A network approach for managing ecosystem services and improving food and nutrition security on smallholder farms

1. Smallholder farmers are some of the poorest and most food insecure people on Earth. Their high nutritional and economic reliance on home--grown produce makes them particularly vulnerable to environmental stressors such as pollinator loss or climate change which threaten agricultural productivity. Improving smallholder agriculture in a way that is environmentally sustainable and resilient to climate change is a key challenge of the 21st century. 2. Ecological intensification, whereby ecosystem services are managed to increase agricultural productivity, is a promising solution for smallholders. However, smallholder farms are complex socio-ecological systems with a range of social, ecological and environmental factors interacting to influence ecosystem service provisioning. To truly understand the functioning of a smallholder farm and identify the most effective management options to support household food and nutrition security, a holistic, systems-based understanding is required. 3. In this paper, we propose a network approach to understand, visualise and model the complex interactions occurring among wild species, crops and people on smallholder farms. Specifically, we demonstrate how networks may be used to (a) identify wild species with a key role in supporting, delivering or increasing the resilience of an ecosystem service; (b) quantify the value of an ecosystem service in a way that is relevant to the food and nutrition security of smallholders; and (c) understand the social interactions that influence the management of shared ecosystem services. 4. Using a case study based on data from rural Nepal, we demonstrate how this framework can be used to connect wild plants, pollinators and crops to key nutrients consumed by humans. This allows us to quantify the nutritional value of an ecosystem service and identify the wild plants and pollinators involved in its provision, as well as providing a framework to predict the effects of environmental change on human nutrition. 5. Our framework identifies mechanistic links between ecosystem services and the nutrients consumed by smallholder farmers and highlights social factors that may influence the management of these services. Applying this framework to smallholder farms in a range of socio-ecological contexts may provide new, sustainable and equitable solutions to smallholder food and nutrition security.Peer reviewe

Pan-cancer proteogenomics connects oncogenic drivers to functional states

Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here, our multi-omics pan-cancer analysis uncovers insights into the impacts of cancer drivers by identifying their significant cis-effects and distal trans-effects quantified at the RNA, protein, and phosphoprotein levels. Salient observations include the association of point mutations and copy-number alterations with the rewiring of protein interaction networks, and notably, most cancer genes converge toward similar molecular states denoted by sequence-based kinase activity profiles. A correlation between predicted neoantigen burden and measured T cell infiltration suggests potential vulnerabilities for immunotherapies. Patterns of cancer hallmarks vary by polygenic protein abundance ranging from uniform to heterogeneous. Overall, our work demonstrates the value of comprehensive proteogenomics in understanding the functional states of oncogenic drivers and their links to cancer development, surpassing the limitations of studying individual cancer types

Estimating the contribution of key populations towards HIV transmission in South Africa

INTRODUCTION: In generalized epidemic settings, there is insufficient understanding of how the unmet HIV prevention and treatment needs of key populations (KPs), such as female sex workers (FSWs) and men who have sex with men (MSM), contribute to HIV transmission. In such settings, it is typically assumed that HIV transmission is driven by the general population. We estimated the contribution of commercial sex, sex between men, and other heterosexual partnerships to HIV transmission in South Africa (SA). METHODS: We developed the "Key-Pop Model"; a dynamic transmission model of HIV among FSWs, their clients, MSM, and the broader population in SA. The model was parameterized and calibrated using demographic, behavioural and epidemiological data from national household surveys and KP surveys. We estimated the contribution of commercial sex, sex between men and sex among heterosexual partnerships of different sub-groups to HIV transmission over 2010 to 2019. We also estimated the efficiency (HIV infections averted per person-year of intervention) and prevented fraction (% IA) over 10-years from scaling-up ART (to 81% coverage) in different sub-populations from 2020. RESULTS: Sex between FSWs and their paying clients, and between clients with their non-paying partners contributed 6.9% (95% credibility interval 4.5% to 9.3%) and 41.9% (35.1% to 53.2%) of new HIV infections in SA over 2010 to 2019 respectively. Sex between low-risk groups contributed 59.7% (47.6% to 68.5%), sex between men contributed 5.3% (2.3% to 14.1%) and sex between MSM and their female partners contributed 3.7% (1.6% to 9.8%). Going forward, the largest population-level impact on HIV transmission can be achieved from scaling up ART to clients of FSWs (% IA = 18.2% (14.0% to 24.4%) or low-risk individuals (% IA = 20.6% (14.7 to 27.5) over 2020 to 2030), with ART scale-up among KPs being most efficient. CONCLUSIONS: Clients of FSWs play a fundamental role in HIV transmission in SA. Addressing the HIV prevention and treatment needs of KPs in generalized HIV epidemics is central to a comprehensive HIV response

Assessing Network Scale-up Estimates for Groups Most at Risk of HIV/AIDS: Evidence From a Multiple-Method Study of Heavy Drug Users in Curitiba, Brazil

