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We present 307 type Ia supernova (SN) light curves from the first 4 yr of the Transiting Exoplanet Survey Satellite mission. We use this sample to characterize the shapes of the early-time light curves, measure the rise times from first light to peak, and search for companion star interactions. Using simulations, we show that light curves must have noise 31 R _⊙ (separations >5.7 × 10 ^12 cm, 99.9% confidence level) and disfavor companions having Roche lobe radii >10 R _⊙ (separations >1.9 × 10 ^12 cm, 95% confidence level). Lastly, we discuss the implications of our results for the intrinsic fraction of single degenerate progenitor systems.

Abstract Background Although global poverty rates have declined in the last decade, the fall in the Asia-Pacific region has been slow relative to the rest of the world. Poverty continues to be a major cause of poor maternal and newborn health, and a barrier to accessing timely antenatal care. Papua New Guinea has one of the highest poverty rates and some of the worst maternal and neonatal outcomes in the Asia-Pacific region. Few studies have investigated equity in antenatal care utilization in this setting. We explored equity in antenatal care utilization and the determinants of service utilization, which include a measure of multidimensional poverty in Papua New Guinea. Methods To explore the association between poverty and antenatal care utilization this study uses data from a ten-cluster randomized controlled trial. The poverty headcount, average poverty gap, adjusted poverty headcount, and multidimensional poverty index of antenatal clinic attendees are derived using the Alkire-Foster method. The distribution of service utilization is explored using the multidimensional poverty index, followed by multivariate regression analyses to evaluate the determinants of service utilization. Results The poverty headcount was 61.06%, the average poverty gap 47.71%, the adjusted poverty headcount 29.13% and the average multidimensional poverty index was 0.363. Further, antenatal care utilization was regressive with respect to poverty. The regression analyses indicated that older women; being a widow (small number of widows (n = 3) asserts interpreting result with caution); or formally employed increase the likelihood of accessing antenatal care more often in pregnancy. Travelling for over an hour to receive care was negatively associated with utilization. Conclusion This study indicated high levels of multidimensional poverty in PNG and that ANC utilization was regressive; highlighting the need to encourage pregnant women, especially those who are economically more vulnerable to visit clinics regularly throughout pregnancy.

The self-collection of vaginal swabs and point-of-care testing and treatment of sexually transmitted infections (STIs) is reported from several low-and middle-income countries. However, the reporting on women’s experiences of self-collection and same-day testing and treatment of STIs is less well described. In this paper, we present the acceptability of self-collected vaginal swabs and point-of-care testing and treatment among pregnant women enrolled in a clinical trial (Women and Newborn Trial of Antenatal Intervention and Management – WANTAIM) in Papua New Guinea. Semi-structured interviews were conducted among 54 women enrolled into WANTAIM to identify the acceptability of the test and treat approach. Analysis of qualitative data used deductive and inductive thematic analysis applying Sekhon, Cartwright and Francis’ acceptability theoretical framework. Most women reported that they understood that the vaginal swab was to identify infections that may affect their unborn baby; however, some were unsure about the specific infections they were being tested for. Among women who tested positive for an STI, some were unsure what they had been treated for. Overall, the self-collection of vaginal swabs for STI testing during pregnancy was highly acceptable.

Global methylation analysis of gene promoters is promising for detection of high-grade squamous intraepithelial lesions or worse (HSIL+) in high-risk human papillomavirus (hrHPV)-positive women. However, diagnostic performance of methylation data at individual CpG-sites is limited. We explored methylation for predicting HSIL+ in self- and clinician-collected samples from Papua New Guinea.Methylation of EPB41L3 (1–6 CpG-sites), hTERT (1–10 CpG-sites) and FAM19A4 (1–5 CpG-sites) was assessed through pyrosequencing from 44 HPV+ samples (4 cancers, 19 HSIL, 4 low-grade squamous intraepithelial lesions (LSIL), 17 normal). New primers were designed for FAM19A4 directed to the first exon region not explored previously.In clinician-collected samples, methylation at CpG-sites 4 and 5 of EPB41L3 were the best HSIL predictors (AUC >0.83) and CpG-site 4 for cancer (0.925). Combination of EPB41L3 sites 2/4 plus FAM19A4 site 1 were the best HSIL+ markers [100% sensitivity, 63.2% specificity].Methylation at CpG-site 5 of FAM19A4 was the best HSIL predictor (0.67) in self-collected samples, and CpG-sites 1 and 3 of FAM19A4 for cancer (0.77). Combined, FAM19A4 site 1 plus HPV 16/18 detection yielded sensitivity of 82.6% and specificity of 61.9%.In conclusion, methylation at individual CpG-sites of EPB41L3 and FAM19A4 outperformed global analysis and improved HSIL+ detection, warranting further investigation.

