Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

BACKGROUND: Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. RESULTS: Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. CONCLUSIONS: Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

Evaluating Stakeholder Engagement in North Carolina Sea Grant’s Strategic Planning Process

In order to develop a strategic plan that will guide their priorities and resource allocation for 2018-2021, North Carolina Sea Grant has implemented a multi-stage process designed to increase stakeholder engagement and to better assess and serve the coastal priorities of North Carolinians. This project explores strengths and potential areas for improvement within NC Sea Grant’s planning process with a specific focus on maximizing stakeholder engagement. By interviewing staff, observing focus groups, and creating a survey instrument for public distribution, we developed a set of recommendations highlighting the ways that NC Sea Grant can better facilitate inclusion of stakeholder, public, and staff input in its strategic planning process, such as holding some stakeholder events outside of typical business hours and discussing ways to incorporate diversity into the strategic plan.

A non-Newtonian computational fluid dynamics study of the stencil printing process

This paper describes the application of computational fluid dynamics (CFD) to simulate the macroscopic bulk motion of solder paste ahead of a moving squeegee blade in the stencil printing process during the manufacture of electronic components. The successful outcome of the stencil printing process is dependent on the interaction of numerous process parameters. A better understanding of these parameters is required to determine their relation to print quality and improve guidelines for process optimization. Various modelling techniques have arisen to analyse the flow behaviour of solder paste, including macroscopic studies of the whole mass of paste as well as microstructural analyses of the motion of individual solder particles suspended in the carrier fluid. This work builds on the knowledge gained to date from earlier analytical models and CFD investigations by considering the important non-Newtonian rheological properties of solder pastes which have been neglected in previous macroscopic studies. Pressure and velocity distributions are obtained from both Newtonian and non-Newtonian CFD simulations and evaluated against each other as well as existing established analytical models. Significant differences between the results are observed, which demonstrate the importance of modelling non-Newtonian properties for realistic representation of the flow behaviour of solder paste.

Correlation of solder paste rheology with computational simulations of the stencil printing process

Soldering technologies continue to evolve to meet the demands of the continuous miniaturisation of electronic products, particularly in the area of solder paste formulations used in the reflow soldering of surface mount devices. Stencil printing continues to be a leading process used for the deposition of solder paste onto printed circuit boards (PCBs) in the volume production of electronic assemblies, despite problems in achieving a consistent print quality at an ultra-fine pitch. In order to eliminate these defects a good understanding of the processes involved in printing is important. Computational simulations may complement experimental print trials and paste characterisation studies, and provide an extra dimension to the understanding of the process. The characteristics and flow properties of solder pastes depend primarily on their chemical and physical composition and good material property data is essential for meaningful results to be obtained by computational simulation.This paper describes paste characterisation and computational simulation studies that have been undertaken through the collaboration of the School of Aeronautical, Mechanical and Manufacturing Engineering at Salford University and the Centre for Numerical Modelling and Process Analysis at the University of Greenwich. The rheological profile of two different paste formulations (lead and lead-free) for sub 100 micron flip-chip devices are tested and applied to computational simulations of their flow behaviour during the printing process.

A unified 3D model of the VAR process

A 3D time-dependent model of the VAR process has been developed using CFD techniques. The model solves the coupled field equations for fluid flow, heat transfer (including phase change) and electromagnetic field, for both the electrode and the ingot. The motion of the electic arc 'preferred spot' can be specified based on observations. Correlations are sought between the local gap height, resulting from instantaneous liquid pool surface shape and electrode tip shape, and the arc motion. The detailed behaviour of the melting film on the electrode tip is studies using a spectral free surface technique, which allows investigation of the drops' detachment and drip shorts.

Surface-enhanced Raman scattering studies of rhodanines: Evidence for substrate surface-induced dimerization

The surface-enhanced Raman scattering (SERS) spectra of rhodanine adsorbed on silver nanoparticles have been examined using 514.5 and 632.8 nm excitation. There is evidence that, under the experimental conditions used, rhodanine undergoes a nanoparticle surface-induced reaction resulting in the formation of a dimeric species via the active methylene group in a process which is analogous to the Knoevenagel reaction. The experimental observations are supported by DFT calculations at the B3-LYP/cc-pVDZ level. Calculated energies for the interaction of the E and Z isomers of the dimers of rhodanine with silver nanoparticles support a model in which the (intra-molecular hydrogen bonded) E isomer dimer is of lower energy than the Z isomer. A strong band, at 1566 cm(-1), in the SERS spectrum of rhodanine is assigned to the nu(C=C) mode of the dimer species.

Thixotropic studies of lead-based solder, lead-free solder and conductive adhesive pastes

The stencil printing process is an important process in the assembly of Surface Mount Technology (SMT)devices. There is a wide agreement in the industry that the paste printing process accounts for the majority of assembly defects. Experience with this process has shown that typically over 60% of all soldering defects are due to problems associated with the flow properties of solder pastes. Therefore, the rheological measurements can be used as a tool to study the deformation or flow experienced by the pastes during the stencil printing process. This paper presents results on the thixotropic behaviour of three pastes; lead-based solder paste, lead-free solder paste and isotropic conductive adhesive (ICA). These materials are widely used as interconnect medium in the electronics industry. Solder paste are metal alloys suspended in a flux medium while the ICAs consist of silver flakes dispersed in an epoxy resin. The thixotropy behaviour was investigated through two rheological test; (i) hysteresis loop test and (ii) steady shear rate test. In the hysteresis loop test, the shear rate were increased from 0.001 to 100s-1 and then decreased from 100 to 0.001s-1. Meanwhile, in the steady shear rate test, the materials were subjected to a constant shear rate of 0.100, 100 and 0.001s-1 for a period of 240 seconds. All the pastes showed a high degree of shear thinning behaviour with time. This might be due to the agglomeration of particles in the flux or epoxy resin that prohibits pastes flow under low shear rate. The action of high shear rate would break the agglomerates into smaller pieces which facilitates the flow of pastes, thus viscosity is reduced at high shear rate. The solder pastes exhibited a higher degree of structural breakdown compared to the ICAs. The area between the up curve and down curve in the hysteresis curve is an indication of the thixotropic behavior of the pastes. Among the three pastes, lead-free solder paste showed the largest area between the down curve and up curve, which indicating a larger structural breakdown in the pastes, followed by lead-based solder paste and ICA. In a steady shear rate test, viscosity of ICA showed the best recovery with the steeper curve to its original viscosity after the removal of shear, which indicating that the dispersion quality in ICA is good because the high shear has little effect on the microstructure of ICA. In contrast, lead-based paste showed the poorest recovery which means this paste undergo larger structural breakdown and dispersion quality in this paste is poor because the microstructure of the paste is easily disrupted by high shear. The structural breakdown during the application of shear and the recovery after removal of shear is an important characteristic in the paste printing process. If the paste’s viscosity can drop low enough, it may contribute to the aperture filling and quick recovery may prevent slumping.

Numerical and experimental studies of a substructural identification strategy

For structural health monitoring it is impractical to identify a large structure with complete measurement due to limited number of sensors and difficulty in field instrumentation. Furthermore, it is not desirable to identify a large number of unknown parameters in a full system because of numerical difficulty in convergence. A novel substructural strategy was presented for identification of stiffness matrices and damage assessment with incomplete measurement. The substructural approach was employed to identify large systems in a divide-and-conquer manner. In addition, the concept of model condensation was invoked to avoid the need for complete measurement, and the recovery process to obtain the full set of parameters was formulated. The efficiency of the proposed method is demonstrated numerically through multi-storey shear buildings subjected to random force. A fairly large structural system with 50 DOFs was identified with good results, taking into consideration the effects of noisy signals and the limited number of sensors. Two variations of the method were applied, depending on whether the sensor could be repositioned. The proposed strategy was further substantiated experimentally using an eight-storey steel plane frame model subjected to shaker and impulse hammer excitations. Both numerical and experimental results have shown that the proposed substructural strategy gave reasonably accurate identification in terms of locating and quantifying structural damage.

Can benthic community structure be used to predict the process of bioturbation in real ecosystems

Disentangling the roles of environmental change and natural environmental variability on biologically mediated ecosystem processes is paramount to predict future marine ecosystem functioning. Bioturbation, the biogenic mixing of sediments, has a regulating role in marine biogeochemical processes. However, our understanding of bioturbation as a community level process and of its environmental drivers is still limited by loose use of terminology, and a lack of consensus about what bioturbation is. To help resolve these challenges, this empirical study investigated the links between four different attributes of bioturbation (bioturbation depth, activity and distance, and biodiffusive transport); the ability of an index of bioturbation (BPc) to predict each of them; and their relation to seasonality, in a shallow coastal system – the Western Channel Observatory, UK. Bioturbation distance depended on changes in benthic community structure, while the other three attributes were more directly influenced by seasonality in food availability. In parallel, BPc successfully predicted bioturbation distance but not the other attributes of bioturbation. This study therefore highlights that community bioturbation results from this combination of processes responding to environmental variability at different time-scales. However, community level measurements of bioturbation across environmental variability are still scarce, and BPc is calculated using commonly available data on benthic community structure and the functional classification of invertebrates. Therefore, BPc could be used to support the growth of landscape scale bioturbation research, but future uses of the index need to consider which bioturbation attributes the index actually predicts. As BPc predicts bioturbation distance, estimated here using a random-walk model applicable to community settings, studies using either of the metrics should be directly comparable and contribute to a more integrated future for bioturbation research.

