Thesis submitted in fulfillment of the requirements of the award of the Degree of Doctor of Philosophy (Library and Information Science) at the University of Zululand, South Africa, 2011. / ICT is a compound term that is used to refer to the convergence of a wide array of new technologies presently being developed and used in the creation, processing and transmission of information. Broadly speaking, these technologies encompass all aspects of data / information recording, handling and transmission, and include computers, telecommunications, satellites, fibre optics, video-based multimedia applications, automated speech outputs, and electronic broadcast technologies. The public services referred to in this study are government departments, and they are responsible for servicing society, devising policies, and ensuring that they are implemented. The civil servants referred to in this study are government employees. The focus of this study was to examine the use, types, interaction, and availability of ICTs in four government departments in KwaZulu-Natal, South Africa, in the context of work productivity and creativity. In order to achieve the stated aim, the following research had to be answered: What types of ICTs are available in government departments? What problems are experienced by the civil servants in their utilization of ICTs? How can the education and training needs of the civil servants be addressed? To what extent are ICTs used by the civil servants in their work activities? What strategies and solutions can address the problems faced by the civil servants? This study adopted mixed methods where aspects of both quantitative and qualitative approaches were employed. The quantitative method was used to solicit information from the civil servants, while the qualitative approach was used in the review of different social informatics studies. The literature review was undertaken across a broad spectrum of sources including conference papers, journals, government policy documents and several Internet sources. The study used multistage probability sampling to select the elements for the survey and to achieve the desired representation from the population. Probability samples helped the researcher acquire a demonstrable degree of reliability and validity. The sampling techniques used were simple random, systematic, and stratified sampling. Simple random sampling was first used to identify government departments in the province that have considerable reach and are service intensive, namely the Departments of Arts and Culture, Home Affairs, Education, and Health. Secondly, systematic sampling was used to select suitable district municipalities. This sampling technique was used in order to increase the chances of obtaining a representative sample and to prevent bias in the selection process. The initial starting municipality in this technique was selected randomly and every second district municipality from a list was selected thereafter. The departments were selected from the following district municipalities: uMgungundlovu, uMzinyathi, Zululand, uThungulu and Sisonke. The first stage of stratified sampling consisted of the division of the service area into rural and urban based areas. In the second stage, stratification of personnel in the selected departments into top, medium and lower level management was done. This was to ensure that all the levels of management were represented in the study. In the last stage, a simple random sample was used to select the sample elements from the different levels of management. Government departments in South Africa have a well defined organogram such that the number of managers is almost equal across all departments. A sample size of 20 % of the population elements was used and this resulted in 65 personnel being selected from each ministry and a target sample of 260 managers. A questionnaire was used to collect quantitative data. The data collected was analyzed using thematic categorization and tabulation, and the findings were presented descriptively. The findings show that a variety of ICTs have been adopted in the sector. All the civil servants surveyed indicated that they used ICTs to communicate with fellow colleagues, for spreadsheet purposes, word processing, printing, and to disseminate departmental information. The respondents’ level of interaction with some of the ICTs, such as e-mail, personal computers, Internet, printers and telephones, was very high, while the use of ICTs such as video conferencing, television and radio was very poor. The most common obstacles to the effective use of ICTs in government departments were found to be lack of skills / competence, the lack of a comprehensive ICT policy, and the lack of proper planning for the adoption and diffusion of ICTs in the sector. The civil servants particularly voiced the need for training on database searching and information retrieval. The contextual conditions that need to be adapted in order to improve the use of ICTs in government departments include the need for adequate and well structured planning; an introductory a comprehensive ICT policy that would provide sufficient frameworks for ICT development and/or use in the public sector; provision of proper and sufficient ICT infrastructure; funding for the purchase of all necessary facilities and resources for ICTs; and the training of staff on how to use ICTs. The issue of planning revealed here is very important as embarking on any new innovation requires adequate planning. Other recommendations include training sessions for civil servants so that they can use the acquired ICT knowledge and skills in their daily work and activities. Where necessary, the government should continually review the ICT training it offers to civil servants, especially considering the rate of developments in the ICT industry. A good policy would also provide sufficient frameworks for ICT development and/or use in government departments, for instance in areas of strategizing implementation, staff development and communication. Policies to foster the uptake of ICTs are insufficient. Moreover, policies specific to ICT diffusion and use will not, on their own, lead to stronger performance; they should be part of a comprehensive set of actions to create the right conditions for growth and innovation. The diffusion and adoption of ICTs in government departments require expertise at various levels. The South African government is still working on putting together a comprehensive national ICT policy that would guide ICT use in the country. / The University of South Africa

A distributed coalition consisting of a Head Start program, its youth activities program development director, rural youth, an art gallery and its curators, a graphic designer, and a university department are collaborating to design, build, and populate a user controlled content management system to bring the youthsâ work to a global audience, enable computer mediated interaction, provide a venue for exploring artistic expression, and introduce information and communications technologies (ICTs) to the youth and other project participants. Using a project-based approach combined with implicitly constructed scenarios and the iterative and informal processes associated with free / libre / open source software development, the geographically and organizationally distributed project team created the first release of the Growing Tennessee Web site to coincide with a photo exhibition held at a not-for-profit art gallery. The project will build upon its previous accomplishments and introduce additional media and their supporting technologies to rural youth.

