Staphylococcus aureus-Fibronectin Interactions with and without Fibronectin-Binding Proteins and Their Role in Adhesion and Desorption

Adhesion and residence-time-dependent desorption of two Staphylococcus aureus strains with and without fibronectin (Fn) binding proteins (FnBPs) on Fn-coated glass were compared under flow conditions. To obtain a better understanding of the role of Fn-FnBP binding, the adsorption enthalpies of Fn with staphylococcal cell surfaces were determined using isothermal titration calorimetry (ITC). Interaction forces between staphylococci and Fn coatings were measured using atomic force microscopy (AFM). The strain with FnBPs adhered faster and initially stronger to an Fn coating than the strain without FnBPs, and its Fn adsorption enthalpies were higher. The initial desorption was high for both strains but decreased substantially within 2 s. These time scales of staphylococcal bond ageing were confirmed by AFM adhesion force measurement. After exposure of either Fn coating or staphylococcal cell surfaces to bovine serum albumin (BSA), the adhesion of both strains to Fn coatings was reduced, suggesting that BSA suppresses not only nonspecific but also specific Fn-FnBP interactions. Adhesion forces and adsorption enthalpies were only slightly affected by BSA adsorption. This implies that under the mild contact conditions of convective diffusion in a flow chamber, adsorbed BSA prevents specific interactions but does allow forced Fn-FnBP binding during AFM or stirring in ITC. The bond strength energies calculated from retraction force-distance curves from AFM were orders of magnitude higher than those calculated from desorption data, confirming that a penetrating Fn-coated AFM tip probes multiple adhesins in the outermost cell surface that remain hidden during mild landing of an organism on an Fn-coated substratum, like that during convective diffusional flow

Human gait recognition with matrix representation

Human gait is an important biometric feature. It can be perceived from a great distance and has recently attracted greater attention in video-surveillance-related applications, such as closed-circuit television. We explore gait recognition based on a matrix representation in this paper. First, binary silhouettes over one gait cycle are averaged. As a result, each gait video sequence, containing a number of gait cycles, is represented by a series of gray-level averaged images. Then, a matrix-based unsupervised algorithm, namely coupled subspace analysis (CSA), is employed as a preprocessing step to remove noise and retain the most representative information. Finally, a supervised algorithm, namely discriminant analysis with tensor representation, is applied to further improve classification ability. This matrix-based scheme demonstrates a much better gait recognition performance than state-of-the-art algorithms on the standard USF HumanID Gait database

Triple-quark elastic scatterings and thermalization

Triple-quark elastic scattering amplitudes from perturbative QCD are first calculated and then used in a transport equation to study the thermalization of quark matter. By examining momentum isotropy to which the transport equation leads, we can determine thermalization time and offer an initial thermal quark distribution function. With an anisotropic initial quark distribution, which is relevant to quark matter initially created in a central Au-Au collision at \sqrt {s_{NN}}=200 GeV, the transport equation gives a time of the order of 1.8 fm/c for quark matter itself to thermalize by the triple-quark scatterings.Comment: 19 pages, 4 figures, 1 table, LaTex, define u12,u13,u21,u23,u31,u3

qqqbar to qqqbar and qqbarqbar to qqbarqbar Elastic Scatterings and Thermalization of Quark Matter and Antiquark Matter

Thermalization of quark matter and antiquark matter is studied with quark-quark-antiquark as well as quark-antiquark-antiquark elastic scatterings. Squared amplitudes of qqqbar to qqqbar and qqbarqbar to qqbarqbar at order alpha_s^4 are derived in perturbative QCD. Solved by a new technique, solutions of transport equations with the squared amplitudes indicate that the scatterings qqqbar to qqqbar and qqbarqbar to qqbarqbar shorten the thermalization time of quark matter and antiquark matter. It is emphasized that three-parton and other multi-parton scatterings become important at the high parton number density achieved in RHIC Au-Au collisions.Comment: 14 pages, 5 figures, Late

High-Dimensional Stochastic Design Optimization by Adaptive-Sparse Polynomial Dimensional Decomposition

