A Similarity Measure for GPU Kernel Subgraph Matching

Accelerator architectures specialize in executing SIMD (single instruction, multiple data) in lockstep. Because the majority of CUDA applications are parallelized loops, control flow information can provide an in-depth characterization of a kernel. CUDAflow is a tool that statically separates CUDA binaries into basic block regions and dynamically measures instruction and basic block frequencies. CUDAflow captures this information in a control flow graph (CFG) and performs subgraph matching across various kernel's CFGs to gain insights to an application's resource requirements, based on the shape and traversal of the graph, instruction operations executed and registers allocated, among other information. The utility of CUDAflow is demonstrated with SHOC and Rodinia application case studies on a variety of GPU architectures, revealing novel thread divergence characteristics that facilitates end users, autotuners and compilers in generating high performing code

Transcriptional Robustness Complements Nonsense-Mediated Decay in Humans

In eukaryotes, gene expression is a complex, multi-step process involving transcription, splicing, translation, and post-translational modifications. At each individual step, errors can occur that lead to nonfunctional and potentially toxic proteins. Therefore, eukaryotes have evolved a wide array of solutions to minimize the risk of error.This work was supported by NIH grant R01 GM088344 to COW. The funder had no role in the preparation of the article.Cellular and Molecular Biolog

Female Resistance to Invading Males Increases Infanticide in Langurs

BACKGROUND: Infanticide by adult male occurs in many mammalian species under natural conditions, and it is often assumed to be a goal-directed action and explained predominately by sexual selection. Motivation of this behavior in mammals is limitedly involved. METHODOLOGY AND PRINCIPAL FINDINGS: We used long-term reproductive records and direct observation in captivity and in the field of two snub-nosed langur species on the basis of individual identification to investigate how infanticide happened and to be avoided in nonhuman primates. Our observations suggested that infanticide by invading males might be more accidental than goal-directed. The invading male seemed to monopolize all the females including lactating mothers during takeovers. Multiparous mothers who accepted the invading male shortly after takeovers avoided infanticide in most cases. Our results conjectured primiparous mothers would decrease infanticidal possibility if they sexually accepted the invading male during or immediately after takeovers. In the studied langur species, voluntary abortion or mating with the invading male was evidently adopted by females to limit or avoid infanticide by takeover males. CONCLUSIONS AND SIGNIFICANCE: The objective of the invading male was to monopolize all adult females after his takeover. It appeared that the mother's resistance to accepting the new male as a mating partner was the primary incentive for infanticide. Motivation analysis might be helpful to further understand why infanticide occurs in primate species

A holographic model for the fractional quantum Hall effect

Experimental data for fractional quantum Hall systems can to a large extent be explained by assuming the existence of a modular symmetry group commuting with the renormalization group flow and hence mapping different phases of two-dimensional electron gases into each other. Based on this insight, we construct a phenomenological holographic model which captures many features of the fractional quantum Hall effect. Using an SL(2,Z)-invariant Einstein-Maxwell-axio-dilaton theory capturing the important modular transformation properties of quantum Hall physics, we find dyonic diatonic black hole solutions which are gapped and have a Hall conductivity equal to the filling fraction, as expected for quantum Hall states. We also provide several technical results on the general behavior of the gauge field fluctuations around these dyonic dilatonic black hole solutions: We specify a sufficient criterion for IR normalizability of the fluctuations, demonstrate the preservation of the gap under the SL(2,Z) action, and prove that the singularity of the fluctuation problem in the presence of a magnetic field is an accessory singularity. We finish with a preliminary investigation of the possible IR scaling solutions of our model and some speculations on how they could be important for the observed universality of quantum Hall transitions.Comment: 86 pages, 16 figures; v.2 references added, typos fixed, improved discussion of ref. [39]; v.3 more references added and typos fixed, several statements clarified, v.4 version accepted for publication in JHE

