dataesr/scientific-paragraphs-categorization huggingface dataset:
Practicability study outcomes The practicability evaluation was divided into three substudies carried out by trained health care professionals according to 2015 WHO recommendations  [25]. A structured questionnaire was used to obtain socio-demographic data and evaluate the participants' understanding of the instructions for use and their opinions or levels of satisfaction about the practicability of the HIV self-test. Substudy 1: Comprehension of labeling. After participants were provided with an explanation of the objectives of the research, they were asked to move to a private room where the instructions for use of the Exacto 1 Test HIV were given for reading and understanding in their preferred language (French, Lingala or Swahili). After reading the instructions for use, the participants were asked whether they agreed to continue participating in the study by completing a self-administered evaluation questionnaire to gauge their comprehension of the instructions for use.
Statistical analysis All data were entered into an Excel file and analyzed on SPSS 20. 0 (Chicago, IL). Descriptive statistics were computed. Means and standard deviations (SD) were calculated for quantitative variables and proportions for categorical variables. The variable "educational level" included three categories: low (unschooled and primary schooled), middle (college or technical school), and high (undergraduate degree and graduate degree) educational levels. The results were presented as a 95% confidence interval (CI) using the Wilson score bounds. The Pearson's χ 2 test was used for comparison of the frequencies, while Fisher's exact test was used when the validity conditions of the latter test were not verified. Comparisons of means used the Student's t test or ANOVA for variables with more than two classes.
Acknowledgments The authors are grateful to the volunteers for their willingness to participate to the study. Thanks are also due to  Biosynex, Strasbourg, France , for providing the Exacto 1 Test HIV selftests for the study. We also thank the  Programme National de Lutte contre le SIDA, Kinshasa, Democratic Republic of the Congo. We thank  Dr. Thierry Prazuck  as well for the helpful discussion of the design for practicability evaluation of HIV self-testing.
These data indicate that the prenatal exposure to APAP may have perturbed the fetal development leading to subsequent reduced fertility. To further investigate the mechanism and window of sensitivity, Holm and coworkers exposed pregnant dams to 50 mg/kg/day by gavage of APAP in the period 7-13. 5 dpc to assess germ cell numbers. Fetuses from exposure and control groups were collected at 13. 5 dpc and by using the expression levels of Mvh, a stable marker for germ cells, the researchers found a 47% reduction in expression of Mvh in APAP-treated fetuses compared to controls. This reduction was only seen in female fetuses, whereas in male fetuses, no change was seen. The finding may suggest that APAP reduced either the migration of PGC, or the proliferation of oogonia, thus giving rise to fewer primordial follicles.
Anti-lipopolysaccharide factors (ALFs) are antimicrobial peptides with a central β-hairpin structure able to bind to microbial components. Mining sequence databases for ALFs allowed us to show the remarkable diversity of ALF sequences in shrimp. We found at least seven members of the ALF family (Groups A to G), including two novel Groups (F and G), all of which are encoded by different loci with conserved gene organization. Phylogenetic analyses revealed that gene expansion and subsequent diversification of the ALF family occurred in crustaceans before shrimp speciation occurred. The transcriptional profile of ALFs was compared in terms of tissue distribution, response to two pathogens and during shrimp development in Litopenaeus vannamei, the most cultivated species. ALFs were found to be constitutively expressed in hemocytes and to respond differently to tissue damage.
ALFs from Penaeid Shrimp Comprise a Diverse Family Composed of Seven Members By using an exhaustive in silico screening approach, we recovered 47 unique ALF sequences (complete CDS) from both publicly available annotated and non-annotated databases for 10 penaeid shrimp species (Decapoda: Penaeidae) (Table  S1 ). With all predicted amino acid sequences in hand, we performed multiple alignments in order to classify the obtained sequences into the five previously described ALF groups (Groups A to E). Surprisingly, from our sequence analysis, shrimp described ALF groups (Groups A to E). Surprisingly, from our sequence analysis, shrimp ALFs clustered into seven distinct groups with specific amino acid sequence signatures (Figure  1A ). In addition to already documented ALFs from Groups A to E, we identified here two novel groups that were conveniently named Group F and G (Figure  1A ).
