Connecting the vulcanization transition to percolation

The vulcanization transition is addressed via a minimal replica-field-theoretic model. The appropriate long-wave-length behavior of the two- and three-point vertex functions is considered diagrammatically, to all orders in perturbation theory, and identified with the corresponding quantities in the Houghton-Reeve-Wallace field-theoretic approach to the percolation critical phenomenon. Hence, it is shown that percolation theory correctly captures the critical phenomenology of the vulcanization transition associated with the liquid and critical states.Comment: 9 pages, 5 figure

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem have been proposed recently. In this work, we show how to reduce the memory required by the algorithm of [3] that represents de Brujin graphs using Bloom filters. Our method requires 30% to 40% less memory with respect to the method of [3], with insignificant impact to construction time. At the same time, our experiments showed a better query time compared to [3]. This is, to our knowledge, the best practical representation for de Bruijn graphs.Comment: 12 pages, submitte

Detecting and Characterizing Small Dense Bipartite-like Subgraphs by the Bipartiteness Ratio Measure

We study the problem of finding and characterizing subgraphs with small \textit{bipartiteness ratio}. We give a bicriteria approximation algorithm \verb|SwpDB| such that if there exists a subset $S$ of volume at most $k$ and bipartiteness ratio $\theta$, then for any $0<\epsilon<1/2$, it finds a set $S'$ of volume at most $2k^{1+\epsilon}$ and bipartiteness ratio at most $4\sqrt{\theta/\epsilon}$. By combining a truncation operation, we give a local algorithm \verb|LocDB|, which has asymptotically the same approximation guarantee as the algorithm \verb|SwpDB| on both the volume and bipartiteness ratio of the output set, and runs in time $O(\epsilon^2\theta^{-2}k^{1+\epsilon}\ln^3k)$, independent of the size of the graph. Finally, we give a spectral characterization of the small dense bipartite-like subgraphs by using the $k$th \textit{largest} eigenvalue of the Laplacian of the graph.Comment: 17 pages; ISAAC 201

Emerging threat of thrips-borne Melon yellow spot virus on melon and watermelon in Taiwan

The thrips-borne Melon yellow spot virus (MYSV) has recently been found infecting cucurbits in Taiwan. However, this virus was indistinguishable from another thrips-borne virus species Watermelon silver mottle virus (WSMoV), which has been devastating on cucurbits in Taiwan for decades, when the antisera against their nucleocapsid proteins (NPs) were used for diagnosis. To understand the incidences of WSMoV and MYSV in melon and watermelon fields, a survey was conducted in central and southern Taiwan from July 2007 to December 2009. The samples collected from symptomatic plants were tested by indirect enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies (MAbs) specific to the NP of WSMoV or MYSV and the reliability of the results was verified by reverse transcription-polymerase chain reaction (RT-PCR) using species-specific primers. Among a total of 10,480 melon samples collected, 6% and 18.2% of them were found singly infected with WSMoV and MYSV, respectively, and 0.16% infected with both viruses. On the other hand, among 1,811 watermelon samples assayed, 22.4% and 9.2% samples were singly infected with WSMoV and MYSV, respectively, and 0.17% were infected with both viruses. In addition, the aphid-borne viruses Zucchini yellow mosaic virus (ZYMV), Papaya ringspot virus watermelon type (PRSV-W) and Cucumber mosaic virus (CMV) were also detected as prevalent viruses. Our results indicated that mixed infection with the two thrips-borne viruses is rare. Moreover, host preference for both viruses is different; WSMoV prevails on watermelon whereas MYSV is more widespread on melon. We conclude that MYSV has become a serious threat for watermelon and melon production in Taiwan and the possible control measures are discussed

Survival-Time Distribution for Inelastic Collapse

In a recent publication [PRL {\bf 81}, 1142 (1998)] it was argued that a randomly forced particle which collides inelastically with a boundary can undergo inelastic collapse and come to rest in a finite time. Here we discuss the survival probability for the inelastic collapse transition. It is found that the collapse-time distribution behaves asymptotically as a power-law in time, and that the exponent governing this decay is non-universal. An approximate calculation of the collapse-time exponent confirms this behaviour and shows how inelastic collapse can be viewed as a generalised persistence phenomenon.Comment: 4 pages, RevTe

Geochemical analysis of bulk marine sediment by Inductively Coupled Plasma–Atomic Emission Spectroscopy on board the JOIDES Resolution

