Linear-Time Superbubble Identification Algorithm for Genome Assembly

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome constitutes a major algorithmic challenge. Most assembly algorithms utilize de Bruijn graphs constructed from reads for this purpose. A critical step of these algorithms is to detect typical motif structures in the graph caused by sequencing errors and genome repeats, and filter them out; one such complex subgraph class is a so-called superbubble. In this paper, we propose an O(n+m)-time algorithm to detect all superbubbles in a directed acyclic graph with n nodes and m (directed) edges, improving the best-known O(m log m)-time algorithm by Sung et al

NIRT: gated transport through carbon nanotube membranes

Issued as final reportUniversity of California, Berkele

Efficient Computation of Sequence Mappability

Sequence mappability is an important task in genome re-sequencing. In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, our goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that length-$m$ substrings of $T$ starting at positions $i$ and $j$ have at most $k$ mismatches. Previous works on this problem focused on heuristic approaches to compute a rough approximation of the result or on the case of $k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that works in $\mathcal{O}(n \min\{m^k,\log^{k+1} n\})$ time and $\mathcal{O}(n)$ space for $k=\mathcal{O}(1)$. It requires a carefu l adaptation of the technique of Cole et al.~[STOC 2004] to avoid multiple counting of pairs of substrings. We also show $\mathcal{O}(n^2)$-time algorithms to compute all results for a fixed $m$ and all $k=0,\ldots,m$ or a fixed $k$ and all $m=k,\ldots,n-1$. Finally we show that the $(k,m)$-mappability problem cannot be solved in strongly subquadratic time for $k,m = \Theta(\log n)$ unless the Strong Exponential Time Hypothesis fails.Comment: Accepted to SPIRE 201

Development and application of rice starch based edible coating to improve the postharvest storage potential and quality of plum fruit (<i>Prunus salicina</i>)

The study investigated the possibility of enhancing the shelf life of plum fruit coated with rice starch-ι-carrageenan (RS-ι-car) composite coating blended with sucrose fatty acid esters (FAEs). Film solution (starch 3%, carrageenan 1.5% and FAEs 2%) was prepared by mixing the ingredients and properties of stand-alone films (physical, mechanical, barrier and surface morphology) were studied before applying the coating on fruit surface. Fruit were stored at 20 °C for 3 weeks and analyzed for weight loss, ethylene production, respiration rate, color change, firmness, and titratable acidity (TA) and soluble solid content (SSC). Surface morphology of stand-alone film and fruit surface (after applying on the plum fruit) was studied using scanning electron microscopy (SEM). Phytochemical analysis was performed during the storage period and total phenolic content (TPC), total antioxidant capacity (TAC), flavonoid content (FC) and free radical scavenging activity were determined. The rice starch composite coating was shown to be effective in reducing both weight loss (WL) and respiration rate and inhibiting the endogenous ethylene production when compared to the uncoated control fruit stored at room temperature (p &lt; 0.05). TPC, TAC, FC and free radical scavenging activity was unaffected in the coated fruit throughout the storage period (p &lt; 0.05). The findings reported in this study indicate that the RS-ι-car-FAEs coating prolongs the shelf life and maintains the overall quality of plum fruit during storage and could potentially be commercialized as a new edible coating for the plum fruit industry

Tweeting Library and Information Science: a socio-topical distance analysis

The aim of this paper is to demonstrate how topical distance and social distance can provide meaningful results when analysing scholars’ tweets linking to scholarly publications. To do so, we analyse the social and topical distance between tweeted information science papers and their academic tweeters. This allows us to characterize the tweets of scientific papers, the tweeting behavior of scholars, and the relationship between tweets and citations

On the Integrability of the Bukhvostov-Lipatov Model

The integrability of the Bukhvostov-Lipatov four-fermion model is investigated. It is shown that the classical model possesses a current of Lorentz spin 3, conserved both in the bulk and on the half-line for specific types of boundary actions. It is then established that the conservation law is spoiled at the quantum level -- a fact that might indicate that the quantum Bukhvostov-Lipatov model is not integrable, contrary to what was previously believed.Comment: 11 pages, 1 figure, LaTeX2e, AMS; new references adde

Detection of Earth-like Planets Using Apodized Telescopes

The mission of NASA's Terrestrial Planet Finder (TPF) is to find Earth-like planets orbiting other stars and characterize the atmospheres of these planets using spectroscopy. Because of the enormous brightness ratio between the star and the reflected light from the planet, techniques must be found to reduce the brightness of the star. The current favorite approach to doing this is with interferometry: interfering the light from two or more separated telescopes with a $\pi$ phase shift, nulling out the starlight. While this technique can, in principle, achieve the required dynamic range, building a space interferometer that has the necessary characteristics poses immense technical difficulties. In this paper, we suggest a much simpler approach to achieving the required dynamic range. By simply adjusting the transmissive shape of a telescope aperture, the intensity in large regions around the stellar image can be reduced nearly to zero. This approach could lead to construction of a TPF using conventional technologies, requiring space optics on a much smaller scale than the current TPF approach.Comment: Accepted for publication in ApJ Letters, 9 pages, 6 figure

Failure of Mean Field Theory at Large N

We study strongly coupled lattice QCD with $N$ colors of staggered fermions in 3+1 dimensions. While mean field theory describes the low temperature behavior of this theory at large $N$, it fails in the scaling region close to the finite temperature second order chiral phase transition. The universal critical region close to the phase transition belongs to the 3d XY universality class even when $N$ becomes large. This is in contrast to Gross-Neveu models where the critical region shrinks as $N$ (the number of flavors) increases and mean field theory is expected to describe the phase transition exactly in the limit of infinite $N$. Our work demonstrates that close to second order phase transitions infrared fluctuations can sometimes be important even when $N$ is strictly infinite.Comment: 4 pages, 3 figure