dataesr/scientific-paragraphs-categorization huggingface dataset:
Scanning electron microscopy Cells were rinsed twice with D-PBS (Gibco) and then fixed with 2. 5% glutaraldehyde in D-PBS (Sigma-Aldrich) for 1 h at room temperature. After gradual dehydration in ethanol (50, 70, 90 and 100 twice), the samples were immersed in hexamethyldizilazane (Sigma-Aldrich) for 5 min, air dried at room temperature and Fig. 1  EDPs cause fast membrane bleb formation in HT-1080 cells. a Scanning electron microscopy of control (Ctl) and EDP-treated HT-1080 cells after 40 min of incubation. Scale bar: 10 µm. b EDP dose-dependent induction of blebbing was evaluated by counting 10 fields per well under a phase contrast optical microscope after a 40 min incubation. Results were expressed as mean ± S. E. M. Data from one experiment, representative of three independent experiments, are shown.
c HT-1080 cells were treated with 50 µg/mL EDPs from 0 to 120 min. The quantification of the blebbing cell number was evaluated by counting 10 fields per well under a phase contrast optical microscope. Results were expressed as mean ± S. E. M. Data from one experiment, representative of three independent experiments, are shown. d EDPs stimulate cell membrane blebbing in 3D collagen matrix. GFP-Hsp90 transfected HT-1080 cells were seeded in a 3D collagen matrix in the presence of EDPs. 3D confocal imaging was realised after 24 h of incubation to study the HT-1080 cell morphology. In the presence of EDPs, HT-1080 cells adopted an amoeboid morphology with many membrane blebs and shed extracellular vesicles (white arrows). Scale bar: 10 µm. e Real-time imaging and analysis of bleb formation in GFP-Hsp90-transfected cell.
Cells were visualised using a LaB6 electron microscope (JEOL JSM-5400 LV, JEOL) at an acceleration voltage of 20 kV using the secondary electron signal. Transmission electron microscopy Isolated extracellular vesicles were visualised at room temperature using a FEG electron microscope (JEOL2100F, JEOL) fitted with a CCD camera (Orius SC200D, Gatan) at an accelerating voltage of 200 kV. In vitro invasion assay Invasion was performed as previously described. 5 atistical analysis Each experiment was performed at least thrice from separate sets of culture and data were expressed as mean ± S. E. M. Comparisons were performed using Student's t-test. Results were considered significant when *p < 0. 05, **p < 0. 01, ***p < 0. 001. Correlation between different groups was analysed by using nonparametric statistical analysis.
Calcium flux is reported as ratio 350 nm/380 nm fluorescence of FURA-2 in twenty HT-1080 cells. Data from one experiment, representative of five experiments are shown. Calcium-free media (0 Ca) were used to confirm the key role of the extracellular calcium. b Measure of cytosolic calcium concentration using FURA-2 loaded HT-1080 cells in presence of nifedipine after stimulation with EDPs. Calcium flux is reported as ratio 340 nm/380 nm fluorescence of FURA-2 in HT-1080 cells. The results shown are representative experiments (n = 3). Nifedipine was used at 10 µM. c Blebbing inhibition in HT-1080 cells in the presence of EDTA, evaluated by counting 10 fields per well under a phase contrast optical microscope after EDP stimulation for 40 min. Data from one experiment, representative of three independent experiments, are shown.
d Immunolocalisation by confocal microscopy of RhoA, ROCK2, ROCK1, P-LIMK1/2, cofilin, P-ERM, calpain1, actin and snapshot of mCherry-MLC transfected cells after treatment with EDPs versus untreated control HT-1080 cells (Ctl). Snapshot of 3D data was done using Imaris. Scale bar: 10 µm. e Schematic representation of the signalling pathways leading to EDP-induced blebbing and extracellular vesicle shedding. f Images from confocal microscopy analysis of cleaved caspase-3 and annexin-5 distributions after treatment with doxorubicin and EDPs. Cells were cultured on glass slides, fixed with paraformaldehyde and labelled with an anti-cleaved caspase-3 antibody (green) and annexin5-AF568 (red). Scale bar: 10 µm the blebbing, excluding ERC and galectin-3 (Suppl. table II). The use of αvβ5 blocking antibody had no significant effect on EDPinduced blebbing and αvβ3 blocking antibody blocked EDPinduced blebbing by 30% only.
