Reasons for not Using HIV Pre-Exposure Prophylaxis (PrEP) among Gay and Bisexual Men in Australia: Mixed-Methods Analyses from a National, Online, Observational Study

Although approximately 31,000 Australian gay and bisexual men (GBM) are eligible for HIV pre-exposure prophylaxis (PrEP), only 18,500 people currently use it, indicating a need to investigate why GBM do not use it. This article uses data from a national, online, observational study. It adopts a mixed-methods analysis to responses to survey questions asking about reasons Australian GBM were not using PrEP in 2018, according to their level of HIV risk as delineated by the Australian PrEP prescribing guidelines at the time. Participants responded to check-box questions and had the option to respond to a qualitative free-text question. Results showed that just over one-fifth of men were at higher risk of HIV acquisition. Compared to lower-risk men, higher-risk men were more likely to indicate PrEP was too expensive and more likely to cite embarrassment asking for it. Reasons for not using PrEP included a lack of personal relevance, poor accessibility or knowledge, concerns about PrEP’s inability to protect against STIs, potential side effects, and a preference for condoms. We conclude that health promotion more effectively targeting GBM who may benefit the most from PrEP may be valuable

Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays

Tracking the genomic evolution of breast cancer metastasis

Therapeutic choices for metastatic tumors are, in most cases, based upon the histological and molecular analysis of the corresponding primary tumor. Understanding whether and to what extent the genomic landscape of metastasis differs from the tumors from which they originated is critical yet largely unknown. A recent report tackled this key issue by comparing the genomic and transcriptional profile of a metastatic lobular breast tumor with that of the primary tumor surgically removed 9 years earlier. The extent of the differences suggests a high degree of mutational heterogeneity between primary and metastatic lesions and indicates that significant evolution occurs during breast cancer progression

Workplace interventions for increasing standing or walking for decreasing musculoskeletal symptoms in sedentary workers

BACKGROUND: The prevalence of musculoskeletal symptoms among sedentary workers is high. Interventions that promote occupational standing or walking have been found to reduce occupational sedentary time, but it is unclear whether these interventions ameliorate musculoskeletal symptoms in sedentary workers. OBJECTIVES: To investigate the effectiveness of workplace interventions to increase standing or walking for decreasing musculoskeletal symptoms in sedentary workers. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, OSH UPDATE, PEDro, ClinicalTrials.gov, and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) search portal up to January 2019. We also screened reference lists of primary studies and contacted experts to identify additional studies. SELECTION CRITERIA: We included randomised controlled trials (RCTs), cluster-randomised controlled trials (cluster-RCTs), quasi RCTs, and controlled before-and-after (CBA) studies of interventions to reduce or break up workplace sitting by encouraging standing or walking in the workplace among workers with musculoskeletal symptoms. The primary outcome was self-reported intensity or presence of musculoskeletal symptoms by body region and the impact of musculoskeletal symptoms such as pain-related disability. We considered work performance and productivity, sickness absenteeism, and adverse events such as venous disorders or perinatal complications as secondary outcomes. DATA COLLECTION AND ANALYSIS: Two review authors independently screened titles, abstracts, and full-text articles for study eligibility. These review authors independently extracted data and assessed risk of bias. We contacted study authors to request additional data when required. We used GRADE considerations to assess the quality of evidence provided by studies that contributed to the meta-analyses. MAIN RESULTS: We found ten studies including three RCTs, five cluster RCTs, and two CBA studies with a total of 955 participants, all from high-income countries. Interventions targeted changes to the physical work environment such as provision of sit-stand or treadmill workstations (four studies), an activity tracker (two studies) for use in individual approaches, and multi-component interventions (five studies). We did not find any studies that specifically targeted only the organisational level components. Two studies assessed pain-related disability. Physical work environment There was no significant difference in the intensity of low back symptoms (standardised mean difference (SMD) -0.35, 95% confidence interval (CI) -0.80 to 0.10; 2 RCTs; low-quality evidence) nor in the intensity of upper back symptoms (SMD -0.48, 95% CI -.096 to 0.00; 2 RCTs; low-quality evidence) in the short term (less than six months) for interventions using sit-stand workstations compared to no intervention. No studies examined discomfort outcomes at medium (six to less than 12 months) or long term (12 months and more). No significant reduction in pain-related disability was noted when a sit-stand workstation was used compared to when no intervention was provided in the medium term (mean difference (MD) -0.4, 95% CI -2.70 to 1.90; 1 RCT; low-quality evidence). Individual approach There was no significant difference in the intensity or presence of low back symptoms (SMD -0.05, 95% CI -0.87 to 0.77; 2 RCTs; low-quality evidence), upper back symptoms (SMD -0.04, 95% CI -0.92 to 0.84; 2 RCTs; low-quality evidence), neck symptoms (SMD -0.05, 95% CI -0.68 to 0.78; 2 RCTs; low-quality evidence), shoulder symptoms (SMD -0.14, 95% CI -0.63 to 0.90; 2 RCTs; low-quality evidence), or elbow/wrist and hand symptoms (SMD -0.30, 95% CI -0.63 to 0.90; 2 RCTs; low-quality evidence) for interventions involving an activity tracker compared to an alternative intervention or no intervention in the short term. No studies provided outcomes at medium term, and only one study examined outcomes at long term. Organisational level No studies evaluated the effects of interventions solely targeted at the organisational level. Multi-component approach There was no significant difference in the proportion of participants reporting low back symptoms (risk ratio (RR) 0.93, 95% CI 0.69 to 1.27; 3 RCTs; low-quality evidence), neck symptoms (RR 1.00, 95% CI 0.76 to 1.32; 3 RCTs; low-quality evidence), shoulder symptoms (RR 0.83, 95% CI 0.12 to 5.80; 2 RCTs; very low-quality evidence), and upper back symptoms (RR 0.88, 95% CI 0.76 to 1.32; 3 RCTs; low-quality evidence) for interventions using a multi-component approach compared to no intervention in the short term. Only one RCT examined outcomes at medium term and found no significant difference in low back symptoms (MD -0.40, 95% CI -1.95 to 1.15; 1 RCT; low-quality evidence), upper back symptoms (MD -0.70, 95% CI -2.12 to 0.72; low-quality evidence), and leg symptoms (MD -0.80, 95% CI -2.49 to 0.89; low-quality evidence). There was no significant difference in the proportion of participants reporting low back symptoms (RR 0.89, 95% CI 0.57 to 1.40; 2 RCTs; low-quality evidence), neck symptoms (RR 0.67, 95% CI 0.41 to 1.08; two RCTs; low-quality evidence), and upper back symptoms (RR 0.52, 95% CI 0.08 to 3.29; 2 RCTs; low-quality evidence) for interventions using a multi-component approach compared to no intervention in the long term. There was a statistically significant reduction in pain-related disability following a multi-component intervention compared to no intervention in the medium term (MD -8.80, 95% CI -17.46 to -0.14; 1 RCT; low-quality evidence). AUTHORS' CONCLUSIONS: Currently available limited evidence does not show that interventions to increase standing or walking in the workplace reduced musculoskeletal symptoms among sedentary workers at short-, medium-, or long-term follow up. The quality of evidence is low or very low, largely due to study design and small sample sizes. Although the results of this review are not statistically significant, some interventions targeting the physical work environment are suggestive of an intervention effect. Therefore, in the future, larger cluster-RCTs recruiting participants with baseline musculoskeletal symptoms and long-term outcomes are needed to determine whether interventions to increase standing or walking can reduce musculoskeletal symptoms among sedentary workers and can be sustained over time

