dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis Material from eight rats was analyzed for each experimental group and for each parameter studied (total n = 32). All statistical analyses were performed by two-way analysis of variance (ANOVA) with birth condition (CTL and PA) and treatment (Vhi and 17β) as the main factors. When interaction effects were significant, analyses of the simple effects were carried out by post hoc comparisons using Student's t-test (twotailed) adjusted by Bonferroni correction. In any case neither the assumption of normal distribution (Shapiro-Wilk test) nor equality of variances (Levene's test) was rejected. Results were expressed as the mean ± SEM. Differences with a p < 0. 05 were considered to be significant. Statistical analyses were performed using the GraphPad Prism 5. 03 statistical package for Windows (GraphPad software).
The bibliographic analysis realised on the PsycINFO database (keywords «SRs», «development», «child» or «adolescent») revealed that 34% of studies on SRs were carried out in groups of children and/or adolescents in the field of health and illness (e. g. : nutrition, pregnancy, HIV/AIDS, smoking)  [2]. Childhood and adolescence are important periods when social knowledge about the world being developed  [12]. This particular period is an interesting moment for the analysis of genesis and transformation of the SRs. Children are born in the world of SRs shared by adults or by siblings. By being born children become a part of a group that shares certain image of the world, particular representations and during the socialization process children appropriate the social knowledge by interiorisation process  [11; 12].
G:F ratio was calculated from using daily DMI and ADG. Data from feed nutrient analysis were analyzed by ANOVA using GLM Procedures of SAS (Cary, NC). In vitro data were analyzed using MIXED procedure of SAS, with fixed effects of supplement. All performance and intake data were subjected to statistical analysis using MIXED procedures of SAS. The independent variable was diet and dependent variables included beginning weight, final weight, ADG, DMI, and G:F.
Subjects This ancillary PET/MRI study was extracted from the ADELAHYDE longitudinal single-center study, which aimed at identifying factors associated with cognitive decline and white matter diseases in older hypertensive patients with subjective memory complaints (Analyse des DEterminants génétiques et environnementaux de la Leucoaraiose dans une population de sujets Agés Hypertendus présentant des troubles cognitifs DEbutants; ClinicalTrials. gov Identifier: NCT01351961). Inclusion and exclusion criteria have already been detailed elsewhere  (Kearney-Schwartz et al. , 2009). A total of 131 patients participated to the ADELAHYDE-2 study and results of the present study were extracted from the second control visit which comprised a medical examination with measurement of central blood pressure (BP), various neuropsychological tests and a brain MRI  (Ferreira et al.
MRI acquisition and analysis All data were acquired on a 1. 5-T magnet (Signa HDxt, GE Healthcare, Milwaukee, WI, USA) with an 8-element receive head coil (Invivo Corp, Orlando, FL). The protocol involved the recording of a 3dimensional T1-weighted sequence with the following parameters: slice thickness 1. 4 mm; TE/TR/TI = 5/12/350 ms, field of view 240 mm (matrix size 256 × 256), and Fluid-Attenuated Inversion Recovery (FLAIR) images, with the following parameters: slice thickness 5 mm, TE/TR/TI = 158/10000/2300 ms, field of view 240 mm (matrix size 288 × 224). White matter hyperintensities of presumed vascular origin were assessed on the FLAIR images by a blinded experimented radiologist (SB) using the Fazekas score, corresponding to the sum of periventricular and deep white matter hyperintensity ratings  (Fazekas et al.
, 1987). A DTI axial acquisition was also performed with the following parameters: 15 non-collinear gradient directions with b = 1000 s/mm 2 , one b = 0 reference image, contiguous slices of 5 mm thickness; TE/ TR = 72-100/9. 600 ms, field of view 240 mm (matrix size of 128 × 128) covering the entire brain and cerebellum. An automated parcellation of the subcortical white matter was obtained on the 3D T1-weighted images from each patient and by using the "-recon-all" processing pipeline of the FreeSurfer software version 5. 2. This parcellation was thereafter applied to the DTI images through a co-registration and a transformation in the 3D-T1 space of the DTI images ("Dt_recon" function of the FreeSurfer software). Finally, ADC mean values were obtained from the total white matter and from the different lobes using a subcortical white matter parcellation atlas "wmparc"  (Salat et al.
