dataesr/scientific-paragraphs-categorization huggingface dataset:
The region where DNA synthesis switches between the two genomic RNAs, generating the recombinant DNA is defined as a breakpoint. Specifically, a breakpoint corresponds to the region encompassed by the two closest informative sites of each of the parental strains involved in the crossing. As such, its size varies as a function of the density of these sites, with one nucleotide being the smallest size and without an actual upper size limit. In HIV databases, while breakpoints have been mapped along the coding sequences, little is known about the breakpoints in the LTR. However, the increasing numbers of available sequences now also enable the characterization of recombinant LTR from patient isolated strains  [7] [8] [9] [10] [11] [12] [13] [14]. A plethora of HIV recombinants have been identified in the last few decades  15, 16.
Results Analysis of the available CRFs, URFs and HIV-1/MO sequences. Starting with the sequences available in databases, we exploited the sequence diversity found in vivo in heterozygous virions to investigate which of the two copies of genomic RNAs is used during first and second strand transfers (Fig. 1B ,C and F,G, respectively). This approach requires focusing on recombinants, as these viruses are necessarily generated from heterozygous virions. Because, as mentioned above, we wanted to extend the analysis of the recombination pattern not only to the LTR but also to the surrounding sequences, we decided to exclusively consider the recombinant forms for which the full-length sequence, including the LTR, was available (see Materials and Methods). For the sequences of HIV-1/M CRFs and URFs, data on the complete recombination pattern of 13 HIV-1/M CRFs (subtype G 22 , CRF03_AB, CRF08_BC, CRF12_BF, CRF26_AU, CRF31_BC, CRF32_06/A1, CRF42_BF, CRF45_cpx, CRF60_BC, CRF71_BF, CRF87_cpx, CRF88_BC) and that of 5 URFs (URF_SHI 10 , URF_CRN  11  , URF_AUK  11  , URF_WEI  13  , URF_GUI 12 ) were available.
Concerning CRF08, CRF12, CRF42 and URF_CRN, the precise characterization of the recombination pattern in the region encompassing the LTR and the matrix-coding sequence (LTR-MA) was missing from the databases. We therefore completed the recombination analysis in this region using SimPlot  23  (Fig. 2A, B ). For MO recombinants, nine fully sequenced recombinants were considered (see Materials and Methods). For seven of these recombinants (RBF208 8 , YBF274, REC107, BCF212, RBF222, RBF237 and RBF240), the precise characterization of the recombination pattern in nef and the LTR-MA region was also lacking. These recombinants were therefore reanalysed here (Fig. 2C ). Altogether, 27 full-length recombinant sequences were considered, including 13 CRFs, 5 URFs and 9 HIV-1 intergroup recombinants from groups M and O (Supplementary Table  S1 ).
Discussion The generation of retroviral LTR requires two strand transfer events, called first and second strand transfers. These events can be either intra-or intermolecular between the two copies of gRNA present in the viral particle. Inter and intramolecular transfers generate precise patterns of recombination in heterozygous virions. Proviruses with a recombination breakpoint at the U3/R junction are generally attributed to intermolecular first strand transfer, while intramolecular first strand transfer yields LTR without breakpoints. As intra-and intermolecular first strand transfer occur at comparable rates in cell culture  5, 6  , both types of LTR (with a U3/R breakpoint and without breakpoints) are expected to be identified in databases. Although we consistently detect both types of LTR, their distribution is unexpectedly unequal when the proviruses are grouped according to the phylogenetic origin of the sequences adjacent to the LTR (gag and nef).
Materials and Methods Samples. Eleven full-length CRF sequences were retrieved from the Los Alamos HIV sequence database (www. hiv. lanl. gov/). Five full-length URF sequences were searched in the GenBank with the key words "HIV URF" or "HIV recombinant full sequence", and the 200 first hits were screened. Lots of sequences were fulllength in the coding region but not in the LTRs and were therefore discarded. Eight full-length sequence HIV-1/ MO recombinants were retrieved from the literature (97CA-MP645 7 , RBF208 8 , REC024 9 , YBF274  14  ) or from the database of the virology unit at Rouen University Hospital (REC107, BCF212, RBF222 and RBF237; sequences in process of publication). Strains that were already described in publications and in LANL were not further analysed. All the strains used in this study are presented in Supplementary Table  S1.
