Sparse Coding Predicts Optic Flow Specificities of Zebrafish Pretectal Neurons

Zebrafish pretectal neurons exhibit specificities for large-field optic flow patterns associated with rotatory or translatory body motion. We investigate the hypothesis that these specificities reflect the input statistics of natural optic flow. Realistic motion sequences were generated using computer graphics simulating self-motion in an underwater scene. Local retinal motion was estimated with a motion detector and encoded in four populations of directionally tuned retinal ganglion cells, represented as two signed input variables. This activity was then used as input into one of two learning networks: a sparse coding network (competitive learning) and backpropagation network (supervised learning). Both simulations develop specificities for optic flow which are comparable to those found in a neurophysiological study (Kubo et al. 2014), and relative frequencies of the various neuronal responses are best modeled by the sparse coding approach. We conclude that the optic flow neurons in the zebrafish pretectum do reflect the optic flow statistics. The predicted vectorial receptive fields show typical optic flow fields but also "Gabor" and dipole-shaped patterns that likely reflect difference fields needed for reconstruction by linear superposition.Comment: Published Conference Paper from ICANN 2018, Rhode

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared to their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female-preference for rare Y-linked colour variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence

Combining polynomial chaos expansions and genetic algorithm for the coupling of electrophysiological models

The number of computational models in cardiac research has grown over the last decades. Every year new models with di erent assumptions appear in the literature dealing with di erences in interspecies cardiac properties. Generally, these new models update the physiological knowledge using new equations which reect better the molecular basis of process. New equations require the fi tting of parameters to previously known experimental data or even, in some cases, simulated data. This work studies and proposes a new method of parameter adjustment based on Polynomial Chaos and Genetic Algorithm to nd the best values for the parameters upon changes in the formulation of ionic channels. It minimizes the search space and the computational cost combining it with a Sensitivity Analysis. We use the analysis of di ferent models of L-type calcium channels to see that by reducing the number of parameters, the quality of the Genetic Algorithm dramatically improves. In addition, we test whether the use of the Polynomial Chaos Expansions improves the process of the Genetic Algorithm search. We conclude that it reduces the Genetic Algorithm execution in an order of 103 times in the case studied here, maintaining the quality of the results. We conclude that polynomial chaos expansions can improve and reduce the cost of parameter adjustment in the development of new models.Peer ReviewedPostprint (author's final draft

Dynamics of localization in a waveguide

This is a review of the dynamics of wave propagation through a disordered N-mode waveguide in the localized regime. The basic quantities considered are the Wigner-Smith and single-mode delay times, plus the time-dependent power spectrum of a reflected pulse. The long-time dynamics is dominated by resonant transmission over length scales much larger than the localization length. The corresponding distribution of the Wigner-Smith delay times is the Laguerre ensemble of random-matrix theory. In the power spectrum the resonances show up as a 1/t^2 tail after N^2 scattering times. In the distribution of single-mode delay times the resonances introduce a dynamic coherent backscattering effect, that provides a way to distinguish localization from absorption.Comment: 18 pages including 8 figures; minor correction

The transfer matrix in four-dimensional CDT

The Causal Dynamical Triangulation model of quantum gravity (CDT) has a transfer matrix, relating spatial geometries at adjacent (discrete lattice) times. The transfer matrix uniquely determines the theory. We show that the measurements of the scale factor of the (CDT) universe are well described by an effective transfer matrix where the matrix elements are labeled only by the scale factor. Using computer simulations we determine the effective transfer matrix elements and show how they relate to an effective minisuperspace action at all scales.Comment: 32 pages, 19 figure

Secondary hyperparathyroidism in HIV-infected patients: relationship with bone remodeling and response to vitamin D supplementation

