dataesr/scientific-paragraphs-categorization huggingface dataset:
Expression Omnibus  (GEOThis work was supported by the  Northern Portugal Regional Operational Programme  ( NORTE 2020 ), under the Portugal 2020 Partnership Agreement, through the  European Regional Development Fund (FEDER)  ( NORTE-01-0145-FEDER-000013 ) and the  Fundacão para a Ciência e Tecnologia (FCT)  (contracts  PD/BDE/127830/2016  to CF,  SFRH/BD/120127/2016  to IM,  SFRH/BD/ 120371/2016  to AMB,  IF/00474/2014  to  NSO ,  IF/ 01390/2014  to ET,  CEECIND/03628/2017  to AC,  CEECIND/04600/2017  to CC and  IF/00021/2014  to RS), and  Infect-Era Net  (project  INLEISH ). JE also thanks the  Canada Research Chair program  for financial assistance. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Immunosuppression and environmental risk factors Demographic and clinical data was extracted from the patients' medical records (Divat cohort, approved by the French National Commission on Computing and Liberty DR-2025-087, number 914184;  February 15, 2015). The following variables were recorded: level of immunosuppression according to the type of transplantation, induction treatment, number of immunosuppressive drugs, plasma level of calcineurin inhibitors at inclusion, CD4 lymphocyte count at inclusion, and last available gamma globulin dosage (checked routinely once a year). We also recorded all immunological events that led to an increased immunosuppression as well as clinical manifestations associated with over-immunosuppression, such as BK virus, CMV replication and disease, or P. jirovecii pneumonia.
For each episode of diarrhea, patients filled a self-administered questionnaire including characteristics of diarrhea (duration, number of stools per day), associated symptoms (weight loss, low urine production, fever/chills, abdominal pain, nausea/vomiting, asthenia, headache), and data about their lifestyle. All items covered most of the known risk factors for cryptosporidiosis in the previous six months, allowing gaining further insights into the possible source of contamination. Detailed information about contact with water either used for drinking (mineral, tap water, or untreated), for bathing (swimming pool, river, etc. ), recent history of travel abroad, as well as contact with animals or young children or anyone with diarrhea were investigated. Professional activities were also stratified according to the risk of cryptosporidiosis: activities such as contact with animals or biological fluids were considered as high risk; professions with manual activities or with frequent physical contact with people were considered as medium risk, and retired patients or people with solitary professions were considered at low risk.
Acknowledgements We would like to thank  Bénédicte Borsik  for the statistical analysis. Presentation: parts of this work was presented at the following congresses: (1) 26th ECCMID congress, 2016, Amsterdam, Netherland: poster number  P1668 , (2) 17th JNI congress, 2016, Lille, France: poster number ID 01; (3) 1st SFNDT congress, 2016, Strasbourg, France: poster number  P46.
In addition to the expected product (740 nt), in some cell lines a minor product was amplified. Results for 15 representative cell lines is shown in Fig 3A. Sequencing showed that the minor product (542 nt) lacked 198 nt corresponding to exon 8 and retained the original open reading frame (S1A Fig). Interestingly, 12 of the 30 cell lines analyzed did not yield the 542 nt PCR product. Among these 12 lines, nine were homozygous for the minor rs2304256 allele (AA), one was homozygous for the minor rs12720270 allele (AA) and two were homozygous for both minor alleles (Table  2 ). These data suggested that minor alleles (homozygosity) at rs12720270 and/or rs2304256 promote the inclusion of exon 8. Analysis of PBMC samples purified from two genotyped donors confirmed this observation  (Fig 3A). To further assess the effect of the nucleotide variations on exon 8 and exclude potential influence of other polymorphisms on transcript abundance or splicing, we turned to the minigene assay (Cooper, Methods 2005).
