dataesr/scientific-paragraphs-categorization huggingface dataset:
Protein quantification Isobaric quantification was performed using the IsoQuant module of Easyprot's protein export as described previously. Briefly, a false discovery rate of 1% and a minimum of 2 peptides per protein were selected. TMT sixplex was selected as reporter and a mass tolerance of 0. 05 m/z was used. The different protein ratios were calculated. A global normalisation of "median log peptide ratio=0" and a confidence threshold of 95% were selected. EasyProt's Mascat statistical method, inspired by Mascot's quantification module (http://www. matrixscience. com/help/quant_statistics_help. html), and Libra, inspired by the Trans-Proteomic Pipeline's isobaric quantification module (http://tools. proteomecenter. org/wiki/index. php?title=Soft ware:Libra), were chosen, along the generation of the list of proteins featuring a ratio fold over 1.
Statistical analyses For correlation of ctDNA variations and radiological tumour evaluation, image data and ctDNA variations of 16 patients were summarized as binary covariates, progression or non-progression (gathering objective response or stable disease) and increase or decrease between 2 visits, respectively. For early ctDNA variation, increase or decrease was assessed using ctDNA at baseline as reference in only 13 patients. Time to progression (TTP) was calculated from the second blood draw until the first clinical-radiological confirmation of tumour progression. Progression rates were estimated by the Kaplan-Meier method, with 95% confidence intervals (CI). Univariate analyses were performed using the log-rank test. Associations between 2 qualitative covariates were assessed using Fisher's exact test.
Introduction Primary SS (pSS) is a systemic autoimmune disease with characteristic local dryness of the eyes and mouth. Additionally, systemic complications are frequently observed and include multi-organ involvement and fatigue. There is no cure for pSS and treatment options focus on symptom relief, prevention of systemic damage and improvement of quality of life. HCQ is an immunomodulatory drug listed as first line treatment in The Sjo ¨gren's Syndrome Foundation Clinical Practice Guidelines, and is usually prescribed for arthralgias, myalgias and sometimes for fatigue  [1]. Evidence regarding the efficacy of HCQ, however, is limited  [2]. The JOQUER randomized placebo-controlled trial (Gottenberg et al. [3]  JAMA 2014, clinicaltrials. gov identifier NCT00632866) assessed the efficacy of a 24-week HCQ (400 mg/d) treatment in patients with pSS.
Questionnaires, laboratory parameters and objective measures of dryness Acquisition of clinical data and questionnaires is described in Gottenberg et al. [3]. In short, the collected questionnaires included: ESSPRI and ESSDAI to study disease activity; 36-item Medical Outcomes Study Short-Form Health Survey 36 (SF-36) to study quality of life and Hospital Anxiety and Depression Scale to study psychological discomfort. The Schirmer test score and unstimulated salivary flow were measured as objective measures of dryness and several laboratory parameters were included such as serum IgG, IgA and IgM levels, ESR, and CRP measured in each clinical centre.
Acknowledgements The research for this article was (partly) performed within the framework of the  Erasmus Postgraduate School Molecular Medicine. The authors thank patients and healthy volunteers for taking part in this study. I. L. A. B. was involved in analysis and interpretation of data, drafting and revising the article. C. G. vH. -M. was involved in laboratory data acquisition and writing of the manuscript. J. E. G. , M. A. V. and X. M. were involved in conception and study design, data acquisition, data monitoring and interpretation, and revising the article.
Electron Cryo-Tomography Eighteen µ l of cell suspension from the respective cultures was gently mixed with 2 µl protein A-treated 10 nm colloidal gold solution (Cell Microscopy Core, Utrecht, The Netherlands) by pipetting. Aliquots of 3 µl were applied to a plasma-cleaned R2/2 copper Quantifoil grid (Quantifoil Micro Tools, Jena, Germany). Plunge freezing into liquid ethane was carried out using a Leica EMGP (Leica microsystems, Wetzlar, Germany) set to 1 s blotting inside the chamber set at 20 • C and 95% humidity. Grids were stored in liquid nitrogen until imaging. Data acquisition was performed on a Titan Krios transmission electron microscope (Thermo Fisher Scientific, Hillsboro, OR, USA) operating at 300 kV. Images were recorded with a Gatan K2 Summit direct electron detector (Gatan, Pleasanton, CA) equipped with a GIF-quantum energy filter (Gatan) operating with a slit width of 20eV.
