Constrained Min-Cut replication for K-Way hypergraph partitioning

Cataloged from PDF version of article.Replication is a widely-used technique in information retrieval and database systems for providing fault tolerance and reducing parallelization and processing costs. Combinatorial models based on hypergraph partitioning are proposed for various problems arising in information retrieval and database systems. We consider the possibility of using vertex replication to improve the quality of hypergraph partitioning. In this study, we focus on the constrained min-cut replication (CMCR) problem, where we are initially given a maximum replication capacity and a K-way hypergraph partition with an initial imbalance ratio. The objective in the CMCR problem is finding the optimal vertex replication sets for each part of the given partition such that the initial cut size of the partition is minimized, where the initial imbalance is either preserved or reduced under the given replication capacity constraint. In this study, we present a complexity analysis of the CMCR problem and propose a model based on a unique blend of coarsening and integer linear programming (ILP) schemes. This coarsening algorithm is derived from a novel utilization of the Dulmage-Mendelsohn decomposition. Experiments show that the ILP formulation coupled with the Dulmage-Mendelsohn decomposition-based coarsening provides high quality results in practical execution times for reducing the cut size of a given K-way hypergraph partition. © 2014 INFORMS

Compressive Sensing under Matrix Uncertainties: An Approximate Message Passing Approach

In this work, we consider a general form of noisy compressive sensing (CS) when there is uncertainty in the measurement matrix as well as in the measurements. Matrix uncertainty is motivated by practical cases in which there are imperfections or unknown calibration parameters in the signal acquisition hardware. While previous work has focused on analyzing and extending classical CS algorithms like the LASSO and Dantzig selector for this problem setting, we propose a new algorithm whose goal is either minimization of mean-squared error or maximization of posterior probability in the presence of these uncertainties. In particular, we extend the Approximate Message Passing (AMP) approach originally proposed by Donoho, Maleki, and Montanari, and recently generalized by Rangan, to the case of probabilistic uncertainties in the elements of the measurement matrix. Empirically, we show that our approach performs near oracle bounds. We then show that our matrix-uncertain AMP can be applied in an alternating fashion to learn both the unknown measurement matrix and signal vector. We also present a simple analysis showing that, for suitably large systems, it suffices to treat uniform matrix uncertainty as additive white Gaussian noise

A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity

Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1–4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity

Simple and Complex Metafluids and Metastructures with Sharp Spectral Features in a Broad Extinction Spectrum: Particle-Particle Interactions and Testing the Limits of the Beer-Lambert Law

Metallic nanocrystals (NCs) are useful instruments for light manipulation around the visible spectrum. As their plasmonic resonances depend heavily on the NC geometry, modern fabrication techniques afford a great degree of control over their optical responses. We take advantage of this fact to create optical filters in the visible-near IR. Our systems show an extinction spectrum that covers a wide range of wavelengths (UV to mid-IR), while featuring a narrow transparency band around a wavelength of choice. We achieve this by carefully selecting the geometries of a collection of NCs with narrow resonances that cover densely the spectrum from UV to mid-IR except for the frequencies targeted for transmission. This fundamental design can be executed in different kinds of systems, including a solution of colloidal metal NCs (metafluids), a structured planar metasurface or a combination of both. Along with the theory, we report experimental results, showing metasurface realizations of the system, and we discuss the strengths and weaknesses of these different approaches, paying particular attention to particle-particle interaction and to what extent it hinders the intended objective by shifting and modifying the profile of the planned resonances through the hybridization of their plasmonic modes. We have found that the Beer-Lambert law is very robust overall and is violated only upon aggregation or in configurations with nearly-touching NCs. This striking property favors the creation of metafluids with a narrow transparency window, which are investigated here.Comment: Includes Supplementary Information, totaling 32 pages and 8 figure

Cyclic di-GMP-dependent Signaling Pathways in the Pathogenic Firmicute Listeria Monocytogenes

