Automated identification of Fos expression

The concentration of Fos, a protein encoded by the immediate-early gene c-fos, provides a measure of synaptic activity that may not parallel the electrical activity of neurons. Such a measure is important for the difficult problem of identifying dynamic properties of neuronal circuitries activated by a variety of stimuli and behaviours. We employ two-stage statistical pattern recognition to identify cellular nuclei that express Fos in two-dimensional sections of rat forebrain after administration of antipsychotic drugs. In stage one, we distinguish dark-stained candidate nuclei from image background by a thresholding algorithm and record size and shape measurements of these objects. In stage two, we compare performance of linear and quadratic discriminants, nearest-neighbour and artificial neural network classifiers that employ functions of these measurements to label candidate objects as either Fos nuclei, two touching Fos nuclei or irrelevant background material. New images of neighbouring brain tissue serve as test sets to assess generalizability of the best derived classification rule, as determined by lowest cross-validation misclassification rate. Three experts, two internal and one external, compare manual and automated results for accuracy assessment. Analyses of a subset of images on two separate occasions provide quantitative measures of inter- and intra-expert consistency. We conclude that our automated procedure yields results that compare favourably with those of the experts and thus has potential to remove much of the tedium, subjectivity and irreproducibility of current Fos identification methods in digital microscopy

A homomorphism theorem and a Trotter product formula for quantum stochastic flows with unbounded coefficients

We give a new method for proving the homomorphic property of a quantum stochastic ow satisfying a quantum stochastic differential equation with unbounded coefficients, under some further hypotheses. As an application, we prove a Trotter product formula for quantum stochastic ows and obtain quantum stochastic dilations of a class of quantum dynamical semigroups generalizing results of [5

Lyapunov Exponent Pairing for a Thermostatted Hard-Sphere Gas under Shear in the Thermodynamic Limit

We demonstrate why for a sheared gas of hard spheres, described by the SLLOD equations with an iso-kinetic Gaussian thermostat in between collisions, deviations of the conjugate pairing rule for the Lyapunov spectrum are to be expected, employing a previous result that for a large number of particles $N$, the iso-kinetic Gaussian thermostat is equivalent to a constant friction thermostat, up to $1/\sqrt{N}$ fluctuations. We also show that these deviations are at most of the order of the fourth power in the shear rate.Comment: 4 pages, to appear in Rapid Comm., Phys. Rev.

Algorithm for numerical integration of the rigid-body equations of motion

A new algorithm for numerical integration of the rigid-body equations of motion is proposed. The algorithm uses the leapfrog scheme and the quantities involved are angular velocities and orientational variables which can be expressed in terms of either principal axes or quaternions. Due to specific features of the algorithm, orthonormality and unit norms of the orientational variables are integrals of motion, despite an approximate character of the produced trajectories. It is shown that the method presented appears to be the most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur

Inter-specific variation in the potential for upland rush management advocated by agri-environment schemes to increase breeding wader densities

Encroachment of rush Juncus spp. in the United Kingdom uplands poses a threat to declining wader populations due to taller, denser swards that can limit foraging and breeding habitat quality for some species. Rush management via cutting, implemented through agri-environment schemes (AESs), could thus increase wader abundance, but there is insufficient assessment and understanding of how rush management influences upland waders. Across two upland regions of England [South West Peak (SWP) and Geltsdale nature reserve, Cumbria], we surveyed waders over four visits in fields where rush was managed according to AES prescriptions (treatment; n = 21) and fields without rush management that were otherwise ecologically similar (control; n = 22) to assess how the densities of breeding wader pairs respond to rush management in the short-term. We find evidence for regional variation in the response of waders to rush management, with densities of Common Snipe Gallinago gallinago significantly higher in treatment than control fields in the SWP, but not Geltsdale. There were no statistically significant responses to treatment on densities of Eurasian Curlew Numenius arquata or Northern Lapwing Vanellus vanellus. The 95% confidence intervals for the treatment parameter estimates suggest that this may be due to limited statistical power in the case of Lapwing. For Curlew, however, any potential increases in densities are negligible. There was no evidence that variation in rush cover, which ranged from 10 to 70%, influenced densities of any of our three focal species. Our results suggest that rush management through AES prescriptions delivered in isolation of other interventions may not lead to general increases in breeding wader densities in the short-term, but benefits may arise in some situations due to regional and inter-specific variation in effectiveness. Rush management supported with interventions that improve soil conditions and thus food availability, or reduce predation pressure, may enable AES rush management to generate benefits. Additional research is required to maximise the potential benefits of rush management for each species through the development of prescriptions that tailor to individual species’ optimum sward structure

