Family-based association analysis with ordered categorical phenotypes, covariates and interactions

Genetic association analyses of family-based studies with ordered categorical phenotypes are often conducted using methods either for quantitative or for binary traits, which can lead to suboptimal analyses. Here we present an alternative likelihood-based method of analysis for single nucleotide polymorphism (SNP) genotypes and ordered categorical phenotypes in nuclear families of any size. Our approach, which extends our previous work for binary phenotypes, permits straightforward inclusion of covariate, gene-gene and gene-covariate interaction terms in the likelihood, incorporates a simple model for ascertainment and allows for family-specific effects in the hypothesis test. Additionally, our method produces interpretable parameter estimates and valid confidence intervals. We assess the proposed method using simulated data, and apply it to a polymorphism in the c-reactive protein (CRP) gene typed in families collected to investigate human systemic lupus erythematosus. By including sex interactions in the analysis, we show that the polymorphism is associated with anti-nuclear autoantibody (ANA) production in females, while there appears to be no effect in males.

Warranty cost analysis for products with a dormant state

Most building services products are installed while a building is constructed, but they are not operated until the building is commissioned. The warranty of the products may cover the time starting from their installation to the end of the warranty period. Prior to the commissioning of the building, the products are at a dormant mode (i.e., not operated) but protected by the warranty. For such products, both the usage intensity and the failure patterns are different from those with continuous usage intensity and failure patterns. This paper develops warranty cost models for repairable products with a dormant mode from both the manufacturer's and buyer's perspectives. Relationships between the failure patterns at the dormant mode and at the operational mode are also discussed. Numerical examples and sensitivity analysis are used to demonstrate the applicability of the methodology derived in the paper.

Characterization and classification of tumor lesions using computerized fractal-based texture analysis and support vector machines in digital mammograms

Objective: This paper presents a detailed study of fractal-based methods for texture characterization of mammographic mass lesions and architectural distortion. The purpose of this study is to explore the use of fractal and lacunarity analysis for the characterization and classification of both tumor lesions and normal breast parenchyma in mammography. Materials and methods: We conducted comparative evaluations of five popular fractal dimension estimation methods for the characterization of the texture of mass lesions and architectural distortion. We applied the concept of lacunarity to the description of the spatial distribution of the pixel intensities in mammographic images. These methods were tested with a set of 57 breast masses and 60 normal breast parenchyma (dataset1), and with another set of 19 architectural distortions and 41 normal breast parenchyma (dataset2). Support vector machines (SVM) were used as a pattern classification method for tumor classification. Results: Experimental results showed that the fractal dimension of region of interest (ROIs) depicting mass lesions and architectural distortion was statistically significantly lower than that of normal breast parenchyma for all five methods. Receiver operating characteristic (ROC) analysis showed that fractional Brownian motion (FBM) method generated the highest area under ROC curve (A z = 0.839 for dataset1, 0.828 for dataset2, respectively) among five methods for both datasets. Lacunarity analysis showed that the ROIs depicting mass lesions and architectural distortion had higher lacunarities than those of ROIs depicting normal breast parenchyma. The combination of FBM fractal dimension and lacunarity yielded the highest A z value (0.903 and 0.875, respectively) than those based on single feature alone for both given datasets. The application of the SVM improved the performance of the fractal-based features in differentiating tumor lesions from normal breast parenchyma by generating higher A z value. Conclusion: FBM texture model is the most appropriate model for characterizing mammographic images due to self-affinity assumption of the method being a better approximation. Lacunarity is an effective counterpart measure of the fractal dimension in texture feature extraction in mammographic images. The classification results obtained in this work suggest that the SVM is an effective method with great potential for classification in mammographic image analysis.

A lightweight technique for assessing risks in requirements analysis

A simple and practical technique for assessing the risks, that is, the potential for error, and consequent loss, in software system development, acquired during a requirements engineering phase is described. The technique uses a goal-based requirements analysis as a framework to identify and rate a set of key issues in order to arrive at estimates of the feasibility and adequacy of the requirements. The technique is illustrated and how it has been applied to a real systems development project is shown. How problems in this project could have been identified earlier is shown, thereby avoiding costly additional work and unhappy users.

