Adjustment of a turbulent boundary layer to a 'canopy' of roughness elements

A model is developed for the adjustment of the spatially averaged time-mean flow of a deep turbulent boundary layer over small roughness elements to a canopy of larger three-dimensional roughness elements. Scaling arguments identify three stages of the adjustment. First, the drag and the finite volumes of the canopy elements decelerate air parcels; the associated pressure gradient decelerates the flow within an impact region upwind of the canopy. Secondly, within an adjustment region of length of order Lc downwind of the leading edge of the canopy, the flow within the canopy decelerates substantially until it comes into a local balance between downward transport of momentum by turbulent stresses and removal of momentum by the drag of the canopy elements. The adjustment length, Lc, is proportional to (i) the reciprocal of the roughness density (defined to be the frontal area of canopy elements per unit floor area) and (ii) the drag coefficient of individual canopy elements. Further downstream, within a roughness-change region, the canopy is shown to affect the flow above as if it were a change in roughness length, leading to the development of an internal boundary layer. A quantitative model for the adjustment of the flow is developed by calculating analytically small perturbations to a logarithmic turbulent velocity profile induced by the drag due to a sparse canopy with L/Lc≪1, where L is the length of the canopy. These linearized solutions are then evaluated numerically with a nonlinear correction to account for the drag varying with the velocity. A further correction is derived to account for the finite volume of the canopy elements. The calculations are shown to agree with experimental measurements in a fine-scale vegetation canopy, when the drag is more important than the finite volume effects, and a canopy of coarse-scale cuboids, when the finite volume effects are of comparable importance to the drag in the impact region. An expression is derived showing how the effective roughness length of the canopy, \z0eff, is related to the drag in the canopy. The value of \z0eff varies smoothly with fetch through the adjustment region from the roughness length of the upstream surface to the equilibrium roughness length of the canopy. Hence, the analysis shows how to resolve the unphysical flow singularities obtained with previous models of flow over sudden changes in surface roughness

Drift, partial drift and Darwin's proposition

A body moves at uniform speed in an unbounded inviscid fluid. Initially, the body is infinitely far upstream of an infinite plane of marked fluid; later, the body moves through and distorts the plane and, finally, the body is infinitely far downstream of the marked plane. Darwin (1953) suggested that the volume between the initial and final positions of the surface of marked fluid (the drift volume) is equal to the volume of fluid associated with the ‘added-mass’ of the body. We re-examine Darwin's (1953) concept of drift and, as an illustration, we study flow around a sphere. Two lengthscales are introduced: ρmax, the radius of a circular plane of marked particles; and x0, the initial separation of the sphere and plane. Numerical solutions and asymptotic expansions are derived for the horizontal Lagrangian displacement of fluid elements. These calculations show that depending on its initial position, the Lagrangian displacement of a fluid element can be either positive – a Lagrangian drift – or negative – a Lagrangian reflux. By contrast, previous investigators have found only a positive horizontal Lagrangian displacement, because they only considered the case of infinite x0. For finite x0, the volume between the initial and final positions of the plane of marked fluid is defined to be the ‘partial drift volume’, which is calculated using a combination of the numerical solutions and the asymptotic expansions. Our analysis shows that in the limit corresponding to Darwin's study, namely that both x0 and ρmax become infinite, the partial drift volume is not well-defined: the ordering of the limit processes is important. This explains the difficulties Darwin and others noted in trying to prove his proposition as a mathematical theorem and indicates practical, as well as theoretical, criteria that must be satisfied for Darwin's result to hold. We generalize our results for a sphere by re-considering the general expressions for Lagrangian displacement and partial drift volume. It is shown that there are two contributions to the partial drift volume. The first contribution arises from a reflux of fluid and is related to the momentum of the flow; this part is spread over a large area. It is well-known that evaluating the momentum of an unbounded fluid is problematic since the integrals do not converge; it is this first term which prevented Darwin from proving his proposition as a theorem. The second contribution to the partial drift volume is related to the kinetic energy of the flow caused by the body: this part is Darwin's concept of drift and is localized near the centreline. Expressions for partial drift volume are generalized for flow around arbitrary-shaped two- and three-dimensional bodies. The partial drift volume is shown to depend on the solid angles the body subtends with the initial and final positions of the plane of marked fluid. This result explains why the proof of Darwin's proposition depends on the ratio ρmax/x0. An example of drift due to a sphere travelling at the centre of a square channel is used to illustrate the differences between drift in bounded and unbounded flows