Quantifying Missing Heritability at Known GWAS Loci

Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing due to poor tagging or additional causal variants at known GWAS loci. Here, we use variance components to quantify the heritability explained by all SNPs at known GWAS loci in nine diseases from WTCCC1 and WTCCC2. After accounting for expectation, we observed all SNPs at known GWAS loci to explain 1.29 X more heritability than GWAS-associated SNPs on average (P = 3.3 X 10[superscript -5]). For some diseases, this increase was individually significant:2.07 X for Multiple Sclerosis (MS) (P = 6.5 X 10 [superscript -9]) and for Crohn's Disease (CD) (P = 1.3 X 10[superscript -3]); all analyses of autoimmune diseases excluded the well-studied MHC region. Additionally, we found that GWAS loci from other related traits also explained significant heritability. The union of all autoimmune disease loci explained 7.15 X more MS heritability than known MS SNPs (P 20,000 Rheumatoid Arthritis (RA) samples typed on ImmunoChip, with 2.37 X more heritability from all SNPs at GWAS loci (P = 2.3 X 10[superscript -6]) and more heritability from all autoimmune disease loci (P < 1 X 10[superscript -16]) compared to known RA SNPs (including those identified in this cohort). Our methods adjust for LD between SNPs, which can bias standard estimates of heritability from SNPs even if all causal variants are typed. By comparing adjusted estimates, we hypothesize that the genome-wide distribution of causal variants is enriched for low-frequency alleles, but that causal variants at known GWAS loci are skewed towards common alleles. These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture.National Institutes of Health (U.S.) (Grant R03HG006731)National Institutes of Health (U.S.) (Fellowship F32GM106584

Prescribing indicators at primary health care centers within the WHO African region: a systematic analysis (1995-2015)