Rs2304256 is associated with increased TYK2 Having shown above that rs2304256 and rs12720270 favour exon 8 inclusion, we wondered if these variants contribute to a higher level of global TYK2. Interestingly, in the Genotype-Tissue Expression (GTEx) database, rs2304256 is associated with a modest increase of TYK2 in several tissues (S1 Table ), including whole blood (Fig  6A ) (https://gtexportal. org/). We therefore performed an eQTL analysis using TYK2 NanoString data obtained on whole blood of 1000 healthy donors of European ancestry (Milieu Interieur cohort)  [27, 28]. In non-stimulated blood, rs2304256 showed a tendency toward higher TYK2. The effect was modest but significant (P = 0. 0048) (Fig 6B ).
The nucleotide variation may at the same time disrupt an ESE recognized by SF2/ASF (CAGTCGGC). Interestingly, among the 13 human immune cell types analyzed in the DICE project (https://dice-database. org)  [37] , SRp55 was found to be particularly abundant in naïve B cells. The genotyped cell lines and primary cells we have analyzed (carriers of major alleles) exhibit a very low level of the alternate transcript ΔE8 relative to full-length TYK2 (Figs  3  and 5 ). The low-abundance ΔE8 transcript may result from noisy splicing  [38, 39]  and may have no biological implication. However, we do not favour this hypothesis, since the alternate ΔE8 transcript is protein-coding, not subject to nonsense-mediated decay and potentially functional. Alternative splicing is most often cell-specific, tissue-specific or stimulus-induced and the possibility exists that TYK2 ΔE8 is more abundant and functionally relevant in cells possessing a proper repertoire of splicing regulatory factors.
Genic regions located between exons from the pseudo-transcript were then used as introns. Quantification of gene expression from exonic parts and introns was done using HT-Seq  [64]. For the quantification of splice junction, we used the filter_cs script from leafcutter package  [65]  to extract all spliced reads with an overhang of at least 6 nucleotides into each exon and count reads across each exon-exon junction. EQTL analyses were performed using Matrix EQTL  [66] , including for population of origin as a covariate. TYK2 mRNA levels were measured in whole blood of healthy donors from the Milieu Interieur cohort by the NanoString hybridization-based multiplex assay  [28]. The Milieu Interieur cohort is composed of 500 men and 500 women from 20 to 69 years of age  [67, 68]. The NanoString TYK2 probe is complementary to the exon 3/exon 4 junction: GGGCCTGAGCATCGAAGAGGGCAAAGAGATTGAAGCAAGGAGGAGTGATACCAACTTTATG TGCAATGTGGATGCAGACTTCCTCAGCTGTCAGCGATGA.
Funding: Research in the Unit of  Cytokine Signaling  funded by the  Institut Pasteur , the  Fondation pour la Recherche Medicale (Equipe FRM   DEQ20170336741 ) and the  Institut National de la Santeet de la Recherche Medicale (INSERM). ZL is supported by the  Centre National de la Recherche Scientifique (CNRS). Research in the  Unit of Human Evolutionary Genetics  funded by the  Institut Pasteur , the  French Government 's  Investissement d'Avenir program ,  Laboratoires d'Excellence "Integrative Biology of Emerging Infectious Diseases"  ( ANR-10-LABX-62-IBEID ), " Milieu Interieur " ( ANR-10-LABX-69-01 ) and the  Fondation pour la Recherche Medicale (Equipe FRM   DEQ20180339214 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Comparable catalytic activity was indicated by the basal P-TYK2 in non-treated samples (Fig 2B). arthritis; IBD: inflammatory bowel disease; AS: ankylosing spondylitis; IIM: idiopathic inflammatory myopathies. https://doi. org/10. 1371/journal. pone. 0225289. t001 a Major and minor allele in European population and (+) strand nucleotide. b Minor allele frequency, according to Ensembl database. c Odds ratio (OR) for the minor allele. Abbreviations, TK: tyrosine kinase; MS: multiple sclerosis; SLE: systemic lupus erythematosus; T1D: type I diabetes, RA: rheumatoid.
LC-MS/MS system & analysis procedure The chromatography and mass spectrometry detection were performed as previously described [19]. The multiple reaction monitoring transitions were as follows (precursor ion (m/z) → product ions (m/z) (collision energy (%)): 158. 1 → 67. 2 (25), 95. 1 (16), 123. 2 (10) for tranexamic acid and 144. 1 → 81. 1 (22), 109. 4 (15), 126. 1 (11)  for the internal standard; the first transition being used for quantification. Data acquisition and processing were performed using Xcalibur v4. 2. 28. 14 (Thermo Fisher Scientific).
Accuracy & precision Accuracy (measured concentration/nominal concentration) and precision (CV) were calculated for the QC and the LLOQ. Each QC level was processed six-times the same day for the intraday assay and on three different days for the interday assay. The data were analyzed using variance analysis (ANOVA). Accuracy had to be within 85-115% of the nominal concentrations and precision of ± 15%. For the LLOQ, an accuracy between 80-120% and a precision of ± 20% were accepted.
Analysis of study samples To confirm the suitability of the method for the analysis of clinical samples, it was applied to measure tranexamic acid concentration in whole blood samples from five volunteers participating in a clinical trial (PharmacoTXA, NCT03777488). Patients gave written inform consent for their participation to the study. Those patients received either 1 g TXA through the intravenous or intramuscular route or 2 g through the oral route and one liquid whole blood sample and one capillary blood sample on a VAMS device were collected 3-6 h after drug administration. The liquid blood sample was obtained by venipuncture and stored frozen at -80 • C while the fingerstick method was used for VAMS capillary blood sampling and the devices stored at ambient temperature.
Calibration curve The calibration range has been determined with the eight calibration standards in the range 0. 1-1000. 0 mg/l. The data were fitted with an ordinary least square model, as guided by the visual inspection of the graphs plotting the peak area ratios of tranexamic acid to the IS versus concentration. Data heteroscedasticity were suggested by heterogeneity in the pattern of residuals plotted as a function of the concentration. Therefore, a weighted least square regression model was applied with a 1/x weighing factor  [29]. Means fitted equation obtained from seven  curves for human liquid whole blood and whole blood dried on VAMS devices were y = 0. 00454 ( ± 0. 00058) x -0. 00080 ( ± 0. 00074; mean ± SD) and y = 0. 00572 ( ± 0. 00094) x -0. 00084 ( ± 0. 00054), respectively, with corresponding mean least square linear regression correlation coefficient (r 2 ) of 0.
2. 4. Statistical analysis The data that support the findings of this study are available from the corresponding author upon reasonable request. The highest single-dnDSA MFIs were used in the statistical analysis. Fisher's test was used to assess the putative link between the assay results (FC-XM, C1qScreen TM , and the presence of IgG1 and/or IgG3 subclasses) and morphological features of the biopsy (ABMR and C4d deposits). The threshold for statistical significance was set to p<0. 05. The DSA MFIs for each group were compared using Student's t-test.
Another approach is to use multifunctional CARs which can encode by-products, such as cytokines, to augment tumor killing. CAR antigens have to be expressed on the cell surface but most solid tumor antigens are intracellular, so lessons can be learned from the use of TCR transgenic T cells. The first report of autologous T cells transduced with a TCR directed against the NY-ESO-1 antigen showed remarkable tumor regression in patients with synovial cell sarcoma or metastatic melanoma. 2 Patients who demonstrated responses to therapy were those with T cell persistence. Poor persistence of transferred CD8+ cells and insufficient CD4+ T cell support are two key challenges of adoptive T cell therapy. In a currently ongoing trial (NCT03691376), autologous engineered hematopoietic stem cells with tumor-recognizing CD4 TCRs are being used for long-term support of NY-ESO-1 CD8 TCR transduced T cells in recurrent or treatment-refractory ovarian cancer, with the aim of promoting long-term persistence of TCR T cells.