Reference panel. To study the phylogenetic relationships and the recombination patterns of the HIV-1/MO intergroup recombinants as well as the HIV-1/M intragroup recombinants (CRFs and URFs), a panel of HIV-1/M reference strains was generated with sequences from HIV-1/M pure subtypes, CRF01_AE and CRF02_AG, as well as HIV-1/O and HIV-1/P sequences, gathered from the LANL sequence database and aligned with MEGA 7  30. In this study, we considered that subtype G is a recombinant and CRF02 a pure subtype, as demonstrated by Abecasis et al. in 2007  22. Very few sequences were complete in the LTRs. Namely no sub-subtype A2 and F2, and no subtypes H, J and K were available (Supplementary Table  S3 ). Study of the mosaic structure of the HIV recombinants. Three CRFs (CRF08, CRF12, CRF42) from the LANL HIV database were not fully described in the LTR.
One URF (URF_CRN) was fully described but one breakpoint, located between U5 and the beginning of gag was not precisely defined. We thus retrieved the full sequence of these four viruses for further analysis. The coding sequence of these four strains was computed with jpHMM software  31  (http://jphmm. gobics. de) to generate and verify the mosaic structure in their coding sequence (Fig. 2A ). Moreover, for each of the four strains, the sequence going from the 5′ border of the LTR till the end of the MA coding sequence (LTR-MA) was aligned with the panel of selected HIV-1/M reference strains to study the precise recombination pattern in this region. The alignment was gap-stripped and the SimPlot software  23  was used to perform similarity plot (SP), informative sites (IS) and BootScan (BS) analyses (Fig.
The BS analysis was then run to confirm the location of the breakpoint. Concerning HIV-1/MO recombinants, the non-coding sequence of the RBF208 HIV-1/MO recombinant  8  was not described and HIV-1/MO recombinants (YBF274, REC107, BCF212, RBF222, RBF240 and RBF237) are not yet published. For these recombinants, the nef coding sequence and the LTR-MA region were analysed. For each recombinant, the part of the nef coding sequence that does not overlap with U3 was concatenated with the LTR-MA sequence into a nef-LTR-MA sequence (see Supplementary sequences). The nef-LTR-MA sequences were aligned with the reference panel with MEGA 7  30  , the alignment was gap-stripped and a recombination analysis was performed with the SimPlot software  23  as described for HIV-1/M CRFs and URFs. For each recombinant, the SimPlot analysis was performed using HIV-1/O reference sequences and the HIV-1/M subtype reference sequences corresponding to the strain whose sequence was present in the coding region of the recombinants (for instance, subtype D for RBF208, which is a recombinant between HIV-1/O and HIV-1/M subtype D).
Patients The French Hospital Database on HIV (FHDH, ANRS CO4) is a nationwide hospital-based cohort created in 1989, in which clinical and biological data on HIV-infected patients throughout France are prospectively recorded  [12]. To date more than 140 000 patients have been included and signed an informed consent. Data submitted by the participating centres to the data coordinating and analysis centre are anonymized, then encrypted. The FHDH was approved by the institutional ethic committees, Commission Nationale de l'Informatique et des Libertes (CNIL) on 27 November 1991 (Journal Officiel, 17 January 1992). Using the same definition as previously  [11]  we characterize two groups of HIV1-infected adults who attended an FHDH follow-up visit in 2005 while asymptomatic and antiretroviral-naïve, and who had had at least three CD4 cell counts measurements during the previous 5 years.
1 in univariable analyses. Backward selection retained only those variables with p values below 0. 1. For the HIC group, only two variables could be entered in the multivariable model, owing to an insufficient number of events. For continuous variables, the choice of metric (categorized or continuous) was based on the lowest value of Akaike's criterion (AIC). SAS software version 9. 4 (SAS Institute, Cary, NC) was used for all analyses. P values <0. 05 were considered to denote statistical significance.
Results In 2005, among the 202 LTNP patients included in our previous analysis  [11] , 184 patients (91%) still had LTNP status: an update showed that 12 patients started antiretroviral treatment before 2006, 4 patients had developed AIDS, and data were missing for 2 patients. Among these 184 LTNP patients, 171 had a follow-up visit after 2005 and were thus included in this analysis. Of them 22 had a CD4 cell count nadir of at least 600/ml, and a positive CD4 cell slope and were previously referred as "Elite LTNP"  [11]. Among the 101 previously studied HIC patients, an update showed that 18 patients started antiretroviral treatment before 2006, one patient developed AIDS, and two patients were also infected by HIV-2. Among the remaining 80 HIC patients, 72 had a follow-up visit after 2005 and were thus included in this analysis.