Tomograms were recorded at a nominal magnification of 42,000x (pixel size of 3. 513 Å). Using UCSF tomography data collection software  (Zheng et al. , 2007) , all tilt series were collected using a bidirectional tilt scheme which started with 0 • to -54 • followed by 0 • to 54 • tilting with a 2 • increment. Defocus was set to -8 µm. The cumulative exposure was 120 e-/ Å 2. Drift correction and bead-tracking based tilt series alignment were done using software package IMOD  (Kremer et al. , 1996). Tomograms were reconstructed using simultaneous iterative reconstruction (SIRT) with iteration number set to 4. Line scans perpendicular to the OM or sheath membrane was done using IMOD. Twenty nine measurements from five cells each were recorded.
The flow rate was set to 300 nL/ min. The data acquisition mode for the initial label-free quantification study was set to obtain one high-resolution MS scan at a resolution of 60,000 (m/z 200) with scanning range from 375 to 1500 m/z followed by MS/MS scans of the 10 most intense ions. To increase the efficiency of MS/MS shots, the charged state screening modus was adjusted to exclude unassigned and singly charged ions. The dynamic exclusion duration was set to 30 s. The ion accumulation time was set to 50 ms (both MS and MS/MS). The automatic gain control (AGC) was set to 3 × 10 6 for MS survey scans and 1 × 10 5 for MS/MS scans. For label-free quantification the MS raw data were analyzed with Progenesis QI software (Non-linear Dynamics, version 2. 0). MS/MS search of aligned LC-MS runs was performed using MASCOT against a decoy database of the uniprot Vibrio cholerae protein database (UniProt Consortium, 2018).
The following search parameters were used: full tryptic specificity required (cleavage after lysine or arginine residues); two missed cleavages allowed; carbamidomethylation (C) set as a fixed modification; and oxidation (M) set as a variable modification. The mass tolerance was set to 10 ppm for precursor ions and 0. 02 Da for fragment ions for high energy-collision dissociation (HCD). Results from the database search were imported back to Progenesis, mapping peptide identifications to MS1 features. The peak heights of all MS1 features annotated with the same peptide sequence were summed, and protein abundance was calculated per LC-MS run. Next, the data obtained from Progenesis were evaluated using SafeQuant R-package version 2. 2. 2  (Glatter et al. , 2012). Hereby, 1% false discovery rates (FDR) of identification and quantification as well as intensity-based absolute quantification (iBAQ) values were calculated.
To further gain more information on the detected proteins, their localization was predicted using PSORTdb  (Peabody et al. , 2016)  and Fur binding boxes were inferred from  Panina et al. (2001) ;  Mey et al. (2005). Data from a microarray study  (Asakura et al. , 2007)  and RNA sequencing analysis  (Xu et al. , 2018)  of V. cholerae VBNC cells are included for comparison (see Table  S3 ). In addition, the abundance of predicted enzymes of metabolic pathways were mapped using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database  (Kanehisa and Goto, 2000; Kanehisa et al. , 2017)  (see Table  S5 ). Finally, the proteomic data was further sorted according to their predicted regulons as inferred from RegPrecise 3. 0  (Novichkov et al. , 2013).
V. cholerae Enters the VBNC State After Prolonged Incubation In order to simulate the aquatic habitats as closely as possible in our laboratory setting, we used water samples collected from environmental sources, including fresh water (NFW), brackish water (NBW) and salt water (NSW). Cells introduced into the 50 ml microcosms of NFW, NBW and NSW had all lost their ability to form colonies on LB plates over the course of 200 days (Figure  1 ). At the final time point 69% (NFW), 70% (NBW) and 65% (NSW) of the cells were viable according to live/ dead staining with Syto9 and propidium iodide (data not shown). From the initial ∼2 × 10 9 cells/ ml the final total cell count showed a reduction of the cells per ml to 6. 3× 10 6 ± 2. 4 × 10 6 (NFW), 2. 8× 10 7 ± 1. 2 × 10 7 (NBW) and 1. 3× 10 7 ± 3.
Proteins that were detected with n >= 3 peptides were analyzed in more detail. Components that were more abundant in VBNC cells fell, among others, into the categories of bacterial chemotaxis, flagellar assembly, ribosomal proteins, arginine biosynthesis, and ABC transporters. Less abundant proteins in VBNC cells were predominantly allocated to metabolic categories such as carbon metabolism, tricarboxylic acid cycle (TCA) cycle, amino acid, amino sugar and nucleotide sugar metabolism (Table  S4 ). For more detailed analysis, the components of individual structures or pathways were further refined using published data or the VchoCyc database  (Shi et al. , 2006).