Macrophage subpopulation identity in Drosophila is modulated by apoptotic cell clearance and related signalling pathways

In Drosophila blood, plasmatocytes of the haemocyte lineage represent the functional equivalent of vertebrate macrophages and have become an established in vivo model with which to study macrophage function and behaviour. However, the use of plasmatocytes as a macrophage model has been limited by a historical perspective that plasmatocytes represent a homogenous population of cells, in contrast to the high levels of heterogeneity of vertebrate macrophages. Recently, a number of groups have reported transcriptomic approaches which suggest the existence of plasmatocyte heterogeneity, while we identified enhancer elements that identify subpopulations of plasmatocytes which exhibit potentially pro-inflammatory behaviours, suggesting conservation of plasmatocyte heterogeneity in Drosophila. These plasmatocyte subpopulations exhibit enhanced responses to wounds and decreased rates of efferocytosis when compared to the overall plasmatocyte population. Interestingly, increasing the phagocytic requirement placed upon plasmatocytes is sufficient to decrease the size of these plasmatocyte subpopulations in the embryo. However, the mechanistic basis for this response was unclear. Here, we examine how plasmatocyte subpopulations are modulated by apoptotic cell clearance (efferocytosis) demands and associated signalling pathways. We show that loss of the phosphatidylserine receptor Simu prevents an increased phagocytic burden from modulating specific subpopulation cells, while blocking other apoptotic cell receptors revealed no such rescue. This suggests that Simu-dependent efferocytosis is specifically involved in determining fate of particular subpopulations. Supportive of our original finding, mutations in amo (the Drosophila homolog of PKD2), a calcium-permeable channel which operates downstream of Simu, phenocopy simu mutants. Furthermore, we show that Amo is involved in the acidification of the apoptotic cell-containing phagosomes, suggesting that this reduction in pH may be associated with macrophage reprogramming. Additionally, our results also identify Ecdysone receptor signalling, a pathway related to control of cell death during developmental transitions, as a controller of plasmatocyte subpopulation identity. Overall, these results identify fundamental pathways involved in the specification of plasmatocyte subpopulations and so further validate Drosophila plasmatocytes as a heterogeneous population of macrophage-like cells within this important developmental and immune model

Upland rush management advocated by agri‐environment schemes increases predation of artificial wader nests

Farmland birds, including breeding waders, have declined across Europe. One frequently advocated strategy to facilitate population recovery is using agri-environment schemes (AES) to improve vegetation structure. A key example is cutting dense rush Juncus to open the sward which aims to increase the abundance of wading birds, for example by improving foraging conditions. Effects on breeding success are, however, unknown. This is a critical knowledge gap as high nest and chick predation rates are a key driver of wader declines. For wader species that nest across a range of sward structures, for example Eurasian curlew Numenius arquata and common snipe Gallinago gallinago, converting denser swards to more open ones may reduce opportunities for nest concealment and thus increase predation risk. Due to the difficulties of locating large numbers of wader nests, we assess rush management impacts on nest predation risk using artificial wader nests (n = 184) in two upland areas of England, using fields in which rush is managed according to AES prescriptions (treatment; n = 21) or un-managed (control; n = 22) fields. Daily nest predation rates (DPRs) were twice as high in treatment (0.064 day−1) than control fields (0.027 day−1). Within treatment fields, DPRs were twice as high for nests in cut rush patches (0.108 day−1) than in uncut rush (0.055 day−1). Modelling links higher DPRs associated with rush cutting to the resultant shorter and less dense vegetation. Our results highlight the need to assess how AES prescriptions that alter vegetation structure impact all aspects of the target species’ fitness and thus determine population recovery. Studies using real wader nests should test whether AES rush management inadvertently creates an ecological trap by altering vegetation structure, and identify the sward structure and configuration that optimizes trade-offs between foraging conditions and nest predation risk