dataesr/scientific-paragraphs-categorization huggingface dataset:
All track calculations were performed using T cell Analyser version 1. 7. 0 software (http://spider. science. strath. ac. uk/sipbs/showPage. php?page=software_imaging), written by J. Dempster (University of Strathclyde, Glasgow, Scotland)  (40). Data were transferred and plotted in GraphPad Prism 6 (GraphPad Software Inc. ) for creation of the graphs. Electron microscopy. WT and Ccr7 -/-mice were euthanized and immediately perfused with 4% paraformaldehyde and 2. 5% glutaraldehyde in PBS. Anterior s. c. fat containing brachial LNs was excised and cut in the midsection with respect to the region containing the afferent lymphatic vessel  (14) , and blocks were prepared and processed for standard transmission electron microscopy by the University of Virginia Advanced Microscopy and Histology Core.
Sections were evaluated using a Joel 1220 electron microscope. Analysis of adventitial wall diameter and luminal diameter of lymphatic collecting vessel. Single 2-photon-generated videos were analyzed at Washington University School of Medicine and Hannover Medical School by individuals blinded to the genotype and age of the mice used to generate the data. For analysis, multiple Z-stacks per mouse were examined in the middle region (along the z axis) of the vessel, and the thickness of the lymphatic collector wall and the diameter of the lumen of the collector vessel were quantified using Imaris software. Further, the ratio between the lymphatic lumen diameter and the lymphatic wall diameter was calculated. After data were unblinded, graphical depictions of the results were prepared using GraphPad Prism 6.
Estimation of surface area of contact between lymphatic vessel and DCs. Surfaces of the lymphatic vessel and DCs were created using the surface function in Imaris. The surfaces were then imported into MATLAB as X, Y, and Z Cartesian coordinates. To determine the contact between the vessel and the cell, a threshold was predetermined (1 micron), and the distance between each vessel and cell Cartesian coordinate was calculated using the Euclidean distance formula (Equation  1 ). The points of the vessel that were within the distance threshold were then used to estimate the surface area, as these were the points considered to be in contact with a cell. The subset of vessel points was then projected onto the plane of most variance, found using singular value decomposition (Equation  2 ). The surface area was estimated from this 2D object by finding its convex hull and then calculating the area of the convex hull using MATLAB.
Cells were stained with combinations of the following mAbs for 25 minutes on ice, protected from light. mAbs included those directed against CD45 V500-conjugated Abs (BD Horizon, clone 30-F11) or Pacific Blue-conjugated Abs (BioLegend, clone 30-F11), CD11c Pe-Cy7-conjugated Abs (Bio-Legend, clone N418), CD11b APC-Cy7-conjugated Abs (Biolegend, clone M1/70), CD24 PerCP-Cy5. 5-conjugated Abs (BD Biosciences -Pharmingen, clone M1/69), CD64 APC-conjugated Abs (BD Biosciences -Pharmingen, clone X54-5/7. 1), F4/80 APC-Cy7-conjugated Abs (BioLegend, clone CI:A3-1), and MHC II eFluor450-or FITC-conjugated Abs (eBioscience, clone M5/14. 15. 2). Abs to MerTK (BAF 591) were from R&D Systems and were used in combination with streptavidin PerCP-Cy5. 5-conjugated Abs (BioLegend). Cells were analyzed on the LSR Fortessa (BD) instrument equipped with DIVA software.
Samples were later analyzed using FlowJo software (Tree Star). 2-Photon microscopy. Mice were anesthetized by i. p. injection of ketamine (50 mg/kg) and xylazine (10 mg/kg) and maintained with halved doses administered every hour. Mice analyzed at Hannover Medical School received 1 i. p. injection of ketamine (100 mg/kg) and medetomidine (1 mg/kg). Mouse legs were carefully shaved with Nair (Church & Dwight Co. ) and washed with 1× PBS to remove the extra lotion. The superficial layer of the skin was removed, and the lymphatic collecting vessels in the popliteal region were visualized via s. c. injection of 10 to 20 μl of DyLight 594-conjugated tomato lectin (Vector Laboratories) into the footpad. During the acquisition, mouse status was closely monitored. Images were collected at Washington University using a customized Leica SP8 2-photon microscope equipped with a ×25/0.
