Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics.

This paper reports an array-designed C84-embedded Si substrate fabricated using a controlled self-assembly method in an ultra-high vacuum chamber. The characteristics of the C84-embedded Si surface, such as atomic resolution topography, local electronic density of states, band gap energy, field emission properties, nanomechanical stiffness, and surface magnetism, were examined using a variety of surface analysis techniques under ultra, high vacuum (UHV) conditions as well as in an atmospheric system. Experimental results demonstrate the high uniformity of the C84-embedded Si surface fabricated using a controlled self-assembly nanotechnology mechanism, represents an important development in the application of field emission display (FED), optoelectronic device fabrication, MEMS cutting tools, and in efforts to find a suitable replacement for carbide semiconductors.

Uncertainty Comparison of Visual Sensing in Adverse Weather Conditions.

This paper focuses on flood-region detection using monitoring images. However, adverse weather affects the outcome of image segmentation methods. In this paper, we present an experimental comparison of an outdoor visual sensing system using region-growing methods with two different growing rules-namely, GrowCut and RegGro.

Text mining for identifying topics in the literatures about adolescent substance use and depression.

Background: Both adolescent substance use and adolescent depression are major public health problems, and have the tendency to co-occur. Thousands of articles on adolescent substance use or depression have been published. It is labor intensive and time consuming to extract huge amounts of information from the cumulated collections.

First-principles study of the structural and dynamic properties of the liquid and amorphous Li-Si alloys.

We have performed density functional theory calculations and ab initio molecular dynamics to investigate the structures and dynamic properties of the liquid and amorphous LixSi alloys over a range of composition from x = 1.0 - 4.8.

Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels.

Lung adenocarcinoma is one of the most deadly human diseases. However, the molecular mechanisms underlying this disease, particularly RNA splicing, have remained underexplored. Here, we report a triple-level (gene-, transcript-, and exon-level) analysis of lung adenocarcinoma transcriptomes from 77 paired tumor and normal tissues, as well as an analysis pipeline to overcome genetic variability for accurate differentiation between tumor and normal tissues.

Visual Sensing for Urban Flood Monitoring.

With the increasing climatic extremes, the frequency and severity of urban flood events have intensified worldwide. In this study, image-based automated monitoring of flood formation and analyses of water level fluctuation were proposed as value-added intelligent sensing applications to turn a passive monitoring camera into a visual sensor. Combined with the proposed visual sensing method, traditional hydrological monitoring cameras have the ability to sense and analyze the local situation of flood events.

Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome.

The Core Pattern Analysis on Chinese Herbal Medicine for Sjögren's syndrome: A Nationwide Population-Based Study.

This large-scale survey aimed to evaluate frequencies and patterns of Chinese herbal medicine (CHM) used for Sjögren's syndrome (SS) in Taiwan by analyzing the National Health Insurance Research Database (NHIRD) for cases in which CHM was used as an alternative therapy to Western medicine for improving patients' discomforts. We analyzed cases of SS principal diagnosis (ICD-9:710.2) with a catastrophic illness certificate (CIC) in traditional Chinese medicine (TCM) outpatient clinics from three cohorts of the Longitudinal Health Insurance Database (LHID) in the NHIRD between 2002 and 2011.

Connectomics-based analysis of information flow in the Drosophila brain.

Understanding the overall patterns of information flow within the brain has become a major goal of neuroscience. In the current study, we produced a first draft of the Drosophila connectome at the mesoscopic scale, reconstructed from 12,995 images of neuron projections collected in FlyCircuit (version 1.1).

Cyber surveillance for flood disasters.

Regional heavy rainfall is usually caused by the influence of extreme weather conditions. Instant heavy rainfall often results in the flooding of rivers and the neighboring low-lying areas, which is responsible for a large number of casualties and considerable property loss. The existing precipitation forecast systems mostly focus on the analysis and forecast of large-scale areas but do not provide precise instant automatic monitoring and alert feedback for individual river areas and sections.

