A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

Theory of Thermodynamic Magnetic Oscillations in Quasi-One-Dimensional Conductors

The second order correction to free energy due to the interaction between electrons is calculated for a quasi-one-dimensional conductor exposed to a magnetic field perpendicular to the chains. It is found that specific heat, magnetization and torque oscillate when the magnetic field is rotated in the plane perpendicular to the chains or when the magnitude of magnetic filed is changed. This new mechanism of thermodynamic magnetic oscillations in metals, which is not related to the presence of any closed electron orbits, is applied to explain behavior of the organic conductor (TMTSF)$_2$ClO$_4$.Comment: 11 pages + 5 figures (included

China and the crisis : global power, domestic caution and local initiative

Even though the global crisis had a quick and dramatic impact on Chinese exports, the Chinese government responded with a range of policy responses that have helped maintain high rates of growth. This success has helped propel China to the centre of global politics, accelerating what many perceive to be a power shift from the West to China. But these gains were achieved by reversing policy in previous years designed to make a fundamental shift in China‟s mode of development, and have highlighted the problems associated with making such a transition. At the moment that many are looking at the Chinese "model" as a potential alternative to the Washington Consensus, one of the consequences of the crisis is to further question the long term efficacy of this "model" in China itself

Quantum Hall Effect in Three-dimensional Field-Induced Spin Density Wave Phases with a Tilted Magnetic Field

The quantum Hall effect in the three-dimensional anisotropic tight-binding electrons is investigated in the field-induced spin density wave phases with a magnetic field tilted to any direction. The Hall conductivity, $\sigma_{xy}$ and $\sigma_{xz}$, are shown to be quantized as a function of the wave vector of FISDW, while $\sigma_{yz}$ stays zero, where $x$ is the most conducting direction and $y$ and $z$ are perpendicular to $x$.Comment: 18 pages, REVTeX 3.0, 1 figure is available upon request, to be published in Physical Review

Role of the dimerized gap due to anion ordering in spin-density wave phase of (TMTSF)2_2ClO4_4 at high magnetic fields

Magnetoresistance measurements have been carried out along the highly conducting a axis in the FISDW phase of hydrogened and deuterated (TMTSF)$_2$ClO$_4$ for various cooling rates through the anion ordering temperature. With increasing the cooling rate, a) the high field phase boundary $\beta_{\rm {HI}}$, observed at 27 T in hydrogened samples for slowly cooled, is shifted towards a lower field, b) the last semimetallic SDW phase below $\beta_{\rm {HI}}$ is suppressed, and c) the FISDW insulating phase above $\beta_{\rm {HI}}$ is enhanced in both salts. The cooling rate dependence of the FISDW transition and of $\beta_{\rm {HI}}$ in both salts can be explained by taking into account the peculiar SDW nesting vector stabilized by the dimerized gap due to anion ordering.Comment: 6pages,6figures(EPS), accepted for publication in PR

Demonstration of multi-channel 80 Gbit/s integrated transmitter and receiver for wavelength-division multiplexing passive optical network and fronthauling applications

The performance evaluation of a multi-channel transmitter that employs an arrayed reflective electroabsorption modulator-based photonic integrated circuit and a low-power driver array in conjunction with a multi-channel receiver incorporating a pin photodiode array and integrated arrayed waveguide grating is reported. Due to their small footprint, low power consumption and potential low cost, these devices are attractive solutions for future mobile fronthaul and next generation optical access networks. A BER performance of <10(-9) at 10.3 Gbit/s per channel is achieved over 25 km of standard single mode fibre. The transmitter/receiver combination can achieve an aggregate bit rate of 82.4 Gbit/s when eight channels are active

Discretely guided electromagnetic effective medium

A material comprised of an array of subwavelength coaxial waveguides decomposes incident electromagnetic waves into spatially discrete wave components, propagates these components without frequency cut-off, and reassembles them on the far side of the material. The propagation of these wave components is fully controlled by the physical properties of the waveguides and their geometrical distribution in the array. This allows for an exceptional degree of control over the electromagnetic response of this effective medium, with numerous potential applications. With the development of nanoscale subwavelength coaxial waveguides, these applications (including metamaterial functionality) can be enabled in the visible frequency range

Towards spectrally selective catastrophic response

We study the large-amplitude response of classical molecules to electromagnetic radiation, showing the universality of the transition from linear to nonlinear response and breakup at sufficiently large amplitudes. We demonstrate that a range of models, from the simple harmonic oscillator to the successful Peyrard-Bishop-Dauxois type models of DNA, which include realistic effects of the environment (including damping and dephasing due to thermal fluctuations), lead to characteristic universal behavior: formation of domains of dissociation in driving force amplitude-frequency space, characterized by the presence of local boundary minima. We demonstrate that by simply following the progression of the resonance maxima in this space, while gradually increasing intensity of the radiation, one must necessarily arrive at one of these minima, i.e., a point where the ultrahigh spectral selectivity is retained. We show that this universal property, applicable to other oscillatory systems, is a consequence of the fact that these models belong to the fold catastrophe universality class of Thom's catastrophe theory. This in turn implies that for most biostructures, including DNA, high spectral sensitivity near the onset of the denaturation processes can be expected. Such spectrally selective molecular denaturation could find important applications in biology and medicine

SDW and FISDW transition of (TMTSF)2_2ClO4_4 at high magnetic fields

The magnetic field dependence of the SDW transition in (TMTSF)$_2$ClO$_4$ for various anion cooling rates has been measured, with the field up to 27T parallel to the lowest conductivity direction $c^{\ast}$. For quenched (TMTSF)$_2$ClO$_4$, the SDW transition temperature $T_{\rm {SDW}}$ increases from 4.5K in zero field up to 8.4K at 27T. A quadratic behavior is observed below 18T, followed by a saturation behavior. These results are consistent with the prediction of the mean-field theory. From these behaviors, $T_{\rm {SDW}}$ is estimated as $T_{\rm {SDW_0}}$=13.5K for the perfect nesting case. This indicates that the SDW phase in quenched (TMTSF)$_2$ClO$_4$, where $T_{\rm {SDW}}$ is less than 6K, is strongly suppressed by the two-dimensionality of the system. In the intermediate cooled state in which the SDW phase does not appear in zero field, the transition temperature for the field-induced SDW shows a quadratic behavior above 12T and there is no saturation behavior even at 27T, in contrast to the FISDW phase in the relaxed state. This behavior can probably be attributed to the difference of the dimerized gap due to anion ordering.Comment: 4pages,5figures(EPS), accepted for publication in PR

Magnetic Determination of Hc2H_{c2} under Accurate Alignment in (TMTSF)2_2ClO4_4

Cantilever magnetometry has been used to measure the upper critical magnetic field $H_{c2}$ of the quasi-one dimensional molecular organic superconductor (TMTSF)$_2$ClO$_4$. From simultaneous resistivity and torque magnetization experiments conducted under precise field alignment, $H_{c2}$ at low temperature is shown to reach 5T, nearly twice the Pauli paramagnetic limit imposed on spin singlet superconductors. These results constitute the first thermodynamic evidence for a large $H_{c2}$ in this system and provide support for spin triplet pairing in this unconventional superconductorComment: Submitted July 1, 2003, Accepted December 9, 2003, Physical Review Letter