OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences

Insertion sequences (ISs) are simple transposable elements present in most bacterial and archaeal genomes and play an important role in genomic evolution. The recent expansion of sequenced genomes offers the opportunity to study ISs comprehensively, but this requires efficient and accurate tools for IS annotation. We have developed an open-source program called OASIS, or Optimized Annotation System for Insertion Sequences, which automatically annotates ISs within sequenced genomes. OASIS annotations of 1737 bacterial and archaeal genomes offered an unprecedented opportunity to examine IS evolution. At a broad scale, we found that most IS families are quite widespread; however, they are not present randomly across taxa. This may indicate differential loss, barriers to exchange and/or insufficient time to equilibrate across clades. The number of ISs increases with genome length, but there is both tremendous variation and no increase in IS density for genomes >2 Mb. At the finer scale of recently diverged genomes, the proportion of shared IS content falls sharply, suggesting loss and/or emergence of barriers to successful cross-infection occurs rapidly. Surprisingly, even after controlling for 16S rRNA sequence divergence, the same ISs were more likely to be shared between genomes labeled as the same species rather than as different species.Organismic and Evolutionary Biolog

Geometric, electronic properties and the thermodynamics of pure and Al--doped Li clusters

The first--principles density functional molecular dynamics simulations have been carried out to investigate the geometric, the electronic, and the finite temperature properties of pure Li clusters (Li$_{10}$, Li$_{12}$) and Al--doped Li clusters (Li$_{10}$Al, Li$_{10}$Al$_2$). We find that addition of two Al impurities in Li$_{10}$ results in a substantial structural change, while the addition of one Al impurity causes a rearrangement of atoms. Introduction of Al--impurities in Li$_{10}$ establishes a polar bond between Li and nearby Al atom(s), leading to a multicentered bonding, which weakens the Li--Li metallic bonds in the system. These weakened Li--Li bonds lead to a premelting feature to occur at lower temperatures in Al--doped clusters. In Li$_{10}$Al$_2$, Al atoms also form a weak covalent bond, resulting into their dimer like behavior. This causes Al atoms not to `melt' till 800 K, in contrast to the Li atoms which show a complete diffusive behavior above 400 K. Thus, although one Al impurity in Li$_{10}$ cluster does not change its melting characteristics significantly, two impurities results in `surface melting' of Li atoms whose motions are confined around Al dimer.Comment: 9 pages, 7 figure

Studies of the Stability and Dynamics of Levitated Drops

This is a review of our experimental and theoretical studies relating to equilibrium and stability of liquid drops, typically of low viscosity, levitated in air by a sound field. The major emphasis here is on the physical principles and understanding behind the stability of levitated drops. A comparison with experimental data is also given, along with some fascinating pictures from high-speed photography. One of the aspects we shall deal with is how a drop can suddenly burst in an intense sound field; a phenomenon which can find applications in atomization technology. Also, we are currently investigating the phenomenon of suppression of coalescence between drops levitated in intense acoustic fields

NIR-to-VIS Face Recognition via Embedding Relations and Coordinates of the Pairwise Features

NIR-to-VIS face recognition is identifying faces of two different domains by extracting domain-invariant features. However, this is a challenging problem due to the two different domain characteristics, and the lack of NIR face dataset. In order to reduce domain discrepancy while using the existing face recognition models, we propose a 'Relation Module' which can simply add-on to any face recognition models. The local features extracted from face image contain information of each component of the face. Based on two different domain characteristics, to use the relationships between local features is more domain-invariant than to use it as it is. In addition to these relationships, positional information such as distance from lips to chin or eye to eye, also provides domain-invariant information. In our Relation Module, Relation Layer implicitly captures relationships, and Coordinates Layer models the positional information. Also, our proposed Triplet loss with conditional margin reduces intra-class variation in training, and resulting in additional performance improvements. Different from the general face recognition models, our add-on module does not need to pre-train with the large scale dataset. The proposed module fine-tuned only with CASIA NIR-VIS 2.0 database. With the proposed module, we achieve 14.81% rank-1 accuracy and 15.47% verification rate of 0.1% FAR improvements compare to two baseline models

Rapid and sensitive insulated isothermal PCR for point-of-need feline leukaemia virus detection