For instance, the sequence MjALF-A2  [11]  is actually a member of Group G and not an ALF from Group A, whereas the cationic MjALF-D1 (GenBank: KU160499) belongs to Group F and not to Group D (which gathers anionic sequences only). More surprisingly, the sequence MjALF-E1 (GenBank: KY627760), previously classified as a cationic member of Group E, did not fit in any ALF Group. Indeed, its mature sequence contains an additional cysteine residue (apart of the two cysteines holding the central β-hairpin structure) that is not found in ALFs from either marine chelicerates or crustaceans. Interestingly, coding sequences related to MjALF-E1 were also found in P. monodon and L. vannamei. Unlike the three-cysteine-containing sequences from M. japonicus and P. monodon, the sequences identified in L.
ALF Sequence Diversity Is Gene-Encoded To gain insights into the origin of the molecular diversity of the shrimp ALF family, we searched for ALF gene sequences in both annotated (GenBank Nucleotide) and non-annotated (Whole-Genome Shotgun Contigs) databases. From our in silico mining analysis, seven unique genomic sequences were identified in P. monodon: ALFPm2 from Group A (GenBank: EF523561), ALFPm3 from Group B (GenBank: EF523562), ALFPm6 from Group C (GenBank: JN562340), ALFPm8 from Group D (GenBank: NIUS010164210), ALFPm9 from Group E (GenBank: NIUS010076396), ALFPm10 from Group F (GenBank: NIUS011801312) and ALFPm11 from Group G (GenBank: NIUS010749450). Each genomic sequence corresponded to a specific ALF member and we found no evidences that ALFs from different Groups could be encoded by a same genomic sequence.
Indeed, the ALF clade gathered sequences from both crustaceans and marine chelicerates. Regarding the crustacean group, ALFs were split into two main clades (Figure  2A ). The first clade included ALFs from Group A, while the second clade gathered ALFs from six additional groups (B to G). Interestingly, sequences from non-penaeid species (Pleocyemata) were found in all shrimp ALF groups, but they also formed exclusive groups distinct from those found in penaeids (Figure  2A ). Cationic and anionic ALF groups from penaeid shrimp are displayed in blue and red, respectively. Posterior probabilities (Bayesian) and bootstrap values (neighbor-joining) higher than 50% are shown in the nodes. The list of the ALF sequences included in analyses (annotations, sequences and GenBank accession numbers) is provided in Table  S1.
Similarly, molecular tools such as in situ hybridization could reveal the tissue specificity of ALFs and thus, they would help in uncovering other biological functions. Finally, a classification of all crustacean ALFs (from both decapod and non-decapod species) based on robust phylogenetic reconstructions may avoid misleading classifications and lead to consensus among researchers. With the identification of two novel ALF groups, we found that ALFs from Groups E and G share a common ancestor gene. Interestingly, Group G is lacking in species of the genus Fenneropenaeus whereas it is found in species of the genera Farfantepenaeus, Litopenaeus, Marsupenaeus and Penaeus. Although it cannot be ruled out that data are missing from publicly accessible databases, the absence of Group G in Fenneropenaeus could result from a gene loss event within this genus.
Database Searches and Phylogenetic Reconstructions ALF sequences were methodically collected from publicly accessible databases and used for the search of homologous sequences in both annotated and non-annotated databases. Only fulllength coding sequences were considered. Homology searches were performed using tBLASTx at NCBI. Exon-intron boundaries were defined by alignment of the cDNA and genomic sequences. All nucleotide sequences were manually inspected and analyzed using open-access bioinformatics tools. Three-dimensional models for L. vannamei ALFs were built with SWISS-MODEL (https: //swissmodel. expasy. org/) using ALFPm3 NMR resolution (PDB: 2JOB1) as a template. Deduced amino acid sequences were aligned using MAFFT multiple alignment program (https://mafft. cbrc. jp/alignment/server/).