A circuit mechanism for irrationalities in decision-making and NMDA receptor hypofunction: behaviour, computational modelling, and pharmacology

Decision-making biases can be systematic features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases in health and disease. Monkeys performed an evidence integration task in which they showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a neural mechanism for this behaviour. Because NMDA receptor (NMDA-R) hypofunction is a leading hypothesis for neuropathology in schizophrenia, we simulated behavioural effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were tested experimentally using the NMDA-R antagonist ketamine, yielding changes in decision-making consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent. Significance People can make apparently irrational decisions because of underlying features in their decision circuitry. Deficits in the same neural circuits may also underlie debilitating cognitive symptoms of neuropsychiatric patients. Here, we reveal a neural circuit mechanism explaining an irrationality frequently observed in healthy humans making binary choices – the pro-variance bias. Our circuit model could be perturbed by introducing deficits in either excitatory or inhibitory neuron function. These two perturbations made specific, dissociable predictions for the types of irrational decisionmaking behaviour produced. We used the NMDA-R antagonist ketamine, an experimental model for schizophrenia, to test if these predictions were relevant to neuropsychiatric pathophysiology. The results were consistent with impaired excitatory neuron function, providing important new insights into the pathophysiology of schizophrenia

A circuit mechanism for decision-making biases and NMDA receptor hypofunction

Decision-making biases can be features of normal behaviour, or deficits underlying neuropsychiatric symptoms. We used behavioural psychophysics, spiking-circuit modelling and pharmacological manipulations to explore decision-making biases during evidence integration. Monkeys showed a pro-variance bias (PVB): a preference to choose options with more variable evidence. The PVB was also present in a spiking circuit model, revealing a potential neural mechanism for this behaviour. To model possible effects of NMDA receptor (NMDA-R) antagonism on this behaviour, we simulated the effects of NMDA-R hypofunction onto either excitatory or inhibitory neurons in the model. These were then tested experimentally using the NMDA-R antagonist ketamine, a pharmacological model of schizophrenia. Ketamine yielded an increase in subjects' PVB, consistent with lowered cortical excitation/inhibition balance from NMDA-R hypofunction predominantly onto excitatory neurons. These results provide a circuit-level mechanism that bridges across explanatory scales, from the synaptic to the behavioural, in neuropsychiatric disorders where decision-making biases are prominent

Ecological and life-history drivers of avian skull evolution

One of the most famous examples of adaptive radiation is that of the Galápagos finches, where skull morphology, particularly the beak, varies with feeding ecology. Yet increasingly studies are questioning the strength of this correlation between feeding ecology and morphology in relation to the entire neornithine radiation, suggesting that other factors also significantly affect skull evolution. Here, we broaden this debate to assess the influence of a range of ecological and life history factors, specifically habitat density, migration, and developmental mode, in shaping avian skull evolution. Using 3D geometric morphometric data to robustly quantify skull shape for 354 extant species spanning avian diversity, we fitted flexible phylogenetic regressions and estimated evolutionary rates for each of these factors across the full dataset. The results support a highly significant relationship between skull shape and both habitat density and migration, but not developmental mode. We further found heterogenous rates of evolution between different character states within habitat density, migration, and developmental mode, with rapid skull evolution in species which occupy dense habitats, are migratory, or are precocial. These patterns demonstrate that diverse factors impact the tempo and mode of avian phenotypic evolution, and that skull evolution in birds is not simply a reflection of feeding ecology

DECIPHER: Improving genetic diagnosis through dynamic integration of genomic and clinical data.

