Multiscale analysis of protein functions and stochastic modelling of gene transcriptional regulatory networks

Genomic and proteomic analyses have attracted a great deal of interests in biological research in recent years. Many methods have been applied to discover useful information contained in the enormous databases of genomic sequences and amino acid sequences. The results of these investigations inspire further research in biological fields in return. These biological sequences, which may be considered as multiscale sequences, have some specific features which need further efforts to characterise using more refined methods. This project aims to study some of these biological challenges with multiscale analysis methods and stochastic modelling approach. The first part of the thesis aims to cluster some unknown proteins, and classify their families as well as their structural classes. A development in proteomic analysis is concerned with the determination of protein functions. The first step in this development is to classify proteins and predict their families. This motives us to study some unknown proteins from specific families, and to cluster them into families and structural classes. We select a large number of proteins from the same families or superfamilies, and link them to simulate some unknown large proteins from these families. We use multifractal analysis and the wavelet method to capture the characteristics of these linked proteins. The simulation results show that the method is valid for the classification of large proteins. The second part of the thesis aims to explore the relationship of proteins based on a layered comparison with their components. Many methods are based on homology of proteins because the resemblance at the protein sequence level normally indicates the similarity of functions and structures. However, some proteins may have similar functions with low sequential identity. We consider protein sequences at detail level to investigate the problem of comparison of proteins. The comparison is based on the empirical mode decomposition (EMD), and protein sequences are detected with the intrinsic mode functions. A measure of similarity is introduced with a new cross-correlation formula. The similarity results show that the EMD is useful for detection of functional relationships of proteins. The third part of the thesis aims to investigate the transcriptional regulatory network of yeast cell cycle via stochastic differential equations. As the investigation of genome-wide gene expressions has become a focus in genomic analysis, researchers have tried to understand the mechanisms of the yeast genome for many years. How cells control gene expressions still needs further investigation. We use a stochastic differential equation to model the expression profile of a target gene. We modify the model with a Gaussian membership function. For each target gene, a transcriptional rate is obtained, and the estimated transcriptional rate is also calculated with the information from five possible transcriptional regulators. Some regulators of these target genes are verified with the related references. With these results, we construct a transcriptional regulatory network for the genes from the yeast Saccharomyces cerevisiae. The construction of transcriptional regulatory network is useful for detecting more mechanisms of the yeast cell cycle.

Empirical analysis of freeway traffic oscillation : its safety impact and evolution

Traffic oscillations are typical features of congested traffic flow that are characterized by recurring decelerations followed by accelerations. However, people have limited knowledge on this complex topic. In this research, 1) the impact of traffic oscillations on freeway crash occurrences has been measured using the matched case-control design. The results consistently reveal that oscillations have a more significant impact on freeway safety than the average traffic states. 2) Wavelet Transform has been adopted to locate oscillations' origins and measure their characteristics along their propagation paths using vehicle trajectory data. 3) Lane changing maneuver's impact on the immediate follower is measured and modeled. The knowledge and the new models generated from this study could provide better understanding on fundamentals of congested traffic; enable improvements to existing traffic control strategies and freeway crash countermeasures; and instigate people to develop new operational strategies with the objective of reducing the negative effects of oscillatory driving.

On the empirical eigenvalue distribution of slotted amplify-and-forward relaying protocol model

In this paper we consider the case of large cooperative communication systems where terminals use the protocol known as slotted amplify-and-forward protocol to aid the source in its transmission. Using the perturbation expansion methods of resolvents and large deviation techniques we obtain an expression for the Stieltjes transform of the asymptotic eigenvalue distribution of a sample covariance random matrix of the type HH† where H is the channel matrix of the transmission model for the transmission protocol we consider. We prove that the resulting expression is similar to the Stieltjes transform in its quadratic equation form for the Marcenko-Pastur distribution.

Correlation of the expression of human kallikrein-related peptidases 4 and 7 with the prognosis in oral squamous cell carcinoma

Background Very few articles have been written about the expression of kallikreins (KLK4 and KLK7) in oral cancers. Therefore, the purpose of this study was to examine and report on their prognostic potential. Methods Eighty archival blocks of primary oral cancers were sectioned and stained for KLK4 and KLK7 by immunohistochemistry. The percentage and the intensity of malignant keratinocyte staining were correlated with patient survival using Cox regression analysis. Results Both kallikreins were expressed strongly in the majority of tumor cells in 68 of 80 cases: these were mostly moderately or poorly differentiated neoplasms. Staining was particularly intense at the infiltrating front. Patients with intense staining had significantly shorter overall survival (p < .05). Conclusion This is the first observation on the patient survival influenced by kallikrein expression in oral carcinoma. The findings are consistent with those for carcinomas at other sites, in particular the prostate and ovary. KLK4 and/or KLK7 immunohistochemistry seems to have diagnostic and prognostic potential in this disease.

Diversification and value-at-risk

A pervasive and puzzling feature of banks’ Value-at-Risk (VaR) is its abnormally high level, which leads to excessive regulatory capital. A possible explanation for the tendency of commercial banks to overstate their VaR is that they incompletely account for the diversification effect among broad risk categories (e.g., equity, interest rate, commodity, credit spread, and foreign exchange). By underestimating the diversification effect, bank’s proprietary VaR models produce overly prudent market risk assessments. In this paper, we examine empirically the validity of this hypothesis using actual VaR data from major US commercial banks. In contrast to the VaR diversification hypothesis, we find that US banks show no sign of systematic underestimation of the diversification effect. In particular, diversification effects used by banks is very close to (and quite often larger than) our empirical diversification estimates. A direct implication of this finding is that individual VaRs for each broad risk category, just like aggregate VaRs, are biased risk assessments.

Empirical research in business process management : introduction to the special issue

In this editorial letter, we provide the readers of Information Systems and e-Business Management with an introduction to Business Process Management and the challenges of empirical research in this field. We then briefly describe selected examples of current research efforts in this fields and how the papers accepted for this special issue contribute to extending our body of knowledge.

Empirical evaluation of an autonomous vehicle in an urban environment

Operation in urban environments creates unique challenges for research in autonomous ground vehicles. Due to the presence of tall trees and buildings in close proximity to traversable areas, GPS outage is likely to be frequent and physical hazards pose real threats to autonomous systems. In this paper, we describe a novel autonomous platform developed by the Sydney-Berkeley Driving Team for entry into the 2007 DARPA Urban Challenge competition. We report empirical results analyzing the performance of the vehicle while navigating a 560-meter test loop multiple times in an actual urban setting with severe GPS outage. We show that our system is robust against failure of global position estimates and can reliably traverse standard two-lane road networks using vision for localization. Finally, we discuss ongoing efforts in fusing vision data with other sensing modalities.

Empirical minimization

We investigate the behavior of the empirical minimization algorithm using various methods. We first analyze it by comparing the empirical, random, structure and the original one on the class, either in an additive sense, via the uniform law of large numbers, or in a multiplicative sense, using isomorphic coordinate projections. We then show that a direct analysis of the empirical minimization algorithm yields a significantly better bound, and that the estimates we obtain are essentially sharp. The method of proof we use is based on Talagrand’s concentration inequality for empirical processes.

On the optimality of sample-based estimates of the expectation of the empirical minimizer

We study sample-based estimates of the expectation of the function produced by the empirical minimization algorithm. We investigate the extent to which one can estimate the rate of convergence of the empirical minimizer in a data dependent manner. We establish three main results. First, we provide an algorithm that upper bounds the expectation of the empirical minimizer in a completely data-dependent manner. This bound is based on a structural result due to Bartlett and Mendelson, which relates expectations to sample averages. Second, we show that these structural upper bounds can be loose, compared to previous bounds. In particular, we demonstrate a class for which the expectation of the empirical minimizer decreases as O(1/n) for sample size n, although the upper bound based on structural properties is Ω(1). Third, we show that this looseness of the bound is inevitable: we present an example that shows that a sharp bound cannot be universally recovered from empirical data.

Are low CO2 emitters in rural areas also socially excluded? An empirical investigation of travel diary data from rural Northern Ireland

The reduction of CO2 emissions and social exclusion are two key elements of UK transport strategy. Despite intensive research on each theme, little effort has so far been made linking the relationship between emissions and social exclusion. In addition, current knowledge on each theme is limited to urban areas; little research is available on these themes for rural areas. This research contributes to this gap in the literature by analysing 157 weekly activity-travel diary data collected from three case study areas with differential levels of area accessibility and area mobility options, located in rural Northern Ireland. Individual weekly CO2 emission levels from personal travel diaries (both hot exhaust emission and cold-start emission) were calculated using average speed models for different modes of transport. The socio-spatial patterns associated with CO2 emissions were identified using a general linear model whereas binary logistic regression analyses were conducted to identify mode choice behaviour and activity patterns. This research found groups that emitted a significantly lower level of CO2 included individuals living in an area with a higher level of accessibility and mobility, non-car, non-working, and low-income older people. However, evidence in this research also shows that although certain groups (e.g. those working, and residing in an area with a lower level of accessibility) emitted higher levels of CO2, their rate of participation in activities was however found to be significantly lower compared to their counterparts. Based on the study findings, this research highlights the need for both soft (e.g. teleworking) and physical (e.g. accessibility planning) policy measures in rural areas in order to meet government’s stated CO2 reduction targets while at the same time enhancing social inclusion.