Curable sexually transmitted infections (STIs) are neglected in public health policy, services and society at large. Effective interventions are available for some STI but seem not to be prioritised at global, regional or local levels. Zambia and Papua New Guinea (PNG) have a high burden of STIs among pregnant women but little is known about the prioritisation of STI treatment and care among this group. We undertook a qualitative study to explore how STIs are prioritised among pregnant women in local health systems in Zambia and PNG. Semi-structured interviews were conducted with 19 key informants-health care workers providing antenatal care, and policy and programme advisers across the two countries. Audio recordings were transcribed and translated into English and stored, managed, and coded in NVivo v12. Analysis used deductive and inductive thematic analysis. Findings were coded against the World Health Organization health system building blocks. Participants spoke about the stigma of STIs at the community level. They described a broad understanding of morbidity associated with undiagnosed and untreated STIs in pregnant women. The importance of testing and treating STIs in pregnancy was well recognised but many spoke of constraints in providing these services due to stock outs of test kits for HIV and syphilis and antibiotics. In both settings, syndromic management remains the mainstay for treating curable STIs. Clinical practice and treatment were not in alignment with current STI guidelines in either country, with participants recognising the need for mentorship and in-service training, as well as the availability of commodities to support their clinical practice. Local disruptions to screening and management of syphilis, HIV and other curable STIs were widely reported in both countries. There is a need to galvanise priority at national and regional levels to ensure ongoing access to supplies needed to undertake STI testing and treatment.

Abstract Background Little research has explored the sexual and reproductive health (SRH) experience of female sex workers (FSW), including girls aged

Abstract Background Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of bacteria genomes at an unprecedented speed. However, most current TGS assemblers were specifically designed for human or other species that do not have a circular genome. Besides, the repetitive DNA fragments in many bacterial genomes plus the high error rate of long sequencing data make it still very challenging to accurately assemble their genomes even with a relatively small genome size. Therefore, there is an urgent need for the development of an optimized method to address these issues. Results We developed B-assembler, which is capable of assembling bacterial genomes when there are only long reads or a combination of short and long reads. B-assembler takes advantage of the structural resolving power of long reads and the accuracy of short reads if applicable. It first selects and corrects the ultra-long reads to get an initial contig. Then, it collects the reads overlapping with the ends of the initial contig. This two-round assembling procedure along with optimized error correction enables a high-confidence and circularized genome assembly. Benchmarked on both synthetic and real sequencing data of several species of bacterium, the results show that both long-read-only and hybrid-read modes can accurately assemble circular bacterial genomes free of structural errors and have fewer small errors compared to other assemblers. Conclusions B-assembler provides a better solution to bacterial genome assembly, which will facilitate downstream bacterial genome analysis.

Abstract Background In Papua New Guinea (PNG) members of key populations, including female sex workers (FSW), men who have sex with men (MSM) and transgender women (TGW), have higher rates of HIV compared to the general adult population and low engagement in HIV care. This paper examines the socio-ecological factors that encourage or hinder HIV treatment initiation and adherence among HIV positive members of key populations in PNG. Methods As part of a larger biobehavioural survey of key populations in PNG, 111 semi-structured interviews were conducted with FSW, MSM and TGW, of whom 28 identified as living with HIV. Interviews from 28 HIV positive participants are used in this analysis of the influences that enabled or inhibited HIV treatment initiation and treatment adherence. Results Enablers included awareness of the biomedical benefits of treatment; experiences of the social, familial and health benefits of early treatment initiation and adherence; support provided by family and friends; and non-judgmental and supportive HIV service provision. Factors that inhibited treatment initiation and adherence included perception of good health and denial of HIV diagnosis; poor family support following positive diagnosis; and anonymity and stigma concerns in HIV care services. Conclusion Exploring health promotion messages that highlight the positive health impacts of early treatment initiation and adherence; providing client-friendly services and community-based treatment initiation and supply; and rolling out HIV viral load testing across the country could improve health outcomes for these key populations.

