the milk samples and conducted the interviews.
During the F3 rags condition, we provided wildcats with F3 on rags immediately before the beginning of each daily session of behavioural data collection. After that, during the new visual object condition, we used five white blocks hung on the outside of the enclosure mesh in the same positions as the cloth rags to ascertain whether any effect had been due to the presence of such novel objects (Figure  1B ). The cats could observe and smell the objects, but they could not reach, manipulate, or play with them. enclosure mesh in the same positions as the cloth rags to ascertain whether any effect had been due to the presence of such novel objects (Figure  1B ). The cats could observe and smell the objects, but they could not reach, manipulate, or play with them. The stimuli were placed on the first day of each condition and were removed at the end of each condition.
Data Collection and Analysis We used continuous focal animal sampling  [34]  to record the duration of individual and social behaviours during all experimental conditions. Behavioural categories are listed in the ethogram (Table  1 ). Each condition lasted five consecutive days. For each experimental condition, we carried out ten 20-min sessions (two per day, one session in the morning and one session in the afternoon, consecutively over five days) for each of the five wild cats. Thus, for each condition, we collected behavioural data of the study subjects during 50 sessions (200 sessions over all four conditions) for a total of 4000 min of observations. Table  1. Ethogram (based on  [33] , modified).
Social inactivity A wildcat sleeps or rests in contact with another subject. Not observed A wildcat is hiding or is not distinctly visible. During the study period, the zoo was open to the public and the behavioural observations were conducted during opening hours, avoiding the fasting day and the following day. The same observer (V. B. ) collected behavioural data throughout the overall study period by carrying out live observations of the study subjects in their social context. Individuals were identified through physical features. The same observer had also collected data on the same study group for our previous study  [33]. We defined the daily time budget, both the total during the overall study period and for each condition, to investigate the differences and similarities of the activity budget across the conditions and to assess the behavioural indicators of wellbeing (i.
e. , positive welfare indicators: species-specific behaviours, meaning the repertoire of behaviours that is shared by virtually all members of a given species; negative welfare indicators: stress-related, self-directed, and abnormal behaviours;  [11] ) of the study subjects. We analysed data using non-parametric statistical tests. Specifically, we used the Friedman test to compare the duration of the behavioural categories between the four conditions. As a post hoc test, we used the Nemenyi test because it is a conservative test that was developed to account for a family-wise error  [32, 35, 36]. We set the significance level at p < 0. 05 and used the statistical software XLSTAT (v. 2020. 4. 1. 1023).
Time Budget The most performed behavioural category by the wildcats over the entire study period was individual inactivity (36%), followed by exploration (19%), and social inactivity (11%). Animals 2023, 13, 1762 6 of 13 Among the other observed behaviours, when considering the overall study period, the least performed behavioural categories were maintenance and agonistic behaviours (around 1% each). Figure  2  shows the total duration as percentages of all the behaviours performed by the study subjects (self-grooming, attention, locomotion, territorial behaviour, social interspecific, not observed). During the entire study period, none of the study subjects displayed abnormal behaviours. level at p < 0. 05 and used the statistical software XLSTAT (v. 2020. 4. 1. 1023).