Background: Patient-reported outcomes (PROs) provide clinicians with further understanding of the impact of treatment on patients' daily lives. In addition, real-world studies, which employ broader inclusion criteria than randomized trials, may help to inform prescribing decisions when selecting a disease-modifying therapy (DMT) to treat relapsing forms of MS (RMS). We sought to use PROs to determine patient treatment satisfaction and other treatment outcomes, and report safety and tolerability associated with teriflunomide, in the global, phase 4 Teri-PRO study (NCT01895335). Methods: Patients with RMS (N = 1000) received teriflunomide for 48 weeks per local labeling. The primary endpoint was Global Satisfaction with teriflunomide treatment measured by the Treatment Satisfaction Questionnaire for Medication (TSQM, V1.
, 2014; O'Connor et al. , 2011)  in two phase 3 trials. In addition, teriflunomide has been shown to be effective in patients with a first demyelinating episode suggestive of MS  (Miller et al. , 2014). Teriflunomide has also demonstrated a manageable safety and tolerability profile that is consistent across phase 2 and 3 clinical trials  (Comi et al. , 2016; Confavreux et al. , 2014; O'Connor et al. , 2011 O'Connor et al. , , 2006)) , and their extensions  (Confavreux et al. , 2012; Freedman et al. , 2016; O'Connor et al. , 2016). Studies in the teriflunomide clinical development program assessed clinical and radiologic outcomes traditionally used in clinical trials of DMTs for the treatment of MS. The Teri-PRO (Teriflunomide Patient-Reported Outcomes, NCT01895335) study evaluated PROs, including treatment satisfaction, disability, and quality of life with teriflunomide, as well as its clinical effectiveness, safety, and tolerability, in routine clinical practice worldwide.
The Treatment Satisfaction Questionnaire for Medication (TSQM, Version 1. 4), used in this study to assess patient-reported satisfaction with teriflunomide treatment, is a measure that has been increasingly used to assess DMTs in real-world practice  (Calkwood et al. , 2014; Kresa-Reahl et al. , 2015; Saiz et al. , 2015; Wicks et al. , 2016). The TSQM has shown good measurement properties using traditional psychometric methods applied to data from a range of chronic diseases (migraine, arthritis, hypertension, asthma, diabetes, psoriasis, hypercholesterolemia, and depression)  (Atkinson et al. , 2004) , as well as data from patients with MS from both this study  (Hobart et al. , 2016)  and the TENERE (NCT00883337) phase 3 trial  (Vermersch et al. , 2017).
Cognition was measured using the Symbol Digit Modalities Test (SDMT)  (Vollmer et al. , 2016) , which involves a simple substitution task; the total score is the proportion of correct answers, with higher scores indicating a higher level of cognitive function. Further information pertaining to cognitive function was provided by the cognitive subscale of the MSPS. Data regarding adherence to treatment and adverse events (AEs) were also collected during the course of the study. The timings of assessments are shown in Fig. 1.
, 2016; O'Connor et al. , 2016). Assessment of cognitive impairment using both the physician-rated SDMT and the patient-rated Cognitive Symptom subscale of the MSPS also showed stability over time. Teriflunomide treatment was previously shown to be associated with a significant improvement in cognitive performance vs placebo in the TEMSO phase 3 trial (NCT00134563), as measured by the Paced Auditory Serial Addition Test  (Miller et al. , 2011)    course  (Achiron and Barak, 2006)  and imposes a significant burden on patients in terms of their capacity to remain in employment, while also adversely impacting personal relationships and quality of life  (Cadden and Arnett, 2015; Multiple Sclerosis International Federation, 2013). Cognitive decline in MS is also associated with other manifestations of the disease, including brain volume loss  (Vollmer et al.
, 2016) , which is known to occur at an accelerated rate in patients with MS relative to the general population  (De Stefano et al. , 2014). Teriflunomide has previously been shown to reduce the rate of brain volume loss vs placebo in an analysis of the TEMSO MRI data  (Radue et al. , 2015) , which may account for the observed effects on cognitive function. Quality of life outcomes, measured by MusiQoL and the Stern Leisure Activity Scale, also remained stable with statistically significant improvements seen on some MusiQoL subscales. In the TOWER phase 3 trial, significant benefits in quality of life (as measured by the Short-Form 36) were reported with teriflunomide 14 mg treatment vs placebo  (Confavreux et al. , 2014). The safety and tolerability profile of teriflunomide in this study was consistent with that seen in phase 2 and 3 clinical trials  (Comi et al.
