Inapproximability of maximal strip recovery

In comparative genomic, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in the genomic maps need to be removed first. Maximal Strip Recovery (MSR) is an optimization problem proposed by Zheng, Zhu, and Sankoff for reliably recovering syntenic blocks from genomic maps in the midst of noise and ambiguities. Given $d$ genomic maps as sequences of gene markers, the objective of \msr{d} is to find $d$ subsequences, one subsequence of each genomic map, such that the total length of syntenic blocks in these subsequences is maximized. For any constant $d \ge 2$, a polynomial-time 2d-approximation for \msr{d} was previously known. In this paper, we show that for any $d \ge 2$, \msr{d} is APX-hard, even for the most basic version of the problem in which all gene markers are distinct and appear in positive orientation in each genomic map. Moreover, we provide the first explicit lower bounds on approximating \msr{d} for all $d \ge 2$. In particular, we show that \msr{d} is NP-hard to approximate within $\Omega(d/\log d)$. From the other direction, we show that the previous 2d-approximation for \msr{d} can be optimized into a polynomial-time algorithm even if $d$ is not a constant but is part of the input. We then extend our inapproximability results to several related problems including \cmsr{d}, \gapmsr{\delta}{d}, and \gapcmsr{\delta}{d}.Comment: A preliminary version of this paper appeared in two parts in the Proceedings of the 20th International Symposium on Algorithms and Computation (ISAAC 2009) and the Proceedings of the 4th International Frontiers of Algorithmics Workshop (FAW 2010

Metal-to-insulator transition in anatase TiO2 thin films induced by growth rate modulation

We demonstrate control of the carrier density of single phase anatase TiO2 thin films by nearly two orders of magnitude by modulating the growth kinetics during pulsed laser deposition, under fixed thermodynamic conditions. The resistivity and the intensity of the photoluminescence spectra of these TiO2 samples, both of which correlate with the number of oxygen vacancies, are shown to depend strongly on the growth rate. A quantitative model is used to explain the carrier density changes.Comment: 13 pages 3 figure

Detection of high k turbulence using two dimensional phase contrast imaging on LHD

High k turbulence, up to 30 cm(-1), can be measured using the two dimensional CO₂ laser phase contrast imaging system on LHD. Recent hardware improvements and experimental results are presented. Precise control over the lens positions in the detection system is necessary because of the short depth of focus for high k modes. Remote controllable motors to move optical elements were installed, which, combined with measurements of the response to ultrasound injection, allowed experimental verification and shot-to-shot adjustment of the object plane. Strong high k signals are observed within the first 100-200 ms after the initial electron cyclotron heating (ECH) breakdown, in agreement with gyrotron scattering. During later times in the discharge, the entire k spectrum shifts to lower values (although the total amplitude does not change significantly), and the weaker high k signals are obscured by leakage of low k components at low frequency, and detector noise, at high frequency

Evidence of a link between the evolution of clusters and their AGN fraction

‘The definitive version is available at www3.interscience.wiley.com .' Copyright Blackwell Publishing / Royal Astronomical Society. DOI: 10.1111/j.1365-2966.2009.14513.xPeer reviewe

Sub-Cycle Optical Response Caused by Dressed State with Phase-Locked Wavefunctions

The coherent interaction of light with matter imprints the phase information of the light field on the wavefunction of the photon-dressed electronic state. Driving electric field, together with a stable phase that is associated with the optical probe pulses, enables the role of the dressed state in the optical response to be investigated. We observed optical absorption strengths modulated on a sub-cycle timescale in a GaAs quantum well in the presence of a multi-cycle terahertz driving pulse using a near-infrared probe pulse. The measurements were in good agreement with the analytical formula that accounts for the optical susceptibilities caused by the dressed state of excitons, which indicates that the output probe intensity was coherently reshaped by the excitonic sideband emissions

Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair

Nucleotide excision repair (NER) in yeast is effected by the concerted action of a large complex of proteins. Recently, we identified a stable subcomplex containing the yeast Rad7 and Rad16 proteins. Here, we report the identification of autonomously replicating sequence binding factor 1 (ABF1) as a component of the Rad7/Rad16 NER subcomplex. Yeast ABF1 protein is encoded by an essential gene required for DNA replication, transcriptional regulation, and gene silencing. We show that ABF1 plays a direct role in NER in vitro. Additionally, consistent with a role of ABF1 protein in NER in vivo, we show that certain temperature-sensitive abf1 mutant strains that are defective in DNA replication are specifically defective in the removal of photoproducts by NER and are sensitive to killing by ultraviolet (UV) radiation. These studies define a novel and unexpected role for ABF1 protein during NER in yeast