Each data point represents analysis of 1 Z-stack, with 5 to 7 Z-stacks examined per mouse. Other measurements assessed from these videos were mean DC velocity (C), meandering index (D), and motility coefficient(E). From 4 to 5 mice per genotype were examined, with multiple areas along the lymphatic collecting vessel analyzed per mouse. For C-E, each data point represents tracking from an individual cell, with 7 to 10 cells tracked from 4 to 5 mice per genotype. In C-E, each mouse is plotted using a distinct symbol shape. Mann-Whitney U tests were performed for assessment of statistical significance. **P < 0. 01; ***P < 0. 001.
Acknowledgments We thank  Theresa  and  Ken Murphy  and  Kory Lavine  for providing mice and for advice. We also thank  Guillermo Oliver  ( Northwestern University ) for provision of Prox1-ERT2-Cre mice. The  Advanced Microscopy Facility at the University of Virginia  expertly embedded and prepared sections on grids for use in electron microscopy. G. J. Randolph  was affiliated with the.
The Study In January 2010, France introduced sentinel surveillance for C. trachomatis proctitis, approved by the country's Data Protection Authority, to monitor the LGV outbreak. Laboratories perform routine testing for C. trachomatis, and positive anorectal specimens are referred to the French National Reference Center for Chlamydiae (Bordeaux, France) for LGV testing, using a real-time PCR targeting a 36-bp deletion in the pmpH gene  (9). For each patient, clinical, biological, and sexual behavior data are collected after written consent is obtained. During January 2010-April 2015, we retrospectively selected 179 LGV-positive anorectal specimens from the surveillance samples. To ensure that samples were representative of infections in the LGV-infected population, we used the following criteria for selecting samples for each year of the study: 1) the percentage of specimens analyzed each year was the same and corresponded to ≈12% of anorectal LGV cases diagnosed in France per year; 2) the residences of patients were classified as in the Paris area versus other regions of France to respect the geographic distribution of cases during each year of the survey; 3) samples were distributed over the 12 months of each year, except 2015; and 4) specimens had a high bacterial load, defined as a cycle threshold of <30 using the pmpH real-time PCR.
We analyzed 23 C. trachomatis specimens from 2010, 24 from 2011, 24 from 2012, 40 from 2013, 49 from 2014, and 19 from January-April 2015. Amplification of the ompA gene was performed directly on specimens. A 1,100-bp fragment was amplified by nested PCR, using the NLO and NRO primers and PCTM3 and SERO2A primers  (10) , and sequenced in both directions. An L genovar was confirmed for all specimens by ompA sequencing. Most specimens (52. 5%, 94/179) had ompA sequences identical to that of the C. trachomatis L2b/ UCH-1/proctitis reference strain (GenBank accession no. AM884177. 1); 61 (34%) specimens had sequences identical to that of reference strain L2/434/BU (GenBank accession no. AM884176. 1). In the remaining 24 specimens, we identified 4 genetic L2b ompA variants that had nonsynonymous single-nucleotide polymorphisms, compared with nucleotide sequence of the L2b/UCH-1/proctitis reference strain.
One variant, L2b ompA variant 1 (designated L2bV1; GenBank accession no. JX971936), was found in 19 specimens and featured a C→A substitution at position 517 (Leu173Ile)  (8, 11). A second variant, L2bV2 (Gen-Bank accession no. KU518893), was detected in 1 specimen and had an A→C substitution at position 515 (Lys-172Thr). The third variant, L2bV3 (GenBank accession no. KU518894), was detected in 2 specimens and shared a C→A substitution at position 493 (His165Asn). The fourth variant, L2bV4 (GenBank accession no. KU18892), was detected in 2 specimens and featured a C→A point mutation at position 286 (Ala96Thr). All specimens were from men. Symptoms (rectal syndrome, rectal pains, anal discharge, rectal bleeding) were present in all cases, and clinical features were similar. Data about sexually transmitted bacterial co-infections (e.
