Charged particle dynamics in the presence of non-Gaussian L\'evy electrostatic fluctuations

Full orbit dynamics of charged particles in a $3$-dimensional helical magnetic field in the presence of $\alpha$-stable L\'evy electrostatic fluctuations and linear friction modeling collisional Coulomb drag is studied via Monte Carlo numerical simulations. The L\'evy fluctuations are introduced to model the effect of non-local transport due to fractional diffusion in velocity space resulting from intermittent electrostatic turbulence. The probability distribution functions of energy, particle displacements, and Larmor radii are computed and showed to exhibit a transition from exponential decay, in the case of Gaussian fluctuations, to power law decay in the case of L\'evy fluctuations. The absolute value of the power law decay exponents are linearly proportional to the L\'evy index $\alpha$. The observed anomalous non-Gaussian statistics of the particles' Larmor radii (resulting from outlier transport events) indicate that, when electrostatic turbulent fluctuations exhibit non-Gaussian L\'evy statistics, gyro-averaging and guiding centre approximations might face limitations and full particle orbit effects should be taken into account.Comment: 5 pages, 5 figures. Accepted as a letter in Physics of Plasma

Geminivirus Rep Protein Interferes with the Plant DNA Methylation Machinery and Suppresses Transcriptional Gene Silencing

Viruses are masters at circumventing host defenses and manipulating the cellular environment for their own benefit. The replication of the largest known family of single-stranded DNA viruses, Geminiviridae, is impaired by DNA methylation but the fact that plants might use methylation as a defense against geminiviruses and the impact that viral genome methylation may have during the infection, remain controversial. We have found that geminiviruses reduce the expression of the plant maintenance DNA methyltransferases, MET1 and CMT3, in both, locally and systemically infected tissues. Furthermore, we demonstrated that the virus-mediated repression of these two maintenance DNA methyltransferases is widely spread among different geminivirus species and we have identified Rep as the geminiviral protein responsible for the repression of MET1 and CMT3. The presence of Rep, suppresses transcriptional gene silencing (TGS) of an Arabidopsis transgene and of host loci whose expression is strongly controlled by MET1. Bisulfite sequencing analyses showed that the expression of Rep caused a substantial reduction in the levels of DNA methylation at certain loci at CG sites. The biological relevance of these findings and the role of Rep as a TGS suppressor will be discussed.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

PAMP-triggered immunity against Pseudomonas syringae involves microRNA-mediated regulation of several uncharacterized R genes

Two main types of noncoding small RNA molecules have been found in plants: microRNAs (miRNAs) and small interfering RNAs (siRNAs). They differ in their biogenesis and mode of action, but share similar sizes (20-24 nt). Their precursors are processed by Dicer-Like RNase III (dcl) proteins present in Arabidopsis thaliana, and in their mature form can act as negative regulators of gene expression, being involved in a vast array of plant processes, including plant development, genomic integrity or response to stress. Small-RNA mediated regulation can occurs at transcriptional level (TGS) or at post-transcriptional level (PTGS). In recent years, the role of gene silencing in the regulation of expression of genes related to plant defence responses against bacterial pathogens is becoming clearer. Comparisons carried out in our lab between the expression profiles of different mutants affected in gene silencing, and plants challenged with Pseudomonas syringae pathovar tomato DC3000, led us to identify a set of uncharacterized R genes, belonging to the TIR-NBS-LRR gene family, differentially expressed in these conditions. Through the use of bioinformatics tools, we found a miRNA* of 22 nt putatively responsible for down-regulating expression of these R genes through the generation of siRNAs. We have also found that the corresponding pri-miRNA is down-regulated after PAMP-perception in a SA-dependent manner. We also demonstrate that plants with altered levels of miRNA* (knockdown lines or overexpression lines) exhibit altered PTI-associated phenotypes, suggesting a role for this miRNA* in this defence response against bacteria. In addition we identify one of the target genes as a negative regulator of defence response against Pseudomonas syringae.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. MINECO, FEDE