Pervasive brain monitoring and data sharing based on multi-tier distributed computing and linked data technology.

EEG-based Brain-computer interfaces (BCI) are facing basic challenges in real-world applications. The technical difficulties in developing truly wearable BCI systems that are capable of making reliable real-time prediction of users' cognitive states in dynamic real-life situations may seem almost insurmountable at times. Fortunately, recent advances in miniature sensors, wireless communication and distributed computing technologies offered promising ways to bridge these chasms.

Microyielding of core-shell crystal dendrites in a bulk-metallic-glass matrix composite.

In-situ synchrotron x-ray experiments have been used to follow the evolution of the diffraction peaks for crystalline dendrites embedded in a bulk metallic glass matrix subjected to a compressive loading-unloading cycle. We observe irreversible diffraction-peak splitting even though the load does not go beyond half of the bulk yield strength. The chemical analysis coupled with the transmission electron microscopy mapping suggests that the observed peak splitting originates from the chemical heterogeneity between the core (major peak) and the stiffer shell (minor peak) of the dendrites.

Investigation into the mechanical properties of single-walled carbon nanotube heterojunctions.

The mechanical properties of finite-length (6,0)/(8,0) single-walled carbon nanotube (SWCNT) heterojunctions with respect to different kinds of connection segments, either coaxial or bias, are investigated using molecular dynamics simulation calculations. It is found that the resulting significant deformation of structure and significant drop of stress under yielding strain is due to the strain localization. Moreover, the deformation is occurred below the heptagon ring in the thinner segment of the heterojunctions under tension at different temperatures, whereas under compression it occurs on the heptagon ring.

A novel aerosol-mediated drug delivery system for inner ear therapy: intratympanic aerosol methylprednisolone can attenuate acoustic trauma.

We developed a novel aerosol-mediated drug delivery system for inner ear therapy by using a silicon-based multiple-Fourier horn nozzle. Intratympanic aerosol (ITA) methylprednisolone (MP) delivery can protect hearing after acoustic trauma. The highest concentration of MP (38.

Modeling sound transmission of human middle ear and its clinical applications using finite element analysis.

We have developed a new finite element (FE) model of human right ear, including the accurate geometry of middle ear ossicles, external ear canal, tympanic cavity, and mastoid cavity. The FE model would be suitable to study the dynamic behaviors of pathological middle ear conditions, including changes of stapedial ligament stiffness, tensor tympani ligament (TTL), and tympanic membrane (TM) stiffness and thickness. Increasing stiffness of stapedial ligament has substantial effect on stapes footplate movement, especially at low frequencies, but less effect on umbo movement.

Target molecular simulations of RecA family protein filaments.

Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon.

Fuzzy adaptive interacting multiple model nonlinear filter for integrated navigation sensor fusion.

In this paper, the application of the fuzzy interacting multiple model unscented Kalman filter (FUZZY-IMMUKF) approach to integrated navigation processing for the maneuvering vehicle is presented. The unscented Kalman filter (UKF) employs a set of sigma points through deterministic sampling, such that a linearization process is not necessary, and therefore the errors caused by linearization as in the traditional extended Kalman filter (EKF) can be avoided. The nonlinear filters naturally suffer, to some extent, the same problem as the EKF for which the uncertainty of the process noise and measurement noise will degrade the performance.

Adsorption and dissociation of NH3 on clean and hydroxylated TiO2 rutile (110) surfaces: a computational study.

The adsorption and dissociation of NH(3) on the clean and hydroxylated TiO(2) rutile (110) surfaces have been investigated by the first-principles calculations. The monodentate adsorbates such as H(3)N-Ti(a), H(2)N-Ti(a), N-Ti(a), H(2)N-O(a), HN-O(a), N-O(a) and H-O(a), as well as the bidentate adsorbate, Ti-N-Ti(a) can be formed on the clean surface. It is found that the hydroxyl group enhances the adsorption of certain adsorbates on the five-fold-coordinated Ti atoms (5c-Ti), namely H(2)N-Ti(a), HN-Ti(a), N-Ti(a) and Ti-N-Ti(a).