Abstract Background Biobehavioral data about men who have sex with men (MSM) and transgender women (TGW) in Papua New Guinea (PNG) are limited to those who sell sex. Information about those MSM and TGW who do not sell sex is necessary to guide HIV prevention and treatment efforts. Methods We conducted respondent-driven sampling (RDS) surveys among MSM and TGW in Port Moresby, Lae, and Mt. Hagen, PNG from in 2016 and 2017. Eligibility criteria was: aged > 12 years, born male, could speak English or Tok Pisin and had oral or anal sex with another person born male in the past 6 months. Participants were interviewed face-to-face and offered rapid HIV testing. Weighted data analysis was conducted using RDS-Analyst (v. 0.62). Results We enrolled 400 participants in Port Moresby, 352 in Lae, and 111 in Mt. Hagen. In the last six months, 73.2% of MSM/TGW in Port Moresby, 77.9% in Lae, and 75.9% in Mt. Hagen, had a concurrent sexual partnership. Upwards of 70% of MSM/TGW in all three cities had sex with a woman in the same period. Less than half of MSM/TGW had ever tested for HIV. HIV prevalence among MSM/TGW was 8.5% in Port Moresby and 6.9% in Lae. Among participants in Mt. Hagen it was 1.3%. HIV was associated with not having sex with a woman in the last six months and sexually transmitted disease symptoms in the last 12 months in Port Moresby and Lae. In Port Moresby, it was also associated with an uncut foreskin, and in Lae with earning income in the formal sector and being unable to rely on other MSM or TGW to accompany them to healthcare services. Conclusions The large proportion of MSM and TGW with concurrent sexual partnerships, combined with the low testing coverage, indicates strong potential for the spread of HIV. The different correlates of HIV in Port Moresby and Lae highlight the importance of conducting surveys in multiple locations and using data to develop locally appropriate interventions even within a country.

Abstract Background Papua New Guinea (PNG) has a high prevalence of sexually transmitted infections (STIs). There is increasing evidence that anorectal STIs are important in terms of the dual epidemics of HIV and STIs in this setting. At the time of this study, anorectal STI testing was not possible, and there was no mechanism for self-collection of anorectal specimen among at risk ‘key populations’. This paper documents the development of a culturally appropriate tool that has been used to facilitate self-collection of anorectal specimens with key populations in PNG. Methods This qualitative study involved four focus groups conducted with a purposive sample of 35 participants, including female sex workers, men who have sex with men and transgender women in Port Moresby and Goroka in 2015. During focus groups, participants reviewed and provided critical feedback for the adaption of a previously piloted and published pictorial anorectal specimen collection tool for use with key populations in PNG. Results The final instruction tools are presented in English language and Tok Pisin. To develop these, participants feedback resulted in six key areas of the existing instruction document being modified to ensure it was appropriate for use in PNG. These included translating complex words for sexual health issues (i.e. ‘STIs’, ‘anorectal STIs’, ‘anus’, ‘anal sex’), biomedical instruments (i.e. ‘specimen bottle’, ‘specimen packet’ and ‘swab’), and aspects of the clinical procedure (i.e. inserting the swab 3–4 cm into the anus to collect a specimen). The visual identity of the graphics was redesigned to localise the images for use in PNG. Conclusions This paper describes the development of a culturally and linguistically appropriate tool for a biomedical and clinical intervention with key populations in PNG based around self-collection of anorectal specimens for molecular STI testing. The final tools have been used to facilitate the self-collection of anorectal specimens following a clear clinical protocol during a large bio-behavioural survey in PNG.

