Search

Large scale changes in biodiversity and conservation management require long-term goals and planning across multiple sectors in the face of increasing global change. Major trends in land use and management interventions, species additions or losses, and climate are well recognized, but responses are still often short-term and fragmented across agencies and sectors. Scenario-building can be a powerful tool to imagine possible futures, integrating across sectors and disciplines and promoting long-term thinking and planning. As an interdisciplinary team of experts, we developed potential scenarios for a range of future environmental conditions. The scenarios explored: increasing land ownership and stewardship of land by indigenous peoples (Māori); widespread afforestation using native tree species; national-scale eradication of invasive mammalian predators; and increasing frequency of extreme weather events. We explored the implications of these globally-relevant trends at a national scale using Aotearoa New Zealand as our study system. Detailed descriptions of these scenarios were developed by experts using environmental, economic, social science and policy lenses. Across scenarios several common themes were consistently highlighted, including the importance of land use in driving other conservation outcomes. How the value of ecosystem services is recognized and prioritized was also important to a wide range of outcomes. Furthermore, each scenario presented both opportunities and risks to equality, indigenous empowerment and human capital, emphasizing the importance of good policy responses to maximize benefits and minimize unintended harm. These scenarios will be used to stimulate new questions and ideas for biodiversity conservation and management, such as considering the implications of different potential futures for the management of biological invasions. This approach is explicitly designed to be generalisable across different sites or regions and provides a method for considering the implications of potential future changes for a broad range of disciplines or needs.

Oral bacteria play important roles in human health and disease. Oral samples collected using ethanol-containing mouthwash are widely used for oral microbiome studies. However, ethanol is flammable and not ideal for transportation/storage in large quantities, and some individuals may avoid ethanol due to the burning sensation or due to various personal, medical, religious, and/or cultural factors. Here, we compared ethanol-free and ethanol-containing mouthwashes using multiple microbiome metrics and assessed the stability of the mouthwash samples stored up to 10 days before processing. Forty volunteers provided oral wash samples collected using ethanol-free and ethanol-containing mouthwashes. From each sample, one aliquot was immediately frozen, one was stored at 4°C for 5 days and frozen, while the third aliquot was stored for 5 days at 4°C and 5 days at ambient temperature to mimic shipping delays and then frozen. DNA was extracted, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatic processing was performed using QIIME 2. Microbiome metrics measured in the two mouthwash types were very similar, with intraclass correlation coefficients (ICCs) for alpha and beta diversity metrics greater than 0.85. Relative abundances of some taxa were significantly different, but ICCs of the top four most abundant phyla and genera were high (> 0.75) for the comparability of the mouthwashes. Stability during delayed processing was also high for both mouthwashes based on alpha and beta diversity measures and relative abundances of the top four phyla and genera (ICCs ≥ 0.90). These results demonstrate ethanol-free mouthwash performs similarly to ethanol-containing mouthwash for microbial analyses, and both mouthwashes are stable for at least 10 days without freezing prior to laboratory processing. Ethanol-free mouthwash is suitable for collecting and shipping oral wash samples, and these results have important implications for planning future epidemiologic studies of the oral microbiome.

[This corrects the article DOI: 10.1371/journal.pone.0193730.].

The objective of this study was to elicit experts' opinions and gather estimates on the perceived probability of introduction and spread of avian influenza (AI) virus in the Australian broiler and layer industry. Using a modified Delphi method and a 4-step elicitation process, 11 experts were asked to give initial individual estimates for the various pathways and practices in the presented scenarios using a questionnaire. Following this, a workshop was conducted to present group averages of estimates and discussion was facilitated to obtain final individual estimates. For each question, estimates for all experts were combined using a discrete distribution, with weights allocated representing the level of expertise. Indirect contact with wild birds either via a contaminated water source or fomites was considered the most likely pathway of introduction of low pathogenic avian influenza (LPAI) on poultry farms. Presence of a water body near the poultry farm was considered a potential pathway for introduction only when the operation type was free range and the water body was within 500m distance from the shed. The probability that LPAI will mutate to highly pathogenic avian influenza (HPAI) was considered to be higher in layer farms. Shared personnel, equipment and aerosol dispersion were the most likely pathways of shed to shed spread of the virus. For LPAI and HPAI spread from farm to farm, shared pick-up trucks for broiler and shared egg trays and egg pallets for layer farms were considered the most likely pathways. Findings from this study provide an insight on most influential practices on the introduction and spread of AI virus among commercial poultry farms in Australia, as elicited from opinions of experts. These findings will be used to support parameterization of a modelling study assessing the risk of AI introduction and spread among commercial poultry farms in Australia.