Acknowledgments We thank members of the French surveillance of Chlamydia trachomatis proctitis network, all biologists who sent biologic samples and physicians who reported cases of lymphogranuloma venereum to the surveillance system. Dr. Peuchant works in the laboratory for Mycoplasmal and Chlamydial Infections in Humans at the  University of Bordeaux. Her primary research interests are the epidemiology of and genotyping methods for C. trachomatis.
Additionally, we studied the impact of the following factors on outcomes: age (considered as a continuous variable), type of disease (myeloid versus lymphoid), and previous autograft (yes versus no). The log-rank test was used for univariate comparisons. For all prognostic analyses, the median value of continuous variables was used as a cut-off point. Factors associated with a P value less than. 10 by univariate analysis were included in the final multivariate model, using forward Cox proportional hazards. All tests were 2-sided. The type I error rate was fixed at. 05 for determination of significant factors associated with time-to-event outcomes. Statistical analyses were performed using the SAS 9. 3 (SAS Institute Inc. , SAS Campus Drive, Cary, NC) software package.
4; BD Pharmingen) and streptavidin-APC (BD Pharmingen). Endogenous green fluorescent protein (GFP) was used to detect Foxp3 expression. Dead cells were gated out using propidium iodide. Data acquisition and analysis were performed using a FACSCanto (BD) and the FlowJo (Tree Star) software, respectively. In vivo suppression assays. Splenic nTreg (CD4 ϩ CD25 ϩ Foxp3 EGFPϩ ) and naive CD4 ϩ T cells (CD4 ϩ CD25 Ϫ Foxp3 EGFPϪ ) were isolated from C57BL/6-Foxp3 EGFP mice as described above. Suppression assays were performed in vivo by coinjecting intravenously (i. v. ) a fixed number of naive CD4 ϩ T cells with titrated numbers of nTreg into irradiated syngeneic wild-type or C57BL/6-CD4 Ϫ/Ϫ mice. Mice were infected i. p. with P. berghei ANKA within 3 h. Development of CM and parasitemia served as a readout of suppression activity.
Control wells included unstimulated duplicates or plain medium. Supernatants were harvested, and cytokine and chemokine production of nTreg were simultaneously measured by a multiplexed bead assay, using the Milliplex Map Mouse cytokine/chemokine premixed 22 Plex (Millipore), according to the manufacturer's protocols. Cytokine concentrations were determined by the Luminex 100 system (Austin, TX) using the STarStation software (Applied Cytometry, Sheffield, United Kingdom) in two independent assays. Statistical analysis. Data were analyzed with the Prism software package (GraphPad). Survival times were compared with a nonparametric log-rank test (Mantel-Cox). We used the Mann-Whitney test for the analysis of parasitemia data. P values of Յ0. 05 were considered significant.
ACKNOWLEDGMENTS We thank  Isabelle Lanctin  ( Institut Pasteur, Paris [IPP])  for kindly providing WLA mice. We are grateful to  Monique Bauzou  ( INSERM U511 ,  Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris, France ),  Marie-Christine Wagner ,  Hinde Benjelloun ,  Barbara Jaron , and  Pierre-Henri Commere  (all  IPP ) for technical assistance,  Cécile Pham  ( IPP ) for administrative assistance, and the staff of the IPP animal facility for animal care. We thank  Peter David ,  Thomas Fehr , and  Gary Burkhart  for critical review of the manuscript. We thank  Fabien Herbert  for statistical analysis and critical analysis of the manuscript. Anne-Laurence Blanc ,  Sylviane Pied , and  Pierre-André Cazenave  conceived and designed the experiments. Anne-Laurence Blanc ,  Sylviane Pied ,  Olivier Gorgette , and Pierre-André Cazenave performed the experiments.
