Parametric uncertainty in complex environmental models: a cheap emulation approach for models with high-dimensional output

In order to understand underlying processes governing environmental and physical processes, and predict future outcomes, a complex computer model is frequently required to simulate these dynamics. However there is inevitably uncertainty related to the exact parametric form or the values of such parameters to be used when developing these simulators, with \emph{ranges} of plausible values prevalent in the literature. Systematic errors introduced by failing to account for these uncertainties have the potential to have a large effect on resulting estimates in unknown quantities of interest. Due to the complexity of these types of models, it is often unfeasible to run large numbers of training runs that are usually required for full statistical emulators of the environmental processes. We therefore present a method for accounting for uncertainties in complex environmental simulators without the need for very large numbers of training runs and illustrate the method through an application to the Met Office's atmospheric transport model NAME. We conclude that there are two principle parameters that are linked with variability in NAME outputs, namely the free tropospheric turbulence parameter and particle release height. Our results suggest the former should be significantly larger than is currently implemented as a default in NAME, whilst changes in the latter most likely stem from inconsistencies between the model specified ground height at the observation locations and the true height at this location. Estimated discrepancies from independent data are consistent with the discrepancy between modelled and true ground height

Sticky stuff : redefining bedform prediction in modern and ancient environments

This work was funded by the UK Natural Environment Research Council (NERC) under the COHBED project (NE/1027223/1). Paterson was funded by the Marine Alliance for Science and Technology for Scotland (MASTS).The dimensions and dynamics of subaqueous bedforms are well known for cohesionless sediments. However, the effect of physical cohesion imparted by cohesive clay within mixed sand-mud substrates has not been examined, despite its recognized influence on sediment stability. Here we present a series of controlled laboratory experiments to establish the influence of substrate clay content on subaqueous bedform dynamics within mixtures of sand and clay exposed to unidirectional flow. The results show that bedform dimensions and steepness decrease linearly with clay content, and comparison with existing predictors of bedform dimensions, established within cohesionless sediments, reveals significant over-prediction of bedform size for all but the lowermost clay contents examined. The profound effect substrate clay content has on bedform dimensions has a number of important implications for interpretation in a range of modern and ancient environments, including reduced roughness and bedform heights in estuarine systems and the often cited lack of large dune cross-sets in turbidites. The results therefore offer a step change in our understanding of bedform formation and dynamics in these, and many other, sedimentary environments.Publisher PDFPeer reviewe

Settling velocity and mass settling flux of flocculated estuarine sediments

New formulations are presented for the settling velocity and mass settling flux (the product of settling velocity and sediment concentration) of flocculated estuarine mud. Physics-based formulae for these are developed based on assumptions of a two-class floc population (microflocs and Macroflocs) in quasi-equilibrium with the flow. The settling velocities of microflocs and Macroflocs are related to floc size and density via the Kolmogorov microscale as a function of turbulent shear-stress and sediment concentration, including height-dependence and floc-density-dependence. Coefficients in the formulae are calibrated against an existing large data-set of in situ observations of floc size and settling velocity from Northern European estuaries. Various measures of performance show that the resulting formulae achieve an improved level of agreement with data compared with other published prediction methods. The new formulae, with the original calibration coefficients, perform well in tests against independent measurements made in two estuaries

Quantifying the 3D structure and function of porosity and pore space in natural sediment flocs

Purpose: Flocculated cohesive suspended sediments (flocs) play an important role in all aquatic environments, facilitating the transport and deposition of sediment and associated contaminants with consequences for aquatic health, material fluxes, and morphological evolution. Accurate modelling of the transport and behaviour of these sediments is critical for a variety of activities including fisheries, aquaculture, shipping, and waste and pollution management and this requires accurate measurement of the physical properties of flocs including porosity. Methods: Despite the importance of understanding floc porosity, measurement approaches are indirect or inferential. Here, using μCT, a novel processing and analysis protocol, we directly quantify porosity in natural sediment flocs. For the first time, the complexity of floc pore spaces is observed in 3-dimensions, enabling the identification and quantification of important pore space and pore network characteristics, namely 3D pore diameter, volume, shape, tortuosity, and connectivity. Results: We report on the complexity of floc pore space and differentiate effective and isolated pore space enabling new understanding of the hydraulic functioning of floc porosity. We demonstrate that current methodological approaches are overestimating floc porosity by c. 30%. Conclusion: These new data have implications for our understanding of the controls on floc dynamics and the function of floc porosity and can improve the parameterisation of current cohesive sediment transport models

UK emissions of the greenhouse gas nitrous oxide

Signatories of the Kyoto Protocol are obliged to submit annual accounts of their anthropogenic greenhouse gas emissions, which include nitrous oxide (N2O). Emissions from the sectors industry (3.8 Gg), energy (14.4 Gg), agriculture (86.8 Gg), wastewater (4.4 Gg), land use, land-use change and forestry (2.1 Gg) can be calculated by multiplying activity data (i.e. amount of fertilizer applied, animal numbers) with simple emission factors (Tier 1 approach), which are generally applied across wide geographical regions. The agricultural sector is the largest anthropogenic source of N2O in many countries and responsible for 75 per cent of UK N2O emissions. Microbial N2O production in nitrogen-fertilized soils (27.6 Gg), nitrogen-enriched waters (24.2 Gg) and manure storage systems (6.4 Gg) dominate agricultural emission budgets. For the agricultural sector, the Tier 1 emission factor approach is too simplistic to reflect local variations in climate, ecosystems and management, and is unable to take into account some of the mitigation strategies applied. This paper reviews deviations of observed emissions from those calculated using the simple emission factor approach for all anthropogenic sectors, briefly discusses the need to adopt specific emission factors that reflect regional variability in climate, soil type and management, and explains how bottom-up emission inventories can be verified by top-down modelling

