Protein sliding and hopping kinetics on DNA

Using Monte-Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (1) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of ms; (2) sliding dominates the root mean square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (3) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins

Asymmetry of localised states in a single quantum ring: polarization dependence of excitons and biexcitons

We performed spectroscopic studies of a single GaAs quantum ring with an anisotropy in the rim height. The presence of an asymmetric localised state was suggested by the adiabatic potential. The asymmetry was investigated in terms of the polarization dependence of excitons and biexcitons, where a large energy di erence (0.8 meV) in the exciton emission energy for perpendicular polarizations was observed and the oscillator strengths were also compared using the photoluminescence decay rate. For perpendicular polarizations the biexciton exhibits twice the energy di erence seen for the exciton, a fact that may be attributed to a possible change in the selection rules for the lowered symmetry.Comment: accepted in Applied physics Letter

Excited exciton and biexciton localised states in a single quantum ring

We observe excited exciton and biexciton states of localised excitons in an anisotropic quantum ring, where large polarisation asymmetry supports the presence of a crescent-like localised structure. We also find that saturation of the localised ground state exciton with increasing excitation can be attributed to relatively fast dissociation of biexcitons (? 430 ps) compared to slow relaxation from the excited state to the ground state (? 1000 ps). As no significant excitonic Aharonov-Bohm oscillations occur up to 14 T, we conclude that phase coherence around the rim is inhibited as a consequence of height anisotropy in the quantum ring.Comment: 4 pages, 4 figure

QCD axion and quintessential axion

The axion solution of the strong CP problem is reviewed together with the other strong CP solutions. We also point out the quintessential axion(quintaxion) whose potential can be extremely flat due to the tiny ratio of the hidden sector quark mass and the intermediate hidden sector scale. The quintaxion candidates are supposed to be the string theory axions, the model independent or the model dependent axions.Comment: 15 pages. Talk presented at Castle Ringberg, June 9-14, 200

Re-embedding a 1-Plane Graph into a Straight-line Drawing in Linear Time

Thomassen characterized some 1-plane embedding as the forbidden configuration such that a given 1-plane embedding of a graph is drawable in straight-lines if and only if it does not contain the configuration [C. Thomassen, Rectilinear drawings of graphs, J. Graph Theory, 10(3), 335-341, 1988]. In this paper, we characterize some 1-plane embedding as the forbidden configuration such that a given 1-plane embedding of a graph can be re-embedded into a straight-line drawable 1-plane embedding of the same graph if and only if it does not contain the configuration. Re-embedding of a 1-plane embedding preserves the same set of pairs of crossing edges. We give a linear-time algorithm for finding a straight-line drawable 1-plane re-embedding or the forbidden configuration.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016). This is an extended abstract. For a full version of this paper, see Hong S-H, Nagamochi H.: Re-embedding a 1-Plane Graph into a Straight-line Drawing in Linear Time, Technical Report TR 2016-002, Department of Applied Mathematics and Physics, Kyoto University (2016

Lesion detection and Grading of Diabetic Retinopathy via Two-stages Deep Convolutional Neural Networks

We propose an automatic diabetic retinopathy (DR) analysis algorithm based on two-stages deep convolutional neural networks (DCNN). Compared to existing DCNN-based DR detection methods, the proposed algorithm have the following advantages: (1) Our method can point out the location and type of lesions in the fundus images, as well as giving the severity grades of DR. Moreover, since retina lesions and DR severity appear with different scales in fundus images, the integration of both local and global networks learn more complete and specific features for DR analysis. (2) By introducing imbalanced weighting map, more attentions will be given to lesion patches for DR grading, which significantly improve the performance of the proposed algorithm. In this study, we label 12,206 lesion patches and re-annotate the DR grades of 23,595 fundus images from Kaggle competition dataset. Under the guidance of clinical ophthalmologists, the experimental results show that our local lesion detection net achieve comparable performance with trained human observers, and the proposed imbalanced weighted scheme also be proved to significantly improve the capability of our DCNN-based DR grading algorithm

Effectiveness of Hindman's theorem for bounded sums

We consider the strength and effective content of restricted versions of Hindman's Theorem in which the number of colors is specified and the length of the sums has a specified finite bound. Let $\mathsf{HT}^{\leq n}_k$ denote the assertion that for each $k$-coloring $c$ of $\mathbb{N}$ there is an infinite set $X \subseteq \mathbb{N}$ such that all sums $\sum_{x \in F} x$ for $F \subseteq X$ and $0 < |F| \leq n$ have the same color. We prove that there is a computable $2$-coloring $c$ of $\mathbb{N}$ such that there is no infinite computable set $X$ such that all nonempty sums of at most $2$ elements of $X$ have the same color. It follows that $\mathsf{HT}^{\leq 2}_2$ is not provable in $\mathsf{RCA}_0$ and in fact we show that it implies $\mathsf{SRT}^2_2$ in $\mathsf{RCA}_0$. We also show that there is a computable instance of $\mathsf{HT}^{\leq 3}_3$ with all solutions computing $0'$. The proof of this result shows that $\mathsf{HT}^{\leq 3}_3$ implies $\mathsf{ACA}_0$ in $\mathsf{RCA}_0$

Certainly Unsupervisable States

This paper proposes an abstraction method for compositional synthesis. Synthesis is a method to automatically compute a control program or supervisor that restricts the behaviour of a given system to ensure safety and liveness. Compositional synthesis uses repeated abstraction and simplification to combat the state-space explosion problem for large systems. The abstraction method proposed in this paper finds and removes the so-called certainly unsupervisable states. By removing these states at an early stage, the final state space can be reduced substantially. The paper describes an algorithm with cubic time complexity to compute the largest possible set of removable states. A practical example demonstrates the feasibility of the method to solve real-world problems

The neonicotinoid insecticide Imidacloprid repels pollinating flies and beetles at field-realistic concentrations

Neonicotinoids are widely used systemic insecticides which, when applied to flowering crops, are translocated to the nectar and pollen where they may impact upon pollinators. Given global concerns over pollinator declines, this potential impact has recently received much attention. Field exposure of pollinators to neonicotinoids depends on the concentrations present in flowering crops and the degree to which pollinators choose to feed upon them. Here we describe a simple experiment using paired yellow pan traps with or without insecticide to assess whether the commonly used neonicotinoid imidacloprid repels or attracts flying insects. Both Diptera and Coleoptera exhibited marked avoidance of traps containing imidacloprid at a field-realistic dose of 1 μg L-1, with Diptera avoiding concentrations as low as 0.01 μg L-1. This is to our knowledge the first evidence for any biological activity at such low concentrations, which are below the limits of laboratory detection using most commonly available techniques. Catch of spiders in pan traps was also slightly reduced by the highest concentrations of imidacloprid used (1 μg L-1), but catch was increased by lower concentrations. It remains to be seen if the repellent effect on insects occurs when neonicotinoids are present in real flowers, but if so then this could have implications for exposure of pollinators to neonicotinoids and for crop pollination. © 2013 Easton, Goulson