For instance, the diet may exert a direct positive effect on the immune system for example, antineoplastic effects exerted by polyphenols. A plant-based high-fiber diet is consistent with current dietary recommendations in cancer, although these recommendations are primarily based on data on cancer prevention. Future studies should prospectively investigate the effects of dietary fiber on the gut microbiome and immune response in the setting of immune checkpoint inhibitors. Diet should be assessed in all observational microbiome cohorts and both habitual diet and baseline microbiota may influence response to microbiome modulation interventions including FMT and probiotic use. In conclusion, the gut microbiota and its metabolites may mediate the effect of diet. The function of the microbiome is more important than its composition and this is shaped by diet.
For surface CX3CR1 staining on circulating monocytes, lysed blood cells were incubated or not with 50, 100, or 200 nM murine CX3CL1-AF647 (Almac, Edinburgh, Scotland) for 30 min at 37 • C. Cell were washed once in PBS and cell surface staining was performed using Panel-2 (Supplemental Table  1 ). When circulating Mo were not incubated with CX3CL1-AF647, CX3CR1 was detected using Anti-CX3CR1-PE. Specificity of CX3CR1 staining was controlled using either CX3CR1-deficient Mo isolated from Cx3cr1 EGFP/EGFP mice or incubating CX3CR1proficient Mo in the presence of unlabeled CX3CL1 at 1µM before staining. Sample acquisitions were performed on the LSRFortessa X-20 Flow cytometry (BD) using FACSDIVA software (BD), and data were analyzed with FlowJo software (BD) and Cytobank analysis platform (21) (Beckman Coulter, Santa Clara, CA).
ACKNOWLEDGMENTS This work was supported by grants from  Inserm ,  Sorbonne University, Fondation pour la recherche Médicale Equipe labelisée , and from  Agence Nationale de la Recherche , project  CMOS (CX3CR1 expression on monocytes during sepsis) 2015  ( ANR-EMMA-050 ). AM-K was supported by post-doctoral fellowship both from the  ANR  and  FRM.
Microcomputed tomography (microCT) Bone biopsies of patients with SM, still in the fixative, were scanned on a computerized microtomograph (Skyscan 1172, Bruker microCT, Kontich, Belgium) according to previously published protocol applied to human bone biopsies  [13, 19]. The following parameters were determined with the Ct-An 1. 11 software: bone volume fraction (BV/TV3D, in %), trabecular thickness (Tb. Th3D, in mm), number (Tb. N3D, in /mm) and separation (Tb. Sp3D, in mm), Trabecular Bone Pattern factor (Tb. Pf, an index of trabecular connectivity) and structure model index (SMI) that quantifies the plate-versus-rod characteristic of trabecular bone.
Acknowledgments The authors also thank  Mrs Stéphanie Lemière  and  Nadine Gaborit  for their skillful technical assistance with microCT and histotechnology. Many thanks to all the MD who send us patients for the diagnosis of their disease:  E. Hoppé ,  C. Masson ,  R. Levasseur ,  A. B. Beucher ,  M. Drouet  and  A. Schmidt-Tanguy  from our  University Hospital.
Data acquisition was performed on an EPICS-CYAN flow cytometer (Beckman Coulter France S. A. S. ), and data were analyzed using Summit 4. 3 software. The DiI and APC fluorescence intensities were recorded on the FL2 and FL8 channels, respectively. Quadrants were determined based on the negative control staining with a corresponding isotype Ab. Fluorescence-activated cell sorting (FACS): cell sorting was performed on a FACS ARIA III sorter (Beckman Coulter France S. A. S. ). Spheres were dissociated, and the single-cell suspension was adjusted to a concentration of 10 6 cells/mL in RPMI. After excluding cell debris, the collection gates were set according to the negative (DiI-negative) control cells. Cells with positive fluorescence corresponded to the DiI-positive cell subset. The collected cells were centrifuged, rinsed, and replated for sphere, cell cycle analysis, and in vivo experiments.
