CLiDE version 1.0 user guide

The Dynamic Environmental Sensitivity to Change (DESC) project coupled cellular automaton (CA) modelling from various backgrounds and produced the CAESAR-Lisflood-DESC (CLiDE) modelling platform: a geomorphological simulator that allows a variety of Earth system interactions to be explored. A derived version of the well established Cellular Automaton Evolutionary Slope and River (CAESAR) model (Coulthard and Van De Wiel, 2006), CAESAR-Lisflood, which incorporates the Lisflood hydrodymanic model (Coulthard et al., 2013) to simulate channel and overbank flow, is used as the platform kernel. The two dimensional modular design allows great versatility in the range of simulated spatio-temporal scales to which it can be applied. CAESAR has been used to investigate a variety of sediment transport, erosional and depositional processes under differing climatic and land use pressures in river reaches and catchments (Hancock et at., 2011). The recent addition of Lisflood to the code improves the representation of surface water flow within the model by incorporating momentum. However, as with many landscape evolution models (LEMs), CAESAR over-simplifies the representation of some of the hydrological processes and interactions that drive sediment transport. Specifically, it does not simulate groundwater flow and its discharge to rivers. To address these limitations, the non-Lisflood controlled surface hydrological processes within the CLiDE platform are replaced with a bespoke distributed hydrological model that includes a groundwater model. This hydrological model partitions rainfall between surface run-off and recharge to groundwater using a soil water balance model, which is applied at each grid cell. To simulate groundwater flow to river channels we incorporate a single layer finite difference model into the code. This solves the governing partial differential groundwater flow equation using a forward time-stepping, or explicit, solution method (Wang and Anderson, 1982), which can be considered as a cellular automaton (CA) model (Ravazzani et al., 2011). The groundwater model is coupled to the surface model through the exchange of recharge and baseflow. In addition to the hydrological modifications, a debris flow component has been added to the platform. The triggering aspect of this component is linked to simulated groundwater levels

Were rivers flowing across the Sahara during the last interglacial? Implications for human migration through Africa.

Human migration north through Africa is contentious. This paper uses a novel palaeohydrological and hydraulic modelling approach to test the hypothesis that under wetter climates c.100,000 years ago major river systems ran north across the Sahara to the Mediterranean, creating viable migration routes. We confirm that three of these now buried palaeo river systems could have been active at the key time of human migration across the Sahara. Unexpectedly, it is the most western of these three rivers, the Irharhar river, that represents the most likely route for human migration. The Irharhar river flows directly south to north, uniquely linking the mountain areas experiencing monsoon climates at these times to temperate Mediterranean environments where food and resources would have been abundant. The findings have major implications for our understanding of how humans migrated north through Africa, for the first time providing a quantitative perspective on the probabilities that these routes were viable for human habitation at these times

Simulating the influences of groundwater on regional geomorphology using a distributed, dynamic, landscape evolution modelling platform

A dynamic landscape evolution modelling platform (CLiDE) is presented that allows a variety of Earth system interactions to be explored under differing environmental forcing factors. Representation of distributed surface and subsurface hydrology within CLiDE is suited to simulation at sub-annual to centennial time-scales. In this study the hydrological components of CLiDE are evaluated against analytical solutions and recorded datasets. The impact of differing groundwater regimes on sediment discharge is examined for a simple, idealised catchment, Sediment discharge is found to be a function of the evolving catchment morphology. Application of CLiDE to the upper Eden Valley catchment, UK, suggests the addition of baseflow-return from groundwater into the fluvial system modifies the total catchment sediment discharge and the spatio-temporal distribution of sediment fluxes during storm events. The occurrence of a storm following a period of appreciable antecedent rainfall is found to increase simulated sediment fluxes