ACKNOWLEDGEMENTS In memory of my father  Guy Brassart  (1945Brassart ( -2018) ) and my grandmother. The authors thank  Dr Joon Kim  ( Korea University, South Korea ) for the GFP-Hsp90 plasmid and  Dr Steven Hooper  ( Cancer Research UK London Research Institute, United Kingdom ) for the mCherry-MLC plasmid. We are grateful to  Aurélie Dupont-Deshorgue ,  Dr Sandra Audonnet  ( Flow Cytometry Core URCACyt, URCA, Reims, France ),  Dr Frederique Nolin  and  Laurence Wortham  ( EA4682 ,  URCA, Reims, France ) for their skilful technical assistance. This work was supported by grants from the  Centre National de la Recherche Scientifique  ( UMR 7369 ), the  University of Reims Champagne-Ardenne , the  Region Champagne-Ardenne  and the  Ligue Nationale contre le Cancer.
Results We generated shotgun Illumina sequence data from four archival blood slides derived from malaria patients sampled between 1942 and 1944 in Spain's Ebro Delta. The majority of reads that mapped to P. vivax (89. 09%) derived from a single slide dated to 1944. In total, 481,245 DNA reads (0. 44% of the total reads generated) mapped to P. vivax, yielding a composite genome, we term Ebro-1944, at 1. 4Â coverage (1. 28Â deriving from the newly analyzed 2017 slide), and spanning 66. 42% of the (PvP01) reference. The mtDNA genome was recovered at 32Â coverage (supplementary figs. 1-5 and tables 1-3, Supplementary Material online). Although working with low coverage ancient genomes is challenging, the fact that our genome is haploid and displays low levels of  van Dorp et al. doi:10. 1093/molbev/msz264 MBE postmortem sequencing errors suggests it can be reliably used in most evolutionary analyses.
Therefore, to infer the temporal relationship of Ebro-1944 to strains from the Americas, we included our historic sample together with 15 closely related publicly available genomes sampled over a range of time periods (supplementary table 5, Supplementary Material online). We selected strains predominantly from the Americas, with three additional genomes included from India, Myanmar, and North Korea to root the topology and increase the time span of our data set. To account for the possible confounding effect of genetic recombination, we filtered the resulting alignment for a set of high confidence congruent SNPs. Specifically, we removed all homoplasic that is SNPs in the alignment in conflict with the maximum parsimony phylogeny (see Materials and Methods). This approach identifies, with no required prior knowledge, regions of the genome that are hypervariable, deriving from recombination or mixed infections, as well as filtering SNPs which may have been erroneously called due to low sequence quality or postmortem damage.
The resultant data set included 131,309 SNPs and 277 strains. We used this catalog to genotype all remaining samples in the data set. For the individual genotyping, we called SNPs with GATK v3. 7 UnifiedGenotyper as before, removing all heterozygous calls, and all variants with a minor allele frequency below 0. 01%. The final data set comprised 338 samples and 128,081 SNPs. The genotypes for Ebro-1944 were called by selecting one random read that mapped each position of the data set, a pseudo-haploid calling approach which is advocated for low coverage aDNA  (Mathieson et al. 2015). This resulted in the Ebro-1944 sequence covering 77,425 of the 128,081 total included positions (supplementary table 3, Supplementary Material online).
Phylogenetic Analysis and Data Set The whole-genome sequences of 15 modern P. vivax samples and Ebro-1944 were mapped against the PvP01 reference assembly  (Auburn et al. 2016 ) (supplementary table 5, Supplementary Material online). These strains were selected with a focus on the Americas and also to include strains sampled over a large temporal span as is required for phylogenetic tip dating. The main motivation for using the PvP01 reference genome for mapping sequence data for phylogenetic analyses stems from this assembly offering a better definition of sub-telomeric genes and repetitive pir genes that usually lie in recombinant regions, thus providing greater power to identify and exclude these parts of the genome  (Auburn et al. 2016). After calling variants with GATK version 3. 7 UnifiedGenotyper, polymorphisms were further filtered by selecting only those SNPs with a coverage >1 an average mapping quality >30, a genotype quality >30, and by removing heterozygous positions.
Acknowledgments We are grateful to  Thomas D. Otto  ( University of Glasgow ) and  Thomas Lavsten  ( University of Copenhagen ) for helpful comments and suggestions and to the descendants of  Dr Canicio ,  Miquel , and  Ildefons Oliveras  for sharing with us their slides. We additionally would like to thank  Dr George Busby  and  Dr Jacob Almagro  for useful discussions on chromosome painting of Plasmodium sp. This research was supported by a grant from  Obra Social "La Caixa," Secretaria d'Universitats i Recerca Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya  ( GRC 2017 SGR 880 ),  Secretaria d'Universitats i Recerca  ( GRC2017-SGR880 ), and by  FEDER-Ministry of Science, Innovation and Universities (MCIU)  ( PGC2018-095931-B-100 ) to C. L. -F. and an  European Research Council (ERC)   Consolidator Grant  ( 681396-Extinction Genomics ) to M.
