Considering the Role of Adaptive Evolution in Models of the Ocean and Climate System

Numerical models have been highly successful in simulating global carbon and nutrient cycles in today's ocean, together with observed spatial and temporal patterns of chlorophyll and plankton biomass at the surface. With this success has come some confidence in projecting the century-scale response to continuing anthropogenic warming. There is also increasing interest in using such models to understand the role of plankton ecosystems in past oceans. However, today's marine environment is the product of billions of years of continual evolution-a process that continues today. In this paper, we address the questions of whether an assumption of species invariance is sufficient, and if not, under what circumstances current model projections might break down. To do this, we first identify the key timescales and questions asked of models. We then review how current marine ecosystem models work and what alternative approaches are available to account for evolution. We argue that for timescales of climate change overlapping with evolutionary timescales, accounting for evolution may to lead to very different projected outcomes regarding the timescales of ecosystem response and associated global biogeochemical cycling. This is particularly the case for past extinction events but may also be true in the future, depending on the eventual degree of anthropogenic disruption. The discipline of building new numerical models that incorporate evolution is also hugely beneficial in itself, as it forces us to question what we know about adaptive evolution, irrespective of its quantitative role in any specific event or environmental changes.

Protocol of a two arm randomised, multi-centre, 12-month controlled trial: evaluating the impact of a Cognitive Behavioural Therapy (CBT)-based intervention Supporting UPtake and Adherence to antiretrovirals (SUPA) in adults with HIV

Background

Delay to start antiretroviral therapy (ART) and nonadherence compromise the health and wellbeing of people living with HIV (PLWH), raise the cost of care and increase risk of transmission to sexual partners. To date, interventions to improve adherence to ART have had limited success, perhaps because they have failed to systematically elicit and address both perceptual and practical barriers to adherence. The primary aim of this study is to determine the efficacy of the Supporting UPtake and Adherence (SUPA) intervention.

Methods

This study comprises 2 phases. Phase 1 is an observational cohort study, in which PLWH who are ART naïve and recommended to take ART by their clinician complete a questionnaire assessing their beliefs about ART over 12 months. Phase 2 is a randomised controlled trial (RCT) nested within the observational cohort study to investigate the effectiveness of the SUPA intervention on adherence to ART. PLWH at risk of nonadherence (based on their beliefs about ART) will be recruited and randomised 1:1 to the intervention (SUPA intervention + usual care) and control (usual care) arms. The SUPA intervention involves 4 tailored treatment support sessions delivered by a Research Nurse utilising a collaborative Cognitive Behavioural Therapy (CBT) and Motivational Interviewing (MI) approach. Sessions are tailored to individual needs and preferences based on the individual patient’s perceptions and practical barriers to ART. An animation series and intervention manual have been developed to communicate a rationale for the personal necessity for ART and illustrate concerns and potential solutions. The primary outcome is adherence to ART measured using Medication Event Monitoring System (MEMS). Three hundred seventy-two patients will be sufficient to detect a 15% difference in adherence with 80% power and an alpha of 0.05. Costs will be compared between intervention and control groups. Costs will be combined with the primary outcome in cost-effectiveness analyses. Quality adjusted life-years (QALYs) will also be estimated over the follow-up period and used in the analyses.

Discussion

The findings will enable patients, healthcare providers and policy makers to make informed decisions about the value of the SUPA intervention.

Trial registration

The trial was retrospectively registered 21/02/2014, ISRCTN35514212.

Electronic supplementary material

The online version of this article (10.1186/s12889-019-6893-z) contains supplementary material, which is available to authorized users.

Charmonia in moving frames

Lattice simulation of charmonium resonances with non-zero momentum provides additional information on the two-meson scattering matrices. However, the reduced rotational symmetry in a moving frame renders a number of states with different JP in the same lattice irreducible representation. The identification of JP for these states is particularly important, since quarkonium spectra contain a number of states with different JP in a relatively narrow energy region. Preliminary results concerning spin-identification are presented in relation to our study of charmonium resonances in flight on the Nf = 2 + 1 CLS ensembles.