One of the many challenges hindering the global response to the human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) epidemic is the difficulty of collecting reliable information about the populations most at risk for the disease. Thus, the authors empirically assessed a promising new method for estimating the sizes of most at-risk populations: the network scale-up method. Using 4 different data sources, 2 of which were from other researchers, the authors produced 5 estimates of the number of heavy drug users in Curitiba, Brazil. The authors found that the network scale-up and generalized network scale-up estimators produced estimates 5–10 times higher than estimates made using standard methods (the multiplier method and the direct estimation method using data from 2004 and 2010). Given that equally plausible methods produced such a wide range of results, the authors recommend that additional studies be undertaken to compare estimates based on the scale-up method with those made using other methods. If scale-up-based methods routinely produce higher estimates, this would suggest that scale-up-based methods are inappropriate for populations most at risk of HIV/AIDS or that standard methods may tend to underestimate the sizes of these populations

Use of AUDIT, and measures of drinking frequency and patterns to detect associations between alcohol and sexual behaviour in male sex workers in Kenya

Background: Previous research has linked alcohol use with an increased number of sexual partners, inconsistent condom use and a raised incidence of sexually transmitted infections (STIs). However, alcohol measures have been poorly standardised, with many ill-suited to eliciting, with adequate precision, the relationship between alcohol use and sexual risk behaviour. This study investigates which alcohol indicator - single-item measures of frequency and patterns of drinking (> = 6 drinks on 1 occasion), or the Alcohol Use Disorders Identification Test (AUDIT) - can detect associations between alcohol use and unsafe sexual behaviour among male sex workers. Methods: A cross-sectional survey in 2008 recruited male sex workers who sell sex to men from 65 venues in Mombasa district, Kenya, similar to a 2006 survey. Information was collected on socio-demographics, substance use, sexual behaviour, violence and STI symptoms. Multivariate models examined associations between the three measures of alcohol use and condom use, sexual violence, and penile or anal discharge. Results: The 442 participants reported a median 2 clients/week (IQR = 1-3), with half using condoms consistently in the last 30 days. Of the approximately 70% of men who drink alcohol, half (50.5%) drink two or more times a week. Binge drinking was common (38.9%). As defined by AUDIT, 35% of participants who drink had hazardous drinking, 15% harmful drinking and 21% alcohol dependence. Compared with abstinence, alcohol dependence was associated with inconsistent condom use (AOR = 2.5, 95% CI = 1.3-4.6), penile or anal discharge (AOR = 1.9, 95% CI = 1.0-3.8), and two-fold higher odds of sexual violence (AOR = 2.0, 95% CI = 0.9-4.9). Frequent drinking was associated with inconsistent condom use (AOR = 1.8, 95% CI = 1.1-3.0) and partner number, while binge drinking was only linked with inconsistent condom use (AOR = 1.6, 95% CI = 1.0-2.5). Conclusions: Male sex workers have high levels of hazardous and harmful drinking, and require alcohol-reduction interventions. Compared with indicators of drinking frequency or pattern, the AUDIT measure has stronger associations with inconsistent condom use, STI symptoms and sexual violence. Increased use of the AUDIT tool in future studies may assist in delineating with greater precision the explanatory mechanisms which link alcohol use, drinking contexts, sexual behaviours and HIV transmission

Limited Awareness and Low Immediate Uptake of Pre-Exposure Prophylaxis among Men Who Have Sex with Men Using an Internet Social Networking Site

Background: In 2010, the iPrEx trial demonstrated that oral antiretroviral pre-exposure prophylaxis (PrEP) reduced the risk of HIV acquisition among high-risk men who have sex with men (MSM). The impact of iPrEx on PrEP knowledge and actual use among at-risk MSM is unknown. Online surveys were conducted to assess PrEP awareness, interest and experience among at-risk MSM before and after iPrEx, and to determine demographic and behavioral factors associated with these measures. Methods and Findings: Cross-sectional, national, internet-based surveys were administered to U.S. based members of the most popular American MSM social networking site 2 months before (n = 398) and 1 month after (n = 4 558) publication of iPrEx results. Comparisons were made between these samples with regards to PrEP knowledge, interest, and experience. Data were collected on demographics, sexual risk, and experience with post-exposure prophylaxis (PEP). Regression analyses were performed to identify factors associated with PrEP awareness, interest, and experience post-iPrEx. Most participants were white, educated, and indicated high-risk sexual behaviors. Awareness of PrEP was limited pre- and post-iPrEx (13% vs. 19%), whereas interest levels after being provided with a description of PrEP remained high (76% vs. 79%). PrEP use remained uncommon (0.7% vs. 0.9%). PrEP use was associated with PEP awareness (OR 7.46; CI 1.52–36.6) and PEP experience (OR 34.2; CI 13.3–88.4). PrEP interest was associated with older age (OR 1.01; CI 1.00–1.02), unprotected anal intercourse with ≥1 male partner in the prior 3 months (OR 1.40; CI 1.10–1.77), and perceiving oneself at increased risk for HIV acquisition (OR 1.20; CI 1.13–1.27). Conclusions: Among MSM engaged in online networking, awareness of PrEP was limited 1 month after the iPrEx data were released. Utilization was low, although some MSM who reported high-risk behaviors were interested in using PrEP. Studies are needed to understand barriers to PrEP utilization by at-risk MSM