FUNDING INFORMATION Sylviane Pied received funding from Region Nord Pas de Calais under the ARCIR Dymanique programme (2010-2014), LABEX PARAFRAP ANR-11-LABX-0024. Anne-Laurence Blanc was supported by the Fondation de France (Fonds Inkermann), François Lacoste, and Bertrand Blanc. Tarun Keswani was the recipient of the Raman-Charpack Fellowship 2014 from CEFIPRA (San. No. FT/008/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors declare that no competing financial interests exist.
Acknowledgements We thank  S. Chelbi ,  UNIL, Lausanne, Switzerland, D. Stojanovova, Charles University, Prague, Czech Republic , and  Elisenda Alari Pahissa ,  Ludwig Center, Lausanne , for technical help and Ju ¨rg Tschopp for having contributed tools essential to this project. Studies in the group of G. G. are funded by the  Swiss National Science Foundation  ( PP00P3_139094 ) and the  European Research Council  ( ERC-2012-StG310890 ). E. V. lab is supported by the  European Research Council  ( THINK Advanced Grant ), the  Ligue Nationale contre le Cancer  ( Equipe Labellisee ) and by institutional grants from  INSERM ,  CNRS  and  Aix-Marseille University  to CIML. E. V. is a scholar of the  Institut Universitaire de France.
The bacterial density and the absence of contamination were controlled by plating. The viability of the bacteria in eukaryotic cell culture medium and under different culture conditions was controlled in preliminary studies (data not shown). CGRP and Substance P were obtained from Polypeptides (Strasbourg, France). Gadolinium chloride (GdCl 3 ) was obtained from Sigma-Aldrich (Saint-Quentin Fallavier, France). Cytotoxicity studies. The cytotoxicity of bacteria was studied in the human keratinocyte cell line HaCaT and in RHE. HaCaT Cells, provided by Cell Line Services (Eppelhein, Germany), were grown at 37 °C under a 5% CO 2 atmosphere, in Dulbecco's modified Eagle's medium (DMEM, Lonza, Levallois-Perret, France) supplemented with 10% fetal calf serum and 1% antibiotic cocktail (HyClone Thermo Scientific, Illkirch, France).
Variations in spot intensity and distribution were studied using Bio-Rad PDQuest 2D ® analysis software. Culture medium proteins were excluded and electrophoretic spots of interest were dissected and subjected to in-gel trypsin digestion and analyzed by MALDI-TOF/TOF using an AutoFlex III mass spectrometer (Bruker Daltonics, Wissembourg, France). The spectrometer was used in a positive/reflector mode. Samples were spotted to MTP 384 ground steel targets (Bruker Daltonics, Wissembourg, France) using a freshly prepared matrix solution composed of 2,5-dihydroxybenzoic acid in a solution of trifluoroacetic acid and acetonitrile. Each spectrum was established over an average of 500-1000 laser shots. FlexAnalysis software generated an MS peak list, which was subjected to peptide mass fingerprinting using the integrated software Biotools (Version 3.
2). The NCBI database was searched using the online MASCOT software and statistical sequence analyses were performed using the probability-based Mowse score. For tandem mass spectrometry analysis, all experiments were performed using a LTQ-Orbitrap Elite coupled with an Easy nLC II system (Thermo Scientific, Villebon-sur-Yvette, France). The samples were injected onto an enrichment column (C18 PepMap100, Thermo Scientific, Villebon-sur-Yvette, France). Separation was achieved with an analytical column needle (NTCC-360/100-5-153, NikkyoTechnos, Tokyo, Japan). The mobile phase consisted of H 2 O/0. 1% FA (buffer A) and ACN/FA 0. 1% (buffer B). Tryptic peptides were eluted at a flowrate of 300 nL/min using a three-step linear gradient: from 2 to 40% B over 25 min. The mass spectrometer was operated in positive ion mode with a capillary voltage and a source temperature set at 1.
