A Task-Based and User-Centered Protocol for Bioinformatics Information Search and Retrieval

Joan C. Bartlett
Faculty of Information Studies University of Toronto Toronto, Ontario, Canada 416-978-4715

bartlett@fis.utoronto.ca

ABSTRACT
This paper describes the development of a task-based and usercentered protocol for bioinformatics information search and retrieval in the context of the problem of conducting a functional analysis of a gene sequence. The protocol was developed from data collected by interviews with twenty bioinformatics experts, and validated by both the original participants, and a new cohort of eighteen experts. The protocol describes fourteen steps integrated into three parallel pathways. The details for each step includes not only the flow of data between steps, but also guidelines for the interpretation and use of the information obtained. The protocol forms the basis for a semi-automated information retrieval system to facilitate the process of functionally analyzing a gene sequence. Categories and Subject Descriptors H.3.3 [Information Storage and Retrieval]: Information Search and Retrieval Search process. J.3 [Computer Applications]: Life and Medical Sciences Biology and Genetics. General Terms Design, Human Factors. Keywords Bioinformatics, requirements.

experiments [6]. Yet, in spite of the critical role bioinformatics information retrieval can play in biomedical research, there is an absence of research that explicitly links bioinformatics information retrieval to solving a complex scientific problem. Bioinformaticians (those designing and developing bioinformatics resources) and laboratory scientists can be seen to be working at cross-purposes, with bioinformaticians studying a specific analysis or algorithm in detail, while scientists focus on a biological problem, bringing as many different analytical tools and techniques as necessary to bear on the problem (Hogue, personal communication). Research in bioinformatics has tended to focus on the use or application of a specific database or tool (e.g., [5]) or the details of algorithms for information retrieval or analysis and the subsequent programming and development of a bioinformatics tool (e.g., issues of the journal Bioinformatics). What is not well covered in current research is the integration of bioinformatics information retrieval with a research problem or agenda. This is a complex process; it is not a simple task of using a single bioinformatics resource to retrieve a single piece of information, or to answer a single question. Instead, it involves the integrated use of many different bioinformatics resources in a multi-step process, with the information retrieved at each step adding to the analysis [4]. Anecdotal evidence suggests that it is the process of connecting bioinformatics and laboratory research that is problematic for laboratory scientists (Muskat, personal communication). Instead, biologists tend to use only the simplest tools available [6]. The challenge is knowing which questions to ask, what information to search for and retrieve, and which resources to use to obtain that information; the same process has been found to be challenging in text-based information retrieval environments [10]. Yet information about how to link several different bioinformatics analyses into a cohesive approach to solving a problem is not readily available. Rather than being systematically documented and disseminated in the research literature, knowledge about these processes tends to be passed on from individual to individual, becoming part of the oral history of a research group [3]. One approach to linking information retrieval and a research problem or objective is that of task analysis. Task analysis, defined as the study of what an operator is required to do . . . to achieve a system goal [9], provides a powerful approach for linking information retrieval to a task or goal. It considers factors such as the relationship between goals, tasks and actions, as well as workflow [7]. There are multiple approaches to task analysis. Hierarchical task analysis, considered the best known approach, divides a large job (goal) into individual tasks, which are further

task

analysis,

data

modeling,

interface

1. INTRODUCTION 1.1 Background

As the field of bioinformatics has exploded, there is a need for the techniques of bioinformatics information search, retrieval and use to be brought into the realm of the laboratory scientist. There is a call for a better understanding from the general biologist of the real possibilities given by the analysis of genomes [1] and the need to integrate very tightly the bioinformatics with doing

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divided into sub-tasks until the smallest unit of activity is identified [2]. Procedural analysis considers the sequential flow of steps a user would follow to accomplish the goal [7]. A third approach is to consider task analysis in terms of inputs and outputs [12]. Other factors that are essential to consider are the work domain, constraints within which the work takes place, effective strategies for accomplishing the work, the context in which the work takes place, and the competencies of those doing the work [12]. In the case of an information problem, task analysis provides a means of linking activities such as information retrieval to the overall goal or objective for which the information is needed. For example, Vakkari [11] advocates using task analysis as a basis for studying information searching, while Hersh [8] calls for a taskoriented focus to evaluating information retrieval. The task analysis approach is particularly valuable when the information problem is complex, as in the case of applying bioinformatics information to a scientific problem. Task analysis explicitly studies the connection between the various information retrieval tasks and sub-tasks, and provides the link that integrates each individual information retrieval step into a solution for the overall goal. With the corresponding attention to the person who actually does the task, this approach also shifts the focus to the user of the information, rather than the information retrieval system.

