Urine as a High-Quality Source of Host Genomic DNA from Wild Populations

The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species

Improving the normalization of complex interventions: measure development based on normalization process theory (NoMAD): study protocol

<b>Background</b> Understanding implementation processes is key to ensuring that complex interventions in healthcare are taken up in practice and thus maximize intended benefits for service provision and (ultimately) care to patients. Normalization Process Theory (NPT) provides a framework for understanding how a new intervention becomes part of normal practice. This study aims to develop and validate simple generic tools derived from NPT, to be used to improve the implementation of complex healthcare interventions.<p></p> <b>Objectives</b> The objectives of this study are to: develop a set of NPT-based measures and formatively evaluate their use for identifying implementation problems and monitoring progress; conduct preliminary evaluation of these measures across a range of interventions and contexts, and identify factors that affect this process; explore the utility of these measures for predicting outcomes; and develop an online users’ manual for the measures.<p></p> <b>Methods</b> A combination of qualitative (workshops, item development, user feedback, cognitive interviews) and quantitative (survey) methods will be used to develop NPT measures, and test the utility of the measures in six healthcare intervention settings.<p></p> <b>Discussion</b> The measures developed in the study will be available for use by those involved in planning, implementing, and evaluating complex interventions in healthcare and have the potential to enhance the chances of their implementation, leading to sustained changes in working practices

Accuracy of and preferences for blood-based versus oral-fluid-based HIV self-testing in Malawi: a cross-sectional study

Background: HIV self-testing (HIVST) can use either oral-fluid or blood-based tests. Studies have shown strong preferences for self-testing compared to facility-based services. Despite availability of low-cost blood-based HIVST options, to date, HIVST implementation in sub-Saharan Africa has largely been oral-fluid-based. We investigated whether users preferred blood-based (i.e. using blood sample derived from a finger prick) or oral fluid-based HIVST in rural and urban Malawi. Methods: At clinics providing HIV testing services (n = 2 urban; n = 2 rural), participants completed a semi-structured questionnaire capturing sociodemographic data before choosing to test using oral-fluid-based HVST, blood-based HIVST or provider-delivered testing. They also completed a self-administered questionnaire afterwards, followed by a confirmatory test using the national algorithm then appropriate referral. We used simple and multivariable logistic regression to identify factors associated with preference for oral-fluid or blood-based HIVST. Results: July to October 2018, N = 691 participants enrolled in this study. Given the choice, 98.4% (680/691) selected HIVST over provider-delivered testing. Of 680 opting for HIVST, 416 (61.2%) chose oral-fluid-based HIVST, 264 (38.8%) chose blood-based HIVST and 99.1% (674/680) reported their results appropriately. Self-testers who opted for blood-based HIVST were more likely to be male (50.3% men vs. 29.6% women, p < 0.001), attending an urban facility (43% urban vs. 34.6% rural, p = 0.025) and regular salary-earners (49.5% regular vs. 36.8% non-regular, p = 0.012). After adjustment, only sex was found to be associated with choice of self-test (adjusted OR 0.43 (95%CI: 0.3–0.61); p-value < 0.001). Among 264 reporting blood-based HIVST results, 11 (4.2%) were HIV-positive. Blood-based HIVST had sensitivity of 100% (95% CI: 71.5–100%) and specificity of 99.6% (95% CI: 97.6–100%), with 20 (7.6%) invalid results. Among 416 reporting oral-fluid-based HIVST results 18 (4.3%) were HIV-positive. Oral-fluid-based HIVST had sensitivity of 88.9% (95% CI: 65.3–98.6%) and specificity of 98.7% (95% CI: 97.1–99.6%), with no invalid results. Conclusions: Offering both blood-based and oral-fluid-based HIVST resulted in high uptake when compared directly with provider-delivered testing. Both types of self-testing achieved high accuracy among users provided with a pre-test demonstration beforehand. Policymakers and donors need to adequately plan and budget for the sensitisation and support needed to optimise the introduction of new quality-assured blood-based HIVST products

Protocol: developing a conceptual framework of patient mediated knowledge translation, systematic review using a realist approach