Bayesian phylogenetic analysis was conducted in MrBayes 3. 1. 2 (http: //mrbayes. sourceforge. net/), using WAG + G as substitution model, with two runs of 10 7 generations, sample rate of 1000 and burn-in of 25%. Neighbor-joining analysis was conducted in MEGA X  [27]. Bootstrap sampling was reiterated 1000 times using a 50% bootstrap cutoff. Trees were drawn using FigTree v1. 4. 2 (http://tree. bio. ed. ac. uk/software/figtree/).
The eukaryotic translation elongation factor 1-alpha (LvEF1α) and the ribosomal protein LvL40 were used as reference genes of expression data in hemocytes. Relative transcript levels were determined by the comparative standard curve method using a standard curve derived from 2-fold dilution series of a cDNA pool of all samples. Differences we considered significant at p < 0. 05 (one-way ANOVA and Tukey's multiple comparison test). Gene expression of ALFs during shrimp development was assessed in twelve developmental stages as previously described  [16].
Acknowledgments: The authors are grateful to the  Laboratory of Marine Shrimp  ( Federal University of Santa Catarina, Florianópolis, Brazil ) for providing the shrimp used in this study and to  Pedro Ismael da Silva Jr. ( Butantan Institute, São Paulo, Brazil ) for the culture of Candida albicans MDM8. We are also in debt to  Juan Eberhard  for English correction and editing.
Funding: This research was supported by the Brazilian funding agencies  CNPq  ( MEC/MCTI/CAPES/CNPq/ FAPs PVE 401191/2014-1  and  MCTI/CNPq Universal 406530/2016-5 ) and  CAPES  ( CIMAR 1974/2014 ). P. S. was funded by  FONDECYT  grant  11150009. G. M. M. and N. D. F. were supported by scholarships provided by  FAPESC  and C. B. received a scholarship provided by  CAPES.
1), TIM-3 (7D3) (all from BD-Biosciences), CD45RA (HI100) and CTLA-4 (L3D10) (Biolegend), TIGIT (MBSA43), CD39 and CD73 (eBioscience) and a fixable viability marker (Zombie Fixable Viability Dyes, Biolegend). The production of intracellular cytokines on CD73 + CD4 + and CD73 neg CD4 + Teffs was analyzed using the test previously described (29) with some modifications, in particular the evaluation of IL-22 (22URTI, BD-Biosciences) instead of IL-21. Cells were analyzed on a LSR-Fortessa (BD Biosciences) and data were processed using the FlowJo Software (Tree Star). For the coexpression of i-ICPs, data were analyzed using the Boolean method on the FlowJo software and then represented using SPICE v5. 3 software.
At the end of the experimental time-course, cells were harvested and stained with a viability marker (LIVE/DEAD® Fixable Dead Cell Stains) and fixed in 2% formaldehyde. Cell proliferation was analyzed under an inverted Zeiss microscope (Objective 4x) using an Axiovision 4 software (Zeiss), and by FC (LSR Fortessa, BD Biosciences) according to the CFSE and CTV dilution. For experiments in Transwell Permeable Supports (polycarbonate membrane 0. 4 µm pore Corning), in the 6. 5 mm inserts, 6x10 4 CD73 + CD4 + Teffs alone or in co-culture with Tregs (at a ratio of 1:1) were activated using Expand beads (ratio of 1:4) in the presence, in the bottom wells, of 1. 5x10 5 CD73 neg CD4 + Teffs alone, or in co-culture with Tregs (at a ratio of 1:4) and Expand beads (ratio 1:4), in a total volume of 800 µl.
