Fourier PCA and Robust Tensor Decomposition

Fourier PCA is Principal Component Analysis of a matrix obtained from higher order derivatives of the logarithm of the Fourier transform of a distribution.We make this method algorithmic by developing a tensor decomposition method for a pair of tensors sharing the same vectors in rank-$1$ decompositions. Our main application is the first provably polynomial-time algorithm for underdetermined ICA, i.e., learning an $n \times m$ matrix $A$ from observations $y=Ax$ where $x$ is drawn from an unknown product distribution with arbitrary non-Gaussian components. The number of component distributions $m$ can be arbitrarily higher than the dimension $n$ and the columns of $A$ only need to satisfy a natural and efficiently verifiable nondegeneracy condition. As a second application, we give an alternative algorithm for learning mixtures of spherical Gaussians with linearly independent means. These results also hold in the presence of Gaussian noise.Comment: Extensively revised; details added; minor errors corrected; exposition improve

Oxidative Stress Detection With Escherichia Coli Harboring A katG\u27::lux Fusion

A plasmid containing a transcriptional fusion of the Escherichia coli katG promoter to a truncated Vibrio fischeri lux operon (luxCDABE) was constructed. An E. coli strain bearing this plasmid (strain DPD2511) exhibited low basal levels of luminescence, which increased up to 1,000-fold in the presence of hydrogen peroxide, organic peroxides, redox-cycling agents (methyl viologen and menadione), a hydrogen peroxide-producing enzyme system (xanthine and xanthine oxidase), and cigarette smoke. An oxyR deletion abolished hydrogen peroxide-dependent induction, confirming that oxyR controlled katG\u27::lux luminescence. Light emission was also induced by ethanol by an unexplained mechanism. A marked synergistic response was observed when cells were exposed to both ethanol and hydrogen peroxide; the level of luminescence measured in the presence of both inducers was much higher than the sum of the level of luminescence observed with ethanol and the level of luminescence observed with hydrogen peroxide. It is suggested that this construction or similar constructions may be used as a tool for assaying oxidant and antioxidant properties of chemicals, as a biosensor for environmental monitoring and as a tool for studying cellular responses to oxidative hazards

Detection Of DNA Damage By Use Of Escherichia Coli Carrying recA\u27::lux, uvrA\u27::lux, And alkA\u27::lux Reporter Plasmids

Plasmids were constructed in which DNA damage-inducible promoters recA, uvrA, and alkA from Escherichia coli were fused to the Vibrio fischeri luxCDABE operon. Introduction of these plasmids into E. coli allowed the detection of a dose-dependent response to DNA-damaging agents, such as mitomycin and UV irradiation. Bioluminescence was measured in real time over extended periods. The fusion of the recA promoter to luxCDABE showed the most dramatic and sensitive responses. lexA dependence of the bioluminescent SOS response was demonstrated, confirming that this biosensor\u27s reports were transmitted by the expected regulatory circuitry. Comparisons were made between luxCDABE and lacZ fusions to each promoter. It is suggested that the lux biosensors may have use in monitoring chemical, physical, and genotoxic agents as well as in further characterizing the mechanisms of DNA repair

Aligning Manifolds of Double Pendulum Dynamics Under the Influence of Noise

This study presents the results of a series of simulation experiments that evaluate and compare four different manifold alignment methods under the influence of noise. The data was created by simulating the dynamics of two slightly different double pendulums in three-dimensional space. The method of semi-supervised feature-level manifold alignment using global distance resulted in the most convincing visualisations. However, the semi-supervised feature-level local alignment methods resulted in smaller alignment errors. These local alignment methods were also more robust to noise and faster than the other methods.Comment: The final version will appear in ICONIP 2018. A DOI identifier to the final version will be added to the preprint, as soon as it is availabl

