The Effect of Antinotches on Domain Wall Mobility in Single Crystal Ferroelectric Nanowires

Changes in domain wall mobility, caused by the presence of antinotches in single crystal BaTiO3 nanowires, have been investigated. While antinotches appeared to cause a slight broadening in the distribution of switching events, observed as a function of applied electric field (inferred from capacitance-voltage measurements), the effect was often subtle. Greater clarity of information was obtained from Rayleigh analysis of the capacitance variation with ac field amplitude. Here the magnitude of the domain wall mobility parameter (R) associated with irreversible wall movements was found to be reduced by the presence of antinotches - an effect which became more noticeable on heating toward the Curie temperature. The reduction in this domain wall mobility was contrasted with the noticeable enhancement found previously in ferroelectric wires with notches. Finite element modeling of the electric field, developed in the nanowires during switching, revealed regions of increased and decreased local field at the center of the notch and antinotch structures, respectively; the absolute magnitude of field enhancement in the notch centers was considerably greater than the field reduction in the center of the antinotches and this was commensurate with the manner in, and degree to, which domain wall mobility appeared to be affected. We therefore conclude that the main mechanism by which morphology alters the irreversible component of the domain wall mobility in ferroelectric wire structures is via the manner in which morphological variations alter the spatial distribution of the electric field.

A Low Complexity Video Watermarking in H.264 Compressed Domain

In this paper, a new blind and readable H.264 compressed domain watermarking scheme is proposed in which the embedding/extracting is performed using the syntactic elements of the compressed bit stream. As a result, it is not necessary to fully decode a compressed video stream both in the embedding and extracting processes. The method also presents an inexpensive spatiotemporal analysis that selects the appropriate submacroblocks for embedding, increasing watermark robustness while reducing its impact on visual quality. Meanwhile, the proposed method prevents bit-rate increase and restricts it within an acceptable limit by selecting appropriate quantized residuals for watermark insertion. Regarding watermarking demands such as imperceptibility, bit-rate control, and appropriate level of security, a priority matrix is defined which can be adjusted based on the application requirements. The resulted flexibility expands the usability of the proposed method.

Transonic aeroelastic simulation for instability searches and uncertainty analysis

In this paper the use of eigenvalue stability analysis of very large dimension aeroelastic numerical models arising from the exploitation of computational fluid dynamics is reviewed. A formulation based on a block reduction of the system Jacobian proves powerful to allow various numerical algorithms to be exploited, including frequency domain solvers, reconstruction of a term describing the fluid–structure interaction from the sparse data which incurs the main computational cost, and sampling to place the expensive samples where they are most needed. The stability formulation also allows non-deterministic analysis to be carried out very efficiently through the use of an approximate Newton solver. Finally, the system eigenvectors are exploited to produce nonlinear and parameterised reduced order models for computing limit cycle responses. The performance of the methods is illustrated with results from a number of academic and large dimension aircraft test cases.

Novel Analysis of Oceanic Surface Water Metagenomes Suggests Importance of Polyphosphate Metabolism in Oligotrophic Environments

Polyphosphate is a ubiquitous linear homopolymer of phosphate residues linked by high-energy bonds similar to those found in ATP. It has been associated with many processes including pathogenicity, DNA uptake and multiple stress responses across all domains. Bacteria have also been shown to use polyphosphate as a way to store phosphate when transferred from phosphate-limited to phosphate-rich media - a process exploited in wastewater treatment and other environmental contaminant remediation. Despite this, there has, to date, been little research into the role of polyphosphate in the survival of marine bacterioplankton in oligotrophic environments. The three main proteins involved in polyphosphate metabolism, Ppk1, Ppk2 and Ppx are multi-domain and have differential inter-domain and inter-gene conservation, making unbiased analysis of relative abundance in metagenomic datasets difficult. This paper describes the development of a novel Isofunctional Homolog Annotation Tool (IHAT) to detect homologs of genes with a broad range of conservation without bias of traditional expect-value cutoffs. IHAT analysis of the Global Ocean Sampling (GOS) dataset revealed that genes associated with polyphosphate metabolism are more abundant in environments where available phosphate is limited, suggesting an important role for polyphosphate metabolism in marine oligotrophs.

