Nitrogen doping of carbon nanoelectrodes for enhanced control of DNA translocation dynamics

Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures to achieve this goal, herein we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ~ 290 % and the fluctuation of the nucleobases was reduced by up to ~ 70 %. Given the possibility to be combined with extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap based of carbon nanomaterials.Comment: 11 pages, 4 figure

Distinctive-attribute Extraction for Image Captioning

Image captioning, an open research issue, has been evolved with the progress of deep neural networks. Convolutional neural networks (CNNs) and recurrent neural networks (RNNs) are employed to compute image features and generate natural language descriptions in the research. In previous works, a caption involving semantic description can be generated by applying additional information into the RNNs. In this approach, we propose a distinctive-attribute extraction (DaE) which explicitly encourages significant meanings to generate an accurate caption describing the overall meaning of the image with their unique situation. Specifically, the captions of training images are analyzed by term frequency-inverse document frequency (TF-IDF), and the analyzed semantic information is trained to extract distinctive-attributes for inferring captions. The proposed scheme is evaluated on a challenge data, and it improves an objective performance while describing images in more detail.Comment: 14 main pages, 4 supplementary page

The competition number of a graph having exactly one hole

AbstractLet D be an acyclic digraph. The competition graph of D has the same set of vertices as D and an edge between vertices u and v if and only if there is a vertex x in D such that (u,x) and (v,x) are arcs of D. The competition number of a graph G, denoted by k(G), is the smallest number k such that G together with k isolated vertices is the competition graph of an acyclic digraph. In this paper, we show that the competition number of a graph having exactly one chordless cycle of length at least 4 is at most two. We also give a large family of such graphs whose competition numbers are less than or equal to one

PORTAL: Portal Widget for Remote Target Acquisition and Control in Immersive Virtual Environments

This paper introduces PORTAL (POrtal widget for Remote Target Acquisition and controL) that allows the user to interact with out-of-reach objects in a virtual environment. We describe the PORTAL interaction technique for placing a portal widget and interacting with target objects through the portal. We conduct two formal user studies to evaluate PORTAL for selection and manipulation functionalities. The results show PORTAL supports participants to interact with remote objects successfully and precisely. Following that, we discuss its potential and limitations, and future works

Identifying set-wise differential co-expression in gene expression microarray data

<p>Abstract</p> <p>Background</p> <p>Previous differential coexpression analyses focused on identification of differentially coexpressed gene pairs, revealing many insightful biological hypotheses. However, this method could not detect coexpression relationships between pairs of gene sets. Considering the success of many set-wise analysis methods for microarray data, a coexpression analysis based on gene sets may elucidate underlying biological processes provoked by the conditional changes. Here, we propose a differentially coexpressed gene sets (dCoxS) algorithm that identifies the differentially coexpressed gene set pairs between conditions.</p> <p>Results</p> <p>dCoxS is a two-step analysis method. In each condition, dCoxS measures the interaction score (IS), which represents the expression similarity between two gene sets using Renyi relative entropy. When estimating the relative entropy, multivariate kernel density estimation was used to model gene-gene correlation structure. Statistical tests for the conditional difference between the ISs determined the significance of differential coexpression of the gene set pair. Simulation studies supported that the IS is a representative measure of similarity between gene expression matrices. Single gene coexpression analysis of two publicly available microarray datasets detected no significant results. However, the dCoxS analysis of the datasets revealed differentially coexpressed gene set pairs related to the biological conditions of the datasets.</p> <p>Conclusion</p> <p>dCoxS identified differentially coexpressed gene set pairs not found by single gene analysis. The results indicate that set-wise differential coexpression analysis is useful for understanding biological processes induced by conditional changes.</p

dxz/yzd_{xz/yz} Orbital Subband Structures and Chiral Orbital Angular Momentum in the (001) Surface States of SrTiO3_3

We have performed angle resolved photoemission spectroscopy (ARPES) experiments on the surface states of SrTiO$_3$(001) using linearly and circularly polarized light to investigate the subband structures of out-of-plane $d_{xz/yz}$ orbitals and chiral orbital angular momentum (OAM). The data taken in the first Brillouin zone reveal new subbands for $d_{xz/yz}$ orbitals with Fermi wave vectors of 0.25 and 0.45 $\mathrm{\AA}^{-1}$ in addition to the previously reported ones. As a result, there are at least two subbands for all the Ti 3d t$_{2g}$ orbitals. Our circular dichroism ARPES data is suggestive of a chiral OAM structure in the surface states and may provide clues to the origin of the linear Rashba-like surface band splitting.Comment: 7 pages, 3 figures, Journal pape