5 kV and 275 °C, respectively. The samples were analyzed using the CID (collision induced dissociation) method. The first scan (MS spectra) was recorded in the Orbitrap analyzer (R = 60,000) in the mass range m/z 400-1800. The 20 most intense ions were then selected for MS2 experiments. Singly charged species were excluded for MS2 analysis. Dynamic exclusion of already fragmented precursor ions was applied for 30 s, with a repeat count of 1, a repeat duration of 30 s and an exclusion mass width of ± 10 ppm. Fragmentation occurred in the linear ion trap analyzer with collision energy of 35. All measurements in the Orbitrap analyzer were performed with on-the-fly internal recalibration (lock mass) at m/z 445. 12002 (polydimethylcyclosiloxane). Raw data files were processed using Proteome Discoverer 1.
3 software (Thermo Scientific, Villebon-sur-Yvette, France). Peak lists were searched using the MASCOT search engine (Matrix Science, Boston, USA) against the database Swiss Prot database searches were performed with the following parameters: 1 missed trypsin cleavage site allowed; variable modifications: carbamidomethylation of cystein, and oxidation of methionine; mass tolerance on parent and daughter ions: 10 ppm and 0. 5 Da respectively. Only proteins represented by more than 1 peptide sequence, by 2 folds and with power > 0. 8 were retained. Each protein identification was validated by an ANOVA test. Binding and invasion studies. Binding and invasion studies were performed with HaCaT cells. Cultured keratinocytes were infected for 1 h with S. epidermidis (MFP04) at an MOI of 10:1. In the first series of experiments, at the end of the incubation period HaCaT cells were washed six times with DMEM to remove non-adherent bacteria and then disrupted with 1 mL of 0.
At the end of the experiments, the biofilms were stained with 5 × 10 -6 M Syto 61 red dye or 5 × 10 -6 M SytoX (Molecular Probes, Thermo Fisher Scientific, Villebon-sur-Yvette, France). Observations were made using a confocal laser scanning microscope (LSM 710 confocal laser-scanning microscope; Zeiss, Marly le Roi, France). The biofilm thicknesses and corresponding biovolumes were estimated by measuring field samples from at least 3 independent experiments using COMSTAT software (Matworks, Natick, USA)  49. Characterization of bacterial surface polarity. Stationary phase bacteria were harvested (7,000 × g; 10 minutes) and washed twice in 0. 9% NaCl. The polarity of control and CGRP-treated S. epidermidis MFP04 was studied using the Microbial Adhesion To Solvent (MATS) technique  19  and two solvent couples: chloroform/hexadecane and ethyl acetate/n-decane.
Acknowledgements We wish to thank  Magalie Barreau  and  Olivier Maillot  for technical assistance. A. R. N'Diaye  is a recipient of a doctoral fellowship from the  French Ministry of Research (MRE). This work was supported by grants from the  Communauté d' Agglomération d'Evreux , the  Conseil Général de l'Eure , the  European regional development fund (ERDF)  and the  Normandie Regional Council.
ACKNOWLEDGMENTS Research in the Scherf laboratory is supported by the  European Research Council   Advanced Grant  ( ERC   Plas-moSilencing ),  ANR-13-ISV3-0003-01   NSFC  (n  81361130411 ), and the  French Parasitology consortium Par-aFrap  ( ANR-11-LABX0024 ) awarded to A. S. S. S. V. was supported by the  European Molecular Biology Organization Long-Term Fellowship , the  Marie Sklodowska-Curie International Incoming Fellowship  ( FP7-MC-IIF-302451 ), and the  Pasteur Roux Postdoctoral Fellowship. D. D. is supported by the  ParaFrap Postdoctoral Fellowship. We also acknowledge PlasmoDB, a member of pathogen-databases that are housed under the.