Objectives: Feline leukaemia virus (FeLV), a gamma retrovirus, causes diseases of the feline haematopoietic system that are invariably fatal. Rapid and accurate testing at the point-of-need (PON) supports prevention of virus spread and management of clinical disease. This study evaluated the performance of an insulated isothermal PCR (iiPCR) that detects proviral DNA, and a reverse transcription (RT)-iiPCR that detects both viral RNA and proviral DNA, for FeLV detection at the PON. Methods: Mycoplasma haemofelis, feline coronavirus, feline herpesvirus, feline calicivirus and feline immunodeficiency virus were used to test analytical specificity. In vitro transcribed RNA, artificial plasmid, FeLV strain American Type Culture Collection VR-719 and a clinical FeLV isolate were used in the analytical sensitivity assays. A retrospective study including 116 clinical plasma and serum samples that had been tested with virus isolation, real-time PCR and ELISA, and a prospective study including 150 clinical plasma and serum samples were implemented to evaluate the clinical performances of the iiPCR-based methods for FeLV detection. Results: Ninety-five percent assay limit of detection was calculated to be 16 RNA and five DNA copies for the RT-iiPCR, and six DNA copies for the iiPCR. Both reactions had analytical sensitivity comparable to a reference real-time PCR (qPCR) and did not detect five non-target feline pathogens. The clinical performance of the RT-iiPCR and iiPCR had 98.82% agreement (kappa[κ] = 0.97) and 100% agreement (κ = 1.0), respectively, with the qPCR (n = 85). The agreement between an automatic nucleic extraction/RT-iiPCR system and virus isolation to detect FeLV in plasma or serum was 95.69% (κ = 0.95) and 98.67% (κ = 0.85) in a retrospective (n = 116) and a prospective (n = 150) study, respectively. Conclusions and relevance: These results suggested that both RT-iiPCR and iiPCR assays can serve as reliable tools for PON FeLV detection

A Simple Model for Cavity Enhanced Slow Lights in Vertical Cavity Surface Emission Lasers

We develop a simple model for the slow lights in Vertical Cavity Surface Emission Lasers (VCSELs), with the combination of cavity and population pulsation effects. The dependences of probe signal power, injection bias current and wavelength detuning for the group delays are demonstrated numerically and experimentally. Up to 65 ps group delays and up to 10 GHz modulation frequency can be achieved in the room temperature at the wavelength of 1.3 $\mu$m. The most significant feature of our VCSEL device is that the length of active region is only several $\mu$m long. Based on the experimental parameters of quantum dot VCSEL structures, we show that the resonance effect of laser cavity plays a significant role to enhance the group delays

Enhanced performance of sulfur-infiltrated bimodal mesoporous carbon foam by chemical solution deposition as cathode materials for lithium sulfur batteries

The porous carbon matrix is widely recognized to be a promising sulfur reservoir to improve the cycle life by suppressing the polysulfide dissolution in lithium sulfur batteries (LSB). Herein, we synthesized mesocellular carbon foam (MSUF-C) with bimodal mesopore (4 and 30 nm) and large pore volume (1.72 cm 2 /g) using MSUF silica as a template and employed it as both the sulfur reservoir and the conductive agent in the sulfur cathode. Sulfur was uniformly infiltrated into MSUF-C pores by a chemical solution deposition method (MSUF-C/S CSD) and the amount of sulfur loading was achieved as high as 73% thanks to the large pore volume with the CSD approach. MSUF-C/S CSD showed a high capacity (889 mAh/g after 100 cycles at 0.2 C), an improved rate capability (879 mAh/g at 1C and 420 mAh/g at 2C), and a good capacity retention with a fade rate of 0.16% per cycle over 100 cycles.118Ysciescopu

{BOAO Photometric Survey of Galactic Open Clusters. II. Physical Parameters of 12 Open Clusters

We have initiated a long-term project, the BOAO photometric survey of open clusters, to enlarge our understanding of galactic structure using UBVI CCD photometry of open clusters which have been little studied before. This is the second paper of the project in which we present the photometry of 12 open clusters. We have determined the cluster parameters by fitting the Padova isochrones to the color-magnitude diagrams of the clusters. All the clusters except for Be 0 and NGC 1348 are found to be intermediate-age to old (0.2 - 4.0 Gyrs) open clusters with a mean metallicity of [Fe/H] = 0.0.Comment: 11 page

Anomalous Hall Effect and Skyrmion Number in Real- and Momentum-space

We study the anomalous Hall effect (AHE) for the double exchange model with the exchange coupling $|J_H|$ being smaller than the bandwidth $|t|$ for the purpose of clarifying the following unresolved and confusing issues: (i) the effect of the underlying lattice structure, (ii) the relation between AHE and the skyrmion number, (iii) the duality between real and momentum spaces, and (iv) the role of the disorder scatterings; which is more essential, $\sigma_H$ (Hall conductivity) or $\rho_H$ (Hall resistivity)? Starting from a generic expression for $\sigma_H$, we resolve all these issues and classify the regimes in the parameter space of $J_H \tau$ ($\tau$: elastic-scattering time), and $\lambda_{s}$ (length scale of spin texture). There are two distinct mechanisms of AHE; one is characterized by the real-space skyrmion-number, and the other by momentum-space skyrmion-density at the Fermi level, which work in different regimes of the parameter space.Comment: 4 pages, 1 figure, REVTe