SLoMo: automated site localization of modifications from ETD/ECD mass spectra

Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data

With a Little Help from Our Friends: Social Support as a Source of Well-being and of Coping with Stress

The relationship between one\u27s psycho-emotional and physiological health has long been of interest to social scientists. While many factors have been examined for their impact on causation and prevention, over the past two decades the concepts of social support, stress and well-being have undergone much scrutiny. In this article the authors provide empirical data to enhance our understanding of the interrelatedness of these three concepts. Based on the findings from a study of stress and health in organizations, a model is proposed which elucidates some of the conditions under which social support networks mediate the impact of stress on psychological well-being

Reliability based design optimisation for system-in-package

This paper discusses a reliability based optimisation modelling approach demonstrated for the design of a SiP structure integrated by stacking dies one upon the other. In this investigation the focus is on the strategy for handling the uncertainties in the package design inputs and their implementation into the design optimisation modelling framework. The analysis of fhermo-mechanical behaviour of the package is utilised to predict the fatigue life-time of the lead-free board level solder interconnects and warpage of the package under thermal cycling. The SiP characterisation is obtained through the exploitation of Reduced Order Models (ROM) constructed using high fidelity analysis and Design of Experiments (DoE) methods. The design task is to identify the optimal SiP design specification by varying several package input parameters so that a specified target reliability of the solder joints is achieved and in the same time design requirements and package performance criteria are me

Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-III secretion

BACKGROUND: Like many other pathogens, enterohaemorrhagic and enteropathogenic strains of Escherichia coli employ a type-III secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. This system is encoded by the locus for enterocyte effacement. Many of the genes within this locus have been assigned names and functions through homology with the better characterised Ysc-Yop system from Yersinia spp. However, the functions and homologies of many LEE genes remain obscure. RESULTS: We have performed a fresh bioinformatics analysis of the LEE. Using PSI-BLAST we have been able to identify several novel homologies between LEE-encoded and Ysc-Yop-associated proteins: Orf2/YscE, Orf5/YscL, rORF8/EscI, SepQ/YscQ, SepL/YopN-TyeA, CesD2/LcrR. In addition, we highlight homology between EspA and flagellin, and report many new homologues of the chaperone CesT. CONCLUSION: We conclude that the vast majority of LEE-encoded proteins do indeed possess homologues and that homology data can be used in combination with experimental data to make fresh functional predictions

High-energy optical transitions and optical constants of CH3_3NH3_3PbI3_3 measured by spectroscopic ellipsometry and spectrophotometry

Optoelectronics based on metal halide perovskites (MHPs) have shown substantial promise, following more than a decade of research. For prime routes of commercialization such as tandem solar cells, optical modeling is essential for engineering device architectures, which requires accurate optical data for the materials utilized. Additionally, a comprehensive understanding of the fundamental material properties is vital for simulating the operation of devices for design purposes. In this article, we use variable angle spectroscopic ellipsometry (SE) to determine the optical constants of CH$_3$NH$_3$PbI$_3$ (MAPbI$_3$) thin films over a photon energy range of 0.73 to 6.45 eV. We successfully model the ellipsometric data using six Tauc-Lorentz oscillators for three different incident angles. Following this, we use critical-point analysis of the complex dielectric constant to identify the well-known transitions at 1.58, 2.49, 3.36 eV, but also additional transitions at 4.63 and 5.88 eV, which are observed in both SE and spectrophotometry measurements. This work provides important information relating to optical transitions and band structure of MAPbI$_3$, which can assist in the development of potential applications of the material.Comment: 18 pages, 4 figure

Computational approach for reliable and robust system-in-package design

A computational modelling approach integrated with optimisation and statistical methods that can aid the development of reliable and robust electronic packages and systems is presented. The design for reliability methodology is demonstrated for the design of a SiP structure. In this study the focus is on the procedure for representing the uncertainties in the package design parameters, their impact on reliability and robustness of the package design and how these can be included in the design optimisation modelling framework. The analysis of thermo-mechanical behaviour of the package is conducted using non-linear transient finite element simulations. Key system responses of interest, the fatigue life-time of the lead-free solder interconnects and warpage of the package, are predicted and used subsequently for design purposes. The design tasks are to identify the optimal SiP designs by varying several package input parameters so that the reliability and the robustness of the package are improved and in the same time specified performance criteria are also satisfie

