ANNODA: tool for integrating molecular-biological annotation data

Collecting, analyzing, and making Molecularbiological annotation data accessible in different public data sources is still an ongoing project. Integration of such data from these data sources might lead to valuable biological knowledge. There are numerous annotation data and only some of those are structured. The number and contents of related sources are continuously increasing. In addition, the existing data sources have their own storage structure and implementation. As a result, these could lead to a limitation in the combining of annotation. Here, we proposed a tool, called ANNODA, for integrating Molecular-biological annotation data. Unlike the past work on database interoperation in the bioinformatics community, this database design uses web-links which are very useful for interactive navigation and meanwhile it also supports automated large-scale analysis tasks.

Analyzing inconsistency toward enhancing integration of biological molecular databases

The rapid growth of biological databases not only provides biologists with abundant data but also presents a big challenge in relation to the analysis of data. Many data analysis approaches such as data mining, information retrieval and machine learning have been used to extract frequent patterns from diverse biological databases. However, the discrepancies, due to the differences in the structure of databases and their terminologies, result in a significant lack of interoperability. Although ontology-based approaches have been used to integrate biological databases, the inconsistent analysis of biological databases has been greatly disregarded. This paper presents a method by which to measure the degree of inconsistency between biological databases. It not only presents a guideline for correct and efficient database integration, but also exposes high quality data for data mining and knowledge discovery.

Late Paleozoic depositional history of the Tarim basin, northwest China: an integration of biostratigraphic and lithostratigraphic constraints

This study provides the first detailed lithostratigraphic and biostratigraphic constraints for improving stratigraphic resolution for hydrocarbon prospecting and exploration in the Tarim basin. A total of 49 stratigraphic units (38 formations and 11 members), ranging in age from the latest Devonian to Permian, are reviewed or redefined in terms of nomenclatures, lithology, age constraints, and lateral distributions based on the detailed field works or newly published data. Of these, the Piqiang Formation (new formation) is proposed to include the reefal carbonates of Asselian-Sakmarian age from the northern Tarim. The subsurface upper Paleozoic stratigraphic framework of the desert areas of the basin is also established for the first time. The high-resolution, basinwide stratigraphic correlations reveal that the sedimentation of the basin in the late Paleozoic was extremely uneven. Of these, the Famennian to Changhsingian successions are completely recorded in the south-western margin areas of the basin. Here, five eustatic sedimentary cycles are well recognizable, suggesting the sedimentation was more eustatically controlled and little affected by local tectonism. The late Paleozoic successions of both Kalpin and Taklimakan regions are commonly interrupted by major hiatuses at various horizons, suggesting that the sedimentation was apparently modified by local tectonism. Of these, the northward movement of the Tarim block and its subsequent collision with the Yili microcontinent (part of the Kazakhstan plate) may be principally accountable for the discrepancy in the sedimentation of the various regions in the basin in the late Paleozoic.

Information integration in molecular bioscience

Integrating information in the molecular biosciences involves more than the cross-referencing of sequences or structures. Experimental protocols, results of computational analyses, annotations and links to relevant literature form integral parts of this information, and impart meaning to sequence or structure. In this review, we examine some existing approaches to integrating information in the molecular biosciences. We consider not only technical issues concerning the integration of heterogeneous data sources and the corresponding semantic implications, but also the integration of analytical results. Within the broad range of strategies for integration of data and information, we distinguish between platforms and developments. We discuss two current platforms and six current developments, and identify what we believe to be their strengths and limitations. We identify key unsolved problems in integrating information in the molecular biosciences, and discuss possible strategies for addressing them including semantic integration using ontologies, XML as a data model, and graphical user interfaces as integrative environments.

Seeking mechanisms for improved integration of biodiversity issues in regional natural resource management planning

This article reviews the literature on natural resource management (NRM) planning in Australia, with particular consideration given to exploring how regions might better integrate biodiversity conservation into catchment or regional planning in ways that lead to improved biodiversity conservation practice in the field. Many of the findings of the review are generic, affecting a range of NRM issues (including biodiversity conservation) and the NRM planning process itself, whilst other findings are specific to conservation of biodiversity. Factors affecting the integration of biodiversity include the organizational characteristics of the regional NRM body, clarity in the region of the responsibilities across the three tiers of government, effective participation of stakeholders, existence of detailed NRM plans that include sound biodiversity data and management principles, access to interpreted information, use of a mix of policy instruments capable of delivering biodiversity goals, and effective monitoring frameworks and tools to track the return on investment. there is considerable variability in the ways that NRM planning is practiced across Australia, at the enterprise, regional or catchment levels. However, an overarching issue is how well the planning caters for differences across space, time and human values and this article attempts to identify the considerations that impact on that requirement.