Multi-immunofluorescence stainings on frozen tumor sections Tissue-Tek® O. C. T. (Sakura® Finetek) embedded frozen human primary breast tumors were used to generate 6 m frozen tissue sections with Cryotome TM (Thermo Fisher Scientific). Sections were fixed in paraformaldehyde, permeabilized in Triton X-100 and stained with murine anti-human CD4-AF488 (Biolegend, Clone RPA-T4), rat anti-human FoxP3-APC (Ebioscience, Clone PCH101), and uncoupled rabbit anti-human CD73 (Cell signalling, Clone D7F9A). CD73 staining was revealed with secondary Donkey anti-rabbit antibody (Life Technologies). Immunofluorescence stainings were analyzed on Upright Microscope (Nikon Ni-E) using ImageJ free software.
Of importance, FC analyses reveal the higher propensity of CD73 + CD4 + Teffs to co-produce IFN-γ and IL-17A and co-express CXCR3/CCR6, in line with Th1. 17 compared to CD73 neg CD4 + Teffs. Our results extend the work of Doherty et al (24), who identified the memory CD73 + CD4 + T cells as Th17 cells. Indeed, the exploitation of the transcriptome data from Ramesh et al (27), comparing MDR1 + and MDR1 neg CD4 + memory populations (Gene Expression Omnibus (GEO) repository, accession ID: GSE49702), reveals that nt5e mRNA, coding for CD73, is one of the most significantly upregulated genes in the MDR1 + population (Log2-fold change (FC) = 0. 867; p value = 0. 004). Moreover, CD73 + CD4 + Teffs present a number of features of Th1. 17 cells recently described by Ramesh et al  (27). They express high level of functional MDR1, secrete IL-3 and GM-CSF and present higher expression of IL-23R in contrast to non-pathogenic Th17 that produce only IL-17A, IL-22, IL-10 and IL-21  (26, 27, 34).
Acknowledgments We wish to thank the staff of the core facilities at the  Cancer Research Center of Lyon (CRCL)  for their technical assistance and the  BRC (Biological Resources Centre) of the CLB  for providing human samples. Drs P. Guibert ,  F. Desseigne ,  M. Sarabi  and  L. Mais  are acknowledged for their clinical expertise. We will also thank  Marie Laure Thibult  ( Innate Pharma ) for her assistance for flow cytometry sorting. We are very grateful to  Justine Berthet  for her help and expertise in the development of multi-IF analysis on breast tumor sections. We would also like to thank  Dr. B. Manship  for critical reading of the manuscript.
Patient's selection and data collection Patients were identified retrospectively from two prospective studies, PRIMS and POPARTMUS. The Pregnancy in Multiple Sclerosis (PRIMS) study was the largest observational, prospective study of the natural history of MS during pregnancy and in the following two years  [2] [3]. This multicenter study included 254 women with MS from 12 European countries, followed during 269 pregnancies between January 1993 and July 1995, in a period when no disease-modifying drugs were available. pregnancy, number of relapses during the year before pregnancy, residual DSS score at onset of pregnancy, dates of relapses during pregnancy prior to entry in the study. Data on pregnancy relapses occurring after inclusion, relapses during the first three months of post-partum, use of neuraxial analgesia and breastfeeding were collected prospectively.
A relapse was defined as the appearance, reappearance or worsening of symptoms of neurological dysfunction lasting more than 24 hours. Fatigue alone was not considered as a relapse. Disability was assessed with Kurtzke's Disability Status Scale (DSS), which is based on data from the neurological examination and patient's ability to walk. Residual neurologic disability was defined as the minimal level of persistent disability recorded on two consecutive examinations at least three months apart, excluding any transient worsening of disability related to relapses. Neuraxial analgesia was defined as any type of locoregional analgesia used during delivery, including epidural and spinal analgesia, as no difference has been made between the procedures in the data collection of both studies. For both PRIMS and POPARTMUS, women were included in the present study only if data about use of neuraxial analgesia was available, if the follow-up was at least 3 months post-partum and if they had MS for at least one year prior to conception.