Statistical analyses The results are expressed as the meanstandard error of the mean, and statistical analyses were performed using GraphPad 320 Prism Ò and StatView Ò 5. 0 software (SAS, Cary, NC). Data were analyzed using analysis of variance, followed by Fisher's protected least significant difference post hoc test, with a significance level of P < 0. 05 (*P < 0. 05; **P < 0. 01; ***P < 0. 005; and ****P < 0. 001).
Acknowledgments We would like to thank  Dr. Renata Polakowska  for conceptual and intellectual input and for reviewing the article,  Jean-Pierre Decavel  and  Thierry Chassat  from  PLE-THA , the  Institut Pasteur de Lille animal facility , and  Marie-He  ´lene Gevaert from the histopathological facility core,  Henri Warembourg School of Medicine  for technical assistance. We would also like to thank  Nathalie Jouy  ( Flow Cytometry Platform, Univ Lille, Lille, France ) and  Pauline Ostyn  for their technical assistance.
S1. Data are presented as mean G standard deviation (SD) of at least two independent biological assays, each with 3 technical replicates. Shaded error envelopes depict 95% confidence intervals. (C) EC 50 values of each biological replicate were determined by non-linear regression analysis. EC 50 data are presented as mean G SD from at least 2 independent biological replicates, each with 3 technical replicates. (D) HFF cells were infected with tachyzoites (RH Dku80 UPRT::NLuc-P2A-EmGFP) and incubated with 10 mM AN13762, 5 mM AN3661, or 0. 1% DMSO as control. Cells were fixed 24 h post-infection and then stained with antibodies against the T. gondii inner membrane complex protein GAP45 (magenta). The cytosolic GFP is shown in green. Scale bars, 10 mm. A complete dataset can be found in Figure  S1.
Molecular Docking Suggests a Divergent Resistance Mechanism between Oxaboroles Multiple sequence alignments show a high overall sequence conservation within the metallo-b-lactamase (MBL), Beta-Casp, and RNA specificity domains of CPSF3 within apicomplexan parasites and humans (Figure  4A ). One notable difference between the apicomplexan and human enzyme is the presence of an extended loop or ''apicomplexan specific insert'' whose length varies from 20 to 59 residues. However, conservation of the generated resistant SNVs to AN13762 within T. gondii CPSF3 coding sequence is absolute across species and appears close to the catalytic residues but is never directly involved in the coordination of the catalytic zinc atoms. Next, we visualized the resistance-conferring mutations within the recently obtained structure of Cryptosporidium CPSF3 (ChCPSF3) in co-crystal with AN3661 (pdb id 6Q55)  (Swale et al.
AN13762 Is Active against Cryptosporidium In Vitro and In Vivo The aforementioned data provide evidence that AN13762 targets CPSF3 enzyme. we assessed the anticryptosporidial activity of AN13762 in vitro and in vivo. The ability of AN13762 to inhibit C. parvum INRAE Nluc fast-growing strain in human ileocecal HCT-8 was assessed with its parental scaffold AN3661 as a positive control. Although less potent than AN3661, an efficient in vitro inhibition of C. parvum growth was repeatedly observed with AN13762 (EC 50 13 G 9 mM) (Figures 5A, 5B and S5). AN13762 presented no detectable toxicity for the host cells, even at 100 mM (Figure  5C ). AN13762 activity was therefore assessed in vivo in a neonatal mouse model. Seven-day-old neonates were orally treated with AN13762 mixed in carboxymethyl cellulose (CMC) 4 h after C.
gondii parasites. EMS-mutagenized population of T. gondii tachyzoites was selected in the presence of a lethal concentration of AN13762 to isolate drug-resistant parasites. Analysis of the parental wild-type strain and multiple resistant clones by variant-calling of sequencing reads generated by RNA-seq to identify EMS-induced mutations in coding sequences conferring drug resistance. (B) Schematic of the strategy used to obtain T. gondii-resistant parasites to AN13762. From each mutagenesis experiment a single clone (A1 to F1) was isolated and analyzed by RNA-seq. (C) AN13762-resistant parasites form plaques after 7 days of growth in the presence of 10 mM AN13762. Complete dataset in shown in Figure  S2A. (D) Quantification of plaque sizes of wild-type parasites and resistant lines (A1 to G1) when cultured in the presence of AN13762.