High current density induced damage mechanisms in electronic solder joints: a state-of-the-art review

High current density induced damages such as electromigration in the on-chip interconnection /metallization of Al or Cu has been the subject of intense study over the last 40 years. Recently, because of the increasing trend of miniaturization of the electronic packaging that encloses the chip, electromigration as well as other high current density induced damages are becoming a growing concern for off-chip interconnection where low melting point solder joints are commonly used. Before long, a huge number of publications have been explored on the electromigration issue of solder joints. However, a wide spectrum of findings might confuse electronic companies/designers. Thus, a review of the high current induced damages in solder joints is timely right this moment. We have selected 6 major phenomena to review in this paper. They are (i) electromigration (mass transfer due electron bombardment), (ii) thermomigration (mass transfer due to thermal gradient), (iii) enhanced intermetallic compound growth, (iv) enhanced current crowding, (v) enhanced under bump metallisation dissolution and (vi) high Joule heating and (vii) solder melting. the damage mechanisms under high current stressing in the tiny solder joint, mentioned in the review article, are significant roadblocks to further miniaturization of electronics. Without through understanding of these failure mechanisms by experiments coupled with mathematical modeling work, further miniaturization in electronics will be jeopardize

The effect of heterogeneity on invasion in spatial epidemics: from theory to experimental evidence in a model system

Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade, yet the quantitative investigation of its effects on epidemic spread is still an open problem. In this paper, we test recent theoretical results, which extend the established “percolation paradigm” to the spread of a pathogen in discrete heterogeneous host populations. In particular, we test the hypothesis that the probability of epidemic invasion decreases when host heterogeneity is increased. We use replicated experimental microcosms, in which the ubiquitous pathogenic fungus Rhizoctonia solani grows through a population of discrete nutrient sites on a lattice, with nutrient sites representing hosts. The degree of host heterogeneity within different populations is adjusted by changing the proportion and the nutrient concentration of nutrient sites. The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population. We find a significant, negative correlation between heterogeneity and the probability of pathogen invasion, thereby validating the theory. The value of the correlation is also in remarkably good agreement with the theoretical predictions. We briefly discuss how our results can be exploited in the design and implementation of disease control strategies

Black Holes in Einstein-Aether Theory

We study black hole solutions in general relativity coupled to a unit timelike vector field dubbed the "aether". To be causally isolated a black hole interior must trap matter fields as well as all aether and metric modes. The theory possesses spin-0, spin-1, and spin-2 modes whose speeds depend on four coupling coefficients. We find that the full three-parameter family of local spherically symmetric static solutions is always regular at a metric horizon, but only a two-parameter subset is regular at a spin-0 horizon. Asymptotic flatness imposes another condition, leaving a one-parameter family of regular black holes. These solutions are compared to the Schwarzschild solution using numerical integration for a special class of coupling coefficients. They are very close to Schwarzschild outside the horizon for a wide range of couplings, and have a spacelike singularity inside, but differ inside quantitatively. Some quantities constructed from the metric and aether oscillate in the interior as the singularity is approached. The aether is at rest at spatial infinity and flows into the black hole, but differs significantly from the the 4-velocity of freely-falling geodesics.Comment: 22 pages, 6 figures; v2: minor editing; v3: corrected overall sign in twist formula and an error in the equation for the aether stress tensor. Results unchanged since correct form was used in calculations; v4: corrected minor typ

Using Texture Synthesis for Non-Photorealistic Shading from Paint Samples

This paper presents several methods for shading meshes from scanned paint samples that represent dark to light transitions. Our techniques emphasize artistic control of brush stroke texture and color. We first demonstrate how the texture of the paint sample can be separated from its color gradient. We demonstrate three methods, two real-time and one off-line for producing rendered, shaded images from the texture samples. All three techniques use texture synthesis to generate additional paint samples. Finally, we develop metrics for evaluating how well each method achieves our goal in terms of texture similarity, shading correctness and temporal coherence