The performance of different clinical screening algorithms comprising point-of-care HPV-DNA testing using self-collected vaginal (‘V’) specimens, and visual inspection of the cervix with acetic acid (VIA) was evaluated in Papua New Guinea.Women aged 30–59 years provided V specimens that were tested at point-of-care using the Xpert HPV Test (Cepheid, Sunnyvale, CA). A clinician-collected cervical (‘C’) specimen was then collected for point-of-care Xpert testing, and liquid-based cytology (LBC). Following this, VIA examination was conducted, blind to HPV test results, and ablative cervical cryotherapy provided if indicated. Detection of high-grade squamous intraepithelial lesion (HSIL) by LBC was the reference standard used to evaluate clinical screening algorithms.Of 1005 women, 36 had HSIL+. Xpert HPV Test performance using V specimens (sensitivity 91.7%, specificity 87.0%, PPV 34.0%, NPV 99.3%) was superior to VIA examination alone (51.5%, 81.4%, 17.5%, 95.6% respectively) in predicting underlying HSIL+. A screening algorithm comprising V specimen HPV testing followed by VIA examination had low sensitivity (45.5%) but comparable specificity, PPV and NPV to HPV testing alone (96.3%, 45.5%, 96.3% respectively).A ‘test-and-treat’ screening algorithm based on point-of-care HPV testing of V specimens had superior performance compared with either VIA examination alone, or a combined screening algorithm comprising HPV testing plus VIA. Keywords: Cervical cancer, HPV, Screening, Self-collect, Papua New Guinea, Visual inspection with acetic acid

BackgroundSexually transmitted and genital infections in pregnancy are associated with adverse pregnancy and birth outcomes. Point-of-care tests for these infections facilitate testing and treatment in a single antenatal clinic visit and may reduce the risk of adverse outcomes. Successful implementation and scale-up depends on understanding comparative effectiveness of such programmes and their comparative costs and cost effectiveness. This systematic review synthesises and appraises evidence from economic evaluations of point-of-care testing and treatment for sexually transmitted and genital infections among pregnant women in low- and middle-income countries.MethodsMedline, Embase and Web of Science databases were comprehensively searched using pre-determined criteria. Additional literature was identified by searching Google Scholar and the bibliographies of all included studies. Economic evaluations were eligible if they were set in low- and middle-income countries and assessed antenatal point-of-care testing and treatment for syphilis, chlamydia, gonorrhoea, trichomoniasis, and/or bacterial vaginosis. Studies were analysed using narrative synthesis. Methodological and reporting standards were assessed using two published checklists.ResultsSixteen economic evaluations were included in this review; ten based in Africa, three in Latin and South America and three were cross-continent comparisons. Fifteen studies assessed point-of-care testing and treatment for syphilis, while one evaluated chlamydia. Key drivers of cost and cost-effectiveness included disease prevalence; test, treatment, and staff costs; test sensitivity and specificity; and screening and treatment coverage. All studies met 75% or more of the criteria of the Drummond Checklist and 60% of the Consolidated Health Economics Evaluation Reporting Standards.ConclusionsGenerally, point-of-care testing and treatment was cost-effective compared to no screening, syndromic management, and laboratory-based testing. Future economic evaluations should consider other common infections, and their lifetime impact on mothers and babies. Complementary affordability and equity analyses would strengthen the case for greater investment in antenatal point-of-care testing and treatment for sexually transmitted and genital infections.

Papua New Guinea has among the highest estimated burden of cervical cancer globally, but currently lacks national cervical screening or human papillomavirus (HPV) vaccination programmes. The Papua New Guinean government is committed to introducing the HPV vaccine for primary prevention, but locally-relevant research evidence is not available to guide implementation. Experience from earlier Papua New Guinean health programmes suggests that appropriate engagement with local health cosmologies and cultures for health/wellbeing, illness/disease, and recognition of the role of ‘outsiders’ in preventing, promoting or contributing to sickness, are essential to the successful introduction of biomedical interventions in this setting. We describe findings from a multi-site qualitative study undertaken in three provinces in Papua New Guinea (2012-14). Twenty-one gender specific focus group discussions and 82 semi-structured interviews, with a total of 208 participants, were conducted. There was strong community support for the introduction of the HPV vaccine for cervical cancer prevention in Papua New Guinea. Significantly, and despite being officially discussed in the context of a planned future intervention focusing on vaccinating young girls to prevent cervical cancer, the intervention was de-feminised, where both girls and boys were supported to be vaccinated in any HPV programme in Papua New Guinea.