The influence of fractional diffusion in Fisher-KPP equations

We study the Fisher-KPP equation where the Laplacian is replaced by the generator of a Feller semigroup with power decaying kernel, an important example being the fractional Laplacian. In contrast with the case of the stan- dard Laplacian where the stable state invades the unstable one at constant speed, we prove that with fractional diffusion, generated for instance by a stable L\'evy process, the front position is exponential in time. Our results provide a mathe- matically rigorous justification of numerous heuristics about this model

Separatrix Reconnections in Chaotic Regimes

In this paper we extend the concept of separatrix reconnection into chaotic regimes. We show that even under chaotic conditions one can still understand abrupt jumps of diffusive-like processes in the relevant phase-space in terms of relatively smooth realignments of stable and unstable manifolds of unstable fixed points.Comment: 4 pages, 5 figures, submitted do Phys. Rev. E (1998

A Study of the N-D-K Scalability Problem in Large-Scale Image Classification

Image classification is a extensively studied problem that lies at the heart of computer vision. However, the challenge remains to develop a system that can identify and classify thousands of objects like the human visual system. The accumulation of massive image data sets has permitted the study of this problem at a big-data scale. However current algorithms have been shown to fall short of being practical and accurate at scale. To further understand how these algorithms scale, we developed a library of functions to explore the scalability of the support vector machine (SVM) linear classification algorithm when applied to problems of image classification. Our study provides valuable insights into not only how the SVM algorithm scales up and where it falls short, but also into how to create smarter and more efficient image classifiers that are fine- tuned for the large scale image classification challenge

Anomalous transport in Charney-Hasegawa-Mima flows

Transport properties of particles evolving in a system governed by the Charney-Hasegawa-Mima equation are investigated. Transport is found to be anomalous with a non linear evolution of the second moments with time. The origin of this anomaly is traced back to the presence of chaotic jets within the flow. All characteristic transport exponents have a similar value around $\mu=1.75$, which is also the one found for simple point vortex flows in the literature, indicating some kind of universality. Moreover the law $\gamma=\mu+1$ linking the trapping time exponent within jets to the transport exponent is confirmed and an accumulation towards zero of the spectrum of finite time Lyapunov exponent is observed. The localization of a jet is performed, and its structure is analyzed. It is clearly shown that despite a regular coarse grained picture of the jet, motion within the jet appears as chaotic but chaos is bounded on successive small scales.Comment: revised versio

Adsorption of proteins to thin-films of PDMS and its effect on the adhesion of human endothelial cells

This paper describes a simple and inexpensive procedure to produce thin-films of poly(dimethylsiloxane). Such films were characterized by a variety of techniques (ellipsometry, nuclear magnetic resonance, atomic force microscopy, and goniometry) and used to investigate the adsorption kinetics of three model proteins (fibrinogen, collagen type-I, and bovine serum albumin) under different conditions. The information collected from the protein adsorption studies was then used to investigate the adhesion of human dermal microvascular endothelial cells. The results of these studies suggest that these films can be used to model the surface properties of microdevices fabricated with commercial PDMS. Moreover, the paper provides guidelines to efficiently attach cells in BioMEMS devices.Fil: Chumbimuni Torres, Karin Y.. The University of Texas at San Antonio; Estados UnidosFil: Coronado, Ramon E.. The University of Texas at San Antonio; Estados UnidosFil: Mfuh, Adelphe M.. The University of Texas at San Antonio; Estados UnidosFil: Castro Guerrero, Carlos. The University of Texas at San Antonio; Estados UnidosFil: Silva, María Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Biología Agrícola de Mendoza. Universidad Nacional de Cuyo. Facultad de Ciencias Agrarias. Instituto de Biología Agrícola de Mendoza; ArgentinaFil: Negrete, George R.. The University of Texas at San Antonio; Estados UnidosFil: Bizios, Rena. The University of Texas at San Antonio; Estados UnidosFil: Garcia, Carlos D.. The University of Texas at San Antonio; Estados Unido