Abstract Background Rational medicine use is essential to optimize quality of healthcare delivery and resource utilization. We aim to conduct a systematic review of changes in prescribing patterns in the WHO African region and comparison with WHO indicators in two time periods 1995–2005 and 2006–2015. Methods Systematic searches were conducted in PubMed, Scopus, Web of science, Africa-Wide Nipad, Africa Journals Online (AJOL), Google scholar and International Network for Rational Use of Drugs (INRUD) Bibliography databases to identify primary studies reporting prescribing indicators at primary healthcare centres (PHCs) in Africa. This was supplemented by a manual search of retrieved references. We assessed the quality of studies using a 14-point scoring system modified from the Downs and Black checklist with inclusions of recommendations in the WHO guidelines. Results Forty-three studies conducted in 11 African countries were included in the overall analysis. These studies presented prescribing indicators based on a total 141,323 patient encounters across 572 primary care facilities. The results of prescribing indicators were determined as follows; average number of medicines prescribed per patient encounter = 3.1 (IQR 2.3–4.8), percentage of medicines prescribed by generic name =68.0 % (IQR 55.4–80.3), Percentage of encounters with antibiotic prescribed =46.8 % (IQR 33.7–62.8), percentage of encounters with injection prescribed =25.0 % (IQR 18.7–39.5) and the percentage of medicines prescribed from essential medicines list =88.0 % (IQR 76.3–94.1). Prescribing indicators were generally worse in private compared with public facilities. Analysis of prescribing across two time points 1995–2005 and 2006–2015 showed no consistent trends. Conclusions Prescribing indicators for the African region deviate significantly from the WHO reference targets. Increased collaborative efforts are urgently needed to improve medicine prescribing practices in Africa with the aim of enhancing the optimal utilization of scarce resources and averting negative health consequences

Do rare variant genotypes predict common variant genotypes?

The synthetic association hypothesis proposes that common genetic variants detectable in genome-wide association studies may reflect the net phenotypic effect of multiple rare polymorphisms distributed broadly within the focal gene rather than, as often assumed, the effect of common functional variants in high linkage disequilibrium with the focal marker. In a recent study, Dickson and colleagues demonstrated synthetic association in simulations and in two well-characterized, highly polymorphic human disease genes. The converse of this hypothesis is that rare variant genotypes must be correlated with common variant genotypes often enough to make the phenomenon of synthetic association possible. Here we used the exome genotype data provided for Genetic Analysis Workshop 17 to ask how often, how well, and under what conditions rare variant genotypes predict the genotypes of common variants within the same gene. We found nominal evidence of correlation between rare and common variants in 21-30% of cases examined for unrelated individuals; this rate increased to 38-44% for related individuals, underscoring the segregation that underlies synthetic association

An improved method for undertaking limiting dilution assays for in vitro cloning of Plasmodium falciparum parasites

Abstract. Background: Obtaining single parasite clones is required for many techniques in malaria research. Cloning by limiting dilution using microscopy-based assessment for parasite growth is an arduous and labor-intensive process. An alternative method for the detection of parasite growth in limiting dilution assays is using a commercial ELISA histidine-rich protein II (HRP2) detection kit. Methods. Detection of parasite growth was undertaken using HRP2 ELISA and compared to thick film microscopy. An HRP2 protein standard was used to determine the detection threshold of the HRP2 ELISA assay, and a HRP2 release model was used to extrapolate the amount of parasite growth required for a positive result. Results: The HRP2 ELISA was more sensitive than microscopy for detecting parasite growth. The minimum level of HRP2 protein detection of the ELISA was 0.11ng/ml. Modeling of HRP2 release determined that 2,116 parasites are required to complete a full erythrocytic cycle to produce sufficient HRP2 to be detected by the ELISA. Under standard culture conditions this number of parasites is likely to be reached between 8 to 14 days of culture. Conclusions: This method provides an accurate and simple way for the detection of parasite growth in limiting dilution assays, reducing time and resources required in traditional methods. Furthermore the method uses spent culture media instead of the parasite-infected red blood cells, enabling culture to continue

Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences

Invertebrate biomonitoring can reveal crucial information about the status of restoration projects; however, it is routinely underused because of the high level of taxonomic expertise and resources required. Invertebrate DNA metabarcoding has been used to characterize invertebrate biodiversity but its application in restoration remains untested. We use DNA metabarcoding, a new approach for restoration assessment, to explore the invertebrate composition from pitfall traps at two mine site restoration chronosequences in southwestern Australia. Invertebrates were profiled using two cytochrome oxidase subunit 1 assays to investigate invertebrate biodiversity. The data revealed differences between invertebrate communities at the two mines and between the different age plots of the chronosequences. Several characteristic taxa were identified for each age within the chronosequence, including springtails within the youngest sites (Order: Collembola) and millipedes within the oldest and reference sites (Order: Julida). This study facilitates development of a molecular “toolkit” for the monitoring of ecological restoration projects. We suggest that a metabarcoding approach shows promise in complementing current monitoring practices that rely on alpha taxonomy