Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Generalized conductance sum rule in atomic break junctions

When an atomic-size break junction is mechanically stretched, the total conductance of the contact remains approximately constant over a wide range of elongations, although at the same time the transmissions of the individual channels (valence orbitals of the junction atom) undergo strong variations. We propose a microscopic explanation of this phenomenon, based on Coulomb correlation effects between electrons in valence orbitals of the junction atom. The resulting approximate conductance quantization is closely related to the Friedel sum rule.Comment: 4 pages, 1 figure, appears in Proceedings of the NATO Advanced Research Workshop ``Size dependent magnetic scattering'', Pecs, Hungary, May 28 - June 1, 200

Biochar Extracts Can Modulate the Toxicity of Persistent Free Radicals in the Nematode Caenorhabditis elegans

As an effective soil amendment, biochars require a comprehensive ecological evaluation before they can be widely used in agriculture because endogenous contaminants, such as environmentally persistent free radicals (EPFRs), certainly pose an ecological risk to soil invertebrates. In this study, Caenorhabditis elegans (C. elegans) was used as a model organism to investigate the neurotoxicity of two rice straw biochars pyrolyzed at 500 and 700 °C. After 24 h exposure to unwashed biochar, washed biochar, and leaching fluids (supernatants), the neurobehavioral parameters of C. elegans were determined in a liquid toxicity test. The results showed that the washed 700 °C biochar particles significantly impaired locomotion and prolonged the defecation interval at a biochar concentration of 4 g·well−1, while the unwashed biochar and supernatants caused no apparent impairment. Supporting this, electron paramagnetic resonance (EPR) results showed that the intensity of EPFRs in unwashed 700 °C biochar was stronger than that of the corresponding washed particles. This indicates that, in the liquid test, the EPR signal alone is not indicative of particle toxicity. The accessibility and activity of the EPFRs should be considered. Dissolved organic matter (DOM) was observed in the leaching fluids. The neurotoxic activity of the washed biochar was alleviated after the re-addition of leaching fluids to the washed biochar, suggesting that the dissolved organic materials modulate the reactivity of the EPFRs in the liquid phase. This study suggests that the leaching process may increase the risk of biochar when used in the field environment.National Natural Scientific Foundation of ChinaYunnan Province Basic Research ProjectNSFC-NCNPeer Reviewe

Fast Searching in Packed Strings

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time which is optimal if we can only read one character at the time. However, most strings are stored in a computer in a packed representation with several characters in a single word, giving us the opportunity to read multiple characters simultaneously. In this paper we study the worst-case complexity of string matching on strings given in packed representation. Let $m \leq n$ be the lengths $P$ and $Q$, respectively, and let $\sigma$ denote the size of the alphabet. On a standard unit-cost word-RAM with logarithmic word size we present an algorithm using time O\left(\frac{n}{\log_\sigma n} + m + \occ\right). Here \occ is the number of occurrences of $P$ in $Q$. For $m = o(n)$ this improves the $O(n)$ bound of the Knuth-Morris-Pratt algorithm. Furthermore, if $m = O(n/\log_\sigma n)$ our algorithm is optimal since any algorithm must spend at least \Omega(\frac{(n+m)\log \sigma}{\log n} + \occ) = \Omega(\frac{n}{\log_\sigma n} + \occ) time to read the input and report all occurrences. The result is obtained by a novel automaton construction based on the Knuth-Morris-Pratt algorithm combined with a new compact representation of subautomata allowing an optimal tabulation-based simulation.Comment: To appear in Journal of Discrete Algorithms. Special Issue on CPM 200

Kink Stability of Self-Similar Solutions of Scalar Field in 2+1 Gravity

The kink stability of self-similar solutions of a massless scalar field with circular symmetry in 2+1 gravity is studied, and found that such solutions are unstable against the kink perturbations along the sonic line (self-similar horizon). However, when perturbations outside the sonic line are considered, and taking the ones along the sonic line as their boundary conditions, we find that non-trivial perturbations do not exist. In other words, the consideration of perturbations outside the sonic line limits the unstable mode of the perturbations found along the sonic line. As a result, the critical solution for the scalar collapse remains critical even after the kink perturbations are taken into account.Comment: latex, one figur

Solving variational inequalities defined on a domain with infinitely many linear constraints

We study a variational inequality problem whose domain is defined by infinitely many linear inequalities. A discretization method and an analytic center based inexact cutting plane method are proposed. Under proper assumptions, the convergence results for both methods are given. We also provide numerical examples to illustrate the proposed method

Level-Spacing Distributions and the Bessel Kernel

The level spacing distributions which arise when one rescales the Laguerre or Jacobi ensembles of hermitian matrices is studied. These distributions are expressible in terms of a Fredholm determinant of an integral operator whose kernel is expressible in terms of Bessel functions of order $\alpha$. We derive a system of partial differential equations associated with the logarithmic derivative of this Fredholm determinant when the underlying domain is a union of intervals. In the case of a single interval this Fredholm determinant is a Painleve tau function.Comment: 18 pages, resubmitted to make postscript compatible, no changes to manuscript conten

Conditions for Successful Extended Inflation

We investigate, in a model-independent way, the conditions required to obtain a satisfactory model of extended inflation in which inflation is brought to an end by a first-order phase transition. The constraints are that the correct present strength of the gravitational coupling is obtained, that the present theory of gravity is satisfactorily close to general relativity, that the perturbation spectra from inflation are compatible with large scale structure observations and that the bubble spectrum produced at the phase transition doesn't conflict with the observed level of microwave background anisotropies. We demonstrate that these constraints can be summarized in terms of the behaviour in the conformally related Einstein frame, and can be compactly illustrated graphically. We confirm the failure of existing models including the original extended inflation model, and construct models, albeit rather contrived ones, which satisfy all existing constraints.Comment: 8 pages RevTeX file with one figure incorporated (uses RevTeX and epsf). Also available by e-mailing ARL, or by WWW at http://star-www.maps.susx.ac.uk/papers/infcos_papers.html; Revised to include extra references, results unchanged, to appear Phys Rev

Faster Approximate String Matching for Short Patterns

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have lengths $m$ and $n$, respectively. On a standard unit-cost word RAM with word size $w \geq \log n$ we present an algorithm using time $$O(nk \cdot \min(\frac{\log^2 m}{\log n},\frac{\log^2 m\log w}{w}) + n)$$ When $P$ is short, namely, $m = 2^{o(\sqrt{\log n})}$ or $m = 2^{o(\sqrt{w/\log w})}$ this improves the previously best known time bounds for the problem. The result is achieved using a novel implementation of the Landau-Vishkin algorithm based on tabulation and word-level parallelism.Comment: To appear in Theory of Computing System

Phase diagram of an Ising model with long-range frustrating interactions: a theoretical analysis

We present a theoretical study of the phase diagram of a frustrated Ising model with nearest-neighbor ferromagnetic interactions and long-range (Coulombic) antiferromagnetic interactions. For nonzero frustration, long-range ferromagnetic order is forbidden, and the ground-state of the system consists of phases characterized by periodically modulated structures. At finite temperatures, the phase diagram is calculated within the mean-field approximation. Below the transition line that separates the disordered and the ordered phases, the frustration-temperature phase diagram displays an infinite number of ``flowers'', each flower being made by an infinite number of modulated phases generated by structure combination branching processes. The specificities introduced by the long-range nature of the frustrating interaction and the limitation of the mean-field approach are finally discussed.Comment: 32 pages, 7 figure