Abstract Background Soil-transmitted helminths (STHs) including Ascaris lumbricoides, Necator americanus, Ancylostoma spp. and Trichuris trichiura are cause of significant global morbidity. To mitigate their disease burden, at-risk groups in endemic regions receive periodic mass drug administration using anthelmintics, most commonly albendazole and mebendazole. Assessing the efficacy of anthelmintic drugs is important for confirming that these regimens are working effectively and that drug resistance has not emerged. In this study we aimed to characterise the therapeutic efficacy of albendazole against Ascaris spp. and N. americanus in Timor-Leste, using a quantitative polymerase chain reaction (qPCR) method for parasite detection and quantification. Results A total of 314 participants from 8 communities in Timor-Leste provided stool samples before and 10–14 days after the administration of a single 400 mg dose of albendazole. Helminth infection status and infection intensity (measured in Ct-values and relative fluorescence units) were determined using qPCR. Efficacy was determined by examining the cure rates and infection intensity reduction rates. Albendazole was found to be highly efficacious against Ascaris spp., with a cure rate of 91.4% (95% CI: 85.9–95.2%) and infection intensity reduction rate of 95.6% (95% CI: 88.3–100%). The drug was less efficacious against N. americanus with a cure rate of 58.3% (95% CI: 51.4–64.9%) and infection intensity reduction rate of 88.9% (95% CI: 84.0–97.0%). Conclusions The observed cure rates and infection intensity reduction rates obtained for Ascaris spp. and to a lower extent N. americanus, demonstrate the continued efficacy of albendazole against these species and its utility as a mass chemotherapy agent in Timor-Leste. Furthermore, this study demonstrates the usefulness of qPCR as a method to measure the efficacy of anthelminthic drugs. Additional research is necessary to translate Ct-values into eggs per gram in a systematic way. Trial registration Australian and New Zealand Clinical Trials Registry 12614000680662 (registered 27 June 2014).

Abstract Background Papua New Guinea (PNG) has some of the highest prevalence of urogenital sexually transmitted infections (STIs) in Pacific Asia, but to date, anorectal STI prevalence data do not exist, and diagnosis of anorectal STIs does not occur. The purpose of this study was to document the acceptability of anorectal STI testing and self-collection of anorectal swabs for testing among populations at risk of anorectal STIs, in advance of a large bio-behavioural survey during which this approach to specimen collection was planned among key populations in PNG. Methods Four focus groups were conducted, collecting data from a purposive sample of 35 members of two civil society groups representing female sex workers, men who have sex with men and transgender women in Port Moresby and Goroka. Results All participants were in favour of anorectal STI testing in PNG. Reasons given for willingness to undertake anorectal STI testing included that anal sex is practised; that anorectal STIs are not perceived to exist; there are self-reported experiences of anorectal symptoms indicative of anorectal STIs; that anorectal STI testing will enhance personal health; and that anorectal STI testing is not currently available in PNG. All participants were confident they could obtain self-collected specimens, although several stated that support from trained health workers should be available for community members who may not feel comfortable with self-collection. Conclusions This qualitative research is the first study of acceptability of anorectal STI testing and specimen self-collection procedures in PNG, and Pacific Asia more broadly. Our qualitative findings show support for anorectal STI testing including the use of self-collected swabs among key populations in PNG. Study findings informed the inclusion of anorectal STI testing in a large bio-behavioural survey to be used to estimate anorectal STI prevalence among key populations in PNG for the first time.

