Disease threats to farmed green-lipped mussels Perna canaliculus in New Zealand: Review of challenges in risk assessment and pathway analysis

The endemic green-lipped mussel (GLM) Perna canaliculus is a key cultural and economic species for New Zealand. Unlike other cultured shellfish species, GLMs have experienced relatively few disease issues. The apparent absence of diseases in both wild and farmed GLM populations does not preclude risks from environmental changes or from the introduction of overseas mussel pathogens and parasites. Potential for disease exchange between the GLM and other mytilid species present in New Zealand has yet to be elucidated. After reviewing and discussing relevant scientific literature, we present an initial assessment of GLM vulnerability to disease threats and the potential risk pathways for mussel pathogens and parasites into New Zealand and highlight a number of challenges. These include knowledge gaps relevant to GLM susceptibility to exotic pathogens and parasites, risk pathways into New Zealand and biosecurity risk associated with domestic pathways. Considerations and findings could potentially apply to other farmed aquatic species with limited distribution range and/or low disease exposure

Replica Symmetry Breaking in Attractor Neural Network Models

The phenomenon of replica symmetry breaking is investigated for the retrieval phases of Hopfield-type network models. The basic calculation is done for the generalized version of the standard model introduced by Horner [1] and by Perez-Vicente and Amit [2] which can exhibit low mean levels of neural activity. For a mean activity $\bar a =1/2$ the Hopfield model is recovered. In this case, surprisingly enough, we cannot confirm the well known one step replica symmetry breaking (1RSB) result for the storage capacity which was presented by Crisanti, Amit and Gutfreund [3] (\alpha_c^{\hbox{\mf 1RSB}}\simeq 0.144). Rather, we find that 1RSB- and 2RSB-Ans\"atze yield only slightly increased capacities as compared to the replica symmetric value (\alpha_c^{\hbox{\mf 1RSB}}\simeq 0.138\,186 and \alpha_c^{\hbox{\mf 2RSB}}\simeq 0.138\,187 compared to \alpha_c^{\hbox{\mf RS}}\simeq 0.137\,905), significantly smaller also than the value \alpha_c^{\hbox{\mf sim}} = 0.145\pm 0.009 reported from simulation studies. These values still lie within the recently discovered reentrant phase [4]. We conjecture that in the infinite Parisi-scheme the reentrant behaviour disappears as is the case in the SK-spin-glass model (Parisi--Toulouse-hypothesis). The same qualitative results are obtained in the low activity range.Comment: Latex file, 20 pages, 8 Figures available from the authors upon request, HD-TVP-94-

Crossover effects in a discrete deposition model with Kardar-Parisi-Zhang scaling

We simulated a growth model in 1+1 dimensions in which particles are aggregated according to the rules of ballistic deposition with probability p or according to the rules of random deposition with surface relaxation (Family model) with probability 1-p. For any p>0, this system is in the Kardar-Parisi-Zhang (KPZ) universality class, but it presents a slow crossover from the Edwards-Wilkinson class (EW) for small p. From the scaling of the growth velocity, the parameter p is connected to the coefficient of the nonlinear term of the KPZ equation, lambda, giving lambda ~ p^gamma, with gamma = 2.1 +- 0.2. Our numerical results confirm the interface width scaling in the growth regime as W ~ lambda^beta t^beta, and the scaling of the saturation time as tau ~ lambda^(-1) L^z, with the expected exponents beta =1/3 and z=3/2 and strong corrections to scaling for small lambda. This picture is consistent with a crossover time from EW to KPZ growth in the form t_c ~ lambda^(-4) ~ p^(-8), in agreement with scaling theories and renormalization group analysis. Some consequences of the slow crossover in this problem are discussed and may help investigations of more complex models.Comment: 16 pages, 7 figures; to appear in Phys. Rev.

A two-species model of a two-dimensional sandpile surface: a case of asymptotic roughening

We present and analyze a model of an evolving sandpile surface in (2 + 1) dimensions where the dynamics of mobile grains ({\rho}(x, t)) and immobile clusters (h(x, t)) are coupled. Our coupling models the situation where the sandpile is flat on average, so that there is no bias due to gravity. We find anomalous scaling: the expected logarithmic smoothing at short length and time scales gives way to roughening in the asymptotic limit, where novel and non-trivial exponents are found.Comment: 7 Pages, 6 Figures; Granular Matter, 2012 (Online

Universality in two-dimensional Kardar-Parisi-Zhang growth

We analyze simulations results of a model proposed for etching of a crystalline solid and results of other discrete models in the 2+1-dimensional Kardar-Parisi-Zhang (KPZ) class. In the steady states, the moments W_n of orders n=2,3,4 of the heights distribution are estimated. Results for the etching model, the ballistic deposition (BD) model and the temperature-dependent body-centered restricted solid-on-solid model (BCSOS) suggest the universality of the absolute value of the skewness S = W_3 / (W_2)^(3/2) and of the value of the kurtosis Q = W_4 / (W_2)^2 - 3. The sign of the skewness is the same of the parameter \lambda of the KPZ equation which represents the process in the continuum limit. The best numerical estimates, obtained from the etching model, are |S| = 0.26 +- 0.01 and Q = 0.134 +- 0.015. For this model, the roughness exponent \alpha = 0.383 +- 0.008 is obtained, accounting for a constant correction term (intrinsic width) in the scaling of the squared interface width. This value is slightly below previous estimates of extensive simulations and rules out the proposal of the exact value \alpha=2/5. The conclusion is supported by results for the ballistic deposition model. Independent estimates of the dynamical exponent and of the growth exponent are 1.605 <= z <= 1.64 and \beta = 0.229 +- 0.005, respectively, which are consistent with the relations \alpha + z = 2 and z = \alpha / \beta.Comment: 8 pages, 9 figures, to be published in Phys. Rev.

Comparison of Different Parallel Implementations of the 2+1-Dimensional KPZ Model and the 3-Dimensional KMC Model

We show that efficient simulations of the Kardar-Parisi-Zhang interface growth in 2 + 1 dimensions and of the 3-dimensional Kinetic Monte Carlo of thermally activated diffusion can be realized both on GPUs and modern CPUs. In this article we present results of different implementations on GPUs using CUDA and OpenCL and also on CPUs using OpenCL and MPI. We investigate the runtime and scaling behavior on different architectures to find optimal solutions for solving current simulation problems in the field of statistical physics and materials science.Comment: 14 pages, 8 figures, to be published in a forthcoming EPJST special issue on "Computer simulations on GPU

Implementing efficient concerted rotations using Mathematica and C code

In this article we demonstrate a general and efficient metaprogramming implementation of concerted rotations using Mathematica. Concerted rotations allow the movement of a fixed portion of a polymer backbone with fixed bending angles, like a protein, while maintaining the correct geometry of the backbone and the initial and final points of the portion fixed. Our implementation uses Mathematica to generate a C code which is then wrapped in a library by a Python script. The user can modify the Mathematica notebook to generate a set of concerted rotations suited for a particular backbone geometry, without having to write the C code himself. The resulting code is highly optimized, performing on the order of thousands of operations per second

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism