Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Modeling multi-stakeholder multi-objective decisions during public participation in major infrastructure and construction projects: A decision rule approach

Major infrastructure and construction (MIC) projects are those with significant traffic or environmental impact, of strategic and regional significance and high sensitivity. The decision making process of schemes of this type is becoming ever more complicated, especially with the increasing number of stakeholders involved and their growing tendency to defend their own varied interests. Failing to address and meet the concerns and expectations of stakeholders may result in project failures. To avoid this necessitates a systematic participatory approach to facilitate decision-making. Though numerous decision models have been established in previous studies (e.g. ELECTRE methods, the analytic hierarchy process and analytic network process) their applicability in the decision process during stakeholder participation in contemporary MIC projects is still uncertain. To resolve this, the decision rule approach is employed for modeling multi-stakeholder multi-objective project decisions. Through this, the result is obtained naturally according to the “rules” accepted by any stakeholder involved. In this sense, consensus is more likely to be achieved since the process is more convincing and the result is easier to be accepted by all concerned. Appropriate “rules”, comprehensive enough to address multiple objectives while straightforward enough to be understood by multiple stakeholders, are set for resolving conflict and facilitating consensus during the project decision process. The West Kowloon Cultural District (WKCD) project is used as a demonstration case and a focus group meeting is conducted in order to confirm the validity of the model established. The results indicate that the model is objective, reliable and practical enough to cope with real world problems. Finally, a suggested future research agenda is provided.

Construction of a cDNA clone for a nuclear-coded subunit of cytochrome c oxidase from rat liver

A cDNA library for 6S–9S poly(A)-containing RNA from rat liver was constructed in Image . Initial screening of the clones was carried out using single stranded 32P-labeled cDNA prepared against poly(A)-containing RNA isolated from immunoadsorbed polyribosomes enriched for the nuclear-coded subunit messenger RNAs of cytochrome c oxidase. One of the clones, pCO89, was found to hybridize with the messenger RNA for subunit VIC. The DNA sequence of the insert in pCO89 was carried out and it has got extensive homology with the C-terminal 33 amino acids of subunit VIC from beef heart cytochrome c oxidase. In addition, the insert contained 146 bp, corresponding to a portion of the 3′-non-coding region. Northern blot analysis of rat liver RNA with the nick-translated insert of pCO89 revealed that the messenger RNA for subunit VI would contain around 510 bases.

Following fashion: Visible progressiveness and the social construction of firm value

A central tenet underlying studies on management fashions is that the diffusion of novel forms, models and techniques is driven by an institutional norm of progress, which is the societal expectation that managers will continuously use 'new and improved' management practices. We add to the literature on management fashions by arguing that, if the display of progressiveness in the manner of managing and organizing is expected of organizations, firms that are visibly progressive would be evaluated more positively by organizational audiences following this institutional prescription. Using article counts of co-occurrences of firms and various fashionable management practices in Wall Street Journal, we hypothesize positive effects of such associations on security analysts' evaluations of these firms. Results support this hypothesis. Our study enriches the management fashion literature by highlighting the consequential relevance of organizational adherence to the norm of progress.

Construction of stability multipliers for non-linear feedback systems

This paper is concerned with the analysis of the absolute stability of a non-linear autonomous system which consists of a single non-linearity belonging to a particular class, in an otherwise linear feedback loop. It is motivated from the earlier Popovlike frequency-domain criteria using the ' multiplier ' eoncept and involves the construction of ' stability multipliers' with prescribed phase characteristics. A few computer-based methods by which this problem can be solved are indicated and it is shown that this constitutes a stop-by-step procedure for testing the stability properties of a given system.

The construction of feminism in Indonesian film: Arisan 2!

Feminism in Indonesian society is related to the emancipation term that women nowadays have still been bringing up this issue. However, Arisan 2! film showed a shift in film discourse regarding the representation of cosmopolitan women in Indonesia. This research examines on how Arisan 2! film as a media portrays feminism in the society of Jakarta. Feminism in Arisan 2! film was likely to expose the liberal feminism in nowadays modern society through several issues of women’s emancipation, specifically in the areas of marriage, job, and social life.

Safety impacts of alcohol and other drugs in construction

Estimated 638,400 persons suffered a work-related injury or illness in 2009-2010 and 337 lost their lives as a result in 2009-2010. In 2013-2014, there were 186 fatalities with 29 (16%) occurring in construction. Very little is known about what proportion of accidents are directly attributable to the effects of AOD. Anecdotal evidence highlights issues of AOD and its association with safety risk on construction sites. Research Objective: • To scientifically evaluate the relationship between the use of AOD and the safety impacts within the Australian construction industry to engender a cultural change in the workforce • A nationally consistent and collaborative approach involving government, employers and employees, unions and other key industry stakeholders

The construction of a taxonomy of early childhood educators’ work

Despite considerable research on the impact of early childhood education (ECE), there is little empirical evidence about what the everyday work of educators entails. This paper reports on the development of a tool to capture generalisable data on the everyday work of educators so as to inform effective workforce policy. This tool—a taxonomy of early childhood educators’ work—was developed by drawing on the expertise of six early years’ experts from Australia and the United States of America (USA) and includes time-use diaries, focus groups and interviews with 21 early childhood educators working in long day care and preschool services. The taxonomy, which we present here, consists of 10 domains, each with a number of sub-classes. We propose that this taxonomy is a useful codification system for ascertaining the everyday work tasks, activities and actions of early childhood educators in diverse early years’ settings. It is anticipated that the taxonomy will prove a valuable tool for subsequent research investigating the early childhood workforce.

Construction of inverses with prescribed zero minors and applications to decentralized stabilization

We examine the following question: Suppose R is a principal ideal domain, and that F is an n × m matrix with elements in R, with n>m. When does there exist an m × n matrix G such that GF = Im, and such that certain prescribed minors of G equal zero? We show that there is a simple necessary condition for the existence of such a G, but that this condition is not sufficient in general. However, if the set of minors of G that are required to be zero has a certain pattern, then the condition is necessary as well as sufficient. We then show that the pattern mentioned above arises naturally in connection with the question of the existence of decentralized stabilizing controllers for a given plant. Hence our result allows us to derive an extremely simple proof of the fact that a necessary and sufficient condition for the existence of decentralized stabilizing controllers is the absence of unstable decentralized fixed modes, as well as to derive a very clean expression for these fixed modes. In addition to the application to decentralized stabilization, we believe that the result is of independent interest.

Multiple roles of transfer prices: One vs. two books

This paper investigates multiple roles of transfer prices for shipments of goods and services between entities of a multinational enterprise. At the center is the role of transfer pricing (TP) in tax manipulation, but other roles having to do with internal operations or strategic delegation, etc. are also considered. The interesting question is to what extent and how the different roles of TPs interfere with each other. The answer depends on whether companies use one or two books, i.e. whether they (can) apply different TPs for different purposes. We illustrate, in a stylized model, the competing aims of tax manipulation and strategic delegation. Finally, we briefly look at selected reform proposals, concluding that either TP problems are not addressed, or else new distortions will be introduced instead.

Acoustic emission source location in composite structure by Voronoi construction using geodesic curve evolution

Conventional analytical/numerical methods employing triangulation technique are suitable for locating acoustic emission (AE) source in a planar structure without structural discontinuities. But these methods cannot be extended to structures with complicated geometry, and, also, the problem gets compounded if the material of the structure is anisotropic warranting complex analytical velocity models. A geodesic approach using Voronoi construction is proposed in this work to locate the AE source in a composite structure. The approach is based on the fact that the wave takes minimum energy path to travel from the source to any other point in the connected domain. The geodesics are computed on the meshed surface of the structure using graph theory based on Dijkstra's algorithm. By propagating the waves in reverse virtually from these sensors along the geodesic path and by locating the first intersection point of these waves, one can get the AE source location. In this work, the geodesic approach is shown more suitable for a practicable source location solution in a composite structure with arbitrary surface containing finite discontinuities. Experiments have been conducted on composite plate specimens of simple and complex geometry to validate this method.

Knowledge management research in the construction industry: a review

Purpose: Knowledge management (KM) is important to the knowledge-intensive construction industry. The diversified and changing nature of works in this field warrants us to stocktake, identify changes and map out KM research framework for future exploration. Design/methodology/approach: The study involves three aspects. First, three stages of KM research in construction were distinguished in terms of the time distribution of 217 target publications. Major topics in the stages were extracted for understanding the changes of research emphasis from evolutionary perspective. Second, the past works were summed up in a three-dimensional research framework in terms of management organization, managerial methodology and approach, and managerial objective. Finally, potential research orientations in the future were predicted to expand the existing research framework. Findings: It was found that (1) KM research has significantly blossomed in the last two decades with a great potential; (2) major topics of KM were changing in terms of technology, technique, organization, attribute of knowledge and research objectives; (3) past KM studies centred around management organization, managerial methodology and approach, and managerial objective thus a three-dimensional research framework was proposed; (4) within the research framework, team-level, project-level and firm-level KM were studied to achieve project, organizational and competitive objectives by integrated methodologies of information technology, social technique and KM process tool; and (5) nine potential research orientations were predicted corresponding to the three dimensions. Finally, an expanded research framework was proposed to encourage and guide future research works in this field. Research limitations/implications: The paper only focused on the construction industry. The findings need further exploration in order to discover any possible missing important research works which were not published in English or not included in the time period. Originality/value: The paper formed a systematic framework of KM research in construction and predicted the potential research orientations. It provides much value for the researchers who want to understand the past and the future of global KM research in the construction industry.

Supporting knowledge-intensive construction management tasks in BIM

The delivery of products and services for construction-based businesses is increasingly becoming knowledge-driven and information-intensive. The proliferation of building information modelling (BIM) has increased business opportunities as well as introduced new challenges for the architectural, engineering and construction and facilities management (AEC/FM) industry. As such, the effective use, sharing and exchange of building life cycle information and knowledge management in building design, construction, maintenance and operation assumes a position of paramount importance. This paper identifies a subset of construction management (CM) relevant knowledge for different design conditions of building components through a critical, comprehensive review of synthesized literature and other information gathering and knowledge acquisition techniques. It then explores how such domain knowledge can be formalized as ontologies and, subsequently, a query vocabulary in order to equip BIM users with the capacity to query digital models of a building for the retrieval of useful and relevant domain-specific information. The formalized construction knowledge is validated through interviews with domain experts in relation to four case study projects. Additionally, retrospective analyses of several design conditions are used to demonstrate the soundness (realism), completeness, and appeal of the knowledge base and query-based reasoning approach in relation to the state-of-the-art tools, Solibri Model Checker and Navisworks. The knowledge engineering process and the methods applied in this research for information representation and retrieval could provide useful mechanisms to leverage BIM in support of a number of knowledge intensive CM/FM tasks and functions.

Tuning the beta-turn segment in designed peptide beta-hairpins: Construction of a stable type I ' beta-turn nucleus and hairpin-helix transition promoting segments

Designed octapeptides Boc-Leu-Val-Val-Aib-(D)Xxx-Leu- Val-Val-OMe ((D)Xxx = (D)Ala, 3a; (D)Val, 3c and (D)Pro, 5a) and Boc-Leu-Phe-Val-Aib-DAla-Leu-Phe-Val-OMe (3b) have been investigated to construct models of a stable type I' beta-turn nucleated hairpin and to generate systems for investigating helix-hairpin conformational transitions. Peptide 5a, which contains a central Aib-(D)Pro segment, is shown to adopt a stable type I' beta-turn nucleated hairpin structure, stabilized by four cross-strand hydrogen bonds. The stability of the structure in diverse solvents is established by the observation of all diagnostic NOEs expected in a beta-hairpin conformation. Replacement of (D)Pro5 by (D)Ala/(D)Val (3a-c) results in sequences that form beta-hairpins in hydrogen bonding solvents like CD3OH and DMSO-d(6). However, in CDCl3 evidence for population of helical conformations is obtained. Peptide 6b (Boc-Leu-Phe-Val-Aib-Aib-Leu-Phe-Val-OMe), which contains a centrally positioned Aib-Aib segment, provides a clear example of a system, which exhibits a helical conformation in CDCl3 and a significant population of both helices and hairpins in CD3OH and DMSO-d(6). The coexistence of multiple conformations is established by the simultaneous observation of diagnostic NOEs. Control over stereochemistry of the central beta-turn permits generation of models for robust beta-hairpins and also for the construction of systems that may be used to probe helix-hairpin conformational transitions. (c) 2006 Wiley Periodicals, Inc.

How do construction firms learn on collaborative infrastructure projects?

Construction firms that employ collaborative procurement approaches develop operating routines through joint learning so as to improve infrastructure project performance. This paper reports a study based on a survey sample of 320 construction practitioners which were involved in collaborative infrastructure delivery in Australia. The study developed valid and reliable scales for measuring collaborative learning capability (CLC), and used the scales to evaluate the CLC of contractor and consultant firms within the sample. The evaluation suggests that whilst these firms explore knowledge from both internal and external sources, transform both explicit and tacit knowledge, and apply and internalise new knowledge, they can improve the extent to which these routines are applied to optimise project performance.