Stalking influenza by vaccination with pre-fusion headless HA mini-stem

Inaccuracies in prediction of circulating viral strain genotypes and the possibility of novel reassortants causing a pandemic outbreak necessitate the development of an anti-influenza vaccine with increased breadth of protection and potential for rapid production and deployment. The hemagglutinin (HA) stem is a promising target for universal influenza vaccine as stem-specific antibodies have the potential to be broadly cross-reactive towards different HA subtypes. Here, we report the design of a bacterially expressed polypeptide that mimics a H5 HA stem by protein minimization to focus the antibody response towards the HA stem. The HA mini-stem folds as a trimer mimicking the HA prefusion conformation. It is resistant to thermal/chemical stress, and it binds to conformation-specific, HA stem-directed broadly neutralizing antibodies with high affinity. Mice vaccinated with the group 1 HA mini-stems are protected from morbidity and mortality against lethal challenge by both group 1 (H5 and H1) and group 2 (H3) influenza viruses, the first report of cross-group protection. Passive transfer of immune serum demonstrates the protection is mediated by stem-specific antibodies. Furthermore, antibodies indudced by these HA stems have broad HA reactivity, yet they do not have antibody-dependent enhancement activity.

Evaluation of the Effectiveness of Representative Methods for Determining Young's Modulus and Hardness from Instrumented Indentation Data

The effectiveness of Oliver & Pharr's (O&P's) method, Cheng & Cheng's (C&C's) method, and a new method developed by our group for estimating Young's modulus and hardness based on instrumented indentation was evaluated for the case of yield stress to reduced Young's modulus ratio (sigma(y)/E-r) >= 4.55 x 10(-4) and hardening coefficient (n) <= 0.45. Dimensional theorem and finite element simulations were applied to produce reference results for this purpose. Both O&P's and C&C's methods overestimated the Young's modulus under some conditions, whereas the error can be controlled within +/- 16% if the formulation was modified with appropriate correction functions. Similar modification was not introduced to our method for determining Young's modulus, while the maximum error of results was around +/- 13%. The errors of hardness values obtained from all the three methods could be even larger and were irreducible with any correction scheme. It is therefore suggested that when hardness values of different materials are concerned, relative comparison of the data obtained from a single standard measurement technique would be more practically useful. It is noted that the ranges of error derived from the analysis could be different if different ranges of material parameters sigma(y)/E-r and n are considered.

Finite element analysis on stresses field of normalized layer thickness within ceramic coating on aluminized steel

Multilayer ceramic coatings were fabricated on steel substrate using a combined technique of hot dipping aluminum(HDA) and plasma electrolytic oxidation(PEO). A triangle of normalized layer thickness was created for describing thickness ratios of HDA/PEO coatings. Then, the effect of thickness ratio on stresses field of HDA/PEO coatings subjected to uniform normal contact load was investigated by finite element method. Results show that the surface tensile stress is mainly affected by the thickness ratio of Al layer when the total thickness of coating is unchanged. With the increase of A] layer thickness, the surface tensile stress rises quickly. When Al2O3 layer thickness increases, surface tensile stress is diminished. 'Meanwhile, the maximum shear stress moves rapidly towards internal part of HDA/PEO coatings. Shear stress at the Al2O3/Al interface is minimal when Al2O3 layer and Al layer have the same thickness.

Triple-region structure for turbulent-flow in a square duct - a finite-element approach

The Reynolds-averaged Navier-Stokes equations for describing the turbulent flow in a straight square duct are formulated with two different turbulence models. The governing equations are then expanded as a multi-deck structure in a plane perpendicular to the streamwise direction, with each deck characterized by its dominant physical forces as commonly carried out in analytical work using triple-deck expansion. The resulting equations are numerically integrated using higher polynomial (H-P) finite element technique for each cross-sectional plane to be followed by finite difference representation in the streamwise direction until a fully developed state is reached. The computed results using the two different turbulence models show fair agreement with each other, and concur with the vast body of available experimental data. There is also general agreement between our results and the recent numerical works anisotropic k-epsilon turbulence model.

Descriptive set theory and the ergodic theory of countable groups

The primary focus of this thesis is on the interplay of descriptive set theory and the ergodic theory of group actions. This incorporates the study of turbulence and Borel reducibility on the one hand, and the theory of orbit equivalence and weak equivalence on the other. Chapter 2 is joint work with Clinton Conley and Alexander Kechris; we study measurable graph combinatorial invariants of group actions and employ the ultraproduct construction as a way of constructing various measure preserving actions with desirable properties. Chapter 3 is joint work with Lewis Bowen; we study the property MD of residually finite groups, and we prove a conjecture of Kechris by showing that under general hypotheses property MD is inherited by a group from one of its co-amenable subgroups. Chapter 4 is a study of weak equivalence. One of the main results answers a question of Abért and Elek by showing that within any free weak equivalence class the isomorphism relation does not admit classification by countable structures. The proof relies on affirming a conjecture of Ioana by showing that the product of a free action with a Bernoulli shift is weakly equivalent to the original action. Chapter 5 studies the relationship between mixing and freeness properties of measure preserving actions. Chapter 6 studies how approximation properties of ergodic actions and unitary representations are reflected group theoretically and also operator algebraically via a group's reduced C^*-algebra. Chapter 7 is an appendix which includes various results on mixing via filters and on Gaussian actions.

Algebraic Techniques in Coding Theory: Entropy Vectors, Frames, and Constrained Coding

The study of codes, classically motivated by the need to communicate information reliably in the presence of error, has found new life in fields as diverse as network communication, distributed storage of data, and even has connections to the design of linear measurements used in compressive sensing. But in all contexts, a code typically involves exploiting the algebraic or geometric structure underlying an application. In this thesis, we examine several problems in coding theory, and try to gain some insight into the algebraic structure behind them.

The first is the study of the entropy region - the space of all possible vectors of joint entropies which can arise from a set of discrete random variables. Understanding this region is essentially the key to optimizing network codes for a given network. To this end, we employ a group-theoretic method of constructing random variables producing so-called "group-characterizable" entropy vectors, which are capable of approximating any point in the entropy region. We show how small groups can be used to produce entropy vectors which violate the Ingleton inequality, a fundamental bound on entropy vectors arising from the random variables involved in linear network codes. We discuss the suitability of these groups to design codes for networks which could potentially outperform linear coding.

The second topic we discuss is the design of frames with low coherence, closely related to finding spherical codes in which the codewords are unit vectors spaced out around the unit sphere so as to minimize the magnitudes of their mutual inner products. We show how to build frames by selecting a cleverly chosen set of representations of a finite group to produce a "group code" as described by Slepian decades ago. We go on to reinterpret our method as selecting a subset of rows of a group Fourier matrix, allowing us to study and bound our frames' coherences using character theory. We discuss the usefulness of our frames in sparse signal recovery using linear measurements.

The final problem we investigate is that of coding with constraints, most recently motivated by the demand for ways to encode large amounts of data using error-correcting codes so that any small loss can be recovered from a small set of surviving data. Most often, this involves using a systematic linear error-correcting code in which each parity symbol is constrained to be a function of some subset of the message symbols. We derive bounds on the minimum distance of such a code based on its constraints, and characterize when these bounds can be achieved using subcodes of Reed-Solomon codes.

Anisotropic Bragg diffraction of finite-sized volume holographic grating in photorefractive crystals

Anisotropic diffraction of uniform plane wave by finite-sized volume holographic grating in photorefractive crystals is considered. It is found that the anisotropic diffraction can take place when some special conditions are satisfied. The diffracted image is obtained in experiment for the anisotropic Bragg diffraction in Fe:LiNbO3 crystals. A coupled wave analysis is presented to study the properties of anisotropic diffraction. An analytical integral solution for the amplitudes of the diffracted beams is submitted. A trade off between high diffraction efficiency and the deterioration of reconstruction fidelity is analyzed. Numerical evaluations also show that the finite-sized anisotropic volume grating exhibits strong angular and wavelength selectivity. All the results are useful for the optimizing design of VHOE based on finite-sized volume grating structures. (c) 2006 Elsevier GmbH. All rights reserved.

A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model. © 2011 Elsevier Ltd.

Comparison of Q-factors between TE and TM modes in 3-D microsquares by FDTD simulation

Mode characteristics of three-dimensional (3-D) microsquare resonators are investigated by finite-difference time-domain (FDTD) simulation for the transverse electric (TE)-like and the transverse magnetic (TM)-like modes. For a pillar microsquare with a side length of 2 pin in air, we have Q-factors about 5 X. 103 for TM-like modes at the wavelength of 1550 run, which are one order larger than those of TE-like modes, as vertical refractive index distribution is 3.17/3.4/3.17 and the cororresponding center layer thickness is 0.2 mu m. The mode field patterns show that TM-like modes have much weaker vertical radiation coupling loss than TE-like modes. TM-like modes can have high Q-factors in a microsquare with weak vertical field confinement.

Analysis of mode characteristics for deformed square resonators by FDTD technique

The mode frequencies and quality factors (Q-factors) in two-dimensional (2-D) deformed square resonators are analyzed by finite-difference time-domain (FDTD) technique. The results show that the deformed square cavities with circular and cut corners have larger Q-factors than the perfect ones at certain conditions. For a square cavity with side length of 2 mu m and refractive index of 3.2, the mode Q-factor can increase 13 times as the perfect corners are replaced by a quarter of circle with radius of 0.3 pm. Furthermore the blue shift with the increasing deformations is found as a result of the reduction in effective resonator area. In square cavities with periodic roughness at sidewalls which maintains the symmetry of the square, the Q-factors of the whisperin gallery (WG)-like modes are still one order of magnitude larger that those of non-WG-like modes. However, the Q-tactors of these two types of modes are of the same order in the square cavity with random roughness. We also find that the rectangular and rhombic deformation largely reduce the Q-factors with the increasing offset and cause the splitting of the doubly degenerate modes due to the breaking of certain symmetry properties.

PASSIVATION OF COPPER BY LITHIUM IN P-TYPE GAAS

We report the passivation of two deep copper-related acceptor levels in Cu-diffused p-type GaAs by the group-I element lithium. The deep-level-transient-spectroscopy (DLTS) signals of the well-known Cu-related levels with apparent activation energies 0.15 eV and 0.40 eV disappear in Cu-diffused samples when they are diffused with Li, but can be reactivated by annealing. Photoluminescence measurements show a corresponding disappearance and reappearance of the copper-related luminescence at 1.36 eV. Also we observe with DLT'S an energy level at E(V) + 0.32 eV in the Cu-Li-diff-used samples. The level is neither present in the Cu-diffused samples before Li diffusion nor in Cu-Li-diffused samples after annealing. As the level is not observed in starting materials or solely Li-diffused samples we suggest that it is related to a Cu-Li complex.

Modulation of Photonic Bandgap and Localized States by Dielectric Constant Contrast and Filling Factor in Photonic Crystals

The band structure of 2D photonic crystals (PCs) and localized states resulting from defects are analyzed by finite-difference time-domain (FDTD) technique and Pade approximation. The effect of dielectric constant contrast and filling factor on photonic bandgap (PBG) for perfect PCs and localized states in PCs with point defects are investigated. The resonant frequencies and quality factors are calculated for PCs with different defects. The numerical results show that it is possible to modulate the location, width and number of PBGs and frequencies of the localized states only by changing the dielectric constant contrast and filling factor.

Understanding student stress: a qualitative study of the stress experienced by third level students

Stress can be understood in terms of the meaning of stressful experiences for individuals. The meaning of stressful experiences involves threats to self-adequacy, where self-adequacy is considered a basic human need. Appropriate research methods are required to explore this aspect of stress. The present study is a qualitative exploration of the stress experienced by a group of 27 students at the National Institute of Higher Education, Limerick (since renamed the University of Limerick). The study was carried out by the resident student counsellor at the college. A model of student stress was explored, based on student developmental needs. The data consist of a series of interviews recorded with each of the 27 students over a 3 month period. These interviews were transcribed and the resulting transcripts are the subject of detailed analysis. The analysis of the data is an account of the sense-making process by the student counsellor of the students' reported experiences. The aim of the analysis was to reduce the large amounts of data to their most salient aspects in an ordered fashion, so as to examine the application of a developmental model of stress with this group of students. There were two key elements to the analysis. First, the raw data were edited to identify the key statements contained in the interviews. Second, the statements were categorised, as a means of summarising the data. The results of the qualitative dataanalysis were then applied to the developmental model. The analysis of data revealed a number of patterns of stress amongst the sample of students. Patterns of academic over-identification, parental conflict and social inadequacy were particularly noteworthy. These patterns consisted of an integration of academic, family and social stresses within a developmental framework. Gender differences with regard to the need for separateness and belonging are highlighted. Appropriate student stress intervention strategies are discussed. Based on the present results, the relationship between stress and development has been highlighted and is recommended as a firm basis for future studies of stress in general and student stress in particular.

The abelianization of the Johnson kernel

We prove that the first complex homology of the Johnson subgroup of the Torelli group Tg is a non-trivial, unipotent Tg-module for all g ≥ 4 and give an explicit presentation of it as a Sym H 1(Tg,C)-module when g ≥ 6. We do this by proving that, for a finitely generated group G satisfying an assumption close to formality, the triviality of the restricted characteristic variety implies that the first homology of its Johnson kernel is a nilpotent module over the corresponding Laurent polynomial ring, isomorphic to the infinitesimal Alexander invariant of the associated graded Lie algebra of G. In this setup, we also obtain a precise nilpotence test. © European Mathematical Society 2014.

Muscle-specific variations in use-dependent crossed-facilitation of corticospinal pathways mediated by transcranial direct current (DC) stimulation

The tendency for contractions of muscles in the upper limb to give rise to increases in the excitability of corticospinal projections to the homologous muscles of the opposite limb is well known. Although the suppression of this tendency is integral to tasks of daily living, its exploitation may prove to be critical in the rehabilitation of acquired hemiplegias. Transcranial direct current (DC) stimulation induces changes in cortical excitability that outlast the period of application. We present evidence that changes in the reactivity of the corticospinal pathway induced by DC stimulation of the motor cortex interact systematically with those brought about by contraction of the muscles of the ipsilateral limb. During the application of flexion torques (up to 50% of maximum) applied at the left wrist, motor evoked potentials (MEPs) were evoked in the quiescent muscles of the right arm by magnetic stimulation of the left motor cortex (M1). The MEPs were obtained prior to and following 10 min of anodal, cathodal or sham DC stimulation of left M1. Cathodal stimulation counteracted increases in the crossed-facilitation of projections to the (right) wrist flexors that otherwise occurred as a result of repeated flexion contractions at the left wrist. In addition, cathodal stimulation markedly decreased the excitability of corticospinal projections to the wrist extensors of the right limb. Thus changes in corticospinal excitability induced by DC stimulation can be shaped (i.e. differentiated by muscle group) by focal contractions of muscles in the limb ipsilateral to the site of stimulation. (C) 2008 Elsevier Ireland Ltd. All rights reserved.