Transport and potential attenuation of nitrogen in shallow groundwaters in the lower Rangitikei catchment, New Zealand

Intensive agricultural activities are generally associated with nitrogen leaching from agricultural soils, and this nitrogen has the potential to percolate and contaminate groundwater and surface waters. We assessed surface water and groundwater interactions, and nitrogen leaching and its potential attenuation in shallow groundwater in the lower Rangitikei River catchment (832km²), New Zealand. We combined regional- and local-scale field surveys and experiments, nutrient budget modelling, and hydraulic and geochemical methods, to gain an insight into leaching, transformation and transport of nitrogen via groundwaters to the river in the study area. Concurrent river flow gaugings (in January 2015) and a piezometric map, developed from measured depths to groundwater in 110 bores (in October 2014), suggest groundwater discharges to the Rangitikei River in the upper parts of the study area, while there is groundwater recharge near the coast. The groundwater redox characterisation, based on sampling and analysis of 15 mostly shallow bores (<30m below ground level (bgl)), suggests groundwater across the lower Rangitikei catchment in general is under anoxic/reduced conditions. The groundwater typically has low dissolved oxygen (DO) concentrations (<1mg/L), suggesting the subsurface environment is conducive to potential attenuation by 'denitrification' of NO₃-N in groundwater. We further measured NO₃-N attenuation in shallow groundwater piezometers (3-6mbgl) using single-well push-pull tests. We found generally low levels (<0.5mg/L) of NO₃-N in shallow groundwater piezometers (>5mbgl), despite being installed under intensive land uses, such as dairying and cropping. Our in-field push-pull tests showed NO₃-N reduction at four shallow groundwater piezometers, with the rates of reduction varying from 0.04mgNL^-1h^-1 to 1.57mgNL^-1h^-1. This highlights the importance of a sound understanding of not only the sources, but also transport and transformation, or fate, of nutrients leached from farms, to mitigate the likely impacts of land use on water quality and ecosystem health in agricultural catchments.

Accuracy of self-report of HIV viral load among people with HIV on antiretroviral treatment

OBJECTIVES

The aim of the study was to assess, among people living with HIV, knowledge of their latest HIV viral load (VL) and CD4 count.

METHODS

Agreement between self-report and clinic record was assessed among 2771 HIV-diagnosed individuals on antiretroviral treatment (ART) in the UK Antiretrovirals, Sexual Transmission Risk and Attitudes Study (2011-2012). A confidential self-completed questionnaire collected information on demographic, socioeconomic, HIV-related and health-related factors. Participants were asked to self-report their latest VL [undetectable (≤ 50 copies/mL), detectable (> 50 copies/mL) or "don't know"] and CD4 count (< 200, 200-350, 351-500 or > 500 cells/μL, or "don't know"). Latest clinic-recorded VL and CD4 count were documented.

RESULTS

Of 2678 participants on ART, 434 (16.2%) did not accurately report whether their VL was undetectable. Of 2334 participants with clinic-recorded VL ≤ 50 copies/mL, 2061 (88.3%) correctly reported undetectable VL; 49 (2.1%) reported detectable VL; 224 (9.6%) did not know their VL. Of 344 participants with clinic-recorded VL > 50 copies/mL, 183 (53.2%) correctly reported detectable VL; 76 (22.1%) reported undetectable VL; 85 (24.7%) did not know their VL. Of 2137 participants who reported undetectable VL, clinic-recorded VL was ≤ 50 copies/mL for 2061 (96.4%) and <1000 copies/mL for 2122 (99.3%). In analyses adjusted for gender/sexual orientation, ethnicity, age and time since starting ART, factors strongly associated with inaccurate self-report of VL (including "don't know") included socioeconomic disadvantage [prevalence ratio (95% CI) for "not" vs. "always" having enough money for basic needs: 2.4 (1.9, 3.1)], poor English fluency [3.5 (2.4, 5.1) vs. UK born], nondisclosure of HIV status [1.7 (1.3, 2.1)], ART nonadherence [2.1 (1.7, 2.7) for three or more missed doses vs. none in the past 2 weeks] and depressive symptoms (PHQ-9 score ≥ 10) [1.9 (1.6, 2.2)]. Overall, 612 (22.9%) of 2667 participants on ART did not accurately self-report whether or not their CD4 count was ≤ 350 cells/μL.