DECIPHER (Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources) shares candidate diagnostic variants and phenotypic data from patients with genetic disorders to facilitate research and improve the diagnosis, management, and therapy of rare diseases. The platform sits at the boundary between genomic research and the clinical community. DECIPHER aims to ensure that the most up-to-date data are made rapidly available within its interpretation interfaces to improve clinical care. Newly integrated cardiac case-control data that provide evidence of gene-disease associations and inform variant interpretation exemplify this mission. New research resources are presented in a format optimized for use by a broad range of professionals supporting the delivery of genomic medicine. The interfaces within DECIPHER integrate and contextualize variant and phenotypic data, helping to determine a robust clinico-molecular diagnosis for rare-disease patients, which combines both variant classification and clinical fit. DECIPHER supports discovery research, connecting individuals within the rare-disease community to pursue hypothesis-driven research. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 24 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates

Functional Analysis of Missense Mutations in Kv8.2 Causing Cone Dystrophy with Supernormal Rod Electroretinogram

Mutations in KCNV2 have been proposed as the molecular basis for cone dystrophy with supernormal rod electroretinogram. KCNV2 codes for the modulatory voltage-gated potassium channel α-subunit, Kv8.2, which is incapable of forming functional channels on its own. Functional heteromeric channels are however formed with Kv2.1 in heterologous expression systems, with both α-subunit genes expressed in rod and cone photoreceptors. Of the 30 mutations identified in the KCNV2 gene, we have selected three missense mutations localized in the potassium channel pore and two missense mutations localized in the tetramerization domain for analysis. We characterized the differences between homomeric Kv2.1 and heteromeric Kv2.1/Kv8.2 channels and investigated the influence of the selected mutations on the function of heteromeric channels. We found that two pore mutations (W467G and G478R) led to the formation of nonconducting heteromeric Kv2.1/Kv8.2 channels, whereas the mutations localized in the tetramerization domain prevented heteromer generation and resulted in the formation of homomeric Kv2.1 channels only. Consequently, our study suggests the existence of two distinct molecular mechanisms involved in the disease pathology

Demanding stories: television coverage of sustainability, climate change and material demand

This paper explores the past, present and future role of broadcasting, above all via the medium of television, in shaping how societies talk, think about and act on climate change and sustainability issues. The paper explores these broad themes via a focus on the important but relatively neglected issue of material demand and opportunities for its reduction. It takes the outputs and decision-making of one of the world’s most influential broadcasters, the BBC, as its primary focus. The paper considers these themes in terms of stories, touching on some of the broader societal frames of understanding into which they can be grouped. Media decision-makers and producers from a range of genres frequently return to the centrality of ‘story’ in the development, commissioning and production of an idea. With reference to specific examples of programming, and drawing on interviews with media practitioners, the paper considers the challenges of generating broadcast stories that can inspire engagement in issues around climate change, and specifically material demand. The concluding section proposes actions and approaches that might help to establish material demand reduction as a prominent way of thinking about climate change and environmental issues more widely. This article is part of the themed issue ‘Material demand reduction’

Palynology, Phytoliths and Diatoms in and adjacent to the Great Cave: stratigraphic and taphonomic studies of Late Quaternary vegetation history

Book Chapte

Reconciling persistent and dynamic hypotheses of working memory coding in prefrontal cortex

Competing accounts propose that working memory (WM) is subserved either by persistent activity in single neurons or by dynamic (time-varying) activity across a neural population. Here, we compare these hypotheses across four regions of prefrontal cortex (PFC) in an oculomotor-delayed-response task, where an intervening cue indicated the reward available for a correct saccade. WM representations were strongest in ventrolateral PFC neurons with higher intrinsic temporal stability (time-constant). At the population-level, although a stable mnemonic state was reached during the delay, this tuning geometry was reversed relative to cue-period selectivity, and was disrupted by the reward cue. Single-neuron analysis revealed many neurons switched to coding reward, rather than maintaining task-relevant spatial selectivity until saccade. These results imply WM is fulfilled by dynamic, population-level activity within high time-constant neurons. Rather than persistent activity supporting stable mnemonic representations that bridge subsequent salient stimuli, PFC neurons may stabilise a dynamic population-level process supporting WM