CNVVdb: a database of copy number variations across vertebrate genomes

Summary: CNVVdb is a web interface for identification of putative copy number variations (CNVs) among 16 vertebrate species using the-same-species self-alignments and cross-species pairwise alignments. By querying genomic coordinates in the target species, all the potential paralogous/orthologous regions that overlap ≥80–100% (adjustable) of the query sequences with user-specified sequence identity (≥60%∼≥90%) are returned. Additional information is also given for the genes that are included in the returned regions, including gene description, alternatively spliced transcripts, gene ontology descriptions and other biologically important information. CNVVdb also provides information of pseudogenes and single nucleotide polymorphisms (SNPs) for the CNV-related genomic regions. Moreover, multiple sequence alignments of shared CNVs across species are also provided. With the combination of CNV, SNP, pseudogene and functional information, CNVVdb can be very useful for comparative and functional studies in vertebrates

WTO accession, the changing competitiveness of foreign-financed firms and regional development in Guangdong of southern China

This paper investigates the changing competitiveness of foreign-financed manufacturing firms and its implications for regional development in Guangdong province of southern China in the run-up to World Trade Organization (WTO) accession. It is argued that transnational corporations (TNCs) and some competitive, large-scale, locally-funded firms in Guangdong will triumph after WTO accession. The crowding-out process of small and medium sized enterprises (SMEs) in Guangdong will be accelerated in the near future, as they are competing directly with TNCs, and as their competitive advantages are diminishing, due to bureaucratic red tape and the rigorous enforcement of new government policies. Due to close business linkages with local privately-funded firms, the competitiveness and vitality of foreign-financed enterprises will have profound long term effects on the economic development of Guangdong, before and after WTO accession

Spectral Line-by-Line Pulse Shaping of an On-Chip Microresonator Frequency Comb

We report, for the first time to the best of our knowledge, spectral phase characterization and line-by-line pulse shaping of an optical frequency comb generated by nonlinear wave mixing in a microring resonator. Through programmable pulse shaping the comb is compressed into a train of near-transform-limited pulses of \approx 300 fs duration (intensity full width half maximum) at 595 GHz repetition rate. An additional, simple example of optical arbitrary waveform generation is presented. The ability to characterize and then stably compress the frequency comb provides new data on the stability of the spectral phase and suggests that random relative frequency shifts due to uncorrelated variations of frequency dependent phase are at or below the 100 microHertz level.Comment: 18 pages, 4 figure

Ripple modulated electronic structure of a 3D topological insulator

3D topological insulators, similar to the Dirac material graphene, host linearly dispersing states with unique properties and a strong potential for applications. A key, missing element in realizing some of the more exotic states in topological insulators is the ability to manipulate local electronic properties. Analogy with graphene suggests a possible avenue via a topographic route by the formation of superlattice structures such as a moir\'e patterns or ripples, which can induce controlled potential variations. However, while the charge and lattice degrees of freedom are intimately coupled in graphene, it is not clear a priori how a physical buckling or ripples might influence the electronic structure of topological insulators. Here we use Fourier transform scanning tunneling spectroscopy to determine the effects of a one-dimensional periodic buckling on the electronic properties of Bi2Te3. By tracking the spatial variations of the scattering vector of the interference patterns as well as features associated with bulk density of states, we show that the buckling creates a periodic potential modulation, which in turn modulates the surface and the bulk states. The strong correlation between the topographic ripples and electronic structure indicates that while doping alone is insufficient to create predetermined potential landscapes, creating ripples provides a path to controlling the potential seen by the Dirac electrons on a local scale. Such rippled features may be engineered by strain in thin films and may find use in future applications of topological insulators.Comment: Nature Communications (accepted

Common Variants in CDKAL1, CDKN2A/B, IGF2BP2, SLC30A8, and HHEX/IDE Genes Are Associated With Type 2 Diabetes and Impaired Fasting Glucose in a Chinese Han Population

OBJECTIVE— Genome-wide association studies have identified common variants in CDKAL1, CDKN2A/B, IGF2BP2, SLC30A8, HHEX/IDE, EXT2, and LOC387761 loci that significantly increase the risk of type 2 diabetes. We aimed to replicate these observations in a population-based cohort of Chinese Hans and examine the associations of these variants with type 2 diabetes and diabetes-related phenotypes