Statistical analysis Quantitative variables are expressed as means ± standard deviations, and categorical variables as percentages. Student-t-tests were performed for the unpaired 2-group comparison of quantitative variables. Pearson coefficients were used to assess the correlation between ADC mean , CMRGlc, cardiovascular parameters and/or neuropsychological test scores. A p < 0. 05 was determined as significant. Statistical analyses were performed with SPSS® 20. 0 software. The statistical analyses performed with the SPM software have been already detailed above.
We reconstruct the hadronic system using calorimetry and we obtain an estimate of the threemomentum transfer for each event. The data are subdi-vided into six subranges of momentum transfer up to 0. 8 GeV/c, and within each range we present the observed hadronic energy in the detector. To describe these data, a component of the event rate could be attributed to many-body effects like a two-particle, two-hole (2p2h) process  [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16]. Also, suppression of CCQE interactions is preferred, such as provided by a random phase approximation (RPA) calculation  [7, [17] [18] [19]  applied to a Fermi gas model  [20]. The data were taken between November 2010 and February 2011 with the NuMI beam  [21]  operating in antineutrino mode. The primary beam of 120-GeV protons interacts in a graphite target, producing mesons.
The calorimetric and tracking capabilities of MINERvA are constrained relative to GEANT4 v. 9. 4. p2 (with the Bertini Cascade option) using in-situ  [31]  and hadron test beam measurements  [32]. With no test beam measurements, the neutron response and its uncertainties come after adjusting the cross section to match the data from  [33]  as used by later versions of GEANT4. The kinematics of each event are reconstructed using the measured muon energy and angle, and measured energy deposits attributed to hadrons. The technique is nearly identical to  [6]. A full simulation of the reconstructed sample with calibrated detector response is made using the GEANT4 simulation and GENIE version 2. 8. 4 neutrino event generator  [34]. This simulation is used to obtain a correction  [35] , as a function of the calorimetrically measured hadronic energy, to estimate the energy transfer q 0.
4 < W < 2. 0 GeV. We add two minor (for this analysis < 2% of the total rate) modifications to pion production. The non-resonance, single-pion process is reduced to 43% of the nominal following the comparison of GENIE to bubble chamber experiment neutrino data  [40, 41]. Coherent pion events with pion kinetic energy < 0. 45 GeV are reduced by half  [42] [43] [44]. This base combination of models, compared to reconstructed data, has discrepancies in the region between the CCQE and ∆ process as large as a factor of two, as shown in the top panels of Fig. 3. We have modified the default GENIE version 2. 8. 4 to include advances in modeling the important processes. The CCQE process is modified to include RPA screening based on the IFIC Valencia model  [17, 45]  implemented by weighting GENIE CCQE events  [46].
Data Reconstructed available energy (GeV) Events per 0. 02 GeV FIG. 3 : Reconstructed E avail distributions compared to (top) the base Monte Carlo simulation (GENIE with minor modifications to pion production) for two ranges of reconstructed three momentum transfer. In the improved simulation MnvGENIE-v1 (bottom), the region between the predicted CCQE process (dashed) and the ∆(1232) resonance (dotted) is filled by events generated from the Valencia 2p2h process plus additional 2p2h events (dot-dashed). MINERvA inclusive neutrino data  [6]. The additional events are from weighting up the generated 2p2h events according to a two-dimensional Gaussian in true q 0 , q 3 whose six parameters are fit to the neutrino data version of these distributions. This enhancement adds 50% to the predicted 2p2h strength, but targets the event rate in the kinematic region between the CCQE and ∆ peaks where the rate doubles.
The collection of changes in this and the preceding paragraphs are referred to as "MnvGENIE-v1" and are the central, tuned model for many recent analyses  [48] [49] [50]. The resulting description of the antineutrino data is much improved, as illustrated in Fig. 3  and summarized in Table I using a standard χ 2 test on the reconstructed samples. These models also improve the description of muon-only kinematic distributions of an overlapping subset of the same data set  [50]  selected with no pions in the final state. For this model comparison to reconstructed data, the largest systematic uncertainties include flux, hadron energy scale, and GENIE resonance interaction and final-state rescattering model uncertainties. The GENIE uncertainty on the CCQE axial form factor is reduced to ±9% following the analysis of  [51].
e. , protection against disease and viremia, respectively. Therefore, the capacity to protect against viremia after NHP challenge is considered more an indicator of vaccine potency  (18). For this reason, and for cost and ethical considerations, the protective activity of CYD-TDV in macaques was evaluated only after the first stage of vaccine development using phase I vaccine lots. In this unique study, CYD-TDV was shown to confer almost full protection against wild-type (wt) DENV infection, with the percentage of aviremic animals ranging from 83% (DENV-1 and DENV-4) to 100% (DENV-2 and DENV-3)  (15). Differences in rates of CYD-TDV efficacy between preclinical and clinical data indicated that protective activity in monkeys did not necessarily predict vaccine protection in humans. This offered a unique opportunity to improve the predictive value of the NHP model via a reverse translational approach.