We characterized key components and major targets of the c-di-GMP signaling pathways in the foodborne pathogen Listeria monocytogenes, identified a new c-di-GMP-inducible exopolysaccharide responsible for motility inhibition, cell aggregation, and enhanced tolerance to disinfectants and desiccation, and provided first insights into the role of c-di-GMP signaling in listerial virulence. Genome-wide genetic and biochemical analyses of c-di-GMP signaling pathways revealed that L. monocytogenes has three GGDEF domain proteins, DgcA (Lmo1911), DgcB (Lmo1912) and DgcC (Lmo2174), that possess diguanylate cyclase activity, and three EAL domain proteins, PdeB (Lmo0131), PdeC (Lmo1914) and PdeD (Lmo0111), that possess c-di-GMP phosphodiesterase activity. Deletion of all phosphodiesterase genes (ΔpdeB/C/D) or expression of a heterologous diguanylate cyclase stimulated production of a previously unknown exopolysaccharide. The synthesis of this exopolysaccharide was attributed to the pssA-E (lmo0527-0531) gene cluster. The last gene of the cluster encodes the fourth listerial GGDEF domain protein, PssE, that functions as an I-site c-di-GMP receptor essential for exopolysaccharide synthesis. The c-di-GMP-inducible exopolysaccharide causes cell aggregation in minimal medium and impairs bacterial migration in semi-solid agar, however, it does not promote biofilm formation on abiotic surfaces. The exopolysaccharide also greatly enhances bacterial tolerance to commonly used disinfectants as well as desiccation, which may contribute to survival of L. monocytogenes on contaminated food products and in food-processing facilities. The exopolysaccharide and another, as yet unknown c-di-GMP-dependent target, drastically decrease listerial invasiveness in enterocytes in vitro, and lower pathogen load in the liver and gallbladder of mice infected via an oral route, which suggests that elevated c-di-GMP levels play an overall negative role in listerial virulence

Cyclic di-GMP-Dependent Signaling Pathways in the Pathogenic Firmicute \u3cem\u3eListeria monocytogenes\u3c/em\u3e

We characterized key components and major targets of the c-di-GMP signaling pathways in the foodborne pathogen Listeria monocytogenes, identified a new c-di-GMP-inducible exopolysaccharide responsible for motility inhibition, cell aggregation, and enhanced tolerance to disinfectants and desiccation, and provided first insights into the role of c-di-GMP signaling in listerial virulence. Genome-wide genetic and biochemical analyses of c-di-GMP signaling pathways revealed that L. monocytogenes has three GGDEF domain proteins, DgcA (Lmo1911), DgcB (Lmo1912) and DgcC (Lmo2174), that possess diguanylate cyclase activity, and three EAL domain proteins, PdeB (Lmo0131), PdeC (Lmo1914) and PdeD (Lmo0111), that possess c-di-GMP phosphodiesterase activity. Deletion of all phosphodiesterase genes (ΔpdeB/C/D) or expression of a heterologous diguanylate cyclase stimulated production of a previously unknown exopolysaccharide. The synthesis of this exopolysaccharide was attributed to the pssA-E (lmo0527-0531) gene cluster. The last gene of the cluster encodes the fourth listerial GGDEF domain protein, PssE, that functions as an I-site c-di-GMP receptor essential for exopolysaccharide synthesis. The c-di-GMP-inducible exopolysaccharide causes cell aggregation in minimal medium and impairs bacterial migration in semi-solid agar, however, it does not promote biofilm formation on abiotic surfaces. The exopolysaccharide also greatly enhances bacterial tolerance to commonly used disinfectants as well as desiccation, which may contribute to survival of L. monocytogenes on contaminated food products and in food-processing facilities. The exopolysaccharide and another, as yet unknown c-di-GMP-dependent target, drastically decrease listerial invasiveness in enterocytes in vitro, and lower pathogen load in the liver and gallbladder of mice infected via an oral route, which suggests that elevated c-di-GMP levels play an overall negative role in listerial virulence

A species-wide inventory of NLR genes and alleles in Arabidopsis thaliana

Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with approximately 40 well-chosen wild strains, with half of the pan-NLRome being present in most accessions. We chart NLR architectural diversity, identify new architectures, and quantify selective forces that act on specific NLRs and NLR domains. Our study provides a blueprint for defining pan-NLRomes

Intimate Monolithic integration of Chip-scale Photonic Circuits

Cataloged from PDF version of article.In this paper, we introduce a robust monolithic integration technique for fabricating photonic integrated circuits comprising optoelectronic devices (e.g., surface-illuminated photodetectors, waveguide quantum-well modulators, etc.) that are made of completely separate epitaxial structures and possibly reside at different locations across the wafer as necessary. Our technique is based on the combination of multiple crystal growth steps, judicious placement of epitaxial etch-stop layers, a carefully designed etch sequence, and self-planarization and passivation steps to compactly integrate optoelectronic devices. This multigrowth integration technique is broadly applicable to most III-V materials and can be exploited to fabricate sophisticated, highly integrated, multifunctional photonic integrated circuits on a single substrate. As a successful demonstration of this technique, we describe integrated photonic switches that consume only a 300 x 300 mu m footprint and incorporate InGaAs photodetector mesas and InGaAsP/InP quantum-well modulator waveguides separated by 50 mu m on an InP substrate. These switches perform electrically-reconfigurable optically-controlled wavelength conversion at multi-Gb/s data rates over the entire center telecommunication wavelength band