FDTD analysis of close-coupled 418 MHz radiating devices for human biotelemetry

This paper describes the finite-difference time-domain (FDTD) analysis of antenna-body interaction effects occurring when chest-mounted 418 MHz radio transmitters are used for medical telemetry applications. Whole-body software models (homogeneous, layered and tissue-segmented) were developed for an adult male subject. Using an electrically small (300 mm(2)) planar loop antenna, calculated radiation efficiencies ranged between 33.5% and 39.2% for a whole-body model, and between 60.7% and 66.1% for a torso; radiation patterns were found to be largely independent of model composition. The computed radiation efficiency for a 21.5 kg phantom representing a six-year-old female was within 1.1 dB of measured results (actual body mass 28 kg) and well-correlated azimuthal radiation patterns were noted.

Domain annihilation due to temperature and thickness gradients in single-crystal BaTiO3

The manner in which 90? ferroelectric-ferroelastic domains respond to changes in temperature has been mapped in BaTiO3 single crystals using atomic force microscopy. Domain periodicity remains unaltered until approximately 2 ? C below the Curie temperature (TC ), whereupon domains coarsened dramatically. This behavior was successfully rationalized by considering the temperature dependence of the parameters associated with standard models of ferroelastic domain formation. However, while successful in describing the expected radical increase in equilibrium period with temperature, the model did not predict the unusual mechanism by which domain coarsening occurred; this was not continuous at a local level but instead involved discrete domain annihilation events. Subsequent insights from a combination of free energy analysis for the system and further experimental data from an analogous situation, in which domain period increases with increasing crystal thickness, suggested that domain annihilation is inevitable whenever a component of the relevant gradient that affects domain period is orientated parallel to the domain walls. Consistent with this thesis, we note that, for the observations presented herein, the thermal gradient possessed a significant component parallel to the domain walls. We suggest that domain annihilation is a general feature of domain structures in gradient fields.

Functional analysis of the Campylobacter jejuni N-linked protein glycosylation pathway

We describe in this report the characterization of the recently discovered N-linked glycosylation locus of the human bacterial pathogen Campylobacter jejuni, the first such system found in a species from the domain Bacteria. We exploited the ability of this locus to function in Escherichia coli to demonstrate through mutational and structural analyses that variant glycan structures can be transferred onto protein indicating the relaxed specificity of the putative oligosaccharyltransferase PglB. Structural data derived from these variant glycans allowed us to infer the role of five individual glycosyltransferases in the biosynthesis of the N-linked heptasaccharide. Furthermore, we show that C. jejuni- and E. coli-derived pathways can interact in the biosynthesis of N-linked glycoproteins. In particular, the E. coli encoded WecA protein, a UDP-GlcNAc: undecaprenylphosphate GlcNAc-1-phosphate transferase involved in glycolipid biosynthesis, provides for an alternative N-linked heptasaccharide biosynthetic pathway bypassing the requirement for the C. jejuni-derived glycosyltransferase PglC. This is the first experimental evidence that biosynthesis of the N-linked glycan occurs on a lipid-linked precursor prior to transfer onto protein. These findings provide a framework for understanding the process of N-linked protein glycosylation in Bacteria and for devising strategies to exploit this system for glycoengineering.

Wavelet analysis of bender element signals

Accurate determination of shear wave arrival time using bender elements may be severely affected by a combination of near-field effects and reflected waves. These may mask the first arrival of the shear wave, making its detection difficult in the time domain. This paper describes an approach for measuring the shear wave arrival time through analysis of the output signal in the time-scale domain using a multi-scale wavelet transform. The local maxima lines of the wavelet transform modulus are observed at different scales, and all singularities are mathematically characterised, allowing subsequent detection of the singularity relating to the first arrival. Examples of the use of this approach on typical synthetic and experimental bender element signals are also supplied, and these results are compared with those from other time and frequency domain approaches. The wavelet approach is not affected by near-field effects, but instead is characterised by a relatively consistent singularity related to the shear wave arrival time, across a range of frequencies and noise levels.

Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen Fasciola hepatica:Expansion of a repertoire of virulence-associated factors

Cathepsin L proteases secreted by the helminth pathogen Fasciola hepatica have functions in parasite virulence including tissue invasion and suppression of host immune responses. Using proteomics methods alongside phylogenetic studies we characterized the profile of cathepsin L proteases secreted by adult F. hepatica and hence identified those involved in host-pathogen interaction. Phylogenetic analyses showed that the Fasciola cathepsin L gene family expanded by a series of gene duplications followed by divergence that gave rise to three clades associated with mature adult worms (Clades 1, 2, and 5) and two clades specific to infective juvenile stages (Clades 3 and 4). Consistent with these observations our proteomics studies identified representatives from Clades 1, 2, and 5 but not from Clades 3 and 4 in adult F. hepatica secretory products. Clades 1 and 2 account for 67.39 and 27.63% of total secreted cathepsin Ls, respectively, suggesting that their expansion was positively driven and that these proteases are most critical for parasite survival and adaptation. Sequence comparison studies revealed that the expansion of cathepsin Ls by gene duplication was followed by residue changes in the S2 pocket of the active site. Our biochemical studies showed that these changes result in alterations in substrate binding and suggested that the divergence of the cathepsin L family produced a repertoire of enzymes with overlapping and complementary substrate specificities that could cleave host macromolecules more efficiently. Although the cathepsin Ls are produced as zymogens containing a prosegment and mature domain, all secreted enzymes identified by MS were processed to mature active enzymes. The prosegment region was highly conserved between the clades except at the boundary of prosegment and mature enzyme. Despite the lack of conservation at this section, sites for exogenous cleavage by asparaginyl endopeptidases and a Leu-Ser[downward arrow]His motif for autocatalytic cleavage by cathepsin Ls were preserved.

Secretion and processing of a novel multi-domain cystatin-like protein by intracellular stages of Trichinella spiralis

The excretory-secretory (ES) proteins of nematode parasites are of major interest as they function at the host-parasite interface and are likely to have roles crucial for successful parasitism. Furthermore, the ES proteins of intracellular nematodes such as Trichinella spiralis may also function to regulate gene expression in the host cell. In a recent proteomic analysis we identified a novel secreted cystatin-like protein from T. spiralis L1 muscle larva. Here we show that the protein, MCD-1 (multi-cystatin-like domain protein 1), contains three repeating cystatin-like domains and analysis of the mcd-1 gene structure suggests that the repeated domains arose from duplication of an ancestral cystatin gene. Cystatins are a diverse group of cysteine protease inhibitors and those secreted by parasitic nematodes are important immuno-modulatory factors. The cystatin superfamily also includes cystatin-like proteins that have no cysteine protease inhibitory activity. A recombinant MCD-1 protein expressed as a GST-fusion protein in Escherichia coli failed to inhibit papain in vitro suggesting that the T. spiralis protein is a new member of the non-inhibitory cystatin-related proteins. MCD-1 secreted from T. spiralis exists as high- and low-molecular weight isoforms and we show that a recombinant MCD-1 protein secreted by HeLa cells undergoes pH-dependent processing that may result in the release of individual cystatin-like domains. Furthermore, we found that mcd-1 gene expression is largely restricted to intracellular stages with the highest levels of expression in the adult worms. It is likely that the major role of the protein is during the intestinal stage of T. spiralis infections.

Integrating textual analysis and evidential reasoning for decision making in Engineering design

Decision making is an important element throughout the life-cycle of large-scale projects. Decisions are critical as they have a direct impact upon the success/outcome of a project and are affected by many factors including the certainty and precision of information. In this paper we present an evidential reasoning framework which applies Dempster-Shafer Theory and its variant Dezert-Smarandache Theory to aid decision makers in making decisions where the knowledge available may be imprecise, conflicting and uncertain. This conceptual framework is novel as natural language based information extraction techniques are utilized in the extraction and estimation of beliefs from diverse textual information sources, rather than assuming these estimations as already given. Furthermore we describe an algorithm to define a set of maximal consistent subsets before fusion occurs in the reasoning framework. This is important as inconsistencies between subsets may produce results which are incorrect/adverse in the decision making process. The proposed framework can be applied to problems involving material selection and a Use Case based in the Engineering domain is presented to illustrate the approach. © 2013 Elsevier B.V. All rights reserved.

Towards Utilizing Model-Driven Engineering of Composite Applications for Business Performance Analysis

Composite Applications on top of SAPs implementation of SOA (Enterprise SOA) enable the extension of already existing business logic. In this paper we show, based on a case study, how Model-Driven Engineering concepts are applied in the development of such Composite Applications. Our Case Study extends a back-end business process which is required for the specific needs of a demo company selling wine. We use this to describe how the business centric models specifying the modified business behaviour of our case study can be utilized for business performance analysis where most of the actions are performed by humans. In particular, we apply a refined version of Model-Driven Performance Engineering that we proposed in our previous work and motivate which business domain specifics have to be taken into account for business performance analysis. We additionally motivate the need for performance related decision support for domain experts, who generally lack performance related skills. Such a support should offer visual guidance about what should be changed in the design and resource mapping to get improved results with respect to modification constraints and performance objectives, or objectives for time.

Metamaterials Nanosensor for Label-free Analysis of Conformation and Molecular Interaction of Biomolecules

Analysis of molecular interaction and conformational dynamics of biomolecules is of paramount importance in understanding of their vital functions in complex biological systems, disease detection, and new drug development. Plasmonic biosensors based upon surface plasmon resonance and localized surface plasmon resonance have become the predominant workhorse for detecting accumulated biomass caused by molecular binding events. However, unlike surface-enhanced Raman spectroscopy (SERS), the plasmonic biosensors indeed are not suitable tools to interrogate vibrational signatures of conformational transitions required for biomolecules to interact. Here, we show that plasmonic metamaterials can offer two transducing channels for parallel acquisition of optical transmission and sensitive SERS spectra at the biointerface, simultaneously probing the conformational states and binding affinity of biomolecules, e.g. G-quadruplexes, in different environments (Fig. 1). We further demonstrate the use of the metamaterials for fingerprinting and detection of arginine-glycine-glycine domain of nucleolin, a cancer biomarker which specifically binds to a G-quadruplex, with the picomolar sensitivity. The dual-mode nanosensor will significantly contribute to unraveling the complexes of the conformational dynamics of biomolecules as well as to improving specificity of biodetection assays.

Association Study of 167 Candidate Genes for Schizophrenia Selected by a Multi-Domain Evidence-Based Prioritization Algorithm and Neurodevelopmental Hypothesis

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n = 3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this
ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

Prediction of failure and fracture mechanisms of polymeric composites using finite element analysis. Part 2:Fiber reinforced composites

A robust finite element scheme for the micro-mechanical modeling of the behavior of fiber reinforced polymeric composites under external loads is developed. The developed model is used to simulate stress distribution throughout the composite domain and to identify the locations where maximum stress concentrations occur. This information is used as a guide to predict dominant failure and crack growth mechanisms in fiber reinforced composites. The differences between continuous fibers, which are susceptible to unidirectional transverse fracture, and short fibers have been demonstrated. To assess the validity and range of applicability of the developed scheme, numerical results obtained by the model are compared with the available experimental data and also with the values found using other methods reported in the literature. These comparisons show that the present finite element scheme can generate meaningful results in the analysis of fiber reinforced composites.