Hydrogen-bond structure at the interfaces between water/poly(methyl methacrylate), water/poly(methacrylic acid), and water/poly(2-aminoethylmethacrylamide).

The molecular dynamics approach was employed to study the structural characteristics at the interface of water/poly(methyl methacrylate) (PMMA), water/poly(methacrylic acid) (PMAA), and poly(2-aminoethylmethacrylamide) (PAEMA). It is found that the water on the PMAA surface shows a significant increase in the density at the interface, with a greater number of water molecules permeating into the bulk of the substrate region. The structure of hydrogen bonds of water and the radial distribution function for given polar atoms in the polymer substrate are calculated.

Oxygen vacancy formation and migration in Ce(1-x)Zr(x)O2 catalyst: a DFT+U calculation.

Spin-polarized density functional theory with the inclusion of on-site Coulomb correction (DFT+U) calculation is carried out to study the oxygen vacancy and migration of Ce(1-x)Zr(x)O(2) in a series of Ce/Zr ratios. Substitution of Zr(4+) ion in CeO(2) creates activated oxygen in Ce(1-x)Zr(x)O(2), leading to higher oxygen storage capacity (OCS) compared to CeO(2) due to its structural and electronic modifications. It is found that the oxygen vacancy formation energy (E(f)) is lowered even by small amounts of zirconia; the oxide with a content of 50% zirconia exhibits the lowest E(f) and the best OCS.

Role of hydroxyl groups in the NH(x) (x = 1-3) adsorption on the TiO2 anatase (101) surface determined by a first-principles study.

A spin-polarized density functional theory calculation was carried out to study the adsorption of NH(x) species (x = 1-3) on a TiO2 anatase (101) surface with and without hydroxyl groups by using first-principles calculations. It was found that the present hydroxyl group has the effect of significantly enhancing the adsorption of monodentate adsorbates H2N-Ti(a) compared to that on a bare surface. The nature of the interaction between the adsorbate (NH(x)) and the hydroxylated or bare surface was analyzed by the Mulliken charge and density of states (DOS) calculations.

Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A(H1N1) influenza neuraminidase.

The neuraminidase of the influenza virus is the target of antiviral drugs oseltamivir and zanamivir. Clinical practices have shown that zanamivir and oseltamivir are effective in treating the 2009 A(H1N1) influenza virus. However, drug resistance strains are also emerging.

Potential of mean force of the hepatitis C virus core protein-monoclonal 19D9D6 antibody interaction.

Antigen-antibody interactions are critical for understanding antigen-antibody associations in immunology. To shed further light on this question, we studied a dissociation of the 19D9D6-HCV core protein antibody complex structure. However, forced separations in single molecule experiments are difficult, and therefore molecular simulation techniques were applied in our study.

Predictions of binding for dopamine D2 receptor antagonists by the SIE method.

The control of tetralindiol derivative antagonists released through the inhibition of dopamine D2 receptors has been identified as a potential target for the treatment of schizophrenia. We employed molecular dynamics simulation techniques to identify the predicted D2 receptor structure. Homology models of the protein were developed on the basis of crystal structures of four receptor crystals.

A molecular dynamics simulation of the human lysozyme - camelid VHH HL6 antibody system.

Amyloid diseases such as Alzheimer's and thrombosis are characterized by an aberrant assembly of specific proteins or protein fragments into fibrils and plaques that are deposited in various tissues and organs. The single-domain fragment of a camelid antibody was reported to be able to combat against wild-type human lysozyme for inhibiting in-vitro aggregations of the amyloidogenic variant (D67H). The present study is aimed at elucidating the unbinding mechanics between the D67H lysozyme and VHH HL6 antibody fragment by using steered molecular dynamics (SMD) simulations on a nanosecond scale with different pulling velocities.