This paper describes the level of adoption of biosecurity practices performed on Australian commercial chicken meat and layer farms and farmer-perceived importance of these practices. On-farm interviews were conducted on 25 free range layer farms, nine cage layer farms, nine barn layer farms, six free range meat chicken farms and 15 barn meat chicken farms in the Sydney basin bioregion and South East Queensland. There was a high level of treatment of drinking water across all farm types; town water was the most common source. In general, meat chicken farms had a higher level of adoption of biosecurity practices than layer farms. Cage layer farms had the shortest median distance between sheds (7.75m) and between sheds and waterbodies (30m). Equipment sharing between sheds was performed on 43% of free range meat chicken farms compared to 92% of free range layer farms. There was little disinfection of this shared equipment across all farm types. Footbaths and visitor recording books were used by the majority of farms for all farm types except cage layer farms (25%). Wild birds in sheds were most commonly reported in free range meat chicken farms (73%). Dogs and cats were kept across all farm types, from 56% of barn layer farms to 89% of cage layer farms, and they had access to the sheds in the majority (67%) of cage layer farms and on the range in some free range layer farms (44%). Most biosecurity practices were rated on average as 'very important' by farmers. A logistic regression analysis revealed that for most biosecurity practices, performing a practice was significantly associated with higher perceived farmer importance of that biosecurity practice. These findings help identify farm types and certain biosecurity practices with low adoption levels. This information can aid decision-making on efforts used to improve adoption levels.

IntroductionSex hormones have been implicated in the etiology of a number of diseases. To better understand disease etiology and the mechanisms of disease-risk factor associations, this analysis aimed to investigate the associations of anthropometric, sociodemographic and behavioural factors with a range of circulating sex hormones and sex hormone-binding globulin.MethodsStatistical analyses of individual participant data from 12,330 male controls aged 25-85 years from 25 studies involved in the Endogenous Hormones Nutritional Biomarkers and Prostate Cancer Collaborative Group. Analysis of variance was used to estimate geometric means adjusted for study and relevant covariates.ResultsOlder age was associated with higher concentrations of sex hormone-binding globulin and dihydrotestosterone and lower concentrations of dehydroepiandrosterone sulfate, free testosterone, androstenedione, androstanediol glucuronide and free estradiol. Higher body mass index was associated with higher concentrations of free estradiol, androstanediol glucuronide, estradiol and estrone and lower concentrations of dihydrotestosterone, testosterone, sex hormone-binding globulin, free testosterone, androstenedione and dehydroepiandrosterone sulfate. Taller height was associated with lower concentrations of androstenedione, testosterone, free testosterone and sex hormone-binding globulin and higher concentrations of androstanediol glucuronide. Current smoking was associated with higher concentrations of androstenedione, sex hormone-binding globulin and testosterone. Alcohol consumption was associated with higher concentrations of dehydroepiandrosterone sulfate, androstenedione and androstanediol glucuronide. East Asians had lower concentrations of androstanediol glucuronide and African Americans had higher concentrations of estrogens. Education and marital status were modestly associated with a small number of hormones.ConclusionCirculating sex hormones in men are strongly associated with age and body mass index, and to a lesser extent with smoking status and alcohol consumption.

Endometrial cancer (EC) contributes substantially to total burden of cancer morbidity and mortality in the United States. Family history is a known risk factor for EC, thus genetic factors may play a role in EC pathogenesis. Three previous genome-wide association studies (GWAS) have found only one locus associated with EC, suggesting that common variants with large effects may not contribute greatly to EC risk. Alternatively, we hypothesize that rare variants may contribute to EC risk. We conducted an exome-wide association study (EXWAS) of EC using the Infinium HumanExome BeadChip in order to identify rare variants associated with EC risk. We successfully genotyped 177,139 variants in a multiethnic population of 1,055 cases and 1,778 controls from four studies that were part of the Epidemiology of Endometrial Cancer Consortium (E2C2). No variants reached global significance in the study, suggesting that more power is needed to detect modest associations between rare genetic variants and risk of EC.

