How do Researchers Find and Retrieve Scientific Publications – A Case study of the Impact of the Internet on the Construction IT and Construction Management Research Communities

The World Wide Web provides the opportunity for a radically changed and much more efficient communication process for scientific results. A survey in the closely related domains of construction information technology and construction management was conducted in February 2000, aimed at measuring to what extent these opportunities are already changing the scientific information exchange and how researchers feel about the changes. The paper presents the results based on 236 replies to an extensive Web based questionnaire. 65% of the respondents stated their primary research interest as IT in A/E/C and 20% as construction management and economics. The questions dealt with how researchers find, access and read different sources; how much and what publications they read; how often and to which conferences they travel; how much they publish, and what are the criteria for where they eventually decide to publish. Some of the questions confronted traditional and electronic publishing with one final section dedicated to opinions about electronic publishing. According to the survey researchers already download half of the material that they read digitally from the Web. The most popular method for retrieving an interesting publication is downloading it for free from the author’s or publisher’s website. Researchers are not particularly willing to pay for electronic scientific publications. There is much support for a scenario of electronic journals available totally freely on the Web, where the costs could be covered by for instance professional societies or the publishing university. The shift that the Web is causing seems to be towards the "just in time" reading of literature. Also, frequent users of the Web rely less on scientific publications and tend to read fewer articles. If available with little effort, papers published in traditional journals are preferred; if not, the papers should be on the Web. In these circumstances, the role of paper-based journals published by established publishers is shifting from the core "information exchange" to the building of authors' prestige. The respondents feel they should build up their reputations by publishing in journals and relevant conferences, but then make their work freely available on the Web.

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.

Adoption processes for EDM, EDI and BIM technologies in the construction industry

Three strategically important uses of IT in the construction industry are the storage and management of project documents on webservers (EDM), the electronic handling of orders and invoices between companies (EDI) and the use of 3-D models including non-geometrical attributes for integrated design and construction (BIM). In a broad longitudinal survey study of IT use in the Swedish Construction Industry the extent of use of these techniques was measured in 1998, 2000 and 2007. The results showed that EDM and EDI are currently already well-established techniques whereas BIM, although it promises the biggest potential benefits to the industry, only seems to be at the beginning of adoption. In a follow-up to the quantitative studies, the factors affecting the decisions to implement EDM, EDI and BIM as well as the actual adoption processes, were studied using semi-structured interviews with practitioners. The theoretical basis for the interview studies was informed by theoretical frameworks from IT-adoption theory, where in particular the UTAUT model has provided the main basis for the analyses presented here. The results showed that the decisions to take the above technologies into use are made on three differ- ent levels: the individual level, the organizational level in the form of a company, and the organiza- tional level in the form of a project. The different patterns in adoption can to some part be explained by where the decisions are mainly taken. EDM is driven from the organisation/project level, EDI mainly from the organisation/company level, and BIM is driven by individuals pioneering the technique.

A Formalised Model of the Information and Materials Handling Activities in the Construction Process

A model of the information and material activities that comprise the overall construction process is presented, using the SADT activity modelling methodology. The basic model is further refined into a number of generic information handling activities such as creation of new information, information search and retrieval, information distribution and person-to-person communication. The viewpoint could be described as information logistics. This model is then combined with a more traditional building process model, consisting of phases such as design and construction. The resulting two-dimensional matrix can be used for positioning different types of generic IT-tools or construction specific applications. The model can thus provide a starting point for a discussion of the application of information and communication technology in construction and for measurements of the impacts of IT on the overall process and its related costs.

Information Technology in Construction – Domain Definition and Research Issues

This article discusses the scope of research on the application of information technology in construction (ITC). A model of the information and material activities which together constitute the construction process is presented, using the IDEF0 activity modelling methodology. Information technology is defined to include all kinds of technology used for the storage, transfer and manipulation of information, thus also including devices such as copying machines, faxes and mobile phones. Using the model the domain of ITC research is defined as the use of information technology to facilitate and re-engineer the information process component of construction. Developments during the last decades in IT use in construction is discussed against a background of a simplified model of generic information processing tasks. The scope of ITC is compared with the scopes of research in related areas such as design methodology, construction management and facilities management. Health care is proposed as an interesting alternative (to the often used car manufacturing industry), as an IT application domain to compare with. Some of the key areas of ITC research in recent years; expert systems, company IT strategies, and product modelling are shortly discussed. The article finishes with a short discussion of the problems of applying standard scientific methodology in ITC research, in particular in product model research.