Acting at the Nexus : integration of research, policy and practice

This report is the result of an exciting journey of discovery. As with all journeys, we have been to many exotic places, have met extraordinary people, and at times have been challenged to keep going ahead rather than retreating. Good journeys are also enjoyed best in good company. We would like to thank VicHealth for giving us the opportunity to embark on our voyage, but also specifically to some great VicHealth staff: John Biviano, Siân Lloyd, Barb Mouy and Ali Barr have all been travelers along the way, providing us with encouragement, directions and nourishment. We know that our Project Advisory Committee and the then Chief Executive of VicHealth, dr. Rob Moody, have followed our progress on the journey with great interest. A special word of thanks to professor David Hill, chair of our advisory committee and member of the VicHealth Board of Governance, to sit down with us and critically review our navigation procedures. But we could not have reached our destination without the great assistance of the people and agencies that gave us their time, energy, and sometimes precious resources, to engage in data collection for our case studies. Again, a particular word of appreciation, to professor Brian Head, and to Ruth Belben for her incredibly efficient assistance, in organising the ARACY workshop on 24 November, 2006 in which we were given an opportunity to triangulate our position with colleagues from research, policy and practice.

Marketing research and customer analytics : interfunctional knowledge integration

The Customer Analytics (CA) function is increasingly leveraged for Customer Relationship Management (CRM), however it may lack the value of marketing knowledge available from the Marketing Research (MR) function due to inadequate interfunctional knowledge integration. This paper develops a set of sixteen propositions from a synthesis of the marketing and knowledge management literatures relating key organisational influences on the integration of knowledge between the MR and CA functions. A range of strategic, cultural, structural and technical influences is reflected by the propositions. It is planned to test the propositions in future empirical research.

Impact of electronic data interchange in the Australian automotive industry

Information technology continues to play an increasingly significant role in the development of firms competing in the vast array of markets from those classified as global markets, such as the automotive industry, to the smaller nationally-based markets such as retailing. An objective of electronic commerce is to assist organisations to remain competitive and gain entry to markets which were previously unattainable. This study focuses on the organisational impact of one form of electronic commerce (electronic data interchange) on the component sector of the Australian automotive industry and examines the extent to which trading partner relationships have been affected. The research investigates the extent to which the integration of electronic data interchange (EDI) with an organisation’s internal application system may facilitate specific net benefits. The automotive industry became the first Australian industry to cooperatively adopt EDI. Research to date has not adequately examined the organisational impact of the nature and extent of net benefits gained from EDI adoption. To achieve the objective of assessing EDI net benefits, a conceptual model was developed. The model proposed that the level of EDI net benefits expected is influenced by the size of the organisation and the concentration of trade achieved within the industry via intervening links through (a) the level of senior management commitment and (b) the extent of system integration. Nine empirically testable research propositions are derived from the model, each testing the relationship between model constructs. Data was collected from 114 component suppliers to Ford Australia in 1992 and 1994 using a repeated cross-sectional longitudinal design. Structural equation modelling using partial least squares was adopted in the analysis of the data. A pure longitudinal model together with 12 case studies of selected component manufacturers supplemented the research design. The results of the research showed that the proposed conceptual model is a good description of the data. In particular, net benefits obtained from EDI adoption are directly determined by the size of the organisation, and the extent to which firms integrate EDI into their internal application systems. The level of net benefits is only indirectly influenced by the level of senior management commitment to the EDI project through (a) management commitment’s direct effect on integration, and (b) the direct effect the volume of trade a supplier achieves with the automotive industry on senior management commitment and system integration. The major benefits organisations experienced from EDI were enhanced productivity, clerical staff savings, improved data accuracy, enhanced customer service and reduced administration costs. The research showed that few suppliers gained inventory savings from EDI, a frequently claimed benefit from EDI adoption. Evidence of small improvements in product quality emerged from the results. In summary, this research attempts to make two primary contributions to knowledge, first in providing a method by which net benefits from electronic commerce can be measured within an industry adopting electronic trading, and second, by providing organisations with the knowledge of the specific net benefits organisations could expect from EDI adoption, together with the four major factors affecting these benefits. The research concludes with possible directions for future research, in particular an assessment of the impact of incorporating financial EDI into electronic trading.