Geochemical analyses on board the JOIDES Resolution have been enhanced with the addition of a Jobin-Yvon Ultrace inductively coupled plasma-atomic emission spectrometer (ICP-AES) as an upgrade from the previous X-ray fluorescence facility. During Leg 199, we sought to both challenge and utilize the capabilities of the ICP-AES in order to provide an extensive bulk-sediment geochemical database during the cruise. These near real-time analyses were then used to help characterize the recovered sedimentary sequences, calculate mass accumulation rates of the different sedimentary components, and assist with cruise and postcruise sampling requests. The general procedures, sample preparation techniques, and basic protocol for ICP-AES analyses on board ship are outlined by Murray et al. (2000) in Ocean Drilling Program Tech Note, 29. We expand on those concepts and offer suggestions for ICP-AES methodology, calibration by standard reference materials, data reduction procedures, and challenges that are specific to the analysis of bulk-sediment samples. During Leg 199, we employed an extensive bulk-sediment analytical program of ~600 samples of varying lithologies, thereby providing several opportunities for refinement of techniques. We also discuss some difficulties and challenges that were faced and suggest how to alleviate such occurrences for sedimentary chemical analyses during future legs

Entangled light in transition through the generation threshold

We investigate continuous variable entangling resources on the base of two-mode squeezing for all operational regimes of a nondegenerate optical parametric oscillator with allowance for quantum noise of arbitrary level. The results for the quadrature variances of a pair of generated modes are obtained by using the exact steady-state solution of Fokker-Planck equation for the complex P-quasiprobability distribution function. We find a simple expression for the squeezed variances in the near-threshold range and conclude that the maximal two-mode squeezing reaches 50% relative to the level of vacuum fluctuations and is achieved at the pump field intensity close to the generation threshold. The distinction between the degree of two-mode squeezing for monostable and bistable operational regimes is cleared up.Comment: 7 pages, 4 figures; Content changed: more details added to the discussion. To be published in Phys. Rev.

Restoration of kTk_T factorization for low pTp_T hadron hadroproduction

We discuss the applicability of the $k_T$ factorization theorem to low-$p_T$ hadron production in hadron-hadron collision in a simple toy model, which involves only scalar particles and gluons. It has been shown that the $k_T$ factorization for high-$p_T$ hadron hadroproduction is broken by soft gluons in the Glauber region, which are exchanged among a transverse-momentum-dependent (TMD) parton density and other subprocesses of the collision. We explain that the contour of a loop momentum can be deformed away from the Glauber region at low $p_T$, so the above residual infrared divergence is factorized by means of the standard eikonal approximation. The $k_T$ factorization is then restored in the sense that a TMD parton density maintains its universality. Because the resultant Glauber factor is independent of hadron flavors, experimental constraints on its behavior are possible. The $k_T$ factorization can also be restored for the transverse single-spin asymmetry in hadron-hadron collision at low $p_T$ in a similar way, with the residual infrared divergence being factorized into the same Glauber factor.Comment: 12 pages, 2 figures, version to appear in EPJ

From Indexing Data Structures to de Bruijn Graphs

International audienceNew technologies have tremendously increased sequencing throughput com-pared to traditional techniques, thereby complicating DNA assembly. Hence, as-sembly programs resort to de Bruijn graphs (dBG) of k-mers of short reads to compute a set of long contigs, each being a putative segment of the sequenced molecule. Other types of DNA sequence analysis, as well as preprocessing of the reads for assembly, use classical data structures to index all substrings of the reads. It is thus interesting to exhibit algorithms that directly build a dBG of order k from a pre-existing index, and especially a contracted version of the dBG, where non branching paths are condensed into single nodes. Here, we formalise the relation-ship between suffix trees/arrays and dBGs, and exhibit linear time algorithms for constructing the full or contracted dBGs. Finally, we provide hints explaining why this bridge between indexes and dBGs enables to dynamically update the order k of the graph

Transverse Momentum Dependent Parton Distribution/Fragmentation Functions at an Electron-Ion Collider

We present a summary of a recent workshop held at Duke University on Partonic Transverse Momentum in Hadrons: Quark Spin-Orbit Correlations and Quark-Gluon Interactions. The transverse momentum dependent parton distribution functions (TMDs), parton-to-hadron fragmentation functions, and multi-parton correlation functions, were discussed extensively at the Duke workshop. In this paper, we summarize first the theoretical issues concerning the study of partonic structure of hadrons at a future electron-ion collider (EIC) with emphasis on the TMDs. We then present simulation results on experimental studies of TMDs through measurements of single spin asymmetries (SSA) from semi-inclusive deep-inelastic scattering (SIDIS) processes with an EIC, and discuss the requirement of the detector for SIDIS measurements. The dynamics of parton correlations in the nucleon is further explored via a study of SSA in D (`D) production at large transverse momenta with the aim of accessing the unexplored tri-gluon correlation functions. The workshop participants identified the SSA measurements in SIDIS as a golden program to study TMDs in both the sea and valence quark regions and to study the role of gluons, with the Sivers asymmetry measurements as examples. Such measurements will lead to major advancement in our understanding of TMDs in the valence quark region, and more importantly also allow for the investigation of TMDs in the sea quark region along with a study of their evolution.Comment: 44 pages 23 figures, summary of Duke EIC workshop on TMDs accepted by EPJ