Gunrock: A High-Performance Graph Processing Library on the GPU

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs have been two significant challenges for developing a programmable high-performance graph library. "Gunrock", our graph-processing system designed specifically for the GPU, uses a high-level, bulk-synchronous, data-centric abstraction focused on operations on a vertex or edge frontier. Gunrock achieves a balance between performance and expressiveness by coupling high performance GPU computing primitives and optimization strategies with a high-level programming model that allows programmers to quickly develop new graph primitives with small code size and minimal GPU programming knowledge. We evaluate Gunrock on five key graph primitives and show that Gunrock has on average at least an order of magnitude speedup over Boost and PowerGraph, comparable performance to the fastest GPU hardwired primitives, and better performance than any other GPU high-level graph library.Comment: 14 pages, accepted by PPoPP'16 (removed the text repetition in the previous version v5

Superpositions of the Orbital Angular Momentum for Applications in Quantum Experiments

Two different experimental techniques for preparation and analyzing superpositions of the Gaussian and Laguerre-Gassian modes are presented. This is done exploiting an interferometric method on the one hand and using computer generated holograms on the other hand. It is shown that by shifting the hologram with respect to an incoming Gaussian beam different superpositions of the Gaussian and the Laguerre-Gaussian beam can be produced. An analytical expression between the relative phase and the amplitudes of the modes and the displacement of the hologram is given. The application of such orbital angular momenta superpositions in quantum experiments such as quantum cryptography is discussed.Comment: 18 pages, 4 figures. to appear in Journal of Optics

On the iterated Crank-Nicolson for hyperbolic and parabolic equations in numerical relativity

The iterated Crank-Nicolson is a predictor-corrector algorithm commonly used in numerical relativity for the solution of both hyperbolic and parabolic partial differential equations. We here extend the recent work on the stability of this scheme for hyperbolic equations by investigating the properties when the average between the predicted and corrected values is made with unequal weights and when the scheme is applied to a parabolic equation. We also propose a variant of the scheme in which the coefficients in the averages are swapped between two corrections leading to systematically larger amplification factors and to a smaller numerical dispersion.Comment: 7 pages, 3 figure

The status of shark and ray fishery resources in the Gulf of California: applied research to improve management and conservation

Seasonal surveys were conducted during 1998–1999 in Baja California, Baja California Sur, Sonora, and Sinaloa to determine the extent and activities of artisanal elasmobranch fisheries in the Gulf of California. One hundred and forty–seven fishing sites, or camps, were documented, the majority of which (n = 83) were located in Baja California Sur. Among camps with adequate fisheries information, the great majority (85.7%) targeted elasmobranchs during some part of the year. Most small, demersal sharks and rays were landed in mixed species fisheries that also targeted demersal teleosts, but large sharks were usually targeted in directed drift gillnet or, to a lesser extent, surface longline fisheries. Artisanal fishermen were highly opportunistic, and temporally switched targets depending on the local productivity of teleost, invertebrate, and elasmobranch fishery resources. Major fisheries for small sharks ( 1.5 m, “tiburón”) were minor components of artisanal elasmobranch fisheries in Sonora and Sinaloa, but were commonly targeted during summer and early autumn in Baja California and Baja California Sur. The pelagic thresher shark (Alopias pelagicus) and silky shark (Carcharhinus falciformis) were most commonly landed in Baja California, whereas a diverse assemblage of pelagic and large coastal sharks was noted among Baja California Sur landings. Rays dominated summer landings in Baja California and Sinaloa, when elevated catch rates of the shovelnose guitarfish (Rhinobatos productus, 13.2 individuals/vessel/trip) and golden cownose ray (Rhinoptera steindachneri, 11.1 individuals/vesse/trip) primarily supported the respective fisheries. The Sonoran artisanal elasmobranch fishery was the most expansive recorded during this study, and rays (especially R. productus) dominated spring and summer landings in this state. Seasonal catch rates of small demersal sharks and rays were considerably greater in Sonora than in other surveyed states. Many tiburón populations (e.g., C. leucas, C. limbatus, C. obscurus, Galeocerdo cuvier) have likely been overfished, possibly shifting effort towards coastal populations of cazón and rays. Management recommendations, including conducting demographic analyses using available life history data, determining and protecting nursery areas, and enacting seasonal closures in areas of elasmobranch aggregation (e.g., reproduction, feeding), are proposed. Without effective, enforceable management to sustain or rebuild targeted elasmobranch populations in the Gulf of California, collapse of many fisheries is a likely outcome. (PDF contains 243 pages