Life cycle analysis of UK coal fired power plants

This paper examines the life cycle GHG emissions from existing UK pulverized coal power plants. The life cycle of the electricity Generation plant includes construction, operation and decommissioning. The operation phase is extended to upstream and downstream processes. Upstream processes include the mining and transport of coal including methane leakage and the production and transport of limestone and ammonia, which are necessary for flue gas clean up. Downstream processes, on the other hand, include waste disposal and the recovery of land used for surface mining. The methodology used is material based process analysis that allows calculation of the total emissions for each process involved. A simple model for predicting the energy and material requirements of the power plant is developed. Preliminary calculations reveal that for a typical UK coal fired plant, the life cycle emissions amount to 990 g CO2-e/kWh of electricity generated, which compares well with previous UK studies. The majority of these emissions result from direct fuel combustion (882 g/kWh 89%) with methane leakage from mining operations accounting for 60% of indirect emissions. In total, mining operations (including methane leakage) account for 67.4% of indirect emissions, while limestone and other material production and transport account for 31.5%. The methodology developed is also applied to a typical IGCC power plant. It is found that IGCC life cycle emissions are 15% less than those from PC power plants. Furthermore, upon investigating the influence of power plant parameters on life cycle emissions, it is determined that, while the effect of changing the load factor is negligible, increasing efficiency from 35% to 38% can reduce emissions by 7.6%. The current study is funded by the UK National Environment Research Council (NERC) and is undertaken as part of the UK Carbon Capture and Storage Consortium (UKCCSC). Future work will investigate the life cycle emissions from other power generation technologies with and without carbon capture and storage. The current paper reveals that it might be possible that, when CCS is employed. the emissions during generation decrease to a level where the emissions from upstream processes (i.e. coal production and transport) become dominant, and so, the life cycle efficiency of the CCS system can be significantly reduced. The location of coal, coal composition and mining method are important in determining the overall impacts. In addition to studying the net emissions from CCS systems, future work will also investigate the feasibility and technoeconomics of these systems as a means of carbon abatement.

A camera based digit location and recognition system for garment tracking

Garment information tracking is required for clean room garment management. In this paper, we present a camera-based robust system with implementation of Optical Character Reconition (OCR) techniques to fulfill garment label recognition. In the system, a camera is used for image capturing; an adaptive thresholding algorithm is employed to generate binary images; Connected Component Labelling (CCL) is then adopted for object detection in the binary image as a part of finding the ROI (Region of Interest); Artificial Neural Networks (ANNs) with the BP (Back Propagation) learning algorithm are used for digit recognition; and finally the system is verified by a system database. The system has been tested. The results show that it is capable of coping with variance of lighting, digit twisting, background complexity, and font orientations. The system performance with association to the digit recognition rate has met the design requirement. It has achieved real-time and error-free garment information tracking during the testing.

A lightweight technique for assessing risks in requirements analysis

A simple and practical technique for assessing the risks, that is, the potential for error, and consequent loss, in software system development, acquired during a requirements engineering phase is described. The technique uses a goal-based requirements analysis as a framework to identify and rate a set of key issues in order to arrive at estimates of the feasibility and adequacy of the requirements. The technique is illustrated and how it has been applied to a real systems development project is shown. How problems in this project could have been identified earlier is shown, thereby avoiding costly additional work and unhappy users.

Guided growth of neurons and glia using microfabricated patterns of parylene-C on a SiO2 background

This paper describes a simple technique for the patterning of glia and neurons. The integration of neuronal patterning to Multi-Electrode Arrays (MEAs), planar patch clamp and silicon based ‘lab on a chip’ technologies necessitates the development of a microfabrication-compatible method, which will be reliable and easy to implement. In this study a highly consistent, straightforward and cost effective cell patterning scheme has been developed. It is based on two common ingredients: the polymer parylene-C and horse serum. Parylene-C is deposited and photo-lithographically patterned on silicon oxide (SiO2) surfaces. Subsequently, the patterns are activated via immersion in horse serum. Compared to non-activated controls, cells on the treated samples exhibited a significantly higher conformity to underlying parylene stripes. The immersion time of the patterns was reduced from 24 to 3 h without compromising the technique. X-ray photoelectron spectroscopy (XPS) analysis of parylene and SiO2 surfaces before and after immersion in horse serum and gel based eluant analysis suggests that the quantity and conformation of proteins on the parylene and SiO2 substrates might be responsible for inducing glial and neuronal patterning.

A Glacial Geomorphological Map of Victoria Island, Canadian Arctic

Victoria Island lies at the north-western extremity of the region covered by the vast North American Laurentide Ice Sheet (LIS) in the Canadian Arctic Archipelago. This area is significant because it linked the interior of the LIS to the Arctic Ocean, probably via a number of ice streams. Victoria Island, however, exhibits a remarkably complex glacial landscape, with several successive generations of ice flow indicators superimposed on top of each other and often at abrupt (90 degrees) angles. This complexity represents a major challenge to those attempting to produce a detailed reconstruction of the glacial history of the region. This paper presents a map of the glacial geomorphology of Victoria Island. The map is based on analysis of Landsat Enhanced Thematic Plus (ETM+) satellite imagery and contains over 58,000 individual glacial features which include: glacial lineations, moraines (terminal, lateral, subglacial shear margin), hummocky moraine, ribbed moraine, eskers, glaciofluvial deposits, large meltwater channels, and raised shorelines. The glacial features reveal marked changes in ice flow direction and vigour over time. Moreover, the glacial geomorphology indicates a non-steady withdrawal of ice during deglaciation, with rapidly flowing ice streams focussed into the inter-island troughs and several successively younger flow patterns superimposed on older ones. It is hoped that detailed analysis of this map will lead to an improved reconstruction of the glacial history of this area which will provide other important insights, for example, with respect to the interactions between ice streaming, deglaciation and Arctic Ocean meltwater events.