CASSETTE—clindamycin adjunctive therapy for severe Staphylococcus aureus treatment evaluation: Study protocol for a randomised controlled trial

Background Exotoxins are important virulence factors in Staphylococcus aureus. Clindamycin, a protein synthesis inhibitor antibiotic, is thought to limit exotoxin production and improve outcomes in severe S. aureus infections. However, randomised prospective data to support this are lacking. Methods An open-label, multicentre, randomised controlled trial (RCT) will compare outcome differences in severe S. aureus infection between standard treatment (flucloxacillin/cefazolin in methicillin-susceptible S. aureus; and vancomycin/daptomycin in methicillin-resistant S. aureus) and standard treatment plus an additional clindamycin given for 7 days. We will include a minimum of 60 participants (both adult and children) in the pilot study. Participants will be enrolled within 72 h of an index culture. Severe infections will include septic shock, necrotising pneumonia, or multifocal and non-contiguous skin and soft tissue/osteoarticular infections. Individuals who are immunosuppressed, moribund, with current severe diarrhoea or Clostridiodes difficile infection, pregnant, and those with anaphylaxis to β-lactams or lincosamides will be excluded. The primary outcomes measure is the number of days alive and free (1 or 0) of systemic inflammatory response syndrome (SIRS) within the first 14 days post randomisation. The secondary outcomes measure will include all-cause mortality at 14, 42, and 90 days, time to resolution of SIRS, proportion with microbiological treatment failure, and rate of change of C-reactive protein over time. Impacts of inducible clindamycin resistance, strain types, methicillin susceptibility, and presence of various exotoxins will also be analysed. Discussion This study will assess the effect of adjunctive clindamycin on patient-centred outcomes in severe, toxin-mediated S. aureus infections. The pilot study will provide feasibility for a much larger RCT. Trial registration Australian New Zealand Clinical Trials Registry, ACTRN12617001416381p. Registered on 6 October 2017

Information-Geometric Indicators of Chaos in Gaussian Models on Statistical Manifolds of Negative Ricci Curvature

A new information-geometric approach to chaotic dynamics on curved statistical manifolds based on Entropic Dynamics (ED) is proposed. It is shown that the hyperbolicity of a non-maximally symmetric 6N-dimensional statistical manifold M_{s} underlying an ED Gaussian model describing an arbitrary system of 3N degrees of freedom leads to linear information-geometric entropy growth and to exponential divergence of the Jacobi vector field intensity, quantum and classical features of chaos respectively.Comment: 8 pages, final version accepted for publicatio

A Web-Based Cognitive Bias Modification Intervention (Re-train Your Brain) for Emerging Adults With Co-occurring Social Anxiety and Hazardous Alcohol Use: Protocol for a Multiarm Randomized Controlled Pilot Trial

BACKGROUND: Alcohol use and anxiety disorders commonly co-occur, resulting in a more severe clinical presentation and poorer response to treatment. Research has shown that approach bias modification (ApBM) and interpretation bias modification (IBM) cognitive retraining interventions can be efficacious adjunctive treatments that improve outcomes for alcohol use and social anxiety, respectively. However, the acceptability, feasibility, and clinical utility of combining ApBM and IBM programs to optimize treatments among comorbid samples are unknown. It is also unclear whether integrating ApBM and IBM within each training session or alternating them between each session is more acceptable and efficacious. OBJECTIVE: This paper describes the protocol for a randomized controlled pilot trial investigating the feasibility, acceptability, and preliminary efficacy of the Re-train Your Brain intervention-an adjunct web-based ApBM+IBM program-among a clinical sample of emerging adults with hazardous alcohol use and social anxiety. METHODS: The study involves a three-arm randomized controlled pilot trial in which treatment-seeking emerging adults (18-30 years) with co-occurring hazardous alcohol use and social anxiety will be individually randomized to receive the Re-train Your Brain integrated program, delivered with 10 biweekly sessions focusing on both social anxiety and alcohol each week, plus treatment as usual (TAU; ie, the model of care provided in accordance with standard practice at their service; n=30); the Re-train Your Brain alternating program, delivered with 10 biweekly sessions focusing on social anxiety one week and alcohol the next week, plus TAU (n=30); or TAU only (n=30). Primary outcomes include feasibility (uptake, follow-up rates, treatment adherence, attrition, and adverse events) and acceptability (system usability, client satisfaction, user experience, and training format preference). Secondary efficacy outcomes include changes in alcohol approach and interpretation biases, social anxiety, and alcohol use (eg, drinks per day, binge drinking, drinking motives, severity of dependence, and cravings). The primary end point will be posttreatment (6 weeks postbaseline), with a secondary end point at 3 months postbaseline. Descriptive statistics will be conducted for primary outcomes, whereas intention-to-treat, multilevel mixed effects analysis for repeated measures will be performed for secondary outcomes. RESULTS: This study is funded from 2019 to 2023 by Australian Rotary Health. Recruitment is expected to be completed by mid-2022 to late 2022, with follow-ups completed by early 2023. CONCLUSIONS: This study will be the first to evaluate whether an ApBM+IBM program is acceptable to treatment-seeking, emerging adults and whether it can be feasibly delivered via the web, in settings where it will ultimately be used (eg, at home). The findings will broaden our understanding of the types of programs that emerging adults will engage with and whether the program may be an efficacious treatment option for this comorbidity. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry ACTRN12620001273976; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=364131. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/28667