A distributed coalition consisting of a Head Start program, its youth activities program development director, rural youth, an art gallery and its curators, a graphic designer, and a university department are collaborating to design, build, and populate a user controlled content management system to bring the youthsâ work to a global audience, enable computer mediated interaction, provide a venue for exploring artistic expression, and introduce information and communications technologies (ICTs) to the youth and other project participants. Using a project-based approach combined with implicitly constructed scenarios and the iterative and informal processes associated with free / libre / open source software development, the geographically and organizationally distributed project team created the first release of the Growing Tennessee Web site to coincide with a photo exhibition held at a not-for-profit art gallery. The project will build upon its previous accomplishments and introduce additional media and their supporting technologies to rural youth.

The Biochemical Library (BCL) is a protein structure prediction algorithm developed in the Meiler Lab at Vanderbilt University based on the placement of secondary structure elements (SSEs). This algorithm incorporates sparse experimental data constraints from nuclear magnetic resonance (NMR), Cryo- electron microscopy (CryoEM), and electron paramagnetic resonance (EPR), to restrict the conformational sampling space but does not have the capability to use Small Angle X-Ray / Neutron data. This dissertation delineates my work to add this capability to BCL::Fold. Specifically I show and show for what type of structures SAXS/SANS experimental data improves the accuracy BCL:: Fold and importantly where it does not. Furthermore, in collaboration with Oak Ridge National Labs, I present my work on structural determination of the Cellulose Synthase Complex in Arabidopsis Thaliana.

Proteomics allows us to see post-translational modifications and expression patterns that we cannot see with genomics and transcriptomics alone. By itself, proteomics has limited sensitivity to detect genetic variation (e.g. single-nucleotide polymorphisms and insertion/deletion mutations), but we can improve that with access to genomic data: an approach known as proteogenomics. As in many of the -omics fields, reproducibility of proteogenomic results is a problem. Since 2005, the web application âGalaxyâ has been available to improve the transparency and reproducibility of -omic analyses. However, a Galaxy server is not easy to set up, and to work around that, investigators have sometimes distributed their customizations as virtual machines (VMs). In recent years, a more efficient approach for software isolation - âcontainersâ - has become popular. A proteogenomics âflavorâ of Galaxy â Omicron â was created to simplify reproduction of proteogenomic workflows. An easy way for anyone to launch Omicron on Amazon Web Services, paired with a scalable compute cluster, was also created. Using Omicron, results from a 2014 Nature paper were partially reproduced. Due to changes in online reference data and possibly due to different tool versions, it was not possible to perfectly reproduce the previous results. However, other investigators could easily reproduce the Omicron results without digging through methods and supplemental data. Then they could easily apply the same workflow to their own data.

Colorectal Cancer (CRC) remains a leading cause of cancer-related mortality in the United States. A key therapeutic dilemma in the treatment of CRC is whether patients with stage II and stage III disease require adjuvant chemotherapy after surgical resection. Attempts to improve identification of patients at increased risk of recurrence have yielded many predictive models based on gene expression data, but none are FDA approved and none are used in standard clinical practice. To improve recurrence prediction, we utilize an ensemble learning approach to predict recurrence status at 3 years after diagnosis. Multiple views of a microarray dataset were generated then used to train a diverse pool of base learners using 10x 10-fold cross-validation. Stacked generalization was used to train an ensemble model. Our results demonstrate that molecular data predicts recurrence significantly better than basic clinical data. We also demonstrate that the performance of the multiple-view multiple learner (MVML) supervised learning framework exceeds or matches that of the best base learners across all performance metrics.

Thesis under the direction of Dr. Jeremy L. Warner The practice of oncology increasingly relies on genetic information from tumors to determine diagnosis, prognosis and therapy. These tumor molecular profiling reports are generated by clinical laboratories specializing in molecular diagnostics; however, there is no consensus on what the reports should contain, how they should be structured, or how best to transmit and present them to oncologists. This thesis outlines a framework for the data elements, file structure, transmission requirements, clinical information technology requirements and secondary use cases for molecular profiling. This framework is used as a guide to describe the implementation of tumor molecular profile reports into clinical workflows. The experience of implementing automated structured molecular profile reports from a third party laboratory into an electronic health record is described. Using file structures and data elements from the framework, molecular profile genetic data and sample metadata can be accurately parsed, restructured and aggregated for secondary uses. A system of parsing this data into a database and the use cases this database satisfies is described. This framework helps to inform clinical and translational uses of tumor molecular profiling.