Statistical analyses. Analyses of immune or virological parameters were carried out by using variance analysis models (parametric or nonparametric analyses depending on the tested readout). The percentages of positive monkeys (virus or neutralizing antibodies) were compared by using the Fisher test. When multiple comparisons were performed, post hoc adjustments were applied to have a global alpha risk of 5%. The association between postchallenge DENV-2 viremia and prechallenge vaccine-specific humoral responses was assessed by calculating Pearson correlation coefficients. All statistical analyses were performed with SAS v9. 2 software. A margin of error of 5% was used for effects of the main factors.
ACKNOWLEDGMENTS We thank  R. Legrand ,  N. Dereuddre-Bosquet ,  L. Gosse-Ben Braham , and the  IDMIT  staff of the  CEA (Fontenay-Aux-Roses, France)  for conducting NHP challenges and clinical follow-up;  C. Charnay  for logistics and coordination of animal studies; and the  Sanofi Pasteur (SP)  research staff for experimental work. We thank  B. Rokbi  for constant support and advice;  B. Guy  for reviewing the manuscript;  C. Dunod ,  N. Jackson , and  N. Burdin  for scientific support; and  J. S. Persico  for assistance with submission. Wild-type DENV-2 and DENV-4 are the property of  Mahidol University, Thailand (Sutee Yoksan ). CYD dengue vaccine strains are patented by  Sanofi Pasteur. V. B. , F. B. , and J. L. contributed equally to the design of the whole study and to the interpretation of its results.
[45] , but higher than that recorded by Adawy et al. [44]. The gene diversity of AFLP primer sets diverged from 0. 17 (E-AAG/M-CTG) to 0. 48 (E-ACT/M-CAG), with an average of 0. 37, indicating a good level of genetic diversity within barely genotypes. Polymorphic information content (PIC) exhibited a mean of 0. 33 (Table  1 ). This mean was higher than that indicated by Varshney et al. [46]. The difference in this data is a result of the differences in the barely genotypes analyzed, and molecular markers used. The AFLP primer sets revealing a high degree of polymorphism in the present study are recommended for use in future diversity studies of barley germplasm. Moreover, the 40 barley genotypes studied were split into 2 groups based on their geographical location (Western Europe and Eastern Europe).
Data Analysis AFLP fragments were represented as present (1) and absent (0), forming binary data sets. PowerMarker 3. 25  [57]  and GenAlEx 6. 5  [58]  were used to estimate variability indices such as polymorphism, observed heterozygosity (H o ), fixation index (F), polymorphic information content (PIC), gene diversity, and expected heterozygosity (H e ). UPGMA cluster analysis was carried out based on Nei's genetic distance  [59]. The genetic structure of the 40 barley genotypes was studied using STRUCTURE 2. 3 software  [60]. The analyses were done using hypothetical populations numbers (K) ranging from 1 to 11, along with 100,000 burn-in run iteration as well as 100,000 Markov chain Monte Carlo, and with ten runs for each K value. Structure Harvester  [61]  was applied and showed the best likely values of K  [62].
A structure of the EphB2 kinase crystalized with a part of its JM segment in an autoinhibited form (PDB ID 1JPA)  (Wybenga-Groot et al. , 2001 ) may be compared with our model. Interestingly, we see the flexible JM region exploring conformations close to that in the autoinhibited structure of EphB2 (see Figure  S5  and Video S3), although this should be interpreted cautiously given the simplifications inherent in the CG model (see below) employed in these simulations. Thus, we postulate that the flexible JM segment may explore a range of conformations on the surface of the N-lobe of the kinase. (A) Normalized frequency of contacts (defined as the relative number of interacting particles within a 0. 8 nm cutoff distance of the PIP 2 head group) between the kinase domain and the PIP 2 -containing membrane for the mode 1 interaction (see Figure  3 ).