CONCLUSIONS

There is a high level of accuracy of a self-report of undetectable VL in people on ART in the UK. Overall, accurate knowledge of personal VL level varied according to demographic, socioeconomic, HIV-related and health-related factors. Active identification of people who may benefit from increased levels of support and engagement in care is important.

Microbiological problems and biofilms associated with Mycobacterium chimaera in heater-cooler units used for cardiopulmonary bypass

The role of heater-cooler units (HCUs) in the transmission of Mycobacterium chimaera during open heart surgery has been recognized since 2013. Subsequent investigations uncovered a remarkable global outbreak reflecting the wide distribution of implicated devices. HCUs are an essential component of cardiopulmonary bypass operations and their withdrawal would severely affect capacity for life-saving cardiac surgery. However, studies have demonstrated that many HCUs are contaminated with a wide range of micro-organisms, including M. chimaera and complex biofilms. Whole genome sequencing of M. chimaera isolates recovered from one manufacturer's HCUs, worldwide, has demonstrated a high level of genetic similarity, for which the most plausible hypothesis is a point source contamination of the devices. Dissemination of bioaerosols through breaches in the HCU water tanks is the most likely route of transmission and airborne bacteria have been shown to have reached the surgical field even with the use of ultraclean theatre ventilation. Controlling the microbiological quality of the water circulating in HCUs and reducing biofilm formation has been a major challenge for many hospitals. However, enhanced decontamination strategies have been recommended by manufacturers, and, although they are not always effective in eradicating M. chimaera from HCUs, UK hospitals have not reported any new cases of M. chimaera infection since implementing these mitigation strategies. Water safety groups in hospitals should be aware that water in medical devices such as HCUs may act as a vector in the transmission of potentially fatal water-borne infections.

Age, time living with diagnosed HIV infection, and self-rated health

OBJECTIVES

An increasing proportion of people living with HIV are older adults, who may require specialized care. Adverse physical and psychological effects of HIV infection may be greatest among older people or those who have lived longer with HIV.

METHODS

The ASTRA study is a cross-sectional questionnaire study of 3258 HIV-diagnosed adults (2248 men who have sex with men, 373 heterosexual men and 637 women) recruited from UK clinics in 2011-2012. Associations of age group with physical symptom distress (significant distress for at least one of 26 symptoms), depression and anxiety symptoms (scores ≥ 10 on PHQ-9 and GAD-7, respectively), and health-related functional problems (problems on at least one of three domains of the Euroqol 5D-3L)) were assessed, adjusting for time with diagnosed HIV infection, gender/sexual orientation and ethnicity.

RESULTS

The age distribution of participants was: < 30 years, 5%; 30-39 years, 23%; 40-49 years, 43%; 50-59 years, 22%; and ≥ 60 years, 7%. Overall prevalences were: physical symptom distress, 56%; depression symptoms, 27%; anxiety symptoms, 22%; functional problems, 38%. No trend was found in the prevalence of physical symptom distress with age [adjusted odds ratio (OR) for trend across age groups, 0.96; 95% confidence interval (CI) 0.89, 1.04; P = 0.36]. The prevalence of depression and anxiety symptoms decreased with age [adjusted OR 0.86 (95% CI 0.79, 0.94; P = 0.001) and adjusted OR 0.85 (95% CI 0.77, 0.94; P = 0.001), respectively], while that of functional problems increased (adjusted OR 1.28; 95% CI 1.17, 1.39; P < 0.001). In contrast, a longer time with diagnosed HIV infection was strongly and independently associated with a higher prevalence of symptom distress, depression symptoms, anxiety symptoms, and functional problems (P < 0.001 for trends, adjusted analysis).

CONCLUSIONS

Among people living with HIV, although health-related functional problems were more common with older age, physical symptom distress was not, and mental health was more favourable. These results suggest that a longer time with diagnosed HIV infection, rather than age, is the dominating factor contributing to psychological morbidity and lower quality of life.