Abstract Background Timor-Leste has a high prevalence of soil-transmitted helminth (STH) infections. High proportions of the population have been reported as being anaemic, and extremely high proportions of children as stunted or wasted. There have been no published analyses of the contributions of STH to these morbidity outcomes in Timor-Leste. Methods Using baseline cross-sectional data from 24 communities (18 communities enrolled in a cluster randomised controlled trial, and identically-collected data from six additional communities), analyses of the association between STH infections and community haemoglobin and child development indices were undertaken. Stool samples were assessed for STH using qPCR and participant haemoglobin, heights and weights were measured. Questionnaires were administered to collect demographic and socioeconomic data. Intensity of infection was categorised using correlational analysis between qPCR quantification cycle values and eggs per gram of faeces equivalents, with algorithms generated from seeding experiments. Mixed-effects logistic and multinomial regression were used to assess the association between STH infection intensity classes and anaemia, and child stunting, wasting and underweight. Results Very high stunting (60%), underweight (60%), and wasting (20%) in children, but low anaemia prevalence (15%), were found in the study communities. STH were not significantly associated with morbidity outcomes. Male children and those in the poorest socioeconomic quintile were significantly more likely to be moderately and severely stunted. Male children were significantly more likely than female children to be severely underweight. Increasing age was also a risk factor for being underweight. Few risk factors emerged for wasting in these analyses. Conclusions According to World Health Organization international reference standards, levels of child morbidity in this population constitute a public health emergency, although the international reference standards need to be critically evaluated for their applicability in Timor-Leste. Strategies to improve child development and morbidity outcomes, for example via nutrition and iron supplementation programmes, are recommended for these communities. Despite the apparent lack of an association from STH in driving anaemia, stunting, wasting and underweight, high endemicity suggests a need for STH control strategies. Trial registration Australian and New Zealand Clinical Trials Registry ACTRN12614000680662 ; retrospectively registered.

Background: Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and bacterial vaginosis have been associated with preterm birth and low birth weight, and are highly prevalent among pregnant women in many low- and middle-income settings. There is conflicting evidence on the potential benefits of screening and treating these infections in pregnancy. Newly available diagnostic technologies make it possible, for the first time, to conduct definitive field trials to fill this knowledge gap. The primary aim of this study is to evaluate whether antenatal point-of-care testing and immediate treatment of these curable sexually transmitted and genital infections (STIs) leads to reduction in preterm birth and low birth weight. Methods: The Women and Newborn Trial of Antenatal Interventions and Management (WANTAIM) is a cluster-randomised crossover trial in Papua New Guinea to compare point-of-care STI testing and immediate treatment with standard antenatal care (which includes the WHO-endorsed STI ‘syndromic’ management strategy based on clinical features alone without laboratory confirmation). The unit of randomisation is a primary health care facility and its catchment communities. The primary outcome is a composite measure of two events: the proportion of women and their newborns in each trial arm, who experience either preterm birth (delivery

BACKGROUND:No investigations have been undertaken of risk factors for intensity of soil-transmitted helminth (STH) infection in Timor-Leste. This study provides the first analysis of risk factors for intensity of STH infection, as determined by quantitative PCR (qPCR), examining a broad range of water, sanitation and hygiene (WASH) and environmental factors, among communities in Manufahi District, Timor-Leste. METHODS:A baseline cross-sectional survey of 18 communities was undertaken as part of a cluster randomised controlled trial, with additional identically-collected data from six other communities. qPCR was used to assess STH infection from stool samples, and questionnaires administered to collect WASH, demographic, and socioeconomic data. Environmental information was obtained from open-access sources and linked to infection outcomes. Mixed-effects multinomial logistic regression was undertaken to assess risk factors for intensity of Necator americanus and Ascaris infection. RESULTS:2152 participants provided stool and questionnaire information for this analysis. In adjusted models incorporating WASH, demographic and environmental variables, environmental variables were generally associated with infection intensity for both N. americanus and Ascaris spp. Precipitation (in centimetres) was associated with increased risk of moderate-intensity (adjusted relative risk [ARR] 6.1; 95% confidence interval [CI] 1.9-19.3) and heavy-intensity (ARR 6.6; 95% CI 3.1-14.1) N. americanus infection, as was sandy-loam soil around households (moderate-intensity ARR 2.1; 95% CI 1.0-4.3; heavy-intensity ARR 2.7; 95% CI 1.6-4.5; compared to no infection). For Ascaris, alkaline soil around the household was associated with reduced risk of moderate-intensity infection (ARR 0.21; 95% CI 0.09-0.51), and heavy-intensity infection (ARR 0.04; 95% CI 0.01-0.25). Few WASH risk factors were significant. CONCLUSION:In this high-prevalence setting, strong risk associations with environmental factors indicate that anthelmintic treatment alone will be insufficient to interrupt STH transmission, as conditions are favourable for ongoing environmental transmission. Integrated STH control strategies should be explored as a priority.