ACKNOWLEDGMENTS Research in the M. S. P. S. group is supported by the  Wellcome Trust  ( 208361/ Z/17/Z ), and by  BBSRC  ( BB/R00126X/1 ). This work was in part performed using the ARCHER supercomputer via the EPSRC-funded HECBioSim consortium and using the HPC resources from  CALMIP  (Grant- 2017-17036 ). E. Y. J. was supported by  Cancer Research UK  ( A17721 ) and E. S. by the  UK Medical Research Council  ( MR/L018039/1 ). The  Wellcome Center for Human Genetics  is supported by the  Wellcome Trust  ( 203141/Z/16/Z ).
Simulation Analysis VMD  (Humphrey et al. , 1996)  was used to visualize structures and was combined with Tcl scripts to analyse the simulations. The rotation versus distance matrix analyses were performed as described in  (Yamamoto et al. , 2016). Thus we calculated the 2-dimensional normalized histogram of R zz and d z , where d z is the perpendicular distance between the centres of mass of the protein domain and the lipid membrane, and where R zz is the zz component of the rotational matrix required for least squares fitting of a orientation onto a reference orientation. R zz was calculated by using the g_rotmat command in GROMACS (www. gromacs. org) (Hess et al. , 2008; Pronk et al. , 2013). The value of R zz in the density map varies depending on the reference orientation of the PH domain relative to the membrane.
METHODS The DC Cohort is a clinic-based, city-wide, longitudinal observational cohort launched in 2011 to better understand HIV epidemiology in DC, describe clinical outcomes among those in care, and improve the quality of care for people living with HIV in the DC metropolitan area  [13]. At the time of this analysis, there were 13 participating outpatient sites: 8 hospital-based clinics and 5 community-based clinics. Following the provision of written informed consent, participants' clinical data was manually entered or electronically exported from patient medical records and entered into a web-based data entry system called Discovere (Cerner Corporation, Kansas City, MO). Details of the DC Cohort study design have been described previously  [14, 15].
An STI episode may include any combination of chlamydia, gonorrhea, and syphilis diagnosed at the same date. The occurrence and number of incident STI episodes among participants was assessed. To evaluate the HIV transmission potential in individuals with incident STIs, we also examined their plasma HIV VLs. We determined the VLs at the time of STI diagnosis, defined as the VL within ±1 month, 3 months, and 6 months of the STI diagnosis date. If a participant had 2 or more STI episodes within each ±1-, 3-, or 6-month period, the highest VL was selected. Subsequently, we categorized the individuals with STIs as either having any number, 1, or 2 or more STIs, as well as their VLs as either <1500 or ≥1500 copies/mL. This cutoff was used given previous data that HIV-infected persons with VLs higher than 1500 copies/mL had an increased risk of transmitting HIV to others  [8, 16].
RESULTS Around the time this data set was closed, the estimated population of persons with HIV infection receiving care at the 13 DC Cohort sites was 11 235, of which 8732 persons (77. 7%) were approached for enrollment. Of those persons approached, 7004 (80. 2%) were consented, 948 (10. 9%) declined enrollment, 14 (0. 2%) withdrew consent, and 766 (8. 8%) remained undecided. There were significant differences between those consenting and declining, which included female gender (27. 8% of those consenting vs 36. 1% of those declining, P <. 0001), white race/ ethnicity (13. 1% of those consenting vs 6. 6% of those declining, P <. 0001), and private insurance status (27. 6% of those consenting vs 33. 2% of those declining, P <. 0001). Among the 6762 participants enrolled in the study between January 1, 2011, and March 31, 2015, the median age at consent was 47 years (interquartile range, 36.
8% within ±3 months, and 6. 4% at ±6 months. Yet our finding that 41. 8% of participants within 1 month of STI diagnosis had a detectable VL should be an important reminder that presentation for STI evaluation is also a critical opportunity to address ART adherence and virologic suppression. The DC Cohort database is linked semi-annually with the DC Department of Health (DC-DOH) HIV/AIDS surveillance database to enhance data accuracy, as individuals may receive care at multiple clinical sites. After completing our planned STI analyses, we examined linked data and found a 9. 2% increase in the number of chlamydia cases (from 250 to 273 cases) and a 20. 8% increase in the number of cases of gonorrhea (from 212 to 256 cases) during the period of study (unpublished data). These findings highlight that linkage to care and virologic suppression opportunities may also require cross-site communication.
Similarly, the study design also limited the availability of HIV VLs during the same encounter of STI diagnosis. Second, we were unable to distinguish genital or extragenital sites of chlamydia and gonorrhea infection. Third, the population enrolled in the DC Cohort may not be fully representative of the larger HIV-infected population in DC, as enrollment requires some degree of engagement in care, and the demographics of those declining consent differed slightly from those who provided consent. Nonetheless, the strengths of this study include its city-wide, prospective enrollment of participants, its longitudinal study design, and the large sample size that is inclusive of male, female, and transgender participants. Also, our study is unique in linking data from multiple clinical sites with data reported to the local health department.