Four consecutive serial sections of the spleen, lung and cecum of two contact birds (Numbers 3 and 4) from Group 1 were examined in more detail (data not shown). In both animals, one to 15 positive cells per section could be observed in the cecal epithelium and sub-epithelial tissue in at least one serial section. Bird no. 3 also had a single positive cell in the spleen and lung in at least one section, whereas the other bird was negative in all spleen and lung sections (Fig  3 ).
Shedding of chlamydiae The examination of cloacal swabs from all 4-day-old ducklings before inoculation showed a low-level presence of C. psittaci in 11 out of 14 birds (mean Cq = 36. 3). Partial sequencing of the ompA gene from one of these positive cloacal swab samples revealed a sequence identical to the inoculated strain (genotype E/B sub-genotype 06-859, accession number: EU159263. 2). Cloacal swabs from control birds on 10, 28 and 84 dpi were all negative (data not shown). For the challenged groups, the level of cloacal shedding was correlated to the bacterial load detected in their organs. The shedding curves given in Fig 2  I  revealed maximum values of chlamydial genome copies on 7 dpi for Groups 1 and 2, and on 10 dpi for Group 3.
Strain re-isolation and molecular characterization To assess the viability of the C. psittaci detected by PCR, all ceca collected on 10 dpi from Group 1 were inoculated onto embryonated chicken eggs. Isolates were successfully recovered from seven ceca (four inoculated and three contact birds) after one passage (Table  2 ). The ompA gene sequences of these isolates were identical to those of the challenge strain (data not shown).
psittaci shedders. Ducklings included in this study came from a naturally raised flock (non-SPF) and might have been previously infected by vertical transmission  [24] , although no shedding in female ducks had been detected at laying time. At 14 days of age, ducklings from the control group were all PCR negative (organs and cloacal shedding), thus suggesting an early and self-limited infection with spontaneous clearance. These findings were confirmed by follow-up checks carried out on cloacal swabs from control birds (n = 11) aged 4 and 12 weeks and kept in BSL1 after the end of the experiment (data not shown). The initial chlamydial load detected in the 4-day-old ducklings before the start of the experiment was therefore not sufficient to result in development of an active infection and/or carriage.
DDH values were estimated using the GGDC online version 2. 1 (http://ggdc. dsmz. de /distcalc2. php). This analysis yielded 29. 7% Ϯ 2. 45% similarity with Blautia wexlerae (accession no. AXVN00000000), 33. 3% Ϯ 2. 45% with Blautia obeum (accession no. AAVO00000000), 25. 3% Ϯ 2. 40% with Blautia hansenii (accession no. ABYU00000000), 21. 9% Ϯ 2. 35% with Blautia schinkii (accession no. JNKJ00000000), 21. 2% Ϯ 2. 35% with Blautia hydrogenotrophica (accession no. ACBZ00000000), 22. 1% Ϯ 2. 35% with Blautia producta (accession no. ARET00000000), 28. 00% Ϯ 2. 40% with Ruminococcus gnavus (accession no. JAGQ00000000), 34. 4% Ϯ 2. 45% with Ruminococcus torques (accession no. AAVP00000000), and a 31. 6% Ϯ 2. 45% with Blautia coccoides (accession no. BAHT00000000). Accession number(s). The 16S rRNA gene and genome sequences from B.
Statistical analysis For the description of NADE and the analysis of potential determinants of the occurrence of the first NADE during long-term cART, we selected only NADE that occurred after the initial response to cART, i. e. after 4 months of follow-up (M4). Therefore, patients who died or were lost to follow-up before M4 were excluded from analyses. Potential determinants of the occurrence of the first NADE after M4 were studied using Cox proportional hazards regression models. Data were censored at last follow-up in the cohort or death. Plasma HIV RNA, CD4+ cell count (CD4) and CD4/CD8 ratio recorded during follow-up after M4 as well as a composite immune restoration variable built in three categories (CD4< 500/mm 3 , CD4 > 500/mm 3 and CD4/CD8 ratio 1, CD4 > 500/mm 3 and CD4/CD8 ratio > 1), were treated as time-dependent variables.