THE ROLE OF LIPOPROTEIN(a)/APOLIPOPROTEIN(a) IN ENDOTHELIAL DYSFUNCTION: MECHANISTIC STUDIES IN VASCULAR ENDOTHELIUM

Multiple lines of evidence suggest that elevated plasma lipoprotein(a) (Lp(a)) concentrations are a significant risk factor for the development of a number of vascular diseases including coronary heart disease and stroke. Lp(a) consists of a low-density lipoprotein (LDL)-like moiety and an unique glycoprotein, apolipoprotein(a) (apo(a)), that is covalently attached to the apolipoproteinB-100 (apoB-100) component of LDL by a single disulfide bond. Many studies have suggested a role for Lp(a) in the process of endothelial dysfunction. Indeed, Lp(a) has been shown to increase both the expression of adhesion molecules on endothelial cells (EC), as well as monocyte and leukocyte chemotactic activity in these cells. We have previously demonstrated that Lp(a), through its apo(a) moiety, increases actomyosin-driven EC contraction which, as a consequence, increases EC permeability. In this thesis, we have demonstrated a role for the strong lysine-binding site in the kringle IV type 10 domain of apo(a) in increasing EC permeability, which occurs through a Rho/Rho kinase-dependent pathway. We have further validated these findings using mouse mesenteric arteries in a pressure myograph system. We also have dissected another major signaling pathway initiated by apo(a) that involves in a disruption of adherens junctions in EC. In this pathway, apo(a)/Lp(a) activates the PI3K/Akt/GSK3β-dependent pathway to facilitate nuclear translocation of beta-catenin. In the nucleus beta-catenin induced the expression of cyclooxygenase-2 (COX-2) and the secretion of prostaglandin E2 (PGE2) from the EC. Finally, we have presented data to suggest a novel inflammatory role for apo(a) in which it induces the activation of nuclear factor-kappaB through promotion of the dissociation of IkappaB from the inactive cytoplasmic complex; this allows the nuclear translocation of NFkappaB with attendant effects on the transcription of pro-inflammatory genes. Taken together, our findings may facilitate the development of new drug targets for mitigating the harmful effects of Lp(a) on vascular EC which corresponds to an early step in the process of atherogenesis.

Integration Of Strength and Process Modelling of Friction-Stir-Welded Fuselage Panels

In order to reduce potential uncertainties and conservatism in welded panel analysis procedures, understanding of the relationships between welding process parameters and static strength is required. The aim of this study is to determine and characterize the key process induced properties of advanced welding assembly methods on stiffened panel local buckling and collapse performance. To this end, an in-depth experimental and computational study of the static strength of a friction stir welded fuselage skin-stiffener panel subjected to compression loading has been undertaken. Four welding process effects, viz. the weld joint width, the width of the weld Heat Affected Zone, the strength of material within the weld Heat Affected Zone and the magnitude of welding induced residual stress, are investigated. A fractional factorial experiment design method (Taguchi) has been applied to identify the relative importance of each welding process effect and investigate effect interactions on both local skin buckling and crippling collapse performance. For the identified dominant welding process effects, parametric studies have been undertaken to identify critical welding process effect magnitudes and boundaries. The studies have shown that local skin buckling is principally influenced by the magnitude of welding induced residual stress and that the strength of material in the Heat Affected Zone and the magnitude of the welding induced residual stress have the greatest influence on crippling collapse behavior.


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Sequence and Structure Based Protein Folding Studies With Implications

