dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods: The following steps of HCV care cascade were quantified: (1) HIV/HCV co-infected, (2) Diagnosed for both HIV and HCV, (3) treated for HCV infection and (4) achieved sustained virologic response (SVR). The number of HIV/HCV co-infected persons was estimated using modelling and observed HCV prevalence. Data on diagnosed persons were extracted from the national AIDS health information system as of 1 September 2016. Results: Among estimated 3300 persons living with HIV/HCV coinfection in Georgia, 2201 (67%) were not aware of their HIV status and 1099 (33%) were diagnosed with both HIV and HCV. Of those 1099 diagnosed persons, 697 (63%) were treated for hepatitis C with either PEG/RBV-or DAA-based regimen; 480 (69%) of those treated achieved SVR. Rates of SVR were 44% with PEG/RBV and 89% with DAA.
MOAB0303 Efficacy and safety of glecaprevir/pibrentasvir in patients co-infected with hepatitis C virus and human immunodeficiency virus-1: the EXPEDITION-2 study Background: Pangenotypic, once-daily glecaprevir (identified by AbbVie and Enanta)/pibrentasvir (G/P) has demonstrated high rates of sustained virologic response at 12-week post-treatment (SVR12) in patients with hepatitis C virus (HCV) genotype (GT) 1-6 infection. This phase 3 study evaluated the efficacy and safety of G/P in patients with chronic HCV GT1-6 infection and HIV-1 coinfection, including patients with compensated cirrhosis. Methods: EXPEDITION-2 (NCT02738138) is a phase 3, multicentre open-label study evaluating G/P (300mg/120mg) treatment in HCV/HIV-1-co-infected adults without or with compensated cirrhosis for 8 or 12 weeks, respectively.
Methods: This cross-sectional study prospectively included HIVinfected adult patients under c-ART (PROSPEC-HIV; NCT02542020). Liver stiffness measurement (LSM) and controlled attenuation parameter (CAP) by TE were used to estimate liver fibrosis and steatosis, respectively. Exclusion criteria were hepatitis co-infection and c-ART naive. Patients with an unreliable M probe LSM or CAP were excluded from the liver fibrosis and steatosis analyses, respectively. Clinical evaluation, fasting blood tests and TE were performed at the same day. TE exams were performed by a single experimented operator blinded to clinical and laboratory data. Metabolic factors were defined according to the International Diabetes Federation criteria. Alcohol consumption was quantified using the AUDIT score. Presence of liver fibrosis and steatosis was considered when LSM ≥ 8.
MOAB0401 Gaps and opportunities in policy and practice in 20 countries with the highest burden of HIV-associated TB mortality among people living with HIV (PLHIV). In June 2016, Member States adopted the UN Political Declaration on HIV and AIDS, including a target to reduce TB deaths among PLHIV by 75% by 2020. In order to achieve this, gaps in policy, implementation and recording and reporting need to be identified and urgently addressed. Methods: A total of 20 countries were selected with the highest estimated burden of HIV-positive incident TB in 2015. Data on collaborative TB/HIV activities were extracted from the Global TB Programme Database and the UNAIDS online GARPR tool, and trends and progress analysed. Reviews were further conducted of the latest available policy documents, programme reviews, epidemiological assessments, Global Fund Concept Notes and GARPR reports to identify gaps and opportunities in policy and implementation.
The intervention included visual feedback about cliniclevel retention in care (social norms), a self-relevant prime and useful take-home items with the priming image (calendar, pill box). The intervention was implemented at two HIV primary clinics in Shinyanga, Tanzania, in two-week intervals for six months. We conducted a quasi-experimental pilot study (Clinicaltrials. gov: NCT02938533) by reviewing the medical records of a random sample of 438 adult patients living with HIV infection (PLHIV, 320 exposed and 118 unexposed) to compare retention and the proportion of patients achieving a medication possession ratio (MPR) ≥95% after six months. Intervention acceptability was determined through an in-person survey with a convenience sample of 405 PLHIV at baseline (n = 189) and end line (n = 216).
Methods: We analysed data from the national surveillance survey which included 610 FSW and 400 MSM/TG recruited from 22 and 3 districts of Nepal, respectively. Adjusted prevalence ratio (PR) using modified Poisson regression was used to assess the association between independent and outcome variables (non-utilization of HTC in last year). FSW was recruited using two-stage cluster sampling, whereas MSM/TG was recruited using respondent-driven sampling. Results: Non-utilization of HTC in last one year was 54% for FSW and 55% for MSM/TG. The prevalence of depression among study populations was very high (≥50%). About 2 of every 10 FSW experienced forced sex in the last 12 months. The significant factors for FSW related to non-utilization of HTC were: experience of forced sex [PR = 0. 5 (0. 3-0.