1948 and 1968 Czech refugee settlers in Australia : a comparison of the settlement and integration processes among two waves of settlers

Nearly eighteen years ago when I first became interested in the history and sociology of Australian immigration, I was particularly attracted by the fact and opportunity to incorporate immigration settlement, experience and accomplishments in my history teaching in secondary school. In particular it was the area of the settlement of Australia that needed a fuller understanding in the teaching of Australian history. By that I mean it was needed to show that there were many other ethnic groups besides the Anglo-Saxon group which had participated in the development of Australia since 1788. Since the end of World War II, the Australian population has doubled, the population structure and characteristics have changed and knowledge about the diverse groups forming the Australian nation is now sought. Sane ethnic groups, mainly the numerically large, have been studied and numerous reports are available. But many of the smaller groups have attracted little interest among Australian scholars. This was one of the reasons that I decided to research the behaviour of one of the smaller groups - the Czechs - to find out about their immigration history to Australia; their immigration processes such as re-settlement and re-establishment; and their community life since World War II. Because of the scarcity of written materials on Czechs in Australia, I had to rely on interviews, personal reminiscenses, letters and documents translated from the Czech language. I should like to express my gratitude to all people and officials of Czech ethnic organisations and clubs in Australia, who agreed to be interviewed and who provided me with documentary material so important for my work. Respecting the wishes of my interviewees their anonymity had to be preserved. In the course of my research, I have received substantial help and the encouragement from the Editor of the now extinct Czech language paper Newspaper Hlas domova, Mr. F.V., whose co-operation is gratefully recognised. I am also grateful to Associate Professor William D. Rubinstein for his help and encouragement in all stages of my work. The introductory part of the study is covered in Chapter One. She reasons for the need to increase Australia's population after World War II and an analysis of the development of settlement in Australia between 1947 and 1984 are discussed. The emigration of Czechs into Australia and their place in the post-war immigration scheme is introduced. To obtain an overview of how Czechs have emigrated around the world, the literature describing their settlement is compared. Also discussed in the literature on Czech settlement in Australia from an historical point of view. The studies on the concept of ethnicity and settlement in Australia are used to document the theoretical issues for an understanding of Australian society. This chapter also contains aspects of sources and research, shewing the processes of documentary research, interviews and related matters. In Chapter Two the history of Czech emigration is discussed, covering the period from the seventeenth to the twentieth century. The first contacts with Australia are highlighted, continuing into the inter-war period and finally the re-settlement of Czechs after World War II. To understand why Czechs left their ancestral country after World War II, the political situation in Czechoslovakia is analysed. The third chapter concentrates mainly in the 1948 wave of settlers, who left Czechoslovakia after the communist take-over in 1948. Their means of departure from their homeland, selection of Australia as a new homeland and their re-settlement and re-establishment are discussed. Their attitudes after their arrival and their later stages of their settlement are analysed. The formation of numerous Czech ethnic organisations which mushroomed between 1950 and 1954 led to an active community life which began to change about five years after their arrival. These charges led to disorganisation of Czech community's life. The causes of these changes which were influential for the failure of the 1948 group to establish a viable community in Australia are analysed. In Chapter Four the wave of 1968 is viewed, their arrival and settling is covered. The study of their group attitudes and formation of group institutions is the main part of this section. A comparison of my data of the two waves, 1948 and 1968, reveals the information that these two groups did not develop the harmonious relationship expected of them as members of the one ethnic group. Chapter Five discusses immigration typologies and concentrates on the differences between legal and illegal emigrants from the Czechoslovak point of view. The integration processes of Czechs and their incorporation into Australian society are discussed. The sixth chapter sums up the findings of this disertation and states the influences which were responsible for the divisions in Czech ethnic life in Australia in the 1980s.