Merging of the DC Cohort and the DC-DOH databases improved the accuracy of STI diagnosis frequency and provided insight into care received for STIs outside of the primary HIV care site. Finally, to our knowledge, this is the largest cohort to examine the occurrence of STIs and estimated HIV transmission risk in the DC metropolitan area, which has one of the highest incidence rates of HIV in the United States. In conclusion, STIs are frequent among HIV-positive individuals receiving care in DC; thus risk reduction interventions are needed for people living with HIV to help control the spread of STIs, achieve durable HIV virologic suppression, and reduce HIV transmission. These findings will help health care providers and policy makers provide high-impact interventions toward STI control and achievement of virologic suppression among PLWH with the goal of improving the health of the individual and reducing the incidence of HIV in the community.
Acknowledgments Data in this manuscript were collected by the DC Cohort with investigators and research staff located at  Cerner Corporation  ( Harlen Hays ,  Jeffrey Binkley ,  Rachel Hart ,  Dana Franklin ,  Nabil Rayeed ,  Rob Taylor ,  Qingjiang Hou ,  Thilakavathy Subramanian );  Children's National Medical Center Adolescent (Lawrence D'Angelo)  and  Pediatric  ( Natella Rahkmanina ) clinics; The Senior Deputy Director of the  DC Department of Health HAHSTA (Michael Kharfen );  Family and Medical Counseling Service  ( Angela Wood );  Georgetown University (Princy Kumar) ;  George Washington University Medical Faculty Associates (David Parenti) ;  George Washington University Department of Epidemiology and Biostatistics  ( Alan Greenberg ,  Amanda Castel ,  Heather Young ,  James Peterson ,  Lindsey Powers Happ ,  Maria Jaurretche );  Howard University Adult Infectious Disease Clinic (Saumil Doshi ) and  Pediatric Clinic  ( Sohail Rana );  La Clinica Del Pueblo , ( Ricardo Fernandez ); MetroHealth (Annick Hebou);  National Institutes of Health  ( Carl Dieffenbach ,  Henry Masur );  Unity Health Care (Stephen Abbott) ;  Veterans Affairs Medical Center (Debra Benator) ;  Washington Hospital Center (Maria Elena Ruiz) ; and  Whitman-Walker Health  ( Rick Elion ).
Financial support. The DC Cohort is funded by the  National Institute of Allergy and Infectious Diseases  ( UO1 AI69503-03S2 ). Potential conflicts of interest. All authors report no potential conflicts. All authors have submitted the  ICMJE Form for Disclosure of Potential Conflicts of Interest. Prior presentation. Portions of this analysis were presented during ID Week's Poster Abstract Session on October 10, 2015, under the title " Sexually Transmitted Infections among HIV Infected Patients Receiving Care in the District of Columbia: Incidence and Correlates of Syphilis, Gonorrhea, Chlamydia and Viral Hepatitis in the DC Cohort " (Poster No. 1697 ).
2) 0. 4 (0. 2-0. 7) 0. 3 (0. 2-0. 6) 1. 5 (1. 1-2. 0) Abbreviations: CI, confidence interval; HRH, heterosexual; IDU, injection drug user; MSM, men who have sex with men; NA, insufficient data for calculation; STI, sexually transmitted infection. a Rate per 100 person-years of observation using Rothman/Greenland estimation for 95% confidence intervals. b All characteristics are at the time of consent into the DC Cohort.
Methodology We reviewed the availability of reimbursed DAAs and national criteria for DAA reimbursement among countries in the European Union or European Economic Area (including England, Northern Ireland, Scotland, and Wales as separate jurisdictions) and Switzerland. Reimbursement criteria were reviewed for the following DAA regimens: sofosbuvir with ribavirin; sofosbuvir and ledipasvir with or without ribavirin; sofosbuvir and velpatasvir with or without ribavirin; ombitasvir, paritaprevir, and ritonavir, with dasabuvir, and with or without ribavirin; elbasvir and grazoprevir with or without ribavirin; and sofosbuvir and daclatasvir with or without ribavirin. Between Nov 18, 2016, and Aug 1, 2017, most data were extracted from publicly available documentation from government websites and online drug formularies (appendix p 1).