people who are proficient in the use of bioinformatics resources, using them regularly as part of their work. They are also familiar with the process of functionally analyzing a gene sequence, the scientific problem used to gather data. The participants held a variety of positions: eight principal investigators, four graduate students, three post-doctoral fellows, two consultants, one clinician/researcher, one technician and one manager. Most participants held graduate degrees: ten PhD, one MD/PhD, five M.Sc. and four B.Sc. In addition to formal education in the biological sciences, some participants also had formal education in computer science. Seventeen of the participants had been using bioinformatics resources for at least three years. All reported being either moderately or very confident in their ability to use bioinformatics no one was not confident. The participants came from eight different research groups in major research institutions in Canada and the United States. Six of the groups were based in universities, one in government, and one in the private sector. The research groups were either within a biology department (e.g., biochemistry, genetics, microbiology) or a specialized bioinformatics center. Participants were purposefully selected to represent a range of research interests (i.e., human, bacterial and viral research). The purposeful sampling was intended to minimize the bias towards one particular group's house style

1.2 Objective
The objective of this study was to develop a task-based and useroriented protocol describing the application of bioinformatics information retrieval to solving a specific scientific problem, that of conducting a functional analysis of a gene sequence. The protocol forms the specifications for an information retrieval system to link the multiple analyses involved in this task, thus supporting researchers who wish to accomplish the functional analysis of a gene.

2.3 Interviews
Data were collected using semi-structured interviews. Interviews followed a flexible interview script, based on a task analysis approach [7]. The initial question asked the participant to describe the steps he or she would follow, and the databases and tools he or she would use to complete the task of functionally analyzing a gene sequence. Probe questions were used to ensure that essential points were covered. A key element in the data collection was understanding why things were done, not simply recording what was done. Additional questions explored the amount of variation in the process as described by the scientist, in order to understand if the process could be generalized to other situations. Participants also described what parts they believe could be automated. Finally, it was important to understand the key decision points in the process, why particular resources were chosen, and the purpose of each type of analysis.

2. METHODS 2.1 Task

There are many tasks that could have been used to observe bioinformatics analysis, such as gene prediction or protein modeling. The one selected was the task of conducting a functional analysis of a gene sequence, which involves making predictions about the probable biological function of a gene, based on analysis of patterns found in the sequence data. This problem is very timely, as the Human Genome Project and other large sequencing projects have led to an immense amount of gene sequence data for which the function is not known. Determining the function of these genes is one of the next major challenges for biomedical research (Cuticchia, personal communication). Depending on the sequence, the analysis could last from weeks to months in the laboratory. Bioinformatics analysis could last in the order of several hours to a few days, using anywhere from a few to twenty or thirty data sources and tools. The approach is often used to identify which genes are likely to have the functional characteristics of interest to a research project, such as identifying a target gene for a new drug, or determining the biological activity of a disease-associated gene.

2.4 Protocol Development

The interview data was analyzed in an iterative process, using multiple rounds of coding. In the initial round of coding, each interview was analyzed to determine the process followed by that particular expert. The focus was on identifying what was done. The analysis identified the a) type of bioinformatics analysis done at each step, b) the bioinformatics tools used at each step, and c) the order of the steps. The result was twenty individual processes describing how each individual would approach the problem of conducting a functional analysis of a gene. As each individual process was identified, it was also merged into the model protocol. This analysis involved identifying both common and distinct elements of each process. In some cases, similar steps were followed, but were described or named differently by the participants. Points of divergence and convergence among the different processes were identified, and