Combining vector control with trypanocidal treatment can reduce the timeframes necessary to reach operational thresholds for IDTI (<2% seroprevalence in children aged <5 years), but the most informative age groups for serological monitoring are yet to be identified. Measuring progress towards the 2030 goals will require availability of vector surveillance and seroprevalence data at a fine scale, and a more active surveillance system, as well as a better understanding of the risks of vector re-colonization and disease resurgence after vector control cessation. Also, achieving scaling-up in terms of access to treatment to the expected levels (75%) will require a substantial increase in screening asymptomatic populations, which is anticipated to become very costly as CD prevalence decreases. Further modelling work includes refining and extending mathematical models (including transmission dynamics and statistical frameworks) to predict transmission at a sub-national scale, and developing quantitative tools to inform IDTI certification, post-certification and re-certification protocols.
The lowest of all these is currently screening (access to diagnosis <1%). Are current tools able to reliably measure the targets? Force-of-Infection (FOI) models using age-stratified seroprevalence data are a promising tool to measure efficacy of IDTI. Tools are required to evaluate BTT, TTT and CTI. The "0% colonization" target can only be measured very imperfectly with current vector-surveillance tools. What are the biggest unknowns? Prevalence of infection and house infestation in many areas; role of native vector species in transmission; resistance status of vector populations to currently available insecticides; disentangling the impact of chemical vector control from that of housing improvement; efficacy of trypanocidal treatment under various rates of abandonment. What are the biggest risks? Slacking elimination efforts before reaching EPHP; spread of insecticide resistance; not being able to identify and treat congenital cases; treatment of children with false positive results.
The WHO has a project in progress to develop an exhaustive database called the "World Information System for the Control of Chagas Disease" (WISCC), with an agreement with the Computer Centre of the Polytechnic University of Barcelona (Spain), that may be functional to these needs. Additionally, modelling could inform how widely screening should be done in non-endemic countries. Achieving most of the goals currently stated for women and newborns seems challenging with the currently available tools (Table  1 ). Given the long asymptomatic period and the current passive surveillance system for identifying cases of CD in endemic and non-endemic countries, it seems unfeasible that 90% of women of childbearing age will be screened. However, reaching almost 100% of pregnant women is potentially feasible with the recent strategy EMTCT plus (elimination of motherto-child transmission of HIV, syphilis, Chagas, and perinatal hepatitis B), which adds mandatory surveillance tests during pregnancy for CD, planned to be in place in Colombia, Chile and Uruguay as pilot countries over the next few years 34.
" The issue of transfusion-mediated transmission has been or still is pertinent to some non-endemic, developed countries. The Background section, page 3, also states: "So far, 11 out of the 21 recognised endemic countries have been certified as having reached intradomiciliary transmission interruption (IDTI). " This statement inaccurately suggests that there is no vector-borne domestic transmission of in 11 countries. The T. cruzi certifications of IDTI for Central American countries are relevant for , not for , a R. prolixus T. dimidiata widespread vector involved in domestic transmission to humans (Peterson et al. 2019 ). Similarly, the certifications for the Southern Cone countries are relevant for , but in Brazil there are other T. infestans species involved in domestic transmission. On page 4, a reference is needed to justify: "the number of triatomines/house was fitted to data from various locations prior to vector control and applied to cases where there was only one triatomine species present in the dwellings, as well as to situations with mixtures of species and developmental stages, various types of houses and bug densities per house.
Acknowledgments Collaborating Group on Chagas Disease Modelling:  Zulma M Cucunubá  (zulma. cucunuba@imperial. ac. uk, corresponding author) 1,2 ;  Pierre Nouvellet  (pierre. nouvellet@sussex. ac. uk) 3 ;  Sébastien Gourbière  (gourbiere@univ-perp. fr) 4 ;  Juan-Carlos Villar  (jvillarc@cardioinfantil. org) 5,6 ;  Jorge E Rabinovich  (jorge. rabinovich@gmail. com) 7;  Michael Z Levy  (mzlevy@ pennmedicine. upenn. edu) 8;  Fernando Abad-Franch  (abadfr@ yahoo. com) 9,10;  Andy P Dobson  (dobson@princeton. edu) 11;  Maria-Gloria Basañez  (m. basanez@imperial. ac. uk, corresponding author) 1,2 We would like to thank the participants of the " Imperial College Chagas Symposium ",  14-15 February 2018 , for valuable insights on the ideas discussed in this article:  María Dolores Bargues  ( University of Valencia );  Luis Gerardo Castellanos  ( Pan American Health Organization );  Lorenzo Cattarino ,  Julia Halder  and  Elisa Sicuri  ( Imperial College London );  Orin Courtenay  and  Raquel Goncalves  ( University of Warwick );  T Déirdre Hollingsworth  ( University of Oxford ) and  Mauricio J Vera  ( Ministry of Health, Colombia ); the  Infectious Diseases Data Observatory (IDDO) ;  Isabela Ribeiro  and  Sergio Sosa-Estani  (DNDi); and the  Ministry of Health, Brazil.