Association of Aciculin with Dystrophin and Utrophin

Aciculin is a recently identified 60-kDa cytoskeletal protein, highly homologous to the glycolytic enzyme phosphoglucomutase type 1, (Belkin, A. M., Klimanskaya, I. V., Lukashev, M. E., Lilley, K., Critchley, D., and Koteliansky, V. E. (1994) J. Cell Sci. 107, 159-173). Aciculin expression in skeletal muscle is developmentally regulated, and this protein is particularly enriched at cell-matrix adherens junctions of muscle cells (Belkin, A. M., and Burridge, K. (1994) J. Cell Sci. 107, 1993-2003). The purpose of our study was to identify cytoskeletal protein(s) interacting with aciculin in various cell types. Using immunoprecipitation from cell lysates of metabolically labeled differentiating C2C12 muscle cells with anti-aciculin-specific antibodies, we detected a high molecular weight band (M(r) approximately 400,000), consistently coprecipitating with aciculin. We showed that this 400 kDa band comigrated with dystrophin and immunoblotted with anti-dystrophin antibodies. The association between aciculin and dystrophin in C2C12 cells was shown to resist Triton X-100 extraction and the majority of the complex could be extracted only in the presence of ionic detergents. In the reverse immunoprecipitation experiments, aciculin was detected in the precipitates with different anti-dystrophin antibodies. Immunodepletion experiments with lysates of metabolically labeled C2C12 myotubes showed that aciculin is a major dystrophin-associated protein in cultured skeletal muscle cells. Double immunostaining of differentiating and mature C2C12 myotubes with antibodies against aciculin and dystrophin revealed precise colocalization of these two cytoskeletal proteins throughout the process of myodifferentiation in culture. In skeletal muscle tissue, both proteins are concentrated at the sarcolemma and at myotendinous junctions. In contrast, utrophin, an autosomal homologue of dystrophin, was not codistributed with aciculin in muscle cell cultures and in skeletal muscle tissues. Analytical gel filtration experiments with purified aciculin and dystrophin showed interaction of these proteins in vitro, indicating that their association in skeletal muscle is due to direct binding. Whereas dystrophin was shown to be a major aciculin-associated protein in skeletal muscle, immunoblotting of anti-aciculin immunoprecipitates with antibodies against utrophin showed that aciculin is associated with utrophin in cultured A7r5 smooth muscle cells and REF52 fibroblasts. Immunodepletion experiments performed with lysates of metabolically labeled A7r5 cells demonstrated that aciculin is a major utrophin-binding protein in this cell type. Taken together, our data show that aciculin is a novel dystrophin- and utrophin-binding protein. Association of aciculin with dystrophin (utrophin) in various cell types might provide an additional cytoskeletal-matrix transmembrane link at sites where actin filaments terminate at the plasma membrane

Agents, simulated users and humans : an analysis of performance and behaviour

Most of the current models that are used to simulate users in Interactive Information Retrieval (IIR) lack realism and agency. Such models generally make decisions in a stochastic manner, without recourse to the actual information encountered or the underlying information need. In this paper, we develop a more sophisticated model of the user that includes their cognitive state within the simulation. The cognitive state maintains data about what the simulated user knows, has done and has seen, along with representations of what it considers attractive and relevant. Decisions to inspect or judge are then made based upon the simulated user's current state, rather than stochastically. In the context of ad-hoc topic retrieval, we evaluate the quality of the simulated users and agents by comparing their behaviour and performance against 48 human subjects under the same conditions, topics, time constraints, costs and search engine. Our findings show that while naive configurations of simulated users and agents substantially outperform our human subjects, their search behaviour is notably different from actual searchers. However, more sophisticated search agents can be tuned to act more like actual searchers providing greater realism. This innovation advances the state of the art in simulation, from simulated users towards autonomous agents. It provides a much needed step forward enabling the creation of more realistic simulations, while also motivating the development of more advanced cognitive agents and tools to help support and augment human searchers. Future work will focus not only on the pragmatics of tuning and training such agents for topic retrieval, but will also look at developing agents for other tasks and contexts such as collaborative search and slow search

Beam Combining of Quantum Cascade Laser Arrays

Engineering and Applied Science

Responses To Toxicants Of An Escherichia Coli Strain Carrying A uspA\u27::lux Genetic Fusion And An E. Coli Strain Carrying A grpE\u27::lux Fusion Are Similar

A transcriptional fusion of the Escherichia coli uspA promoter to luxCDABE was characterized and compared with a heat shock-responsive grpE\u27::lux fusion. Similarities in range and rank order of inducing conditions were observed; however, the magnitude of induction was typically greater for the grpE\u27::lux fusion strain

Uncertainty quantification in graph-based classification of high dimensional data

Classification of high dimensional data finds wide-ranging applications. In many of these applications equipping the resulting classification with a measure of uncertainty may be as important as the classification itself. In this paper we introduce, develop algorithms for, and investigate the properties of, a variety of Bayesian models for the task of binary classification; via the posterior distribution on the classification labels, these methods automatically give measures of uncertainty. The methods are all based around the graph formulation of semi-supervised learning. We provide a unified framework which brings together a variety of methods which have been introduced in different communities within the mathematical sciences. We study probit classification in the graph-based setting, generalize the level-set method for Bayesian inverse problems to the classification setting, and generalize the Ginzburg-Landau optimization-based classifier to a Bayesian setting; we also show that the probit and level set approaches are natural relaxations of the harmonic function approach introduced in [Zhu et al 2003]. We introduce efficient numerical methods, suited to large data-sets, for both MCMC-based sampling as well as gradient-based MAP estimation. Through numerical experiments we study classification accuracy and uncertainty quantification for our models; these experiments showcase a suite of datasets commonly used to evaluate graph-based semi-supervised learning algorithms.Comment: 33 pages, 14 figure

Approximate t-designs in generic circuit architectures

Unitary t-designs are distributions on the unitary group whose first t moments appear maximally random. Previous work has established several upper bounds on the depths at which certain specific random quantum circuit ensembles approximate t-designs. Here we show that these bounds can be extended to any fixed architecture of Haar-random two-site gates. This is accomplished by relating the spectral gaps of such architectures to those of 1D brickwork architectures. Our bound depends on the details of the architecture only via the typical number of layers needed for a block of the circuit to form a connected graph over the sites. When this quantity is independent of width, the circuit forms an approximate t-design in linear depth. We also give an implicit bound for nondeterministic architectures in terms of properties of the corresponding distribution over fixed architectures.Comment: 29 pages, 8 figure