This paper presents a novel adaptive-sparse polynomial dimensional decomposition (PDD) method for stochastic design optimization of complex systems. The method entails an adaptive-sparse PDD approximation of a high-dimensional stochastic response for statistical moment and reliability analyses; a novel integration of the adaptive-sparse PDD approximation and score functions for estimating the first-order design sensitivities of the statistical moments and failure probability; and standard gradient-based optimization algorithms. New analytical formulae are presented for the design sensitivities that are simultaneously determined along with the moments or the failure probability. Numerical results stemming from mathematical functions indicate that the new method provides more computationally efficient design solutions than the existing methods. Finally, stochastic shape optimization of a jet engine bracket with 79 variables was performed, demonstrating the power of the new method to tackle practical engineering problems.Comment: 18 pages, 2 figures, to appear in Sparse Grids and Applications--Stuttgart 2014, Lecture Notes in Computational Science and Engineering 109, edited by J. Garcke and D. Pfl\"{u}ger, Springer International Publishing, 201

Genome sequence and analysis of the tuber crop potato

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital cro

Graphene oxide functionalized long period fiber grating for highly sensitive hemoglobin detection

We present graphene oxide (GO) nanosheets functionalized long period grating (LPG) for ultrasensitive hemoglobin sensing. The sensing mechanism relies on the measurement of LPG resonant intensity change induced by the adsorption of hemoglobin molecules onto GO, where GO as a bio-interface linkage provides the significant light-matter interaction between evanescent field and target molecules. The deposition technique based on chemical-bonding associated with physical-adsorption was developed to immobilize GO nanosheets on cylindrical fiber device. The surface morphology was characterized by scanning electron microscope, atomic force microscopy, and Raman spectroscopy. With relatively thicker GO coating, the refractive index (RI) sensitivity of GO-LPG was extremely enhanced and achieved −76.5 dB/RIU, −234.2 dB/RIU and +1580.5 dB/RIU for RI region of 1.33-1.38, 1.40-1.44 and 1.45-1.46, respectively. The GO-LPG was subsequently implemented as an optical biosensor to detect human hemoglobin giving a sensitivity of 1.9 dB/(mg/mL) and a detectable concentration of 0.05 mg/mL, which was far below the hemoglobin threshold value for anemia defined by World Health Organization. The proposed GO-LPG architecture can be further developed as an optical biosensing platform for anemia diagnostics and biomedical applications

First Principles Calculations of Fe on GaAs (100)

We have calculated from first principles the electronic structure of 0.5 monolayer upto 5 monolayer thick Fe layers on top of a GaAs (100) surface. We find the Fe magnetic moment to be determined by the Fe-As distance. As segregates to the top of the Fe film, whereas Ga most likely is found within the Fe film. Moreover, we find an asymmetric in-plane contraction of our unit-cell along with an expansion perpendicular to the surface. We predict the number of Fe 3d-holes to increase with increasing Fe thickness on $p$-doped GaAs.Comment: 9 pages, 14 figures, submitted to PR

First-principles study of nucleation, growth, and interface structure of Fe/GaAs

We use density-functional theory to describe the initial stages of Fe film growth on GaAs(001), focusing on the interplay between chemistry and magnetism at the interface. Four features appear to be generic: (1) At submonolayer coverages, a strong chemical interaction between Fe and substrate atoms leads to substitutional adsorption and intermixing. (2) For films of several monolayers and more, atomically abrupt interfaces are energetically favored. (3) For Fe films over a range of thicknesses, both Ga- and As-adlayers dramatically reduce the formation energies of the films, suggesting a surfactant-like action. (4) During the first few monolayers of growth, Ga or As atoms are likely to be liberated from the interface and diffuse to the Fe film surface. Magnetism plays an important auxiliary role for these processes, even in the dilute limit of atomic adsorption. Most of the films exhibit ferromagnetic order even at half-monolayer coverage, while certain adlayer-capped films show a slight preference for antiferromagnetic order.Comment: 11 two-column pages, 12 figures, to appear in Phys. Rev.