Materials and methods 2. 1. Ixodes holocyclus defensins: Identification and prediction of γ-core sequences Data from the I. holocyclus database  (Rodriguez-Valle et al. , 2018)  were used for the bioinformatics analysis to identify the defensin sequences used in this study. Briefly, fully engorged adult female I. holocyclus ticks collected from different locations along the eastern Australian coast were dissected. The salivary glands and viscera were pooled and used for mRNA extraction and preparation of the cDNA libraries that were used in next generation sequencing using Illumina HiSeq 100 bp paired-end read technologies  (Rodriguez-Valle et al. , 2018). The sequences were analyses using the Basic Local Alignment Search Tool (BLAST)  (Altschul et al. , 1990)  against the String v7 database (Von  Mering et al.
, 2006)  and the Unicellular (COG) and Eukaryotic (KOG) Clusters of Orthologous Groups  (Tatusov et al. , 2003). The NCBI conserved domain database (CDD)  (Marchler-Bauer et al. , 2010)  was screened using RPSBLAST  (Goonesekere and Lee, 2008). The selected defensin sequences were then clustered using Markov Cluster Algorithm (MCL)  (Enright et al. , 2002). I. holocyclus mature defensin sequences were aligned with γ-cores previously identified in I. ricinus  (Tonk et al. , 2015a)  and I. scapularis  (Tonk et al. , 2014a)  ticks. Ixodes holocyclus mature defensins and γ-cores were synthesized and their antimicrobial activity was tested.
The steps are repeated for a number of iterations (10,000) computed for 24 h using the protein motion ready-made script and a single cpu. The result is a series of frames that depict protein dynamics. Enthalpy values (kcal/mol) are also recorded during the simulations. To calculate enthalpy, the PELE software uses a force field known as the optimized potentials for liquid simulations (OPLS-2005)  (Jorgensen et al. , 1996). The Metropolis Monte Carlo-based method accepts iteration if the enthalpy is equal to or less than the initial value but is rejected if the enthalpy is greater than the initial value. Further analyses on the molecular simulations were performed using the Visual Molecular Dynamics software (VMD)  (Humphrey et al. , 1996). A threshold of 0. 25 Å every 100 frames for 20 clusters was set for the VMD cluster analysis on the α-carbon backbone of the defensin γ-cores.
Statistical analysis All presented values are mean ± standard deviation including two biological replicates. Since the data were non-normally distributed (Shapiro-Wilk normality test), the Kruskal-Wallis one-way analysis was used, with sum of ranks comparisons performed using Dunn's multiple comparisons test in the GraphPad 6 Prism program (GraphPad Software Inc. ). Differences were considered significant when p-value < 0. 05.
0 Server  (Almagro Armenteros et al. , 2017)  revealed that all holosins (1-5) have a high likelihood (> 0. 99) to be extracellular and soluble molecules. However, despite having a starting codon, no signal peptide was predicted for holosin 2. The furin cleavage site (RVRR) described by  (Krysan et al. , 1999)  was present in all holosins, as well as the six conserved Cys residues that form the three disulfide bridges (Fig. 1 ). After theoretical furin cleavage, the peptides were 36 (holosin 3), 38 (holosins 1, 2 and 4) and 39 (holosin 5) amino acids in length (Table  1 ). In agreement with the above conserved molecular properties, the Conserved Domain Database (CDD) server  (Marchler-Bauer et al. , 2015)  classified holosins 1, 2, 4 and 5 as members of the Defensin-2 family (pfam01097) with Evalues < 2.
29e-05. However, no conserved domain was identified by CDD for holosin 3. The BLAST hits with the lowest E-values and highest % identity were obtained with defensins from the ticks H. longicornis, A. americanum and Ixodes persulcatus (Table  2 ). To further characterize the evolutionary history of holosins, hard and soft tick defensin sequences were collected from GenBank and a Maximum Likehood phylogenetic tree was reconstructed (Fig. 2 ). While most Ixodes defensins clustered together, holosins clustered in different clades suggesting high diversity among I. holocyclus defensins. Holosin 3 was the only defensin from hard ticks that clustered with soft tick defensins.