We constructed a density of infection (DoI) map by combining the ESP map with gridded demographic data from the WorldPop database and a census-based agestructure map. The DoI map shows the estimated number of HIVinfected individuals (15-49 years old) in each square kilometre in Malawi, diagnosed and undiagnosed individuals. We calculated the total number of HIV-infected individuals by aggregating the mapped estimates. Results: The ESP map shows that prevalence (in 15-49 year olds) varies from approximately 1% to 25%, and there is a strong northsouth trend in increasing prevalence and a substantial urban-rural difference. Prevalence is highest in cities in the south (Blantyre and Zomba), Lilongwe in the central region, Mzuzu in the north and villages along Lake Malawi. The DoI map reveals the geographic dispersion pattern of all infected individuals.
TUAD0104 Generic treatments for HIV, HBV, HCV and TB could be mass produced for <$90 per patient A Hill 1 ; M Barber 2 ; D Gotham 3 ; J Fortunak 4 and A Pozniak 5 1 University of Liverpool, Liverpool, UK. 2 London School of Hygiene and Tropical Medicine, London, UK. 3 Imperial College London, London, UK. 4 Howard University, Washington, USA. 5  Chelsea & Westminster Hospital, London, UK Presenting author email: dzintarsgotham@googlemail. com Background: High prices to treat HIV, viral hepatitis and TB can limit treatment access. This analysis aimed to determine prices currently feasible for HIV, HBV, HCV and first-line (1L) DS-TB treatment, assuming competitive generic manufacture. Methods: Data on API exported from India were collected from an online database (www. infodriveindia. com) for July 2014-July 2016.
We measured MTCT rates using early infant diagnosis (EID) programme data collected from January 2007 to November 2013 in Western Kenya and assessed associated HIV transmission risk factors within a spatial context irrespective of treatment guideline changes. Methods: We performed trend analysis for 102,116 HIV-exposed infants (HEIs) using extended Cochran-Mantel-Haenszel stratified test and logistic regression models to determine associations of infant HIV status with maternal and infant characteristics recorded on EID laboratory test request forms. We fitted spatial and spatialtemporal semi-parametric Poisson regression models with infant and maternal covariates to explain MTCT rates. We used R-Integrated Nested Laplace Approximation (INLA) package and Quantum GIS to map raw and fitted estimates.
WEPDB0105 Human Papillomavirus infection and cervical lesions in HIV-1-infected women on antiretroviral treatment in Thailand T Delory 1,2,3 ; N Ngo-Giang-Huong 1,2,4 ; S Rangdaeng 5 ; N Chotivanich 6 ; A Limtrakul 7 ; C Putiyanun 8 ; P Suriyachai 9 ; W Matanasarawut 10 ; T Jarupanich 11 ; P Liampongsabuddhi 12 ; I Heard 13 ; G Jourdain 1,2,4 ; M Lallemant 1,2,4 ; S Le Coeur Background: Rates of Human Papillomavirus (HPV) infections and cervical lesions are both increased in HIV-infected women. The objectives of the study were to estimate the prevalence and factors associated with Human Papillomavirus (HPV) infection, HPV genotypes and cytological/histological high-grade (HSIL +/CIN2+) lesions in HIV-1 infected women receiving combination antiretroviral therapy (cART). Methods: We conducted a cross-sectional study (PapilloV study, NCT01792973) within a prospective cohort (the PHPT cohort) of HIV-infected women on cART in 24 hospitals accross Thailand.
FSWs were provided a small incentive to promote HTS to their clients, who could access the services directly at, or near sex work hotspots. Methods: FSW at high-volume hotspots were given coupons with unique identifier codes (UICs) and basic training to refer clients to an HTS counsellor (and lab technician) located in a room nearby. FSW received USD$1 for each client who agreed to take a test. Each client who accessed HTS was assigned a UIC. Quantitative client data were collected via the CommCare digital platform and analysed for the period September 2015 through December 2016. In addition, the team collected qualitative data via in-depth interviews with 30 clients who attended HTS. Results: Prior to the implementation of this innovation, HTS uptake averaged less than 100 FSW clients per month.