Heralded generation of entangled photon pairs

Entangled photons are a crucial resource for quantum communication and linear optical quantum computation. Unfortunately, the applicability of many photon-based schemes is limited due to the stochastic character of the photon sources. Therefore, a worldwide effort has focused in overcoming the limitation of probabilistic emission by generating two-photon entangled states conditioned on the detection of auxiliary photons. Here we present the first heralded generation of photon states that are maximally entangled in polarization with linear optics and standard photon detection from spontaneous parametric down-conversion. We utilize the down-conversion state corresponding to the generation of three photon pairs, where the coincident detection of four auxiliary photons unambiguously heralds the successful preparation of the entangled state. This controlled generation of entangled photon states is a significant step towards the applicability of a linear optics quantum network, in particular for entanglement swapping, quantum teleportation, quantum cryptography and scalable approaches towards photonics-based quantum computing

Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Evidence-based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of c.25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na=2.27, Ar=2.24, He =0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of c.30% from historical levels (Na=3.36, Ar=3.29, He =0.63). Significant differentiation is seen between current and historical samples (FST =0.156, P=0.0315), and the current population exhibits extremely small Ne (current Ne =2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical Ne =1162.96). Individuals in the current population are related at the level of half- to full-siblings between social groups, and full-siblings or parent-offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential

Coherent spinor dynamics in a spin-1 Bose condensate

Collisions in a thermal gas are perceived as random or incoherent as a consequence of the large numbers of initial and final quantum states accessible to the system. In a quantum gas, e.g. a Bose-Einstein condensate or a degenerate Fermi gas, the phase space accessible to low energy collisions is so restricted that collisions be-come coherent and reversible. Here, we report the observation of coherent spin-changing collisions in a gas of spin-1 bosons. Starting with condensates occupying two spin states, a condensate in the third spin state is coherently and reversibly created by atomic collisions. The observed dynamics are analogous to Josephson oscillations in weakly connected superconductors and represent a type of matter-wave four-wave mixing. The spin-dependent scattering length is determined from these oscillations to be -1.45(18) Bohr. Finally, we demonstrate coherent control of the evolution of the system by applying differential phase shifts to the spin states using magnetic fields.Comment: 19 pages, 3 figure

Preferential regulation of stably expressed genes in the human genome suggests a widespread expression buffering role of microRNAs

In this study, we comprehensively explored the stably expressed genes (SE genes) and fluctuant genes (FL genes) in the human genome by a meta-analysis of large scale microarray data. We found that these genes have distinct function distributions. miRNA targets are shown to be significantly enriched in SE genes by using propensity analysis of miRNA regulation, supporting the hypothesis that miRNAs can buffer whole genome expression fluctuation. The expression-buffering effect of miRNA is independent of the target site number within the 3'-untranslated region. In addition, we found that gene expression fluctuation is positively correlated with the number of transcription factor binding sites in the promoter region, which suggests that coordination between transcription factors and miRNAs leads to balanced responses to external perturbations

Immunoblot analysis of the seroreactivity to recombinant Borrelia burgdorferi sensu lato antigens, including VlsE, in the long-term course of treated patients with Erythema migrans

Objective: We evaluated whether immunoblotting is capable of substantiating the posttreatment clinical assessment of patients with erythema migrans ( EM), the hallmark of early Lyme borreliosis. Methods: In 50 patients, seroreactivity to different antigens of Borrelia burgdorferi sensu lato was analyzed by a recombinant immunoblot test (IB) in consecutive serum samples from a minimum follow-up period of 1 year. Antigens in the IgG test were decorin- binding protein A, internal fragment of p41 (p41i), outer surface protein C (OspC), p39, variable major protein-like sequence expressed (VlsE), p58 and p100; those in the IgM test were p41i, OspC and p39. Immune responses were correlated with clinical and treatment-related parameters. Results: Positive IB results were found in 50% before, in 57% directly after therapy and in 44% by the end of the follow-up for the IgG class, and in 36, 43 and 12% for the IgM class. In acute and convalescence phase sera, VlsE was most immunogenic on IgG testing 60 and 70%), and p41i (46 and 57%) and OspC (40 and 57%) for the IgM class. By the end of the follow-up, only the anti-p41i lgM response was significantly decreased to 24%. Conclusions: No correlation was found between IB results and treatment-related parameters. Thus, immunoblotting does not add to the clinical assessment of EM patients after treatment. Copyright (c) 2008 S. Karger AG, Basel