Structural characterization and thermodynamics of holosins There are 181 defensins (as a keyword) that are structurally resolved in the Protein Databank  (Berman et al. , 2000). The tertiary structures of the I. holocyclus defensins were therefore predicted to further characterize these holosins (Fig. 3a ). Similar to vertebrate βdefensins, the five I. holocyclus holosins are predicted to form a Cysstabilized α/β-fold (CS-αβ) with an amino-terminal α-helix that stabilizes the β-hairpin via three Cys disulfide bridges (I-III; Fig. 3a ). The CSαβ-fold comprises of several structural motifs known as the α-patch, mapped onto the α-helix, and the loops designated by peptide positions at the amine-terminus (n-loop), middle (m-loop) and carboxyl-terminus (c-loop)  (Zhu et al. , 2012). The main structural features common to the I.
holocyclus holosins are the distinct folds at the loop regions, specifically the n-and c-loop, that are characterized by large conformational differences in the first (I) Cys disulfide bridge (Fig. 3a ). The DALI server  (Holm and Laakso, 2016) , a structural heuristic search engine that scans the Protein Databank, was used to identify defensins with the CS-αβ-fold that are similar to the predicted I. holocyclus holosins (Fig. 3a ). According to the DALI server, the closest structural homolog is the antimicrobial defensin, eurocin, from the mold Eurotium amstelodami (Protein Databank accession: 2LT8) that possesses antimicrobial activity against a variety of Gram-positive human pathogens  (Oeemig et al. , 2012). Eurocin, however, is not effective against Gram-negative pathogens  (Oeemig et al.
25) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 1. 7582)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 35 amino acid sequences. All positions containing gaps and missing data were eliminated. There was a total of 40 positions in the final dataset. The percentage of trees (bootstrap values) in which the associated taxa clustered together is shown next to the branches. two C-terminal anti-parallel β-strands; (vi) and an α-helix at the Nterminus.
Acknowledgements JJV is supported by  Project FIT (Pharmacology, Immunotherapy , nanoToxicology), which was funded by the  European Regional Development Fund  and acknowledges a grant from the research organization RVO:  RO0516. Transcriptome analysis of I. holocyclus viscera and salivary glands was funded by the  Australian Research Council  linkage project  LP120200836  and  Elanco Animal Health. MT and AV would like to acknowledge generous funding by the  Hessen State Ministry of Higher Education, Research and the Arts (HMWK)  via the  LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG ) and the  LOEWE Center for Insect Biotechnology and Bioresources.
Immune Phenotyping Whole blood, LN cells and cells from FRT compartments were analyzed by flow cytometry. The cells were incubated with the antibodies listed in Table  S1 , washed, and then fixed with FACS lysing buffer or BD Cell Fix solution. A Fortessa 2-UV 6-Violet 2-Blue 5-Yelgr 3-Red laser configuration was used (BD Biosciences), with Diva (BD) and FlowJo 9. 8. 3 (Tristar, USA) software. At least 500 events for rare cell populations (i. e. , pDC) were recorded.
The antibodies listed in Table  S2  were used for intracellular staining. At least 5,000 events in the CD8 + T cell gate were recorded. The gating strategy was as described elsewhere  (25). Briefly, cytokine and activation marker expression was evaluated in CD4 + and CD8 + T cells, and Boolean gate analyses were performed with FlowJo software. The percentages of cells positive for cytokines and activation markers between unstimulated and MVA-stimulated cells were then compared.
The plates were then washed five times and incubated for 1 h with a 1:20,000 dilution of horseradish peroxidase-conjugated goat anti-monkey H+L chain IgG (Bio-Rad, Marne-la-Coquette, France) or a 1:5,000 dilution of horseradish peroxidase-conjugated goat anti-monkey IgA (Alpha Diagnostic international, San Antonio, TX). The plates were washed five times, then 100 µL o-phenylenediamine dihydrochloride (OPD) (Sigma Aldrich) was added and the plates incubated for 30 min at room temperature in the dark. The reaction was stopped by adding 2N H 2 SO 4. Absorbance was measured at 492 nm with a spectrophotometer (Tecan, Lyon, France), and the data analyzed using Magellan software (Tecan). Antibody titers were calculated by extrapolation from the OD as a function of a serum dilution curve and defined as the dilution of the test serum reaching 2 OD of the corresponding preimmune serum or vaginal fluid, tested at 1:50 and 1:30, respectively.