Here, phylogenetic, epidemiological and virological data deduced factors favouring the selective advantage of large cluster variants. Methods: Population-level phylogenetics across the RT/protease domain deduced temporal dynamics of HIV-1 clustering. Phylogenetics across the viral integrase and V3 loop was performed on representative clusters. Epidemiological data from the SPOT rapid testing site and Montreal primary HIV cohort deduced epidemiological and behavioural risk effects implicated in clustering. Primary HIV-1 strains from MSM associated with large 20+ clusters or singleton/small clusters (cluster size 1-4) were grown in cell culture under dolutegravir (DTG), elvitegravir (EVG) and/or lamivudine (3TC) pressures. Sanger and deep sequencing assessed HIV-1 genotypic changes under drug pressure.
Recently, we have identified unique transmission clusters (TCs) of subtype B circulating in Japan based on their protease-RT gene sequences. In this study, we analysed adaptive evolution of the Env sequences in the TCs to further characterize the immune escape of the Env gene within a TC. Methods: We determined 2673 C2-V5 sequences of Env gp120 from 712 individuals who underwent tropism testing between 2011 and 2015 at Nagoya Medical Center, the second largest medical facility participating in the Japanese Drug Resistance HIV-1 Surveillance Network. The TC of each sequence was identified by searching our TC database, and was confirmed by inferring the phylogenies of gp120 sequences. Neutral evolution of each region within each TC was tested by Kumar's Z-test for the null hypothesis of strict neutrality.
Codon-by-codon neutral selection was analysed by maximum-likelihood computations of synonymous and nonsynonymous substitutions per site using the HyPhy software package. Results: We identified 89 TCs, 77 of which belong to subtype B associated with the MSM population. The nucleotide diversity of the C3 region was greater than that of the V3 region and was similar to that of the V4 region. Regions with greater diversity exhibited significantly positive selection during the evolution of subtypes, whereas the directions of selection during the evolution of TCs were much more variable. Furthermore, different amino acid sites in the C3 region were under positive selection during the evolution of each TC. Viruses circulating in each TC of gp120 have a distinct substitution pattern to confer escape from NAbs.
Current lowest global prices are from public reports and the Global Drugs Fund (TB) and US prices from the Centers for Medicare and Medicaid Services. Patent protection expiry dates are from FDA Orange Book and Medicines Patent Pool Patent Status Database. Abstract TUAD0102-Figure 1. Proportion of ART initiation from new HIV diagnosed Abstracts of the 9th IAS Conference on HIV Science (IAS 2017) Journal of the International AIDS Society 2017, 20 (Suppl 5).
LAM; electronic databases were used to calculate reader agreement between LAM users; and health centre registers were used to calculate workload. Supervision notes, minutes of meetings, training reports and personal observations were used to assess training required, patient MOAD0101 Readiness for antiretroviral therapy: implications for linking HIV-infected individuals to care and treatment Background: Antiretroviral therapy (ART) readiness is a key predictor of ART initiation. However, there is a paucity of data on ART readiness among individuals at the time of HIV diagnosis and ART eligibility assessment. Under a test-and-treat approach, understanding factors associated with ART readiness can inform strategies to support early engagement in care and thereby maximize the benefits of ART.
Methods: Annual data on HIV diagnoses in 2003-2015 were retrieved from a database for HIV/AIDS within the European Surveillance System (TESSy). HIV diagnoses were adjusted for reporting delay and stratified by the presence of an AIDS-defining event within three months of HIV diagnosis and, for individuals without AIDS, by CD4 cell count (≥500, 350-499, 200-349, <200 cells/mm 3 ) at the time of diagnosis. Countries were grouped in sub-regions as defined by United Nations. A back-calculation method based on the ECDC HIV Modelling Tool was used to estimate annual numbers.
Integrating interventions to treat mental disorders into HIV care is a key strategy to improve HIV treatment outcomes in low-and middle-income countries (LMIC), but data on HIV treatment sites' capacities to screen and manage mental disorders are limited. A Parcesepe 1 ; C Mugglin 2 ; M Egger 2 ; F Nalugoda 3 ; C Bernard 4 ; E Yunihastuti 5 ; S Duda 6 ; C William Wester 7 ; D Nash 8 ; IeDEA Network Collaboration 1 Methods: We report preliminary findings from an ongoing sur- vey among a stratified random sample of 142 HIV treatment sites in 36 LMIC that participate in the International epidemio- logic Databases to Evaluate AIDS.