<p>Abstract</p> <p>Background</p> <p>Patient involvement in healthcare represents the means by which to achieve a healthcare system that is responsive to patient needs and values. Characterization and evaluation of strategies for involving patients in their healthcare may benefit from a knowledge translation (KT) approach. The purpose of this knowledge synthesis is to develop a conceptual framework for patient-mediated KT interventions.</p> <p>Methods</p> <p>A preliminary conceptual framework for patient-mediated KT interventions was compiled to describe intended purpose, recipients, delivery context, intervention, and outcomes. A realist review will be conducted in consultation with stakeholders from the arthritis and cancer fields to explore how these interventions work, for whom, and in what contexts. To identify patient-mediated KT interventions in these fields, we will search MEDLINE, the Cochrane Library, and EMBASE from 1995 to 2010; scan references of all eligible studies; and examine five years of tables of contents for journals likely to publish quantitative or qualitative studies that focus on developing, implementing, or evaluating patient-mediated KT interventions. Screening and data collection will be performed independently by two individuals.</p> <p>Conclusions</p> <p>The conceptual framework of patient-mediated KT options and outcomes could be used by healthcare providers, managers, educationalists, patient advocates, and policy makers to guide program planning, service delivery, and quality improvement and by us and other researchers to evaluate existing interventions or develop new interventions. By raising awareness of options for involving patients in improving their own care, outcomes based on using a KT approach may lead to greater patient-centred care delivery and improved healthcare outcomes.</p

Primordial argon isotope fractionation in the atmosphere of Mars measured by the SAM instrument on Curiosity and implications for atmospheric loss

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102170/1/grl51048.pd

Australia and New Zealand Islet and Pancreas Transplant Registry Annual Report 2018—Islet Donations, Islet Isolations, and Islet Transplants

Background. This is an excerpt from chapter 4 of the annual registry report from the Australia and New Zealand islet and pan- creas transplant registry. The full report is available at http://anziptr.org/reports/. Methods. We report data for all allogeneic islet isolation and transplant activity from 2002 to end 2017. Solid organ pancreas transplantation activity is reported separately. New Zealand does not have an islet transplant program. Data analysis was performed using Stata software version 14 (StataCorp, College Station, TX). Results. From 2002 to 2017, a total of 104 allogeneic islet transplants were performed in 62 recipients. Conclusions. The number of islet transplants performed in Australia was slightly lower in 2017 but continues to increase over time

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition

Innovative demand creation strategies to increase voluntary medical male circumcision uptake: a pragmatic randomised controlled trial in Zimbabwe.

INTRODUCTION: Reaching men aged 20-35 years, the group at greatest risk of HIV, with voluntary medical male circumcision (VMMC) remains a challenge. We assessed the impact of two VMMC demand creation approaches targeting this age group in a randomised controlled trial (RCT). METHODS: We conducted a 2×2 factorial RCT comparing arms with and without two interventions: (1) standard demand creation augmented by human-centred design (HCD)-informed approach; (2) standard demand creation plus offer of HIV self-testing (HIVST). Interpersonal communication (IPC) agents were the unit of randomisation. We observed implementation of demand creation over 6 months (1 May to 31 October 2018), with number of men circumcised assessed over 7 months. The primary outcome was the number of men circumcised per IPC agent using the as-treated population of actual number of months each IPC agent worked. We conducted a mixed-methods process evaluation within the RCT. RESULTS: We randomised 140 IPC agents, 35 in each arm. 132/140 (94.3%) attended study training and 105/132 (79.5%) reached at least one client during the trial period and were included in final analysis. There was no evidence that the HCD-informed intervention increased VMMC uptake versus no HCD-informed intervention (incident rate ratio (IRR) 0.87, 95% CI 0.38 to 2.02; p=0.75). Nor did offering men a HIVST kit at time of VMMC mobilisation (IRR 0.65, 95% CI 0.28 to 1.50; p=0.31). Among IPC agents that reported reaching at least one man with demand creation, both the HCD-informed intervention and HIVST were deemed useful. There were some challenges with trial implementation; <50% of IPC agents converted any men to VMMC, which undermined our ability to show an effect of demand creation and may reflect acceptability and feasibility of the interventions. CONCLUSION: This RCT did not show evidence of an effect of HCD-informed demand intervention or HIVST on VMMC uptake. Findings will inform future design and implementation of demand creation evaluations. TRIAL REGISTRATION NUMBER: PACTR201804003064160

Clinician and Parent Perspectives on Parent and Family Contextual Factors that Impact Community Mental Health Services for Children with Behavior Problems

The present study employed qualitative methods to examine multiple stakeholder perspectives regarding the role of parent and family contextual factors on community child mental health treatment for children with behavior problems. Findings suggest agreement between clinicians and parents on the number, types and importance of parent and family factors in children’s mental health services; however, stakeholders differed in reports of which factors were most salient. Specifically, clinicians endorsed most factors as being equally salient, while parents described a few salient factors, with parental stress and inadequate social support being the most frequently discussed. These qualitative data further elucidate the context of community services and have implications for evidence-based practice implementation and improving community care

Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing