Spectral analysis of pair-correlation bandwidth: Application to cell biology images

Images from cell biology experiments often indicate the presence of cell clustering, which can provide insight into the mechanisms driving the collective cell behaviour. Pair-correlation functions provide quantitative information about the presence, or absence, of clustering in a spatial distribution of cells. This is because the pair-correlation function describes the ratio of the abundance of pairs of cells, separated by a particular distance, relative to a randomly distributed reference population. Pair-correlation functions are often presented as a kernel density estimate where the frequency of pairs of objects are grouped using a particular bandwidth (or bin width), Δ>0. The choice of bandwidth has a dramatic impact: choosing Δ too large produces a pair-correlation function that contains insufficient information, whereas choosing Δ too small produces a pair-correlation signal dominated by fluctuations. Presently, there is little guidance available regarding how to make an objective choice of Δ. We present a new technique to choose Δ by analysing the power spectrum of the discrete Fourier transform of the pair-correlation function. Using synthetic simulation data, we confirm that our approach allows us to objectively choose Δ such that the appropriately binned pair-correlation function captures known features in uniform and clustered synthetic images. We also apply our technique to images from two different cell biology assays. The first assay corresponds to an approximately uniform distribution of cells, while the second assay involves a time series of images of a cell population which forms aggregates over time. The appropriately binned pair-correlation function allows us to make quantitative inferences about the average aggregate size, as well as quantifying how the average aggregate size changes with time.

Correlation between NIRS generated and chemically measured feed quality data in barley (Hordeum vulgare), and potential use in QTL analysis identification

A study was performed to investigate the value of near infrared reflectance spectroscopy (NIRS) as an alternate method to analytical techniques for identifying QTL associated with feed quality traits. Milled samples from an F6-derived recombinant inbred Tallon/Scarlett population were incubated in the rumen of fistulated cattle, recovered, washed and dried to determine the in-situ dry matter digestibility (DMD). Both pre- and post-digestion samples were analysed using NIRS to quantify key quality components relating to acid detergent fibre, starch and protein. This phenotypic data was used to identify trait associated QTL and compare them to previously identified QTL. Though a number of genetic correlations were identified between the phenotypic data sets, the only correlation of most interest was between DMD and starch digested (r = -0.382). The significance of this genetic correlation was that the NIRS data set identified a putative QTL on chromosomes 7H (LOD = 3.3) associated with starch digested. A QTL for DMD occurred in the same region of chromosome 7H, with flanking markers fAG/CAT63 and bPb-0758. The significant correlation and identification of this putative QTL, highlights the potential of technologies like NIRS in QTL analysis.

Crude oil and agricultural futures: An analysis of correlation dynamics

Correlations between oil and agricultural commodities have varied over previous decades, impacted by renewable fuels policy and turbulent economic conditions. We estimate smooth transition conditional correlation models for 12 agricultural commodities and WTI crude oil. While a structural change in correlations occurred concurrently with the introduction of biofuel policy, oil and food price levels are also key influences. High correlation between biofuel feedstocks and oil is more likely to occur when food and oil price levels are high. Correlation with oil returns is strong for biofuel feedstocks, unlike with other agricultural futures, suggesting limited contagion from energy to food markets.

Convergence analysis of the Newton algorithm and a pseudo-time marching scheme for diffuse correlation tomography

We propose a self-regularized pseudo-time marching scheme to solve the ill-posed, nonlinear inverse problem associated with diffuse propagation of coherent light in a tissuelike object. In particular, in the context of diffuse correlation tomography (DCT), we consider the recovery of mechanical property distributions from partial and noisy boundary measurements of light intensity autocorrelation. We prove the existence of a minimizer for the Newton algorithm after establishing the existence of weak solutions for the forward equation of light amplitude autocorrelation and its Frechet derivative and adjoint. The asymptotic stability of the solution of the ordinary differential equation obtained through the introduction of the pseudo-time is also analyzed. We show that the asymptotic solution obtained through the pseudo-time marching converges to that optimal solution provided the Hessian of the forward equation is positive definite in the neighborhood of optimal solution. The superior noise tolerance and regularization-insensitive nature of pseudo-dynamic strategy are proved through numerical simulations in the context of both DCT and diffuse optical tomography. (C) 2010 Optical Society of America.