Assessment Baseline TSQM X C PDDS X MSPS X MusiQoL X Stern Leisure Activity Scale SDMT EDSS Relapses Adverse events X Adherence X International Conference on Harmonisation Guidelines for Good Clinical Practice (International Conference on Harmonisation Expert Working Group, 2016), the Declaration of Helsinki (World Medical Association, 2016), and local laws and regulations. This trial is regis- tered with ClinicalTrials. gov, number NCT01895335, and with Clin- icaltrialsregister. eu, EudraCT number 2013-001439-34.
Flow cytometery Flow cytometry experiments were performed using either a LSR Fortessa (Beckton Dickinson) or MACSQuant Analyzer (Miltenyi biotech). Flow cytometry data were analyzed using FlowJo software (FlowJo, LLC). Cells were isolated and incubated with anti-CD16/32 to block Fc receptors, then incubated with the appropriate combination of fluorescent-labeled antibodies. For intracellular staining, cells were stimulated by CD3/CD28 crosslinking as explained above and activation was stopped by adding paraformaldehyde at 4% final concentration. After 15 min at RT, cells were incubated with anti-CD16/32, surface stained with anti-CD4, then permeabilized with methanol, overnight at -20˚C. After washing, cells were incubated with anti-SLP76 pY128 and anti-pERK1/2, followed by anti-mouse-IgG1-PE and anti-rabbit IgG-AlexaFluor647.
Since SLP76 is an essential regulator of T cell lineage development  [3] , we initially addressed the potential effect of Ser376 mutation on thymocyte maturation. We found that the cellularity and the frequencies of CD4 + and CD8 + single-positive, CD4 + CD8 + double-positive and CD4 -CD8 -thymocytes in SLP76-S376A mice were comparable to those observed in control mice (Fig  1A  and Table  1A ). Moreover, immature thymocyte subpopulations, as defined by CD44 and CD25 expression in the triple negative CD3 -CD4 -CD8 -compartment  [18] , were not altered in SLP76-S376A mice (Fig 1B and Table  1B ). These data suggest that SLP76-S376A expression does not significantly affect T cell development. Nevertheless, a high-content screening by multicolor flow cytometry was performed to further extend this analysis.
Similarly, phosphorylation of PLCγ1 at Tyr783 was increased in mutant CD4 + T cells, particularly at early time points of stimulation (Fig 3B  and 3C ). Of note, increased tyrosine phosphorylation of both SLP76 and PLCγ1 dependent on Ser376 mutation is consistent with our previous data in human T cells  [13, 16]. Moreover, increased AKT phosphorylation at Ser473 as well as ERK1 and ERK2 kinases phosphorylation was observed in mutant T cells. The latter result can be a direct consequence of the increased activation of PLCγ1, which acts as an upstream activator of the RAS-RAF-MEK-ERK1/2 signaling cascade through the production of diacylglycerol  [20]. SLP76 and ERK phosphorylation was also analyzed in anti-CD3-stimulated cells by intracellular staining and flow cytometry. These experiments confirmed the increased phosphorylation of both proteins in SLP76-S376A-expressing CD4 + T cells (Fig  4 ).
Acknowledgments We thank  Drs. J. Bouchet  and  S Aguera  ( Lymphocyte Cell Biology Unit, Institut Pasteur ) for critical reading the manuscript;  Drs. P. Bruhns ,  F. Jo  ¨nsson and  C. Gillis  ( Antibodies in Therapy and Pathology Unit, Institut Pasteur ) for helpful discussions, reagents and advice for some experiments;  G. Millot  and  T. Obadia  ( Bioinformatics and Biostatistics Hub-C3BI, Institut Pasteur ;  USR 3756 ,  CNRS ) for their help with statistical analysis. We also thank the  CIPHE-Phenomin (Inserm ,  US012 ) team for generating the SLP76-S376A knock-in mouse line and, in particular,  Lillia Hadjem  for the high-content flow cytometry immunophenotyping. Finally, we thank the  Flow Cytometry  facility of the  Institut Pasteur  for help in T cell sorting. V. H. N. was funded by a doctoral contract of the  French Ministry of Higher Education and Research.
This work was funded by grants from the  Institut Pasteur , the  French National Center for Scientific Research (CNRS) ,  French National Institute of Health and Medical Research (Inserm) , the  Ligue Contre le Cancer-Comitede Paris  (grants nr. RS12/75-107  and  RS13/75-30  to V. D. B. ) and the  Agence National de la Recherche  (grant nr. ANR-11-BSV3-0025  to A. A).