2 FHI360, Country Office, Nairobi, Kenya Presenting author email: smuga@fhi360. org Background: sion among clients on antiretroviral therapy (ART) who had accessed at least one viral load test in the period October 2015 to September 2016. ART was initiated as per the national guide-lines in Kenya. Raw viral load data was assessed from the national viral load database for 139 facilities in five counties (Baringo, Kajiado, Laikipia, Nakuru and Narok) and 38,113 records were analysed. The survey used logistic regression to assess relationships between gender, age and viral load suppression (<1000 copies/ml), with p < 0. 05.
The analysis is based on the ATLAS data set collected in 2015 corresponding to an integrated luminosity of 3. 2 fb -1. Separate measurements of tq and tq production provide sensitivity to the parton distribution functions (PDFs) of the u-quark and the d-quark  [2] , exploiting the different initial states of the two processes as shown in Figure  1. In addition, the cross-section ratio R t ≡ σ(tq)/σ( tq) is measured, featuring smaller systematic uncertainties than the individual cross-sections because of partial cancellations of common uncertainties. In general, measurements of single top-quark production provide insights into the properties of the Wtb vertex. The cross-sections are proportional to the square of the coupling at the production vertex. In the SM, the coupling is given by the Cabibbo-Kobayashi-Maskawa (CKM) matrix element V tb  [3, 4]  multiplied by the universal electroweak coupling constant.
The parton shower, hadronisation, and the underlying event are added using Pythia 6 and the P2012 tune. All top-quark processes are generated assuming a top-quark mass of 172. 5 GeV. The top quark is set to decay exclusively to t → Wb, and the EvtGen v1. 2. 0 program  [36]  is used to model bottom-and charm-hadron decays. To model the W+jets and Z+jets background, the Sherpa v2. 2. 0  [37]  generator is used. Matrix elements are calculated for up to two partons at NLO and up to four partons at LO using the Comix  [38]  and OpenLoops  [39]  ME generators and merged with the Sherpa parton shower  [40]  using the ME+PS@NLO prescription  [41]. The NNPDF 3. 0 PDF set  [42]  is used in conjunction with dedicated parton-shower tuning developed by the Sherpa authors. Diboson events, denoted VV, are also simulated using the Sherpa v2.
5 mm are imposed. Isolation criteria similar to those for electron candidates are imposed. Jets are reconstructed using the anti-k t algorithm  [47]  with a radius parameter of 0. 4. They are calibrated using a combination of an energy-and η-dependent simulation-based scheme and a scheme based on data  [48]. Only jets with p T > 30 GeV and |η| < 3. 5 are accepted. The rapidity range is determined using a W+jets-dominated validation region and defined by requiring good agreement between simulated and measured data. If any jet is close to an electron, with ∆R < 0. 2, the closest jet is removed, as in these cases the jet and the electron are very likely to correspond to the same physical object. Remaining electron candidates overlapping with jets within ∆R < 0. 4 are subsequently rejected. To reduce contributions from muons which stem from heavy-flavour decays inside a jet, muons are removed if they are separated from the nearest jet by ∆R < 0.
The fake-lepton efficiencies are determined from a data sample dominated by nonprompt and fake-lepton background events. This sample is selected by requiring exactly one loose lepton and low E miss T as well as low m T ( E miss T ). The real-lepton efficiencies are also estimated from collision data using a "tag-and-probe" method in Z → ee events. Multijet-background events containing non-prompt muons are modelled with a sample of events enriched in non-isolated muons  [43]. Most of these events originate from b-hadron or c-hadron decays in jets. These events pass the same kinematic requirements as the events of the signal sample. Only some of the muon identification cuts are modified, ensuring that there is no overlap with the signal selection. The normalisation is determined using a binned maximum-likelihood fit.
These uncertainties were determined using √ s = 8 TeV data as described in Ref. [51]  for b-jets and Ref. [50]  for c-jets and light jets, with additional uncertainties to account for the presence of the newly added insertable B-layer and the extrapolation to √ s = 13 TeV. Monte Carlo generators Systematic effects from MC modelling of the signal and the t t background process are either estimated by comparing different generators or by comparing parameter variations in the Powheg-Box + Pythia 6 setup. The Powheg-Box + Herwig++ sample is used for parton shower and hadronisation modelling studies, while MadGraph5_aMC@NLO + Herwig++ is used for studies of the NLO-matching method. Variations of the amount of additional radiation are studied by changing µ r and µ f and the scales in the parton shower simultaneously.