Motor neglect associated with loss of action inhibition

Motor neglect, underuse of one side of the body not explained by weakness or sensory impairment, is a common consequence of stroke that is surprisingly little understood. Behavioural and neuroanatomical hallmarks of the disorder are investigated. Using a masked prime task, it was shown that when patients with left motor neglect plan to move their left hand, irrelevant right limb motor programmes intrude, causing delay. Lesion analysis reveals that such asymmetry of motor programming occurs after infarcts of the right putamen and motor association areas. This demonstration of failure to inhibit ipsilesional limb motor plans suggests potential benefit from interventions that might act to restore balance in action planning

Hyper-resolution mapping of regional storm surge and tide flooding: comparison of static and dynamic models

Storm tide (combination of storm surge and the astronomical tide) flooding is a natural hazard with significant global social and economic consequences. For this reason, government agencies and stakeholders need storm tide flood maps to determine population and infrastructure at risk to present and future levels of inundation. Computer models of varying complexity are able to produce regional-scale storm tide flood maps and current model types are either static or dynamic in their implementation. Static models of storm tide utilize storm tide heights to inundate locations hydrologically connected to the coast, whilst dynamic models simulate physical processes that cause flooding. Static models have been used in regional-scale storm tide flood impact assessments, but model limitations and coarse spatial resolutions contribute to uncertain impact estimates. Dynamic models are better at estimating flooding and impact but are computationally expensive. In this study we have developed a dynamic reduced-complexity model of storm tide flooding that is computationally efficient and is applied at hyper-resolutions (<100 m cell size) over regional scales. We test the performance of this dynamic reduced-complexity model and a separate static model at three test sites where storm tide observational data are available. Additionally, we perform a flood impact assessment at each site using the dynamic reduced-complexity and static model outputs. Our results show that static models can overestimate observed flood areas up to 204 % and estimate more than twice the number of people, infrastructure, and agricultural land affected by flooding. Overall we find that that a reduced-complexity dynamic model of storm tide provides more conservative estimates of coastal flooding and impact

Quantitative T1 and T2 MRI signal characteristics in the human brain: different patterns of MR contrasts in normal ageing

OBJECTIVE: The objective of this study was to examine age-dependent changes in both T(1)-weighted and T(2)-weighted image contrasts and spin-echo T(2) relaxation time in the human brain during healthy ageing. METHODS: A total of 37 participants between the ages of 49 and 87 years old were scanned with a 3 Tesla system, using T(1)-weighted, T(2) weighted and quantitative spin-echo T(2) imaging. Contrast between image intensities and T(2) values was calculated for various regions, including between individual hippocampal subfields. RESULTS: The T(1) contrast-to-noise (CNR) and gray:white signal intensity ratio (GWR) did not change in the hippocampus, but it declined in the cingulate cortex with age. In contrast, T(2) CNR and GWR declined in both brain regions. T(2) relaxation time was almost constant in gray matter and most (but not all) hippocampal subfields, but increased substantially in white matter, pointing to an age effect on water relaxation in white matter. CONCLUSIONS: Changes in T(1) and T(2) MR characteristics influence the appearance of brain images in later life and should be considered in image analyses of aged subjects. It is speculated that alterations at the cell biology level, with concomitant alterations to the local magnetic environment, reduce dephasing and subsequently prolong spin-echo T(2) through reduced diffusion effects in later life. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10334-016-0573-0) contains supplementary material, which is available to authorized users

Magnetic Resonance Imaging to Detect Early Molecular and Cellular Changes in Alzheimer’s Disease

Recent pharmaceutical trials have demonstrated that slowing or reversing pathology in Alzheimer's disease is likely to be possible only in the earliest stages of disease, perhaps even before significant symptoms develop. Pathology in Alzheimer's disease accumulates for well over a decade before symptoms are detected giving a large potential window of opportunity for intervention. It is therefore important that imaging techniques detect subtle changes in brain tissue before significant macroscopic brain atrophy. Current diagnostic techniques often do not permit early diagnosis or are too expensive for routine clinical use. Magnetic Resonance Imaging (MRI) is the most versatile, affordable, and powerful imaging modality currently available, being able to deliver detailed analyses of anatomy, tissue volumes, and tissue state. In this mini-review, we consider how MRI might detect patients at risk of future dementia in the early stages of pathological change when symptoms are mild. We consider the contributions made by the various modalities of MRI (structural, diffusion, perfusion, relaxometry) in identifying not just atrophy (a late-stage AD symptom) but more subtle changes reflective of early dementia pathology. The sensitivity of MRI not just to gross anatomy but to the underlying “health” at the cellular (and even molecular) scales, makes it very well suited to this task