Background Effective medical software is designed to fit the needs of the end users, translating their work into action. User-centered design seeks to involve users at all stages of the design process, but the process itself can be tedious, leading to variable degrees of implementation amongst vendors. This research seeks to create a new method of involving multiple end users remotely in the user-centered design process in order to establish the features and design required for clinicians need to perform effectively. Objectives The objectives of this research are to summarize currently identified necessary pediatric-specific EHR functionalities and create an online software platform to delineate further needs and functionalities, contributing to remote user-centered design of electronic medical record software. Methods We created Vanderbilt Active Interface Design (VandAID), a novel web-based software platform for crowdsourcing user interface design. The platform provides immediate real-time feedback on user interface design and layout decisions using example patient scenarios. The scenarios can pull information from a variety of sources using standards such as a Fast Health Interoperability Resource (FHIR). The design platform allows the selected options to be sent to a REDCap project for statistical analysis or viewed directly in the VandAID platform. We performed a randomized controlled trial to test the usability and utility of this software platform for the design of a neonatal handoff tool. Conclusions This research advances scientific approaches to user-centered design of health information technology by creating a means of collecting remote feedback from multiple users. Results from the randomized controlled trial in the first use case demonstrate this software platform to be a highly usable and effective means of performing cooperative user-centered design.

Electronic health records (EHRs) are rich data sources that can be analyzed to discover new, clinically relevant patterns of disease manifestations. However, sparsity, irregularity, and asynchrony in health records pose challenges for their use in such discovery tasks, as standard statistical and machine learning techniques possess limited ability to handle these complications. Abstracting the clinical data into models and then using elements of those models as input to statistical and machine learning algorithms is one approach to overcoming these challenges. This dissertation provides insight into the use of different models for this purpose. First, I examine the effect of model complexity on algorithm performance. Specifically, I examine how well different models capture the low-specificity information distributed throughout electronic health data. For several predictive algorithms, low-complexity models turn out to be nearly as powerful and much less costly as high-complexity models. I then explore the use of continuous longitudinal models of laboratory results and diagnosis billing codes to discover clinically relevant patterns between and among these data. I look for associations between clusters of specific laboratory values and single billing codes, and identify known associations as well as others that are consistent with current medical knowledge but not expected a priori. Finally, I use the same longitudinal abstraction models as inputs into more complex probabilistic models that adjust for indirect associations, and find that diagnosis codes can be used to predict the laboratory status of a patient.

<p>Information and Communication Technology (ICT) has been considered a tool that can be used to achieve development goals in developing countries. In the same time, the majority of people living in developing countries, and especially those in rural areas lack access to ICT. Even if there have been many attempts to introduce ICT, they have in general not been long-lasting.</p><p>A framework for studying factors that influence use of ICT is desirable. We see it necessary to bring a sustainability aspect into the picture of ICT. In this work the requirement of ‘sustainable ICT use’ stresses that ICT is long-lasting and that ICT meets the needs of the user. Thus, the aim of this work is to develop a tool for conceptualisation that can support the understanding of the conditions for sustainable, and therefore successful, ICT projects in developing countries.</p><p>Our theoretical starting point is taken in the Information System (IS) theories. The theoretical base is then broadened to include theories on international development, theories on sustainable development, and theories on diffusion of innovations and transfer of technology. The theoretical foundation, together with four empirical studies, is used to answer the two research questions in this thesis. The first question is: Which are the critical factors influencing sustainable ICT use in developing countries? By using ‘critical factors’ we emphasise a focus on factors which are crucial (even if possibly not sufficient) for bringing about sustainable ICT use. This question is followed by a second question: How would a framework be structured to properly include these factors in order to support analyses of sustainable ICT use?</p><p>The framework has evolved through the identification of factors from four empirical studies. Forty-one factors were identified and sorted into fifteen subcategories of five major capital assets. The main contribution of our study is that of a generic framework, which can be used as a guideline for planning, implementation, and evaluation of ICT projects in a rural developing country context achieving sustainable ICT. As argued in this thesis technology is not the key resource; it is the combination and system of different resources distributed along a time and space dimension that is the key. With our framework we have demonstrated that the ICT artefact is not the sustainability tool, it is the combination of different resources that makes it sustainable and competitive.</p>