3,694 research outputs found
A Two-loop Test of Buscher's T-duality I
We study the two loop quantum equivalence of sigma models related by
Buscher's T-duality transformation. The computation of the two loop
perturbative free energy density is performed in the case of a certain
deformation of the SU(2) principal sigma model, and its T-dual, using
dimensional regularization and the geometric sigma model perturbation theory.
We obtain agreement between the free energy density expressions of the two
models.Comment: 28 pp, Latex, references adde
Deterministic and Probabilistic Binary Search in Graphs
We consider the following natural generalization of Binary Search: in a given
undirected, positively weighted graph, one vertex is a target. The algorithm's
task is to identify the target by adaptively querying vertices. In response to
querying a node , the algorithm learns either that is the target, or is
given an edge out of that lies on a shortest path from to the target.
We study this problem in a general noisy model in which each query
independently receives a correct answer with probability (a
known constant), and an (adversarial) incorrect one with probability .
Our main positive result is that when (i.e., all answers are
correct), queries are always sufficient. For general , we give an
(almost information-theoretically optimal) algorithm that uses, in expectation,
no more than queries, and identifies the target correctly with probability at
leas . Here, denotes the
entropy. The first bound is achieved by the algorithm that iteratively queries
a 1-median of the nodes not ruled out yet; the second bound by careful repeated
invocations of a multiplicative weights algorithm.
Even for , we show several hardness results for the problem of
determining whether a target can be found using queries. Our upper bound of
implies a quasipolynomial-time algorithm for undirected connected
graphs; we show that this is best-possible under the Strong Exponential Time
Hypothesis (SETH). Furthermore, for directed graphs, or for undirected graphs
with non-uniform node querying costs, the problem is PSPACE-complete. For a
semi-adaptive version, in which one may query nodes each in rounds, we
show membership in in the polynomial hierarchy, and hardness
for
Theoretically Efficient Parallel Graph Algorithms Can Be Fast and Scalable
There has been significant recent interest in parallel graph processing due
to the need to quickly analyze the large graphs available today. Many graph
codes have been designed for distributed memory or external memory. However,
today even the largest publicly-available real-world graph (the Hyperlink Web
graph with over 3.5 billion vertices and 128 billion edges) can fit in the
memory of a single commodity multicore server. Nevertheless, most experimental
work in the literature report results on much smaller graphs, and the ones for
the Hyperlink graph use distributed or external memory. Therefore, it is
natural to ask whether we can efficiently solve a broad class of graph problems
on this graph in memory.
This paper shows that theoretically-efficient parallel graph algorithms can
scale to the largest publicly-available graphs using a single machine with a
terabyte of RAM, processing them in minutes. We give implementations of
theoretically-efficient parallel algorithms for 20 important graph problems. We
also present the optimizations and techniques that we used in our
implementations, which were crucial in enabling us to process these large
graphs quickly. We show that the running times of our implementations
outperform existing state-of-the-art implementations on the largest real-world
graphs. For many of the problems that we consider, this is the first time they
have been solved on graphs at this scale. We have made the implementations
developed in this work publicly-available as the Graph-Based Benchmark Suite
(GBBS).Comment: This is the full version of the paper appearing in the ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA), 201
MIMO free-space optical communication employing subcarrier intensity modulation in atmospheric turbulence channels
In this paper, we analyse the error performance of transmitter/receiver array free-space optical (FSO) communication system employing binary phase shift keying (BPSK) subcarrier intensity modulation (SIM) in clear but turbulent atmospheric channel. Subcarrier modulation is employed to eliminate the need for adaptive threshold detector. Direct detection is employed at the receiver and each subcarrier is subsequently demodulated coherently. The effect of irradiance fading is mitigated with an array of lasers and photodetectors. The received signals are linearly combined using the optimal maximum ratio combining (MRC), the equal gain combining (EGC) and the selection combining (SelC). The bit error rate (BER) equations are derived considering additive white Gaussian noise and log normal intensity fluctuations. This work is part of the EU COST actions and EU projects
Impact of processed earwigs and their faeces on the aroma and taste of 'Chasselas' and 'Pinot Noir' wines
The abundance of the European earwig Forficula auricularia L. (Dermaptera, Forficulidae) in European vineyards increased considerably over the last few years. Although earwigs are omnivorous predators that prey on viticultural pests such as grape moths, they are also known to erode berries and to transfer fungal spores. Moreover, they are suspected to affect the human perception of wines both directly by their processing with the grapes and indirectly by the contamination of grape clusters with their faeces. In this study we artificially contaminated grapes with F. auricularia adults and/or their faeces and determined the impact on aroma and taste of white 'Chasselas' and red 'Pinot noir' wines. Whereas the addition of five living adults/kg grapes affected the olfactory sensation of 'Chasselas' wines only marginally, 0.6 gram of earwig faeces/kg grapes had a strong effect on colour, aroma and the general appreciation of 'Chasselas' wines. Faeces-contaminated wines were less fruity and less floral, the aroma was described as faecal and they were judged to be of lower quality. The contamination of 'Pinot noir' grapes with four different densities of living earwig adults (e.g. 0, 5, 10 and 20 individuals/kg grapes) showed that only wines contaminated with more than 10 earwigs/kg grapes smelled and tasted significantly different than the uncontaminated control wine. Earwig-contaminated 'Pinot noir' wines were judged to be of lower quality. The descriptors “animal”, “reductive”, “vegetal”, “acidic”, “bitter” and “tannic” characterised their sensory perception. In conclusion, our results show that there is a real risk of wine contamination by F. auricularia. In particular, earwig faeces and earwig adults at densities above a threshold of 5 to 10 individuals/kg grapes have the potential to reduce the quality of wines. The evolution of earwig populations in vineyards should therefore be monitored carefully in order to anticipate problems during vinification.