Towards an integration of theories of achievement motivation

This thesis investigated children's school achievement in terms of an integration of three theories of achievement motivation. The three theoretical outlooks were expectancy-value theory (EVT), implicit theories of intelligence (ITI), and flow theory (FT). The first of two studies was an exploratory investigation of the effectiveness of each theory independently and combined to predict children's achievement in four school subjects. The subject areas were maths, reading, instrumental music and sport. Participants were 84 children (40 females and 44 males) aged 9 to 10 years, one of each child's parents, and school teachers of each child in the four subject areas. All data were collected through questionnaires based on the three models. The results indicated that EVT and FT but not ITI accounted for a significant amount of the variance in children's achievement, including effects for subject area and gender. A second confirmatory study tested EVT, FT and an integrated model for the prediction of achievement in maths, reading and instrumental music. The participants were a further 141 children (74 females and 67 males) aged 10 to 11 years, and a parent and teachers of each child. Data collection using questionnaires occurred early in the school year (Timel) and approximately five months later (Time2). For EVT, children and parents’ competence beliefs were significant predictors of children's achievement in each subject area. Females tended to believe themselves more competent at reading and instrumental music and also valued these subjects more highly than boys. Modeling results for flow theory indicated that children's emotional responses to classes (happiness and confusion) were significant predictors of achievement, the type of emotion varying between subject areas and time periods. Females generally had a more positive emotional reaction to reading and instrumental music classes than males did. The integrated model results indicated significant relationships between EVT and flow theories for each subject area, with EVT explaining most achievement variance in the integrated model. Children's and parents’ competence beliefs were the main predictors of achievement at Timel and 2, Subject area and gender differences were found which provide direction for future research. Anecdotal reports of parents and teachers often attest to individual differences in children's involvement in various school domains. Even among children of apparently similar intelligence, it is not uncommon to find one who likes nothing better than to work on a mathematics problem while another much prefers to read a novel or play a musical instrument Some children appear to achieve good results for most of the activities in which they are engaged while others achieve in a less consistent manner, sometimes particularly excelling in one activity. Some children respond to failure experiences with a determination to improve their performance in the future while others react with resignation and acceptance of their low ability. Some children appear to become totally absorbed in the activity of playing sport while others cannot wait for the game to end. The primary research objective guiding the current thesis is how children's thoughts and feelings about school subjects differ and are related to their school achievement. A perusal of the achievement motivation literature indicates several possible models and concepts that can be applied to explain individual differences in children's school achievement. Concepts such as academic self-concept, multiple intelligences, intrinsic and extrinsic motivation, self-beliefs, competence beliefs, subjective task values, mastery and performance goals, ‘Flow’ experiences and social motivation are just some of the constructs used to explain children's achievement motivation, both within and between various activity domains. These constructs are proposed by researchers from different theoretical perspectives to achievement motivation. Although there is much literature relevant to each perspective, there is little research indicating how the various perspectives may relate to each other. The current thesis will begin by reviewing three currently popular theoretical orientations cited in achievement motivation research: subjective beliefs and values; implicit theories of intelligence, and flow experience and family complexity. Following this review, a framework will be proposed for testing the determinants of children's school achievement, both within each of the three theoretical perspectives and also in combination.

Integrating data to facilitate clinical research : a case study

The integration of routine clinical administrative activities into ongoing rigorous clinical research poses challenges for both clinicians and researchers. This case study describes the development of a responsive database system used to facilitate comprehensive longitudinal research into the outcomes of patients waiting for hip and knee replacement surgery in a large public teaching hospital. The initial research procedure was paper-based, with manual patient matching and data entry. This process was time-consuming and associated with substantial risk of error and omissions, necessitating the design of a better system. An integrated database system was designed to receive daily electronic updates of the orthopaedic waiting-list and scheduled clinic and surgery dates. Using readily available software (Microsoft Access), new patients were identified through specifying inclusion and exclusion criteria which allowed rapid and complete recruitment at time of entry to the waiting-list. The integrated system specified the appropriate timing of multiple follow-up assessments, provided prompt information on recruitment for reporting purposes and integrated multiple linked research projects within one database. Seamless exporting of data to statistical programs for analysis was also enabled. This simple integrated approach facilitated efficient execution of a longitudinal study from recruitment to statistical analysis while maximising confidentiality and minimising resources required. This case study describes the development and design of a simple system which could be easily adapted for database management in hospital or clinic-based settings according to local requirements.