4 %. The s-channel production cross-section is calculated at NLO with a total uncertainty of 3. 8 %. For the W+jets and Z+jets backgrounds, an uncertainty of 21 % is assigned. This uncertainty is estimated based on parameter variations in the generation of the Sherpa samples. It was found that correlated variations of the factorisation and renormalisation scales have the biggest impact on the kinematic distributions and produces change covering the unfolded data and their uncertainties  [69]. Diboson processes have an uncertainty of 6 % in the inclusive cross-section including uncertainties on the choice of the factorisation and renormalisation scales and the PDF uncertainty. The multijet background estimate has an uncertainty of 50 %, based on comparisons of the rates obtained using alternative methods described in previous analyses  [19, 43, 70].
The dotted black line indicates the measured value. The combined statistical and systematic uncertainty of the measurement is shown in green, while the statistical uncertainty is represented by the yellow error band. Predictions for all presented PDF sets are within the statistical uncertainty of the measurement. For the purpose of determining f LV • |V tb |, the measured inclusive cross-sections of the tq and the tq process are combined, assuming that each uncertainty is 100 % correlated between the two channels. The statistical uncertainty of the data and the uncertainty due to the limited size of the MC samples, are treated as uncorrelated. The combined cross-section is calculated to be: σ(tq + tq) = 247 ± 6 (stat. ) ± 45 (syst. ) ± 5 (lumi. ) pb = 247 ± 46 pb. To estimate the dependence of the measured cross-sections on the assumed top-quark mass, simulated samples with m top = 170 GeV and m top = 175 GeV are used.
Acknowledgements We thank  E. Orgiu ,  A. Galanti  and  M. Squillaci  ( ISIS ) for valuable discussions,  T. Carney  ( Thermo Fisher Scientific Inc. ) for precious support with the ion gun settings,  Z. Shuai  and T. Zhao ( Tsinghua University ) for help with the charge transport simulations, and  F. Richard  ( ISIS ) for recording the XPS spectra. Device fabrication was carried out in part at the nanotechnology facility STNano (IPCMS) with the assistance of S. Siegwald. We acknowledge funding from the  M-ERA. NET  project  MODIGLIANI , the  European Commission  through the  Graphene Flagship  ( GA-696656 ) and the  Marie-Curie IEF   MULTI2DSWITCH  ( GA-700802 ), the  Agence Nationale de la Recherche  through the  LabEx  project  Chemistry of Complex Systems  ( ANR-10-LABX-0026_CSC ) and the  International Center for Frontier Research in Chemistry (icFRC).
Purified mRNAs were amplified, labeled, and cohybridized according to ref 20 as follows: aRNAs were produced with Message AmpII aRNA amplification kit (Ambion Invitrogen, Waltham, MA, USA) from 200 ng of total RNA. Then, 5 μg of each aRNA were retrotranscribed and labeled with either cyanine-3 (Cy3) or cyanine-5 (Cy5) fluorescent dye (Interchim, Montlucon, France). Labeled samples were combined with 30 pmol of each dye and cohybridized to NimbleGen microarray AryANE v1. 0 containing 126 022 60-mer oligonucleotide probes. 20 Deva software (NimbleGen Roche, Madison, WI, USA) was used to extract pair-data files from the scanned images, obtained using the MS200 microarray scanner (NimbleGen Roche, Madison, WI, USA). Samples at harvest (H) and from cold storage (CS) and 1-MCP treatment (MCP) were interrelated in three comparisons (CS × H; MCP × H; MCP × CS) (Figure  1B ).
22 he normalized values were corrected for the background to estimate gene expression levels. Significant differential gene expression was determined by false discovery rate (FDR) p-values after Benjamini-Hochberg (BH) correction <0. 1. Microarray data is available at Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) under the accession number GSE59728. Further analyses were performed using the sense probes on the array. Differentially expressed probe sequences from AryANE 12X 135 K chip  20  were validated against apple genome assembly v. 1. 0p and v. 3. 0a1contigs at GDR (Genome Database for Rosaceae -http://www. rosaceae. org/) and by maximum likelihood phylogenetic analyses with functionally characterized Arabidopsis proteins. Sequences failing to retrieve coherent transcripts and deduced proteins or phylogenetically divergent from their counterparts in model species were eliminated from the analyses.