Optimal Vertex Cover for the Small-World Hanoi Networks
The vertex-cover problem on the Hanoi networks HN3 and HN5 is analyzed with
an exact renormalization group and parallel-tempering Monte Carlo simulations.
The grand canonical partition function of the equivalent hard-core repulsive
lattice-gas problem is recast first as an Ising-like canonical partition
function, which allows for a closed set of renormalization group equations. The
flow of these equations is analyzed for the limit of infinite chemical
potential, at which the vertex-cover problem is attained. The relevant fixed
point and its neighborhood are analyzed, and non-trivial results are obtained
both, for the coverage as well as for the ground state entropy density, which
indicates the complex structure of the solution space. Using special
hierarchy-dependent operators in the renormalization group and Monte-Carlo
simulations, structural details of optimal configurations are revealed. These
studies indicate that the optimal coverages (or packings) are not related by a
simple symmetry. Using a clustering analysis of the solutions obtained in the
Monte Carlo simulations, a complex solution space structure is revealed for
each system size. Nevertheless, in the thermodynamic limit, the solution
landscape is dominated by one huge set of very similar solutions.Comment: RevTex, 24 pages; many corrections in text and figures; final
version; for related information, see
http://www.physics.emory.edu/faculty/boettcher
Approximate Deadline-Scheduling with Precedence Constraints
We consider the classic problem of scheduling a set of n jobs
non-preemptively on a single machine. Each job j has non-negative processing
time, weight, and deadline, and a feasible schedule needs to be consistent with
chain-like precedence constraints. The goal is to compute a feasible schedule
that minimizes the sum of penalties of late jobs. Lenstra and Rinnoy Kan
[Annals of Disc. Math., 1977] in their seminal work introduced this problem and
showed that it is strongly NP-hard, even when all processing times and weights
are 1. We study the approximability of the problem and our main result is an
O(log k)-approximation algorithm for instances with k distinct job deadlines
A high-throughput in vivo micronucleus assay for genome instability screening in mice.
We describe a sensitive, robust, high-throughput method for quantifying the formation of micronuclei, markers of genome instability, in mouse erythrocytes. Micronuclei are whole chromosomes or chromosome segments that have been separated from the nucleus. Other methods of detection rely on labor-intensive, microscopy-based techniques. Here we describe a 2-d, 96-well plate-based flow cytometric method of micronucleus scoring that is simple enough for a research technician experienced in flow cytometry to perform. The assay detects low levels of genome instability that cannot be readily identified by classic phenotyping, using 25 μl of blood. By using this assay, we have screened >10,000 blood samples and discovered novel genes that contribute to vertebrate genome maintenance, as well as novel disease models and mechanisms of genome instability disorders. We discuss experimental design considerations, including statistical power calculation, we provide troubleshooting tips and we discuss factors that contribute to a false-positive increase in the number of micronucleated red blood cells and to experimental variability.Acknowledgments We thank M. Hitcham and N. Harman for assistance
with blood collections, W. Cheng for assistance with flow cytometry during
high-throughput screening and K. Dry for comments on the manuscript. R.E.M.
is supported by Cancer Research UK (CRUK; project grant C20510/A12401).
D.J.A. is supported by CRUK. D.J.A. and B.L.N. are supported by the Wellcome
Trust. Research in the Jackson Laboratory is funded by CRUK program grant
no. C6/A11224, the European Research Council and the European Community
Seventh Framework Programme grant agreement no. HEALTH-F2-2010-259893
(DDResponse). Core funding is provided by CRUK (C6946/A14492) and the
Wellcome Trust (WT092096). S.P.J. receives his salary from the University of
Cambridge, UK, supplemented by CRUK. G.B. is funded by CRUK program
grant no. C6/A11224.This is the accepted manuscript for a paper published in Nature Protocols 10, 205–215 (2015) doi:10.1038/nprot.2015.010, Published online 31 December 201
Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data
We present two complementary approaches for the interpretation of clusters of
co-regulated genes, such as those obtained from DNA chips and related methods.
Starting from a cluster of genes with similar expression profiles, two basic
questions can be asked:
1. Which mechanism is responsible for the coordinated transcriptional response
of the genes? This question is approached by extracting motifs that are shared
between the upstream sequences of these genes. The motifs extracted are putative
cis-acting regulatory elements.
2. What is the physiological meaning for the cell to express together these
genes? One way to answer the question is to search for potential metabolic
pathways that could be catalyzed by the products of the genes. This can be
done by selecting the genes from the cluster that code for enzymes, and trying
to assemble the catalyzed reactions to form metabolic pathways.
We present tools to answer these two questions, and we illustrate their use with
selected examples in the yeast Saccharomyces cerevisiae. The tools are available
on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/;
http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)
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