Standard protocol approvals, registration and patient consents All patients were informed about the design and purpose of the original studies and all gave their informed, written consent to the protocol. Approval was received from the National French ethical committee on human experimentation for the POPARTMUS study in agreement with French law (March 4, 2002) and the Declaration of Helsinki. The POPARTMUS study is registered with ClinicalTrials. gov under the reference NCT00127075. The PRIMS study did not require such approvals as it was a noninterventional study.
Statistical analysis Bivariate and multivariate associations between the occurrence of a relapse during the first three months post-partum and age at pregnancy onset, MS duration at pregnancy onset, DSS score at pregnancy onset , the occurrence of a relapse in the year before pregnancy, the occurrence of a relapse during the pregnancy and neuraxial analgesia were investigated using logistic regression analysis. Continuous covariates such as age were categorized by using the median. Statistically significant variables in the univariate analysis, with a conservative p value of 0. 20, and clinically relevant variables were included in a multivariate logistic regression model. All statistical analyses were performed using SAS 9. 3 software and a p below 0. 05 was considered significant. Assuming that 25% of women would have a post-partum relapse and that this rate could increase up to 40% if women had an neuraxial analgesia, we calculated that a sample of 393 patients would yield a power of 80%, at a significance level of 0.
ACKNOWLEDGEMENTS Neurology C. Lavie Neuraxial obstetrical analgesia in MS Page 18 We are indebted to the patients for their participation in the PRIMS and POPARTMUS studies and to all the investigators for their active contribution. This work has been supported by grants from patients associations:  Association pour la Recherche sur la Sclérose en Plaques (ARSEP) , the  Myelin Project  and the  European Leukodystrophy Association  (ELA) and Foundation ; and from the  French Ministry of Health  :  Projet Hospitalier de Recherche Clinique -National call  for proposal. Neurology C. Lavie Neuraxial obstetrical analgesia in MS Page 19.
ACKNOWLEDGMENTS This work was supported by the  Agence nationale de recherches sur le sida et les hepatites virales (ANRS)  fund ( ANRS-2014AO21038 ) to M. B. F. R. and  A. Sennepin  were supported by fellowships from  SIDACTION  and  ANRS. We would like to thank the staff of  Institut Cochin IMAGI'C and CYBIO  facilities and  Dr. Benjamin Cheng  ( Icahn School of Medicine at Mount Sinai, New York, NY ) for providing the gag-iGFP HIV-1 plasmids employed in this study.
Methods Materials. Antibodies were obtained as follows. Polyclonal rabbit anti-Tat antibodies (a kind gift of Dr E. Loret, Marseille), monoclonal anti-Tat (SantaCruz sc-65912 or 65913), goat anti-p24 antibodies (Serotec 4999-9007), anti-CypA (sc134910), anti-FKBP12 (Pierce PA1-026A), anti-MAP2 (a generous gift of Pr. Klosen, INCI Strasbourg), anti-DHHC-5 (Sigma HPA014670), anti-DHHC-20 (Sigma SAB 4501054), anti-flotillin-2 (sc-28320) and anti-αtubulin (Sigma T5168) were obtained as indicated. The specificity of anti-CypA antibodies was checked using Jurkat cells deficient for CypA  24. Anti-FLAG M2 antibodies and anti-FLAG M2 Magnetic beads were from Sigma. Kc57-RD1 anti-p24 antibody for FACS analysis was from Beckman-Coulter. Anti-24 antibodies for p24 ELISA (ARP410 and ARP454) were from the NIBSC/CFAR bank (England).