Genomic and functional profiling of gastric cancer

Helicobacter pylori infection is a risk factor for gastric cancer, which is a major health issue worldwide. Gastric cancer has a poor prognosis due to the unnoticeable progression of the disease and surgery is the only available treatment in gastric cancer. Therefore, gastric cancer patients would greatly benefit from identifying biomarker genes that would improve diagnostic and prognostic prediction and provide targets for molecular therapies. DNA copy number amplifications are the hallmarks of cancers in various anatomical locations. Mechanisms of amplification predict that DNA double-strand breaks occur at the margins of the amplified region. The first objective of this thesis was to identify the genes that were differentially expressed in H. pylori infection as well as the transcription factors and signal transduction pathways that were associated with the gene expression changes. The second objective was to identify putative biomarker genes in gastric cancer with correlated expression and copy number, and the last objective was to characterize cancers based on DNA copy number amplifications. DNA microarrays, an in vitro model and real-time polymerase chain reaction were used to measure gene expression changes in H. pylori infected AGS cells. In order to identify the transcription factors and signal transduction pathways that were activated after H. pylori infection, gene expression profiling data from the H. pylori experiments and a bioinformatics approach accompanied by experimental validation were used. Genome-wide expression and copy number microarray analysis of clinical gastric cancer samples and immunohistochemistry on tissue microarray were used to identify putative gastric cancer genes. Data mining and machine learning techniques were applied to study amplifications in a cross-section of cancers. FOS and various stress response genes were regulated by H. pylori infection. H. pylori regulated genes were enriched in the chromosomal regions that are frequently changed in gastric cancer, suggesting that molecular pathways of gastric cancer and premalignant H. pylori infection that induces gastritis are interconnected. 16 transcription factors were identified as being associated with H. pylori infection induced changes in gene expression. NF-κB transcription factor and p50 and p65 subunits were verified using elecrophoretic mobility shift assays. ERBB2 and other genes located in 17q12- q21 were found to be up-regulated in association with copy number amplification in gastric cancer. Cancers with similar cell type and origin clustered together based on the genomic localization of the amplifications. Cancer genes and large genes were co-localized with amplified regions and fragile sites, telomeres, centromeres and light chromosome bands were enriched at the amplification boundaries. H. pylori activated transcription factors and signal transduction pathways function in cellular mechanisms that might be capable of promoting carcinogenesis of the stomach. Intestinal and diffuse type gastric cancers showed distinct molecular genetic profiles. Integration of gene expression and copy number microarray data allowed the identification of genes that might be involved in gastric carcinogenesis and have clinical relevance. Gene amplifications were demonstrated to be non-random genomic instabilities. Cell lineage, properties of precursor stem cells, tissue microenvironment and genomic map localization of specific oncogenes define the site specificity of DNA amplifications, whereas labile genomic features define the structures of amplicons. These conclusions suggest that the definition of genomic changes in cancer is based on the interplay between the cancer cell and the tumor microenvironment.

Construing and Defining the Out of Control : Addiction in the Media 1968-2008.

The four scientific articles comprising this doctoral dissertation offer new information on the presentation and construction of addiction in the mass media during the period 1968 - 2008. Diachronic surveys as well as quantitative and qualitative content analyses were undertaken to discern trends during the period in question and to investigate underlying conceptions of the problems in contemporary media presentations. The research material for the first three articles consists of a sample of 200 texts from Finland s biggest daily newspaper, Helsingin Sanomat, from the period 1968 - 2006. The fourth study examines English-language tabloid material published on the Internet in 2005 - 2008. A number of principal trends are identified. In addition to a significant increase in addiction reporting over time, the study shows that an internalisation of addiction problems took place in the media presentations under study. The phenomenon is portrayed and tackled from within the problems themselves, often from the viewpoint of the individuals concerned. The tone becomes more personal, and technical and detailed accounts are more and more frequent. Secondly, the concept of addiction is broadened. This can be dated to the 1990s. The concept undergoes a conventionalisation: it is used more frequently in a manner that is not thought to require explanation. The word riippuvuus (the closest equivalent to addiction in Finnish) was adopted more commonly in the reporting at the same time, in the 1990s. Thirdly, the results highlight individual self-governance as a superordinate principle in contemporary descriptions of addiction. If the principal demarcation in earlier texts was between us and them , it is now focused primarily on the individual s competence and ability to govern the self, to restrain and master one's behaviour. Finally, in the fourth study investigating textual constructions of female celebrities (Amy Winehouse, Britney Spears and Kate Moss) in Internet tabloids, various relations and functions of addiction problems, intoxication, body and gender were observed to function as cultural symbols. Addiction becomes a sign, or a style, that represents different significations in relation to the main characters in the tabloid stories. Tabloids, as a genre, play an important role by introducing other images of the problems than those featured in mainstream media. The study is positioned within the framework of modernity theory and its views on the need for self-reflexivity and biographies as tools for the creation and definition of the self. Traditional institutions such as the church, occupation, family etc. no longer play an important role in self-definition. This circumstance creates a need for a culture conveying stories of success and failure in relation to which the individual can position their own behaviour and life content. I propose that addiction , as a theme in media reporting, resolves the conflict that emanates from the ambivalence between the accessibility and the individualisation of consumer society, on the one hand, and the problematic behavioural patterns (addictions) that they may induce, on the other.