Data Analysis Comparison between the control group and the SP-exposed group (antibody and T cell responses, and cell population abundance) were analyzed using the two-tailed Mann-Whitney test. The two-tailed Wilcoxon signed rank test was used to compare paired conditions (T cell responses within each animal group). Polyfunctional profiles of MVA-specific CD8 + T cells were compared between the two groups using the Chi-squared test. The statistical threshold of significance was fixed at p < 0. 05 for these tests. Microarray were analyzed using R/Bioconductor software. Gene expression values were quantile normalized. Differentially expressed genes were identified with a paired non-parametric t-test (q-value < 0. 05), based on a 1. 2-fold-change cutoff. Functional enrichment analysis was performed using QIAGEN's Ingenuity Pathway Analysis (IPA, QIAGEN, Redwood City, https://www.
SP Exposures Revealed a Local Specific CD4 + T-Cell Response We evaluated the MVA-specific CD4 + T cell response in the blood, lymph nodes (LNs) and FRT following ex-vivo restimulation of isolated leukocytes. HIV-Gag-specific CD4 + Tcell responses were very weak and mainly detected in the blood. No differences between the two groups were detected (data not shown). MVA-specific CD4 + T-cells were mainly found in the blood and axillary LNs draining the vaccine injection site (Figure  S2A ), as previously described  (24). No differences between the two groups were detected in these compartments. Within the FRT of the control animals, expression of CD154, used as a marker of activated cells, was significantly increased only in CD4 + T cells of the cervix (from 0. 06 to 0. 50% of total CD4 + T cells) following stimulation with MVA and relative to unstimulated cells (Figure  1A , left panel).
SP Exposures Increased Specific CD8 + T Cell Responses in the Cervix We monitored the vaccine response mediated by CD8 + T cells in the blood, LNs and FRT of the control and SPexposed animals using ex vivo re-stimulation assay. HIV-Gagspecific CD8 + T-cell responses were very weak and detected in the blood of few animals. No differences between the two groups were detected (data not shown). MVA-specific CD8 + T cell responses in the blood and LNs were detectable, but not different, between the two groups (Figure  S2B ). By contrast, percentages of IFN-γ (from 0. 27 to 1. 09% of total CD8 + T cells), MIP-1β (from 0. 80 to 1. 55%), TNF-α (from 0. 11 to 0. 53%) and IL-2-producing (from 0. 06 to 0. 24%) CD8 + T cells were statistically higher in the cervix of SP exposed animals compared to controls (Figure  2A ).
NT held a fellowship from the ANRS (France Recherche Nord & Sud Sida-HIV Hépatites). FB held fellowships from the ANRS, Sidaction and Institut Carnot-Pasteur, Microbes & Santé. This work was supported by the Programme Investissement d'Avenir (PIA) managed by the ANR under reference ANR-11-INBS-0008, funding the Infectious Disease Models and Innovative Therapies (IDMIT, Fontenay-aux-Roses, France) infrastructure, the ANR-10-EQPX-02-01, funding the FlowCyTech facility (IDMIT, Fontenay-aux-Roses, France) and the ANR-10-LABX-77-01 funding the Vaccine Research Institute (VRI). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
ACKNOWLEDGMENTS We thank  Drs. Anne-Sophie Beignon ,  Mireille Centlivre , and the  Bmuc division members for scientific discussions. Alex Edelman & Associates  for critical editing of the manuscript. Transgene for providing the wild type MVA strain and  ANRS/INSERM  and the  Vaccine Research Institute the MVA-HIV-B vaccine. Andrea Galli  for preparation of SP pool. Rahima Yousfi  for technical assistance. Dr. Véronique Avettand-Fenoel  for HIV-1 viral load quantification. Dr. Bernard Verrier  for providing the p24 HIV-1 antigen and all members of the  IDMIT infrastructure  for their excellent expertise and outstanding contribution.
FUNDING NT held a fellowship from the ANRS (France Recherche Nord & Sud Sida-HIV Hépatites). FB held fellowships from the ANRS, Sidaction and Institut Carnot-Pasteur, Microbes & Santé. This work was supported by the Programme Investissement d'Avenir (PIA) managed by the ANR under reference ANR-11-INBS-0008, funding the Infectious Disease Models and Innovative Therapies (IDMIT, Fontenay-aux-Roses, France) infrastructure, the ANR-10-EQPX-02-01, funding the FlowCyTech facility (IDMIT, Fontenay-aux-Roses, France) and the ANR-10-LABX-77-01 funding the Vaccine Research Institute (VRI). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.