25 mm i. d. , 0. 25 mm) from SGE. The GC was interfaced with an ISQ mass spectrometer (Thermo Scientific). Compound identification and corresponding structural formulae were assigned using the National Institutes of Standards (NIST) library. Steady-state fluorescence conditions. Fluorescence data were obtained using a FLS980 spectrometer from Edinburgh Instruments. Measurements were performed in a 4 faces polished quartz cuvette filled and sealed in Ar-filled glovebox (O 2 and H 2 O level below 0. 1 ppm). Excitation was ensured by a Xe lamp with two excitation monochromators scanning wavelengths from 250 to 474 nm with a slit aperture of 1 nm. Two emission monochromators fitted with a visible PMT detector probe the emission wavelengths from 262 to 500 nm with a slit aperture of 1 nm. Quantum yield measurements were performed on the same fluorimeter using a Benflec integration sphere.
The single-photon events were collected by a cooled microchannel plate photomultiplier tube R3809U (Hamamatsu) and recorded by a PicoHarp 300 TCSPC system (PicoQuant, 4 ps bintime). The instrumental response function was recorded using colloidal silica (Ludox), and its full width at half-maximum was in the range of 40 ps. The recorded decays were analyzed by FluoFit software package version 4. 6. 6 (PicoQuant). The reduced χ² was below 1. 1. Weighted residuals and autocorrelation function were used to check the quality of the fits. ATR-FTIR conditions. ATR-FTIR measurements were performed using a Nicolet AVATAR 370 DTGS spectrometer (Thermo Scientific). A drop of electrolyte was deposited onto a diamond window and spectra were taken on 16 scans with a resolution of 1 cm -1. Background scans were performed prior to any measurements.
Acknowledgements G. B. , A. N. VN. , I. S. , F. S. wish to thank the  RS2E  and  ANR Labex Storex  for financial support for GB. This work has been accomplished under the  ANR Photo2batt program. The  Conseil Régional de Picardie  and  FEDER  is acknowledged for financial support for IS. The authors wish to acknowledge  Dr. Elodie Salager  ( CEMHTI, CNRS UPR3079 ) for 31 P auto-diffusion NMR measurements and helpful discussion.
Cell suspension was passed through a 70-μm cell strainer. Cells (5. 10 5 ) were incubated with 5 μl/ml purified rat anti-mouse CD16-CD32 mAb (TruStain fcX, Biolegend Inc, San Diego, CA) before incubation with specific anti-mouse antibodies. Cells were marked with CD3-FITC, CD4-APC-Cy7, and CD25-PE (Biolegend Inc), CD8-PerCP-Cy5. 5 and FoxP3-APC (eBioscience Affymetryx, Santa Clara, CA, USA), washed with PBS and fixed with 0. 5% paraformaldehyde. Flow cytometry analysis was performed on FACS LSR Fortessa (BD biosciences, San Jose, CA, USA), and using FlowJo software (Tree Star, Ashland, OR). Cells were gated, based on forward and side scatter and on living cells. Acquisition of multiparameter data was carried out with an appropriate forward scatter (FSC) threshold to exclude debris. At least 50,000 CD3+ cells per sample were analyzed.
Clinical study. All patients who were treated with Nivolumab as second-or third-line treatment for stage IV NSCLC at the Rouen University Hospital between February 2015 and July 2017 were screened. Patients who underwent 18-FDG PET-scan within the 3 months prior to Nivolumab treatment onset were selected for further analysis. Clinical data, imaging, pathology results and molecular analysis were collected from the electronic medical record. 18-FDG PET-scan were reviewed and Metabolic tumor volume was determined using PET VCAR semi-automatic software of AW server 3. 2 (General Electric ® , Milwaukee, USA) for segmentation. Non malig- nant FDG avidity areas were not included in this analysis. MTV cut-off to segregate low versus high MTV patients was determined using ROC curve analysis for overall survival.