Pooled analyses among whites and East Asians have demonstrated positive associations between all-cause mortality and body mass index (BMI), but studies of African Americans have yielded less consistent results. We examined the association between BMI and all-cause mortality in a sample of African Americans pooled from seven prospective cohort studies: NIH-AARP, 1995-2009; Adventist Health Study 2, 2002-2008; Black Women's Health Study, 1995-2009; Cancer Prevention Study II, 1982-2008; Multiethnic Cohort Study, 1993-2007; Prostate, Lung, Colorectal and Ovarian Screening Trial, 1993-2009; Southern Community Cohort Study, 2002-2009. 239,526 African Americans (including 100,175 never smokers without baseline heart disease, stroke, or cancer), age 30-104 (mean 52) and 71% female, were followed up to 26.5 years (mean 11.7). Hazard ratios (HR) and 95% confidence intervals (CI) for mortality were derived from multivariate Cox proportional hazards models. Among healthy, never smokers (11,386 deaths), HRs (CI) for BMI 25-27.4, 27.5-29.9, 30-34.9, 35-39.9, 40-49.9, and 50-60 kg/m(2) were 1.02 (0.92-1.12), 1.06 (0.95-1.18), 1.32 (1.18-1.47), 1.54 (1.29-1.83), 1.93 (1.46-2.56), and 1.93 (0.80-4.69), respectively among men and 1.06 (0.99-1.15), 1.15 (1.06-1.25), 1.24 (1.15-1.34), 1.58 (1.43-1.74), 1.80 (1.60-2.02), and 2.31 (1.74-3.07) respectively among women (reference category 22.5-24.9). HRs were highest among those with the highest educational attainment, longest follow-up, and for cardiovascular disease mortality. Obesity was associated with a higher risk of mortality in African Americans, similar to that observed in pooled analyses of whites and East Asians. This study provides compelling evidence to support public health efforts to prevent excess weight gain and obesity in African Americans.

Pathway analysis of genome-wide association studies (GWAS) offer a unique opportunity to collectively evaluate genetic variants with effects that are too small to be detected individually. We applied a pathway analysis to a bladder cancer GWAS containing data from 3,532 cases and 5,120 controls of European background (n = 5 studies). Thirteen hundred and ninety-nine pathways were drawn from five publicly available resources (Biocarta, Kegg, NCI-PID, HumanCyc, and Reactome), and we constructed 22 additional candidate pathways previously hypothesized to be related to bladder cancer. In total, 1421 pathways, 5647 genes and ∼90,000 SNPs were included in our study. Logistic regression model adjusting for age, sex, study, DNA source, and smoking status was used to assess the marginal trend effect of SNPs on bladder cancer risk. Two complementary pathway-based methods (gene-set enrichment analysis [GSEA], and adapted rank-truncated product [ARTP]) were used to assess the enrichment of association signals within each pathway. Eighteen pathways were detected by either GSEA or ARTP at P≤0.01. To minimize false positives, we used the I(2) statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways ('Aromatic amine metabolism' [P(GSEA) = 0.0100, P(ARTP) = 0.0020], 'NAD biosynthesis' [P(GSEA) = 0.0018, P(ARTP) = 0.0086], 'NAD salvage' [P(ARTP) = 0.0068], 'Clathrin derived vesicle budding' [P(ARTP) = 0.0018], 'Lysosome vesicle biogenesis' [P(GSEA) = 0.0023, P(ARTP)

A recent ovarian cancer genome-wide association study (GWAS) identified a locus on 9p22 associated with reduced ovarian cancer risk. The single nucleotide polymorphism (SNP) markers localize to the BNC2 gene, which has been associated with ovarian development.We analyzed the association of 9p22 SNPs with transvaginal ultrasound (TVU) screening results and CA-125 blood levels from participants without ovarian cancer in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO); 1,106 women with adequate ultrasound screening results and available genotyping information were included in the study.We observed a significantly increased risk of abnormal suspicious TVU results for seven SNPs on 9p22, with odds ratios between 1.68 (95% CI: 1.04-2.72) for rs4961501 and 2.10 (95% CI: 1.31-3.38) for rs12379183. Associations were restricted to abnormal suspicious findings at the first TVU screen. We did not observe an association between 9p22 SNPs and CA-125 levels.Our findings suggest that 9p22 SNPs, which were found to be associated with decreased risk of ovarian cancer in a recent GWAS, are associated with sonographically detectable ovarian abnormalities. Our results corroborate the relevance of the 9p22 locus for ovarian biology. Further studies are required to understand the complex relationship between screening abnormalities and ovarian carcinogenesis and to evaluate whether this locus can influence the risk stratification of ovarian cancer screening.