First-principles analysis of electron correlation, spin ordering and phonons in the normal state of FeSe1-x

We present first-principles density-functional-theory-based calculations to determine the effects of the strength of on-site electron correlation, magnetic ordering, pressure and Se vacancies on phonon frequencies and electronic structure of FeSe1-x. The theoretical equilibrium structure (lattice parameters) of FeSe depends sensitively on the value of the Hubbard parameter U of on-site correlation and magnetic ordering. Our results suggest that there is a competition between different antiferromagnetic states due to comparable magnetic exchange couplings between first- and second-neighbor Fe sites. As a result, a short range order of stripe antiferromagnetic type is shown to be relevant to the normal state of FeSe at low temperature. We show that there is a strong spin-phonon coupling in FeSe (comparable to its superconducting transition temperature) as reflected in large changes in the frequencies of certain phonons with different magnetic ordering, which is used to explain the observed hardening of a Raman-active phonon at temperatures (similar to 100 K) where magnetic ordering sets in. The symmetry of the stripe antiferromagnetic phase permits an induced stress with orthorhombic symmetry, leading to orthorhombic strain as a secondary order parameter at the temperature of magnetic ordering. The presence of Se vacancies in FeSe gives rise to a large peak in the density of states near the Fermi energy, which could enhance the superconducting transition temperature within the BCS-like picture.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Analysis of MAC protocols with correlation receiver for optical CDMA networks – part I

In this paper optical code-division multiple-access (O-CDMA) packet network is considered. Two types of random access protocols are proposed for packet transmission. In protocol 1, all distinct codes and in protocol 2, distinct codes as well as shifted versions of all these codes are used. O-CDMA network performance using optical orthogonal codes (OOCs) 1-D and twodimensional (2-D) wavelength/time single-pulse-per-row (W/TSPR) codes are analyzed. The main advantage of using 2-D codes instead of one-dimensional (1-D) codes is to reduce the errors due to multiple access interference among different users. In this paper, correlation receiver is considered in the analysis. Using analytical model, we compute and compare packet-success probability for 1-D and 2-D codes in an O-CDMA network and the analysis shows improved performance with 2-D codes as compared to 1-D codes.

Experimental analysis of composite single-lap joints using digital image correlation and comparison with theoretical models

The demand for energy efficient, low weight structures has boosted the use of composite structures assembled using increased quantities of structural adhesives. Bonded structures may be subjected to severe working environments such as high temperature and moisture due to which the adhesive gets degraded over a period of time. This reduces the strength of a joint and leads to premature failure. Measurement of strains in the adhesive bondline at any point of time during service may be beneficial as an assessment can be made on the integrity of a joint and necessary preventive actions may be taken before failure. This paper presents an experimental approach of measuring peel and shear strains in the adhesive bondline of composite single-lap joints using digital image correlation. Different sets of composite adhesive joints with varied bond quality were prepared and subjected to tensile load during which digital images were taken and processed using digital image correlation software. The measured peel strain at the joint edge showed a rapid increase with the initiation of a crack till failure of the joint. The measured strains were used to compute the corresponding stresses assuming a plane strain condition and the results were compared with stresses predicted using theoretical models, namely linear and nonlinear adhesive beam models. A similar trend in stress distribution was observed. Further comparison of peel and shear strains also exhibited similar trend for both healthy and degraded joints. Maximum peel stress failure criterion was used to predict the failure load of a composite adhesive joint and a comparison was made between predicted and actual failure loads. The predicted failure loads from theoretical models were found to be higher than the actual failure load for all the joints.

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Chemical bond analysis of the correlation between crystal structure and nonlinear optical properties of complex crystals

Second order nonlinear optical (NLO) properties of single crystals with complex structures are studied, from the chemical bond viewpoint. Contributions of each type of constituent chemical bond to the total linearity and nonlinearity are calculated from the actual crystal structure, using the chemical bond theory of complex crystals and the modified bond charge model. We have quantitatively proposed certain relationships between the crystal structure and its NLO properties. Several relations have been established from the calculation. Our method makes it possible for us to identify, predict and modify new NLO materials according to our needs. (C) 1999 Elsevier Science B.V. All rights reserved.

Cross-correlation frequency resolved optical gating analysis of broadband continuum generation in photonic crystal fiber: Simulations and experiments

Numerical simulations are used to study the temporal and spectral characteristics of broadband supercontinua generated in photonic crystal fiber. In particular, the simulations are used to follow the evolution with propagation distance of the temporal intensity, the spectrum, and the cross-correlation frequency resolved optical gating (XFROG) trace. The simulations allow several important physical processes responsible for supercontinuum generation to be identified and, moreover, illustrate how the XFROG trace provides an intuitive means of interpreting correlated temporal and spectral features of the supercontinuum. Good qualitative agreement with preliminary XFROG measurements is observed. © 2002 Optical Society of America.

Association Analysis of Canonical Wnt Signalling Genes in Diabetic Nephropathy.

Several studies have provided compelling evidence implicating the Wnt signalling pathway in the pathogenesis of diabetic nephropathy. Gene expression profiles associated with renal fibrosis have been attenuated through Wnt pathway modulation in model systems implicating Wnt pathway members as potential therapeutic targets for the treatment of diabetic nephropathy. We assessed tag and potentially functional single nucleotide polymorphisms (SNPs; n = 31) in four key Wnt pathway genes (CTNNB1, AXIN2, LRP5 and LRP6) for association with diabetic nephropathy using a case-control design.