Tat membrane localization was assessed by quantifying Tat/F-actin colocalization using confocal images from 50 < n < 100 cells and Mander's coefficient calculation  20. qRT-PCR. Total RNA was extracted using Trizol before reverse transcription using SuperScript TM III Reverse Transcriptase and oligodT primers. cDNAs were then amplified by real time PCR in triplicates using the LightCycler 480 SYBR Green I Master mix on LightCycler 480 thermo cycler (Roche Applied Science). Primers for DHHCs that are listed in Supplementary Table  2  were chosen using Primer Blast (http://www. ncbi. nlm. nih. gov/tools/primer-blast/) and quantification was performed relative to the expression of GAPDH using the delta delta Ct method  67. Phagocytosis assays. Phagocytosis assays were performed as described  20.
Supernatants were collected and cells were lysed. The amounts of secreted and intracellular GH were then assayed using ELISA (Roche Applied Science). Tat secretion by Jurkat, primary T-cells or PC12 was assayed as described  4, 33. Surface plasmon resonance and microcalorimetry. Surface plasmon resonance (Biacore) and ITC experiments were performed using PI(4,5)P 2 liposomes as described  4. Statistical analyses. Sample size was chosen to insure data significance following statistical analyses. Data are presented as mean ± SEM and individual data points are indicated on bar graphs. Two-sided Student's t-tests were used to compare two conditions, one way ANOVA with Dunnet post-hoc test when more than two conditions were compared, and two way ANOVA with Bonferroni post-hoc test when there were two independent variables (mutations and drugs for instance).
Data analyses were performed using GraphPad Prism 7. p-Values on the figures are indicated as *p < 0. 05, **p < 0. 01, ***p < 0. 001 and n. s. for p > 0. 05. Protein preparation for in-gel digestion. For proteomic analysis, PC12 cells were transfected with Tat-FLAG before immunoprecipitation and SDS-PAGE. Bands around 15 kDa were excised, gel pieces were washed with 25 mM NH 4 HCO 3 , dehydrated with acetonitrile before reduction with 10 mM DTT in 25 mM NH 4 HCO 3 (1 h at 57 °C) and alkylation with 55 mM iodoacetamide. Gel pieces were resuspended in 2 volumes of freshly diluted trypsin (12. 5 ng/μL) and incubated overnight at 37 °C. Digested peptides were then extracted from the gel using 34. 9% H 2 O, 65% acetonitrile and 0. 1% HCOOH before drying. Nano HPLC and MS and MS/MS. The analysis was performed on an Ultra-Performance-LC (Waters).
Samples were separated on a C18 column (Waters Corp. ) using 0. 1% formic acid in water and 0. 1% formic acid in acetonitrile. MS and MS/MS analyzes were performed on SYNAPT™ (Waters) equipped with a Zspray ion source and a lock mass system. The capillary voltage was set at 3. 5 KV and the cone voltage at 35 V. Online calibration was performed with Glu-fibrinopeptide B as the lock-mass. The 3 most abundant peptides (intensity threshold 60 counts/s), preferably doubly and triply charged ions, were selected on each MS spectrum for further isolation and CID fragmentation with 2 energies set. Fragmentation was performed using argon as the collision gas. The complete system was fully controlled by MassLynx 4. 1 (Waters). Raw data were processed with ProteinLynx Browser 2. 5 (Waters). Normal background subtraction type was used for both MS and MS/MS with 5% threshold and polynomial correction of order 5, and deisotoping was performed.
The trypsin peak lists were searched using Mascot (Matrix science). During database search, four variable modifications (oxidation of Methionine (+16 Da), carbamidomethylation of Cysteine (+57 Da), acetylation on Lysine (+42 Da) and palmitoylation on Cysteine (+238 Da)) were considered. The search window was set to 25 ppm for precursor ions and 0. 07 Da for fragment ions. Filtering criteria based on probability-based scoring of the identified peptides were taken into account: 2 peptides were needed to identify a protein and each peptide with a Mascot Ion score >25 is validated. The false discovery rate (FDR) was calculated to be <1 % based on the number of decoy hits. Data availability. All data are available from the authors upon request.