As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has taught us that diversity is the hallmark of their architecture, a fundamental characteristic that enables them to perform the vast array of functionality upon which all of life depends. This diversity, however, is central to one of the most challenging problems in molecular biology: how does a folding polypeptide chain navigate its way through all of the myriad of possible conformations to find its own particular biologically active form? With few overarching structural principles to draw upon that can be applied to all protein architecture, the search for a solution to the protein folding problem has yet to produce an algorithm that can explain and duplicate this fundamental biological process. In this thesis, we take a two-pronged approach for investigating the protein folding process. Our initial statistical studies of the distributions of hydrophobic and hydrophilic residues within α-helices and β-sheets suggest (i) that hydrophobicity plays a critical role in helix and sheet formation; and (ii) that the nucleation of these motifs may result in largely unidirectional growth. Most tellingly, from an examination of the amino acids found in the smallest β-sheets, we do not find any evidence of a β-nucleating code in the primary protein sequence. Complementing these statistical analyses, we have analyzed the structural environments of several ever-widening aspects of protein topology. Our examination of the gaps between strands in the smallest β-sheets reveals a common organizational principle underlying β-formation involving strands separated by large sequential gaps: with very few exceptions, these large gaps fold into single, compact structural modules, bringing the β-strands that are otherwise far apart in the sequence close together in space. We conclude, therefore, that β-nucleation in the smallest sheets results from the co-location of two strands that are either local in sequence, or local in space following prior folding events. A second study of larger β-sheets both corroborates and extends these findings: virtually all large sequential gaps between pairs of β-strands organize themselves into an hierarchical arrangement, creating a bread-crumb model of go-and-come-back structural organization that ultimately juxtaposes two strands of a parental β-structure that are far apart in the sequence in close spatial proximity. In a final study, we have formalized this go-and-come-back notion into the concept of anti-parallel double-strandedness (DS), and measure this property across protein architecture in general. With over 90% of all residues in a large, non-redundant set of protein structures classified as DS, we conclude that DS is a unifying structural principle that underpins all globular proteins. We postulate, moreover, that this one simple principle, anti-parallel double-strandedness, unites protein structure, protein folding and protein evolution.

Legitimising Quality Principles through Critical Incidents in Organisational Development

Purpose – The aim of this paper is to analyse how critical incidents or organisational crises can be used to check and legitimise quality management change efforts in relation to the fundamental principles of quality. Design/methodology/approach – Multiple case studies analyse critical incidents that demonstrate the importance of legitimisation, normative evaluation and conflict constructs in this process. A theoretical framework composed of these constructs is used to guide the analysis. Findings – The cases show that the critical incidents leading to the legitimisation of continuous improvement (CI) were diverse. However all resulted in the need for significant ongoing cost reduction to achieve or retain competitiveness. In addition, attempts at legitimising CI were coupled with attempts at destabilising the existing normative practice. This destabilisation process, in some cases, advocated supplementing the existing approaches and in others replacing them. In all cases, significant conflict arose in these legitimising and normative evaluation processes. Research limitations/implications – It is suggested that further research could involve a critical analysis of existing quality models, tools and techniques in relation to how they incorporate, and are built upon, fundamental quality management principles. Furthermore, such studies could probe the dangers of quality curriculum becoming divorced from business and market reality and thus creating a parallel existence. Practical implications – As demonstrated by the case studies, models, tools and techniques are not valued for their intrinsic value but rather for what they will contribute to addressing the business needs. Thus, in addition to being an opportunity for quality management, critical incidents present a challenge to the field. Quality management must be shown to make a contribution in these circumstances. Originality/value – This paper is of value to both academics and practitioners.

Greek-Turkish Dilemmas and the Cyprus-EU Accession Process

This article compares the processes of foreign policymaking in Greece and Turkey in order to examine why the incentives and pressures of the enlargement process have failed until now to initiate a settlement in the Cyprus bicommunal negotiations. While most studies on the Cyprus problem have focused on the two communities of the island, little at-tention has been paid to the policies of the two â??motherlandsâ??, namely Greece and Turkey. Yet their leverage on the two Cypriot communities and their conflicting expectations with regard to an enlarged Europe in the Eastern Mediterranean constitute a complex security puzzle. The Republic of Cyprus stands as a champion candidate member for the next enlargement, amid fears of Turkish reprisals and hopes for a po-litical settlement on the island. With the benefits of settlement overwhelming the benefits of any other alternative, it is paradoxical that the parties seem to be about to fail to reach a last-minute, mutually beneficial compromise. I try to resolve this paradox by supplementing rational choice theory with cognitivist theories of international relations. While rational choice predicts a direct relationship between external environment and foreign policy shifts, the case of Cyprus suggests that this relationship is actually indirect. Without understanding how the external environment is framed in the domestic political discourse of Greece and Turkey, it is impossible to demonstrate how outside pressure and incentives affect foreign policy shifts.

Finite temperature dense matter studies on next-generation light sources

The construction of short-pulse tunable soft x-ray free electron laser sources based on the self-amplified spontaneous emission process will provide a major advance in capability for dense plasma-related and warm dense matter (WDM) research. The sources will provide 10(13) photons in a 200-fs duration pulse that is tunable from approximately 6 to 100 nm. Here we discuss only two of the many applications made possible for WDM that has been severely hampered by the fact that laser-based methods have been unavailable because visible light will not propagate at electron densities of n(e) greater than or equal to 10(22) cm(-3). The next-generation light sources will remove these restrictions.