The management of individuals with bipolar disorder : a review of the evidence and its integration into clinical practice

Bipolar disorder is a common, debilitating, chronic illness that emerges early in life and has serious consequences such as long-term unemployment and suicide. It confers considerable functional disability to the individual, their family and society as a whole and yet it is often undetected, misdiagnosed and treated poorly. In the past decade, many new treatment strategies have been trialled in the management of bipolar disorder with variable success. The emerging evidence, for pharmacological agents in particular, is promising but when considered alone does not directly translate to real-world clinical populations of bipolar disorder. Data from drug trials are largely based on findings that identify difterences between groups determined in a time-limited manner, whereas clinical management concerns the treatment of individuals over the life-long course of the illness. Considering the findings in the context of the individual and their particular needs perhaps besl bridges the gap between the evidence from research studies and their application in clinical practice. Specifically, only lithium and valproate have moderate or strong evidence for use across all three phases of bipolar disorder, Anticonvulsants, such as lamotrigine. have strong evidence in maintenance; whereas antipsychotics largely have strong evidence in acute mania, with the exception of quetiapine, which has strong evidence in bipolar depression. Maintenance data for antipsychotics is emerging but at present remains weak. Combinations have strong evidence in acute phases of illness but maintenance data is urgently needed. Conventional antidepressants only have weak evidence in bipolar depression and do not have a role in maintenance therapy. Therefore, this paper summarizes the efficacy data for treating bipolar disorder and also applies clinical considerations to these data when

The integration substitute : the role of controls in managing human asset specificity

As the integration solution to the problem of specific assets cannot be replicated on human asset specificity because slavery is illegal, economic theory states that control systems substitute for integration through a balanced structure to help align diverse interests. To understand the intricate design features of the balance, we examine a case-study firm. For low human asset specificity, the restriction and segregation of usable decision rights link with standards. However, incentives are traced to individuals only to the extent task deviations do not create relevant future costs that are difficult to be self-corrected. For high specificity, incentives are related to outputs rather than outcomes, because outcome variations reduce the attractiveness of maintaining the balance. Subjective assessment is used as an efficient alternate ‘balancing’ solution and decision control is shared when available subjective data are inadequate.

Recognising behaviours of multiple people with hierarchical probabilistic model and statistical data association

Recognising behaviours of multiple people, especially high-level behaviours, is an important task in surveillance systems. When the reliable assignment of people to the set of observations is unavailable, this task becomes complicated. To solve this task, we present an approach, in which the hierarchical hidden Markov model (HHMM) is used for modeling the behaviour of each person and the joint probabilistic data association filters (JPDAF) is applied for data association. The main contributions of this paper lie in the integration of multiple HHMMs for recognising high-level behaviours of multiple people and the construction of the Rao-Blackwellised particle filters (RBPF) for approximate inference. Preliminary experimental results in a real environment show the robustness of our integrated method in behaviour recognition and its advantage over the use of Kalman filter in tracking people.

Global and threshold-free transcriptional regulatory networks reconstruction through integrating ChIP-Chip and expression data

Inferring transcriptional regulatory networks from high-throughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed TReNGO (Transcriptional Regulatory Networks reconstruction based on Global Optimization), a global and threshold-free algorithm with simulated annealing for inferring regulatory networks by the integration of ChIP-chip and expression data. Superior to existing methods, TReNGO was expected to find the optimal structure of transcriptional regulatory networks without any arbitrary thresholds or predetermined number of transcriptional modules (TMs). TReNGO was applied to both synthetic data and real yeast data in the rapamycin response. In these applications, we demonstrated an improved functional coherence of TMs and TF (transcription factor)- target predictions by TReNGO when compared to GRAM, COGRIM or to analyzing ChIP-chip data alone. We also demonstrated the ability of TReNGO to discover unexpected biological processes that TFs may be involved in and to also identify interesting novel combinations of TFs.