Purpose of the study: Secondary hyperparathyroidism (SH) is frequent in HIV-infected patients. However, the causes and consequences are not well established. The aim of our study was to determine the relationship between parathyroid hormone (PTH), vitamin D and bone mineral density (BMD) in HIV-infected patients, and the effect of vitamin D replacement on PTH levels. Methods: Prospective study of 506 patients with at least two sequential serum determinations of PTH and 25-hydroxyvitamin D levels. In all cases, a bone dual X-ray absorptiometry (DEXA) was performed at inclusion. Hyperparathyroidism was defined as a PTH level above 65 pg/ml. Summary of results: Mean age was 44 yrs (24–78), and 75% were male. Mean BMI was 23.7 (17.97–33.11), and only 3% were of black race. Median nadir CD4+ was 200 cells/µL (9–499), and median time of HIV infection was 15.3 yrs (1.7–25.2). At inclusion, 488 patients (86%) were on HAART (31% TDF+PI, 44% TDF+NNRTI, 25% non-TDF based regimen) for a median of 929.5 days (154–1969), and 40% were HCV-coinfected. Median eGFR was 97.9 ml/min (62.14–134.08). Overall, mean serum PTH was 56.3 pg/mL (27.2–95.07). SH was observed in 27% of cases, with a marked influence of seasonality (from 44% in January to 10% in August). Mean levels of vitamin D were 17.45 ng/mL (7.6–40.78), with 16% below 10 ng/ml, 59%<20 ng/ml (deficiency), 85%<30 ng/ml (insufficiency). SH was related to vitamin D deficiency (relative risk, RR, 2.44), age (RR 1.04 per year), and a higher decrease in eGFR (RR 1.03 per ml/min), after adjustment by season, antiretroviral therapy, GFR at baseline, and HCV coinfection. DEXA scan showed 18% osteoporosis and 54% osteopenia, and there was an inverse correlation between PTH levels and T and Z score in femoral neck (r=−0.14, p<0.01), higher in those patients below 40 yrs. Vitamin D supplementation in 181 patients produced a significant decrease in serum PTH (57.2 if not treated vs 50.5 pg/ml, p=0.02, 23% continues with SH) and the only factor associated with lack of response was persistent vitamin D deficiency. Conclusion: SH is relatively frequent in HIV patients, in close relation with vitamin D deficiency. It is associated with bone resorption, especially in the femoral neck. The use of vitamin D supplementation improves SH when levels above 20 ng/ml are achieved

Industrial work placement in higher education: a study of civil engineering student engagement

For civil engineering undergraduates, the opportunity to spend a period of time in formal industrial work placement provides an invaluable learning experience. This paper reviews student engagement with short-term industrial placement and provides analysis of questionnaires (n=174) returned by undergraduates studying civil engineering at four Higher Education Institutes (HEI’s) in the West of Scotland. The data captures industrial placement statistics, employability skill-sets and presents brief testimonies from students. Whilst the journey to becoming a professional civil engineer is undoubtedly enhanced by short-term placement clear opportunities exist for HEI’s to affect and change existing pedagogical discourse. Commentary is likely to resonate beyond civil engineering and serve as a timely reminder of the need to re-invigorate academia / industry curriculum partnerships

Spectroscopic variability of two Oe stars

The Oe stars HD45314 and HD60848 have recently been found to exhibit very different X-ray properties: whilst HD60848 has an X-ray spectrum and emission level typical of most OB stars, HD45314 features a much harder and brighter X-ray emission, making it a so-called gamma Cas analogue. Monitoring the optical spectra could provide hints towards the origin of these very different behaviours. We analyse a large set of spectroscopic observations of HD45314 and HD60848, extending over 20 years. We further attempt to fit the H-alpha line profiles of both stars with a simple model of emission line formation in a Keplerian disk. Strong variations in the strengths of the H-alpha, H-beta, and He I 5876 emission lines are observed for both stars. In the case of HD60848, we find a time lag between the variations in the equivalent widths of these lines. The emission lines are double peaked with nearly identical strengths of the violet and red peaks. The H-alpha profile of this star can be successfully reproduced by our model of a disk seen under an inclination of 30 degrees. In the case of HD45314, the emission lines are highly asymmetric and display strong line profile variations. We find a major change in behaviour between the 2002 outburst and the one observed in 2013. This concerns both the relationship between the equivalent widths of the various lines and their morphologies at maximum strength (double-peaked in 2002 versus single-peaked in 2013). Our simple disk model fails to reproduce the observed H-alpha line profiles of HD45314. Our results further support the interpretation that Oe stars do have decretion disks similar to those of Be stars. Whilst the emission lines of HD60848 are explained by a disk with a Keplerian velocity field, the disk of HD45314 seems to have a significantly more complex velocity field that could be related to the phenomenon that produces its peculiar X-ray emission.Comment: Accepted for Publication in A&

Enhanced error estimator based on a nearly equilibrated moving least squares recovery technique for FEM and XFEM

In this paper a new technique aimed to obtain accurate estimates of the error in energy norm using a moving least squares (MLS) recovery-based procedure is presented. We explore the capabilities of a recovery technique based on an enhanced MLS fitting, which directly provides continuous interpolated fields, to obtain estimates of the error in energy norm as an alternative to the superconvergent patch recovery (SPR). Boundary equilibrium is enforced using a nearest point approach that modifies the MLS functional. Lagrange multipliers are used to impose a nearly exact satisfaction of the internal equilibrium equation. The numerical results show the high accuracy of the proposed error estimator