Funding: V. N. was funded by a doctoral contract of the  French Ministry of Higher Education and Research. This work was funded by grants from the  Institut Pasteur  (www. pasteur. fr),the  French National Center for Scientific Research  (www. cnrs. fr), the  Ligue Contre le Cancer -Comitede Paris  (www. ligue-cancer. net;grants nr. RS12/75-107  and  RS13/75-30  to V. D. B. ), the  Agence National de la Recherche  (www. agence-nationale-recherche. fr;grant nr. ANR-11-BSV3-0025  to A. A). French National Institute of Health and Medical Research (Inserm) ; website: www. inserm. fr. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
In the last decade, there have been a few HDPs entering clinical trials, specifically cathelicidins and defensins natural peptides or derivatives such as LL-37, MBI-226 (studies NCT00211523, NCT00211497 and NCT00027248 for the prevention of central venous catheter-related bloodstream infections and acne) and PMX-30063 (study NCT01211470 for acute bacterial skin and skin-structure infection). However, the clinical and commercial development of these peptide-based drugs has some limitations such as high cost of production, susceptibility to proteases and cytotoxicity. For example, the human cathelicidin LL-37 enhances apoptosis of epithelial cells, smooth muscle cells and T cells at levels above 10 µM 37. Besides being cytotoxic, LL-37 is also sensitive to protease cleavage, leading to the abolishment of its antimicrobial properties  38.
The nanoindentation method was used to determine the Young's modulus from the force vs. indentation curves. Mechanical properties were obtained by recording a grid map of 50-by-50 force curves on several bacterial clusters containing at least 10 bacteria electrostatically immobilized onto PEI coated glass substrate. The maximal loading force was 4 nN, the piezodrive was fixed to 2 µm and the approach rate was 2 µm/s. The histograms corresponding to the statistic distribution of the Young modulus were estimated from the analysis of the approach curves according to the Sneddon model  42, 43  where δ is the indentation depth, ν the Poisson coefficient, R is the curvature radius of AFM-tip apex and f BECC the bottom effect correction described by Gavara et Chadwick  42. All the FVI were analysed by mean of an automatic Matlab algorithm described elsewhere  44.
Dead cells were excluded using the LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit (Life Technologies). For OT-I cell transfer experiments, transferred cells were tracked using a combination of PE-Cy7 anti-CD8a (53-6. 7), PerCP-Cy5. 5 anti-CD45. 2 (104), PE anti-CD69 (H1. 2F3), and APC anti-CD25 (PC61). For intracellular staining of cytokines, cells were further fixed using BD Bioscience Cytofix/Cytoperm buffer (BD Biosciences) according to the manufacturer's instructions, and subsequent staining was performed in eBioscience Permeabilization buffer (eBioscience) for 30 min at 4 C using a combination of PE anti-IL-2 (JES6-5H4), PE-Cy7 anti-TNF-a (MP6-XT22), and APC anti-IFNg (XMG1. 2). Data were collected on a FACSCanto II or LSR-II Fortessa flow cytometer and further analyzed using FlowJo software (Tree Star).
ACKNOWLEDGMENTS We thank  Loredana Saveanu  ( CRI, Université Paris 7 ),  Nicolas Cuburu  ( NCI/NIAID ),  Vincenzo Di Bartolo (Institut Pasteur), and Hilde Cheroutre (LIAI)  for helpful discussions and comments on the manuscript. Vincenzo Di Bartolo  and  Matthew Albert  ( Institut Pasteur ) kindly provided the Lm-OVA strain and  Loredana Saveanu  kindly provided the DC2. 4 cell line. We thank the  Penn Vector Core ,  Gene Therapy Program  of the  University of Pennsylvania  for providing the pAAV-1 plasmid (p0001) and the vectorology platform of the  Centre of Research in Myology-UMRS974  for AAV production. We also thank the  Necker Institute Imaging Facility  and the  ARC Foundation  for their help on and funding for the LEICA SP8 confocal microscope used in this study. This work was supported by the  Association Française contre les Myopathies (AFM)  and the  Agence Nationale de la Recherche  ( ANR-11-JSV3 ).
Materials and methods Clinical data. The immunohistochemical detection of gal-1, gal-3, gal-7, and gal-8, CK19, HBME-1 and TPO was studied in two tissue microarrays (TMA) composed of 66 follicular adenomas (FA) and 66 papillary carcinomas (PC). The available population data were gender, age and histopathologic features. This clinical series included 100 women and 32 men. The mean age of patients with FA was 44 years (range, 13-76 years) and 41 years for patients with PC (range, 9-73 years)  (33). The patient samples and clinical data were retrieved from the records of the Lille University Hospital (Lille, France) between August 2000 and September 2001, selected and analysed by two pathologists (Professor E. Leteurtre and Dr F. Renaud). No inclusion and exclusion criteria of the selected patients were used in the current study.