Enhancement of super-exchange pairing in the periodically-driven Hubbard model

We show that periodic driving can enhance electron pairing in strongly-correlated systems. Focusing on the strong-coupling limit of the doped Hubbard model we investigate in-gap, spatially inhomogeneous, on-site modulations and demonstrate that they substantially reduce electronic hopping without suppressing super-exchange interactions and pair hopping. We calculate real-time dynamics for the one-dimensional case, starting from zero and finite temperature initial states, and show that enhanced singlet-pair correlations emerge quickly and robustly in the out-of-equilibrium many-body state. Our results reveal a fundamental pairing mechanism that might underpin optically induced superconductivity in some strongly correlated quantum materials

Visual neglect after right posterior cerebral artery infarction

This article has been made available through the Brunel Open Access Publishing Fund and is available from the specified link - Copyright © 2006 BMJ Publishing Group.Objectives: To investigate the characteristics and neuroanatomical correlates of visual neglect after right-sided posterior cerebral artery (PCA) infarction.Methods: 15 patients with acute PCA strokes were screened for the presence of neglect on a comprehensive battery of cognitive tests. Extra tests of visual perception were also carried out on six patients. To establish which areas were critically associated with neglect, the lesions of patients with and without neglect were compared.Results: Neglect of varying severity was documented in 8 patients. In addition, higher-order visual perception was impaired in 5 of the 6 patients. Neglect was critically associated with damage to an area of white matter in the occipital lobe corresponding to a white matter tract connecting the parahippocampal gyrus with the angular gyrus of the parietal lobe. Lesions of the thalamus or splenium of the corpus callosum did not appear necessary or sufficient to cause neglect, but may mediate its severity in these patients.Conclusions: PCA stroke can result in visual neglect. Interruption of the white matter fibres connecting the parahippocampal gyrus to the angular gyrus may be important in determining whether a patient will manifest neglect

Differentiating Functional Cognitive Disorder from Early Neurodegeneration: A Clinic-Based Study

Functional cognitive disorder (FCD) is a relatively common cause of cognitive symptoms, characterised by inconsistency between symptoms and observed or self-reported cognitive functioning. We aimed to improve the clinical characterisation of FCD, in particular its differentiation from early neurodegeneration. Two patient cohorts were recruited from a UK-based tertiary cognitive clinic, diagnosed following clinical assessment, investigation and expert multidisciplinary team review: FCD, (n = 21), and neurodegenerative Mild Cognitive Impairment (nMCI, n = 17). We separately recruited a healthy control group (n = 25). All participants completed an assessment battery including: Hopkins Verbal Learning Test-Revised (HVLT-R), Trail Making Test Part B (TMT-B); Depression Anxiety and Stress Scale (DASS) and Minnesota Multiphasic Personality Inventory (MMPI-2RF). In comparison to healthy controls, the FCD and nMCI groups were equally impaired on trail making, immediate recall, and recognition tasks; had equally elevated mood symptoms; showed similar aberration on a range of personality measures; and had similar difficulties on inbuilt performance validity tests. However, participants with FCD performed significantly better than nMCI on HVLT-R delayed free recall and retention (regression coefficient −10.34, p = 0.01). Mood, personality and certain cognitive abilities were similarly altered across nMCI and FCD groups. However, those with FCD displayed spared delayed recall and retention, in comparison to impaired immediate recall and recognition. This pattern, which is distinct from that seen in prodromal neurodegeneration, is a marker of internal inconsistency. Differentiating FCD from nMCI is challenging, and the identification of positive neuropsychometric features of FCD is an important contribution to this emerging area of cognitive neurology