Effect of transition-metal substitution in iron-based superconductors

We study theoretically the current debatable issue about the effect of transition-metal (TM) substitution in iron-based superconductors through treating all of the TM ions as randomly distributed impurities. The extra electrons from TM elements are localized at the impurity sites. In the mean time the chemical potential shifts upon substitution. The phase diagram is mapped out and it seems that the TM elements can act as effective dopants. The local density of states (LDOS) is calculated and the bottom becomes V-shaped as the impurity concentration increases. The LDOS at the Fermi energy $\rho(\omega=0)$ is finite and reaches the minimum at the optimal doping level. Our results are in good agreement with the scanning tunneling microscopy experiments.Comment: 5 pages, 4 figure

Studies on Preparation of Photosensitizer Loaded Magnetic Silica Nanoparticles and Their Anti-Tumor Effects for Targeting Photodynamic Therapy

As a fast developing alternative of traditional therapeutics, photodynamic therapy (PDT) is an effective, noninvasive, nontoxic therapeutics for cancer, senile macular degeneration, and so on. But the efficacy of PDT was compromised by insufficient selectivity and low solubility. In this study, novel multifunctional silica-based magnetic nanoparticles (SMNPs) were strategically designed and prepared as targeting drug delivery system to achieve higher specificity and better solubility. 2,7,12,18-Tetramethyl-3,8-di-(1-propoxyethyl)-13,17-bis-(3-hydroxypropyl) porphyrin, shorted as PHPP, was used as photosensitizer, which was first synthesized by our lab with good PDT effects. Magnetite nanoparticles (Fe3O4) and PHPP were incorporated into silica nanoparticles by microemulsion and sol–gel methods. The prepared nanoparticles were characterized by transmission electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy and fluorescence spectroscopy. The nanoparticles were approximately spherical with 20–30 nm diameter. Intense fluorescence of PHPP was monitored in the cytoplasm of SW480 cells. The nanoparticles possessed good biocompatibility and could generate singlet oxygen to cause remarkable photodynamic anti-tumor effects. These suggested that PHPP-SMNPs had great potential as effective drug delivery system in targeting photodynamic therapy, diagnostic magnetic resonance imaging and magnetic hyperthermia therapy

PT-symmetric Solutions of Schrodinger Equation with position-dependent mass via Point Canonical Transformation

PT-symmetric solutions of Schrodinger equation are obtained for the Scarf and generalized harmonic oscillator potentials with the position-dependent mass. A general point canonical transformation is applied by using a free parameter. Three different forms of mass distributions are used. A set of the energy eigenvalues of the bound states and corresponding wave functions for target potentials are obtained as a function of the free parameter.Comment: 13 page

Pair-Hopping Mechanism for Layered Superconductors

We propose a possible charge fluctuation effect expected in layered superconducting materials. In the multireference density functional theory, relevant fluctuation channels for the Josephson coupling between superconducting layers include the interlayer pair hopping derived from the Coulomb repulsion. When interlayer single-electron tunneling processes are irrelevant in the Kohn-Sham electronic band structure calculation, the two-body effective interactions stabilize a superconducting phase. This state is also regarded as a valence-bond solid in a bulk electronic state. The hidden order parameters coexist with the superconducting order parameter when the charging effect of a layer is comparable to the pair hopping. Relevant materials structures favorable for the pair-hopping mechanism are discussed.Comment: 24 pages, 2 figures, to be published in J. Phys. Soc. Jpn. (2009

Generalized Toric Codes Coupled to Thermal Baths

We have studied the dynamics of a generalized toric code based on qudits at finite temperature by finding the master equation coupling the code's degrees of freedom to a thermal bath. As a consequence, we find that for qutrits new types of anyons and thermal processes appear that are forbidden for qubits. These include creation, annihilation and diffusion throughout the system code. It is possible to solve the master equation in a short-time regime and find expressions for the decay rates as a function of the dimension $d$ of the qudits. Although we provide an explicit proof that the system relax to the Gibbs state for arbitrary qudits, we also prove that above a certain crossing temperature, qutrits initial decay rate is smaller than the original case for qubits. Surprisingly this behavior only happens with qutrits and not with other qudits with $d>3$.Comment: Revtex4 file, color figures. New Journal of Physics' versio