The modelling cycle for collective animal behaviour

Collective animal behaviour is the study of how interactions between individuals produce group level patterns, and why these interactions have evolved. This study has proved itself uniquely interdisciplinary, involving physicists, mathematicians, engineers as well as biologists. Almost all experimental work in this area is related directly or indirectly to mathematical models, with regular movement back and forth between models, experimental data and statistical fitting. In this paper, we describe how the modelling cycle works in the study of collective animal behaviour. We classify studies as addressing questions at different levels or linking different levels, i.e. as local, local to global, global to local or global. We also describe three distinct approaches—theory-driven, data-driven and model selection—to these questions. We show, with reference to our own research on species across different taxa, how we move between these different levels of description and how these various approaches can be applied to link levels together

Application of Volcano Plots in Analyses of mRNA Differential Expressions with Microarrays

Volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log10(p-value) from the t test). We review the basic and an interactive use of the volcano plot, and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide an unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility to apply volcano plots to other fields beyond microarray.Comment: 8 figure

Effect of single embryo transfer on the risk of preterm birth associated with in vitro fertilization

To determine whether elective single embryo transfer (eSET) reduces the risk of preterm delivery associated with in vitro fertilization (IVF). This is an observational study of 3125 eSET cycles performed from 2008 to 2009 and reported to the Society for Assisted Reproductive Technology (SART) database. Preterm delivery rates were compared to the overall preterm delivery rate among all patients undergoing IVF over the same time period. The 3125 eSET cycles resulted in 1507 live births (live birth rate 48.2 %) Among these deliveries were 27 twins (1.8 %) and one set of triplets (0.07 %). The overall preterm delivery rate (20-37 weeks gestation) following eSET was 17.6 % (269/1527). This is significantly greater than the preterm birth rate for all patients undergoing IVF over the same time period (12 %, P \u3c 0.001). Elective single embryo transfer does not reduce the risk of preterm delivery associated with in vitro fertilization (IVF)

On the perceptual aesthetics of interactive objects

In this paper we measured the aesthetics of interactive objects (IOs), which are three-dimensional physical artefacts that exhibit autonomous behaviour when ‎handled. The aim of the research was threefold: firstly, to investigate whether aesthetic preference for distinctive objects' structures emerges in compound stimulation; secondly, to explore whether there exists aesthetic preference for distinctive objects’ behaviours; and lastly, to test whether there exists aesthetic preference for specific combinations of objects' structures and behaviours. The following variables were systematically manipulated: 1) IOs’ contour (rounded vs. angular); 2) IOs’ size (small vs. large); 3) IOs’ surface texture (rough vs. smooth); and 4) IOs’ behaviour (Lighting, Sounding, Vibrating, and Quiescent). Results show that behaviour was the dominant factor: it influenced aesthetics more than any other characteristic; Vibrating IOs were preferred over Lighting and Sounding IOs, supporting the importance of haptic processing in aesthetics. Results did not confirm the size and smoothness effects previously reported in vision and touch respectively, which suggests that for the aesthetics preference that emerges in isolated conditions may be different in compound stimulation. Finally, results corroborate the smooth curvature effect

Ultrafast relaxation dynamics of the antiferrodistortive phase in Ca doped SrTiO3

The ultrafast dynamics of the octahedral rotation in Ca:SrTiO3 is studied by time resolved x-ray diffraction after photo excitation over the band gap. By monitoring the diffraction intensity of a superlattice reflection that is directly related to the structural order parameter of the soft-mode driven antiferrodistortive phase in Ca:SrTiO3, we observe a ultrafast relaxation on a 0.2 ps timescale of the rotation of the oxygen octahedron, which is found to be independent of the initial temperaure despite large changes in the corresponding soft-mode frequency. A further, much smaller reduction on a slower picosecond timescale is attributed to thermal effects. Time-dependent density-functional-theory calculations show that the fast response can be ascribed to an ultrafast displacive modification of the soft-mode potential towards the normal state, induced by holes created in the oxygen 2p states

A Gaze-Driven Evolutionary Algorithm to Study Aesthetic Evaluation of Visual Symmetry

Empirical work has shown that people like visual symmetry. We used a gaze-driven evolutionary algorithm technique to answer three questions about symmetry preference. First, do people automatically evaluate symmetry without explicit instruction? Second, is perfect symmetry the best stimulus, or do people prefer a degree of imperfection? Third, does initial preference for symmetry diminish after familiarity sets in? Stimuli were generated as phenotypes from an algorithmic genotype, with genes for symmetry (coded as deviation from a symmetrical template, deviation–symmetry, DS gene) and orientation (0° to 90°, orientation, ORI gene). An eye tracker identified phenotypes that were good at attracting and retaining the gaze of the observer. Resulting fitness scores determined the genotypes that passed to the next generation. We recorded changes to the distribution of DS and ORI genes over 20 generations. When participants looked for symmetry, there was an increase in high-symmetry genes. When participants looked for the patterns they preferred, there was a smaller increase in symmetry, indicating that people tolerated some imperfection. Conversely, there was no increase in symmetry during free viewing, and no effect of familiarity or orientation. This work demonstrates the viability of the evolutionary algorithm approach as a quantitative measure of aesthetic preference

First hint for CP violation in neutrino oscillations from upcoming superbeam and reactor experiments

We compare the physics potential of the upcoming neutrino oscillation experiments Daya Bay, Double Chooz, NOvA, RENO, and T2K based on their anticipated nominal luminosities and schedules. After discussing the sensitivity to theta_{13} and the leading atmospheric parameters, we demonstrate that leptonic CP violation will hardly be measurable without upgrades of the T2K and NOvA proton drivers, even if theta_{13} is large. In the presence of the proton drivers, the fast track to hints for CP violation requires communication between the T2K and NOvA collaborations in terms of a mutual synchronization of their neutrino-antineutrino run plans. Even in that case, upgrades will only discover CP violation in a relatively small part of the parameter space at the 3 sigma confidence level, while 90% confidence level hints will most likely be obtained. Therefore, we conclude that a new facility will be required if the goal is to obtain a significant result with high probability.Comment: 27 pages, 12 figure

Optically induced lattice deformations, electronic structure changes, and enhanced superconductivity in YBa2Cu3O6.48

Resonant optical excitation of apical oxygen vibrational modes in the normal state of underdoped YBa2Cu3O6+x induces a transient state with optical properties similar to those of the equilibrium superconducting state. Amongst these, a divergent imaginary conductivity and a plasma edge are transiently observed in the photo-stimulated state. Femtosecond hard x-ray diffraction experiments have been used in the past to identify the transient crystal structure in this non-equilibrium state. Here, we start from these crystallographic features and theoretically predict the corresponding electronic rearrangements that accompany these structural deformations. Using density functional theory, we predict enhanced hole-doping of the CuO2 planes. The empty chain Cu dy2-z2 orbital is calculated to strongly reduce in energy, which would increase c-axis transport and potentially enhance the interlayer Josephson coupling as observed in the THz-frequency response. From these calculations, we predict changes in the soft x-ray absorption spectra at the Cu L-edge. Femtosecond x-ray pulses from a free electron laser are used to probe these changes in absorption at two photon energies along this spectrum, and provide data consistent with these predictions.Comment: 20 pages with 6 figure