How integrative modelling can break down disciplinary silos

This paper has been published in a peer-reviewed journal as: Kragt, M.E., Robson, B.J. & Macleod, C.J.A. (2013) Modellers’ roles in structuring integrative research projects. Environmental Modelling & Software, 39(1): 322-330. DOI: 10.1016/j.envsoft.2012.06.015Environmental modelling, Interdisciplinary research, Transdisciplinarity, Integration, Research Methods/ Statistical Methods, Q57, Y80, Z19,

A Field Study on the Stability of Road Cut Slopes in Nepal

The density of Nepal’s road network has more than tripled in the last three decades. This growth has been rapid, extensive and in places haphazard, occurring on both the local and strategic road networks, and has resulted in the widespread failure of road cut slopes throughout Nepal. To further understand this effect, field assessments were carried out along roads of different governing grade in Nepal, focusing on the stability of cut slopes and effectiveness of stabilisation measures adopted. This paper summarises the key findings of this study. Although there are multiple guidelines from the Government of Nepal with recommendations on the design and construction of road cut slopes and stabilisation measures, the cut slopes were commonly found to be excavated to steeper inclinations than advised in these guidelines. The cut slopes that were steeper than the advised inclination remained stable before the monsoon, but often failed during the monsoon season due to rainwater infiltration that leads to dissipation of soil suction. Field observations also revealed that the roadside drainage was either not implemented or was blocked. The retaining walls were found to be designed to the same geometry, despite differences in cutting heights and slope materials. This resulted in overturning, bulging, and cracking of the walls. Based on the findings of this study, it is clear that to build resilient road infrastructure in Nepal, the road cuttings need to be excavated according to rigorous engineering guidelines, and standards for the practice of quality assurance need to be implemented

A Computationally Efficient Method to Determine the Probability of Rainfall-Triggered Cut Slope Failure Accounting for Upslope Hydrological Conditions

We present a new computationally efficient methodology to estimate the probability of rainfall-induced slope failure based on mechanical probabilistic slope stability analyses coupled with a hydrogeological model of the upslope area. The model accounts for: (1) uncertainty of geotechnical and hydrogeological parameters; (2) rainfall precipitation recorded over a period of time; and (3) the effect of upslope topography. The methodology provides two key outputs: (1) time-varying conditional probability of slope failure; and (2) an estimate of the absolute frequency of slope failure over any time period of interest. The methodology consists of the following steps: first, characterising the uncertainty of the slope geomaterial strength parameters; second, performing limit equilibrium method stability analyses for the realisations of the geomaterial strength parameters required to calculate the slope probability of failure by a Monte Carlo Simulation. The stability analyses are performed for various phreatic surface heights. These phreatic surfaces are then matched to a phreatic surface time series obtained from the 1D Hillslope-Storage Boussinesq model run for the upslope area to generate Factor of Safety (FoS) time series. A timevarying conditional probability of failure and an absolute frequency of slope failure can then be estimated from these FoS time series. We demonstrate this methodology on a road slope cutting in Nepal where geotechnical tests are not readily conducted. We believe this methodology improves the reliability of slope safety estimates where site investigation is not possible. Also, the methodology enables practitioners to avoid making unrealistic assumptions on the hydrological input. Finally, we find that the time-varying failure probability shows marked variations over time as a result of the monsoon wet–dry weather

Colour vision of green turtle (Chelonia mydas) hatchlings: do they still prefer blue under water?

Background. Several anatomical studies have concluded that green turtles (Chelonia mydas) possess the necessary anatomy for colour vision. Behavioural experiments were conducted with newly emerged hatchlings, testing their attraction towards light sources of different colours on their journey into the ocean. It was concluded that they are attracted to shorter wavelengths compared to longer ones, suggesting a possible attraction towards blue. Methods. Forty-one green turtles at six months of age were tested for their colour discrimination capabilities during a three-choice experiment under water. Three colours were selected for experimentation: blue, yellow, and red. Four different saturations (25, 50, 75, and 100%) of each of these colours were created, in total 12 colours were tested. The colour stimuli was printed and laminated paper colour blocks with food attached to force an interaction. Turtles were individually placed into their housing tanks with three different colours in front of them, from the same level saturation. The colour of the colour plate first approached and bitten by the turtle was noted. Results. The colour of the plate significantly influenced the likelihood that one food plate was selected more than another. Overall blue was selected 66.1%, yellow 18.2% and red 15.7%. There was also a significant interaction between the colour plate selected and the colour of the housing tank. Discussion.The findings of this study are consistent with previous research, concluding that green turtles are attracted to shorter wavelength colours, blue, compared to longer wavelength colours such as yellow or red. As the colour saturation changed and the colours became darker, turtles still chose food from the blue plates compared to the other options. These results indicate an attraction towards the colour blue, and as these research animals have never been in the wild, it is suggested that this attraction be an innate behavioural characteristic for green turtles