Statistical analysis. Statistical analysis was performed using the R language and environment for statistical computing (version 3. 1. 3, R foundation for statistical computing, Vienna, Austria) on RStudio software (version 0. 98. 1103, RStudio ® , Boston, MA, USA). Data were summarized using mean and standard error for mean. In the animal experiments, giving the limited sample size and the high number of groups, we used the non-parametric Kruskall and Wallis test (non-parametric equivalent of the one-way analysis of variance -ANOVA-) for multiple group comparison of the relative tumor volume at day 21 post-treatment initiation. Results were considered statistically significant when p < 0. 05. In the clinical dataset, Kaplan-Meier method was used to estimate progression-free survival (PFS).
Taken together, our results suggest that tumor volume is a predictive factor of anti-PD1 efficacy in NSCLC. That effect may be mediated by T regulator lymphocytes. Tumor debulking appeared to improve treatment outcome in a mouse model and warrants further investigations in the clinical setting. 18FDG PET-scan data from patients treated with anti-PD1 for stage IV NSCLC was reviewed. MTV cut-off to segregate low versus high MTV patients was determined using ROC curve analysis for overall survival (AUC = 0. 81, p = 0. 02). Kaplan-Meier method was used to estimate progression-free survival. MTV, age, histology and Performance Status were compiled in a proportional hazard Cox model to perform multivariate analysis. Comparisons of the 6-months PFS and 1-year OS between groups were performed using Student t-test.
18FDG PET-scan data from patients treated with anti-PD1 for stage IV NSCLC was reviewed. MTV cut-off to segregate low versus high MTV patients was determined using ROC curve analysis for overall survival (AUC = 0. 81, p = 0. 02). Kaplan-Meier method was used to estimate progression-free survival. MTV, age, histology and Performance Status were compiled in a proportional hazard Cox model to perform multivariate analysis. Comparisons of the 6-months PFS and 1-year OS between groups were performed using Student t-test. KLN-205 tumors from DBA/2 allografted mice (n = 9) were harvested at day 21 after treatment initiation. Tumors were dissociated and stained as described in the methods. Flow cytometry analysis was performed on FACS LSR Fortessa (BD biosciences, San Jose, CA, USA), and using FlowJo software (Tree Star, Ashland, OR).
The near full-length genomes or Gag, Pol and Nef regions of proviral DNA were sequenced by Sanger and/or Next Generation Sequencing (NGS). The HLA-A and B alleles were defined by NGS or molecular analysis. The TuTuGenetics software, which moves a sliding window of 8 to 10 amino acids through the amino acid alignment, was combined with the Immune Epitope Data Base (IEDB) to automatically calculate the theoretical binding affinity of identified epitopes to the HLA alleles for each individual. We identified 15 conserved epitopes in Pol (11), Gag (3), and Nef (1) according to their potential presentation by the dominant HLA-A and B alleles and now propose to use the corresponding conserved peptides in a multi-epitopic vaccine (HLA-fitted VAC, HFVAC).
Discussion The aim of the present study was to identify conserved CTL epitopes in integrated HIV-1 with high predicted binding affinity to most common HLA class I alleles to serve as the basis of further T cell immunogen design. Integrated DNA was analysed since virus rebound after cART interruption is believed to originate from such archived DNA. The study has some limitations and raises some important issues. First, we analyzed global archived DNA molecules without differentiating noninfectious and replication competent genomes. It would be pertinent to use and clone CD4+ memory T cells and express the infectious viral particles  [17]. However, there has been an ethical limitation in the available blood volumes. The reading coverage of NGS sequencing was high in the study and since we only rarely observed escape variants at the epitopic areas of interest, we hypothesize but cannot proove that these data would also apply to replication competent infectious genomes inside the DNA molecules analyzed.
As yet it is not possible to know what the effect of peripheral vaccination would be on these tissue cells. Moreover, the full identity of the CTL epitopes archived in the peripheral blood compartment versus the GALT is unclear. Some published data seem to indicate at least that HIV-1 does not evolve in this compartment under efficient cART  [28]. At present we are carrying out a comparative study of the CTL epitopes of archived proviral DNA in these two compartments. In conclusion, we have screened more than 200 patients'HIV proviral sequences for conserved CTL epitopes presented by the most common HLA class I alleles of the studied population. Some of these epitopes have been described in the listing of optimal CTL epitopes of the Los Alamos Immunology database; others are newly described epitopes resulting from our insilico analysis.