In the second outermost track, lines depicting whole-genome RNA-seq data of the T. gondii parental strain (RPKM values of genes are shown). Each bar in the outermost track represents locations of selected archetypal essential genes. See Table  S2  and Figure  S4  for transcriptomic analysis. (G) TgCPSF3 domain architecture as predicted from PFAM databases and crystal structures of Cryptosporidium CPSF3  (Swale et al. , 2019). Positioning of residues that were mutated in parasites resistant to AN13762 (Y328H, G465S, S519C, and E545K, in red) or AN3661 (Y328C, Y483N, and E545K, in blue) are indicated. et al. , 2016; Zhao et al. , 2018). Despite this technical bias, our transcriptomic data indicate that histone mRNAs (e. g. , H2Ba, H4, H2Ax, H2A1, and H2Bb; Table  S2  and Figure  S4 ) were dramatically enriched in drug-resistant lines harboring CPSF3 mutations Y328H, E545K, and S519C, but not in those mutants containing the CPSF3 G456S allele (strains A1 and F1 in Table  1 ).
(D) HFF cells were infected with tachyzoites (RH Dku80 UPRT::NLuc-P2A-EmGFP) and incubated with 10 mM AN13762, 5 mM AN3661, or 0. 1% DMSO as control. Cells were fixed 24 h post-infection and then stained with antibodies against the T. gondii inner membrane complex protein GAP45 (magenta). The cytosolic GFP is shown in green. Scale bars, 10 mm. A complete dataset can be found in FigureS1.
gondii strains expressing the NLuc-P2A-EmGFP reporter gene and incubated with 10 mM AN13762, 5 mM AN3661, or 0. 1% DMSO as control. Cells were fixed 24 h post-infection and then stained with antibodies against the T. gondii inner membrane complex protein GAP45 (magenta). The cytosolic GFP is shown in green. Scale bars, 10 mm. Complete dataset in shown in FigureS3D.
ACKNOWLEDGMENTS We acknowledge  A. Palencia  for initial fruitful discussions. We thank  D. Cannella  and  C. Corrao  for technical assistance. This research was supported by funds from the  Agence Nationale pour la Recherche Project ToxoP53  (grant no. ANR-19-CE15-0026 ) to A. B. , Project  HostQuest  (grant no. ANR-18-CE15-0023 ), and the  European Research Council  ( ERC Consolidator  grant no. 614880  Hosting TOXO) to M. -A. H.
Homology modelling of T. gondii CPSF3 mutations and docking analysis of AN13762 Homology modelling visualization of the T. gondii CPSF3 mutated residues was performed using the Cryptosporidium hominis CPSF3/AN3661 co-crystal structure (pdb id: 6Q55) as a structural model basis. T. gondii point mutations were depicted through direct sequence conservation while AN13762 docking was performed by manual placement of the oxaborole core onto the AN3661 backbone in Coot  (Emsley et al. , 2010)  with no further energy minimization performed. Schematics were produced using Pymol (Schrödinger, LLC) and UCSF Chimera.
(E) Fluorescence microscopy showing intracellular growth of WT and the CPSF3-edited parasites (G456Sand E545K). HFF cells were infected with tachyzoites of the indicated T. gondii strains expressing the NLuc-P2A-EmGFP reporter gene and incubated with 10 mM AN13762, 5 mM AN3661, or 0. 1% DMSO as control. Cells were fixed 24 h post-infection and then stained with antibodies against the T. gondii inner membrane complex protein GAP45 (magenta). The cytosolic GFP is shown in green. Scale bars, 10 mm. Complete dataset in shown in FigureS3D.