Individual differences in excitation and inhibition in visual cortex

The formation of a visual percept in the human brain involves multiple processes, the extent of which may be related to each other within individuals but may show variability between participants. The aim of this thesis was to investigate the relationships between individual variability in various measures of visual processing. The non-invasive neuroimaging methods of magnetic resonance imaging (MRI), magnetic resonance spectroscopy (MRS), magnetoencephalography (MEG) and functional MRI (fMRI) were employed to measure brain structure, neurotransmitter concentration, neuronal oscillations and haemodynamic activity, respectively. Reductions in haemodynamic activity in non-stimulated areas of visual cortex (negative blood oxygen level-dependent responses) were shown to hold useful information about the stimulus, in addition to the responses in stimulated cortex. In general, there were no strong relationships between increased or decreased functional responses in visual cortex and measures of brain structure or of neurotransmitter concentration. Age was the major determinant of individual variability in the frequency of neuronal oscillations. These findings do not replicate results from previous studies that have shown links between individual differences in these measures. This discrepancy was not due to poor repeatability of MRS measures, since methods for optimisation of MRS were identified in this thesis. Simulations were also conducted to determine the sample sizes required in correlational studies involving neuroimaging measures with associated measurement noise. The lack of replication of relationships between neuroimaging measures of individual differences in visual processing is likely to be influenced by low statistical power, due to the small sample sizes and weak relationships tested. Such studies should therefore be conducted and interpreted cautiously, bearing in mind issues of power, demographic mediators of relationships and the likely strength of relationships inferred from the physiological mechanisms linking the variables tested

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A>T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Evolution of nesting habitats and metapleural glands in ants

The metapleural gland is a unique and complex structure located on the propodeum of ants. Given its function in immune defence against microbes, it has undoubtedly played an important role in the ecological success of ants by enforcing colony hygiene and preventing diseases. Although this gland has an important antimicrobial function, it has been lost several times. It has been proposed that these losses are due to a shift in nesting habit, i.e. ants living in trees can afford to loose the metapleural gland because this environment harbours fewer microbes. Here we test this idea, the 'Arboreality Hypothesis', by constructing a phylogeny for 48 formicine ant species using eight markers (nuclear and mitochondrial) and Bayesian tree building methods. Character mapping for the presence/absence of the gland and nesting habitat was carried out with SIMMAP including 1000 trees from the posterior distribution of the MCMC run. Our results show several independent losses and regains of the metapleural gland across the subfamily. We also find a significant correlation between the two traits, suggesting that the 'Arboreality Hypothesis' can indeed explain the pattern of presence/absence of the metapleural gland in this group of ants

Capability Analysis of Earth Observation Data for Integrated Emergency Management

Space is one of the UK’s fastest-growing industry sectors of the last decade. Recognising this, in 2021 the UK Government’s first National Space Strategy established a new vision to make the nation one of the most innovative and attractive worldwide space economies. As part of the strategic funding programme, in 2023, the UK Space Agency (UKSA) funded a scoping study to assess the potential of satellite data to address issues that the three North East England Local Resilience Forums face at all stages of implementing the UK’s Integrated Emergency Management Framework (IEMF). Through dedicated workshops convened by two North East England universities, regional stakeholders from the emergency domain and related industries identified three case studies ripe for applying satellite data in support of multi-agency IEMF activities. Master’s students in the UK’s Centre for Doctoral Training in Geospatial Systems then undertook a month-long integrated group project to assess the potential for satellite imagery to be applied in the identified application areas. The research reported in this paper demonstrates how satellite imagery may be adopted to help address challenges posed during power outages, for mitigating illegal waste site fires, and during periods of snow and extreme cold. While the maturity levels of satellite applications vary in the three case studies due to data availability and image resolution, all three cases demonstrate that space data, particularly when augmented with additional geospatial information, help to enhance IEMF analysis. It is anticipated that the findings from the study will help stakeholders involved in IEMF management appreciate the added value of integrating satellite data into their current processes and analyses. By empowering key stakeholders to use satellite applications more effectively, it is predicted that better decisions will be achieved, thereby improving emergency risk management. A prototype dashboard, an output of the research to demonstrate the potential of space data for emergency management, is available online