Scaling laws for the photo-ionisation cross section of two-electron atoms

The cross sections for single-electron photo-ionisation in two-electron atoms show fluctuations which decrease in amplitude when approaching the double-ionisation threshold. Based on semiclassical closed orbit theory, we show that the algebraic decay of the fluctuations can be characterised in terms of a threshold law $\sigma \propto |E|^{\mu}$ as $E \to 0_-$ with exponent $\mu$ obtained as a combination of stability exponents of the triple-collision singularity. It differs from Wannier's exponent dominating double ionisation processes. The details of the fluctuations are linked to a set of infinitely unstable classical orbits starting and ending in the non-regularisable triple collision. The findings are compared with quantum calculations for a model system, namely collinear helium.Comment: 4 pages, 1 figur

Rapid fluorescence-based reporter-gene assays to evaluate the cytotoxicity and antitumor drug potential of platinum complexes

BackgroundThe need for new platinum antitumor drugs is underscored by the usefulness of cisplatin and carboplatin in chemotherapy and the resistance of many tumors to these compounds. Combinatorial chemistry could aid in the search for cisplatin analogs if fast, high-throughput assays were available. Our goal was to develop rapid cell-based assays suitable for high-throughput screening that accurately predict the cytotoxicity of platinum complexes. We examined the effects of platinum complexes and other agents on reporter-gene expression in cancer cells.ResultsHeLa Tet-On cells with inducible enhanced green fluorescent protein (EGFP) were prepared. Cisplatin and other cis-disubstituted platinum complexes inhibited EGFP expression, with a strong positive correlation between EGFP inhibition and cytotoxicity. By contrast, trans-[Pt(NH3)2Cl2], other trans-platinum complexes, methyl methanesulfonate or heat shock stimulated EGFP expression. Northern and nuclear run-on analyses revealed that the changes in EGFP expression were at the level of transcription. In another reporter-gene assay in Jurkat cells, cisplatin, but not trans-[Pt(NH3)2Cl2] or K2[PtCl4], inhibited β-lactamase expression, as measured by hydrolysis of the fluorescent substrate CCF2.ConclusionsThe EGFP results indicate that cytotoxic stress enhances transcription from the inducible promoter, whereas compounds able to form the 1,2-intrastrand platinum-DNA cross-links repress transcription. Both fluorescence-based reporter-gene assays afford promising new approaches to platinum anticancer drug discovery

Semiclassical theory of the emission properties of wave-chaotic resonant cavities

We develop a perturbation theory for the lifetime and emission intensity for isolated resonances in asymmetric resonant cavities. The inverse lifetime $\Gamma$ and the emission intensity $I(\theta)$ in the open system are expressed in terms of matrix elements of operators evaluated with eigenmodes of the closed resonator. These matrix elements are calculated in a semiclassical approximation which allows us to represent $\Gamma$ and $I(\theta)$ as sums over the contributions of rays which escape the resonator by refraction.Comment: 4 pages, 2 color figure

Cortistain is expressed in a distinct subset of cortical interneurons

Cortistatin is a presumptive neuropeptide that shares 11 of its 14 amino acids with somatostatin. In contrast to somatostatin, administration of cortistatin into the rat brain ventricles specifically enhances slow wave sleep, apparently by antagonizing the effects of acetylcholine on cortical excitability. Here we show that preprocortistatin mRNA is expressed in a subset of GABAergic cells in the cortex and hippocampus that partially overlap with those containing somatostatin. A significant percentage of cortistatin-positive neurons is also positive for parvalbumin. In contrast, no colocalization was found between cortistatin and calretinin, cholecystokinin, or vasoactive intestinal peptide. During development there is a transient increase in cortistatin-expressing cells in the second postnatal week in all cortical areas and in the dentate gyrus. A transient expression of preprocortistatin mRNA in the hilar region at P16 is paralleled by electrophysiological changes in dentate granule cells. Together, these observations suggest mechanisms by which cortistatin may regulate cortical activity