Design for design: support for creative practice in computer-supported collaborative work (CSCW) in design

This paper describes a novel methodology for observing and analysing collaborative design by using the concepts of cognitive dimensions related to concept-based misfit analysis. The study aims at gaining an insight into support for creative practice of graphical communication in collaborative design processes of designers while sketching within a shared white board and audio conferencing environment. Empirical data on design processes have been obtained from observation of groups of student designers solving an interior space-planning problem of a lounge-diner in a shared virtual environment. The results of the study provide recommendations for the design and development of interactive systems to support such collaborative design activities.

Phylogeny, function, and evolution of the cupins, a structurally conserved, functionally diverse superfamily of proteins

The cupin superfamily is a group of functionally diverse proteins that are found in all three kingdoms of life, Archaea, Eubacteria, and Eukaryota. These proteins have a characteristic signature domain comprising two histidine- containing motifs separated by an intermotif region of variable length. This domain consists of six beta strands within a conserved beta barrel structure. Most cupins, such as microbial phosphomannose isomerases (PMIs), AraC- type transcriptional regulators, and cereal oxalate oxidases (OXOs), contain only a single domain, whereas others, such as seed storage proteins and oxalate decarboxylases (OXDCs), are bi-cupins with two pairs of motifs. Although some cupins have known functions and have been characterized at the biochemical level, the majority are known only from gene cloning or sequencing projects. In this study, phylogenetic analyses were conducted on the conserved domain to investigate the evolution and structure/function relationships of cupins, with an emphasis on single- domain plant germin-like proteins (GLPs). An unrooted phylogeny of cupins from a wide spectrum of evolutionary lineages identified three main clusters, microbial PMIs, OXDCs, and plant GLPs. The sister group to the plant GLPs in the global analysis was then used to root a phylogeny of all available plant GLPs. The resulting phylogeny contained three main clades, classifying the GLPs into distinct subfamilies. It is suggested that these subfamilies correlate with functional categories, one of which contains the bifunctional barley germin that has both OXO and superoxide dismutase (SOD) activity. It is proposed that GLPs function primarily as SODs, enzymes that protect plants from the effects of oxidative stress. Closer inspection of the DNA sequence encoding the intermotif region in plant GLPs showed global conservation of thymine in the second codon position, a character associated with hydrophobic residues. Since many of these proteins are multimeric and enzymatically inactive in their monomeric state, this conservation of hydrophobicity is thought to be associated with the need to maintain the various monomer- monomer interactions. The type of structure-based predictive analysis presented in this paper is an important approach for understanding gene function and evolution in an era when genomes from a wide range of organisms are being sequenced at a rapid rate.

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Characterization of an escherichia coli elaC deletion mutant

The elaC gene of Escherichia coli encodes a binuclear zinc phosphodiesterase (ZiPD). ZiPD homologs from various species act as 3' tRNA processing endoribonucleases, and although the homologous gene in Bacillus subtilis is essential for viability [EMBO J. 22 (2003) 4534], the physiological function of E. coli ZiPD has remained enigmatic. In order to investigate the function of E. coli ZiPD we generated and characterized an E. coli elaC deletion mutant. Surprisingly, the E. coli elaC deletion mutant was viable and had wild-type like growth properties. Micro array-based transcriptional analysis indicated expression of the E. coli elaC gene at basal levels during aerobic growth. The elaC gene deletion had no effect on the expression of genes coding for RNases or amino-acyl tRNA synthetases or any other gene among a total of > 1300 genes probed. 2D-PAGE analysis showed that the elaC mutation, likewise, had no effect on the proteome. These results strengthen doubts about the involvement of E. coli ZiPD in tRNA maturation and suggest functional diversity within the ZiPD/ElaCl protein family. In addition to these unexpected features of the E. coli elaC deletion mutant, a sequence comparison of ZiPD (ElaCl) proteins revealed specific regions for either enterobacterial or mammalian ZiPD (ElaCl) proteins. (C) 2004 Elsevier Inc. All rights reserved.