2.2 Participants
Participants in this study were twenty bioinformatics experts,

incorporated into the model. As a visual aid to the development of the model, flowcharts were used to represent the model at high level. The second round of coding focused on understanding the reasoning behind each step of the process, that is, why each participant followed their particular process. This analysis shed light on some of the variations between the individual processes, by explaining the reasoning behind the choice of bioinformatics analyses. Second round coding also identified the data input and output at each step of the process, and how the information obtained would be used. These findings were incorporated into the model protocol.

analysis or resource is intended to provide all of the information needed to generate a solution. Another key feature of the individual processes was the role of, and need for, human decision-making. While the parameters surrounding some decisions could be defined and articulated, others could not. Instead, participants reported that they relied on their own judgement in a particular situation, and could not specify the factors that determined the decision. Instead, this was referred to as the art rather than the science of the process. The participants also reported that while parts of the process they followed could be automated, there were other points that could not be thus, the processes had the potential for semi-automation, but not full. When merged together, the twenty processes generated a sixteenstep consensus protocol, describing the application of bioinformatics information retrieval to the problem of predicting gene function. The sixteen steps were linked together into three, parallel pathways, each describing a variation in the approach to the functional analysis of a gene sequence. The validation process led to the removal of two analytical steps from the process the two in question (EST Expression Pattern and Identify Genome Location) were determined not to fit within the scope of the functional analysis of a gene. The final, validated protocol therefore consisted of fourteen steps, twelve analytical steps and two decision steps. These are listed and described in Table 1. The data flow diagram in Figure 1 illustrates the relationship among the steps. Each rounded square box refers to one of the twelve analytical steps. The two diamond shaped boxes refer to the two major decision points, at which the protocol branches into one of the three parallel pathways. While decision points are not typically shown in data flow diagrams, these two were included, as the points they define are critical components of the protocol. Finally, the arrows between the boxes are labeled with the data that flows from one box (step) to the next. The protocol has as its starting point the sequence data (either cDNA or genomic DNA) of a novel gene with unknown function. The first three steps prepare this data for the analysis. The first analysis in the protocol is Step 1 - Contig Assembly. If the initial sequence exists in fragments, these are assembled together into a complete (or more complete) contig. The longer DNA sequence is used as input for the next step of the process, Step 2 - Open Reading Frame Prediction. Ideally, this analysis will yield one open reading frame (ORF) on which to base further analysis. If it is not possible to identify which of the six open reading frames is correct, the subsequent analyses must be done in parallel with all possible ORFs. The final preparatory step is Step 3 - Translation. The DNA sequence of the ORF is translated into the corresponding amino acid sequence, which is used as the basis for the remaining analyses. Amino acid sequence is used rather than DNA sequence because of the redundancy in the genetic code. Step 4 - Homology Searching is the first step to analyze the amino acid sequence. While commonly referred to as homology searching, the analysis actually identifies sequences based on sequence similarity or identify, rather than by a definite evolutionary link. If two or more proteins are similar at the sequence level, then there is likely a similarity in function. Homology searching was a common element in the individual processes, and is therefore included in the protocol prior to the branching of the three alternate approaches.

2.5 Validation of the Protocol

To ensure the integrity of the protocol, it was submitted to testing of both internal and external validity. Internal validity testing had the goal of determining if the protocol reflected reality. It involved participant validation, in which the original interview participants commented on the protocol, and whether it accurately reflected what they had reported. Participants responded to a web-based survey, in which they commented on the detail of each analytical step in the protocol, and on the order and grouping of individual steps in the protocol. Twelve of the original twenty participants completed the validation survey. External validity relates to the generalizability of research findings. The findings from qualitative research are typically limited in generalizability, relating only to the study group, or other very similar groups. However, the goal of this research was to develop a protocol that could be used by a larger population of scientists to facilitate the functional analysis of a gene. It was therefore essential to determine if the protocol was applicable beyond the original study group. Accordingly, a second cohort of bioinformatics experts, similar in background and experience to the first, were surveyed using webbased questionnaires. A combination of key informant and snowball techniques yielded names of potential participants. Additional participants were recruited through messages sent to bioinformatics related listservs (MOLBIOSIG and SIGBIOINFORM). A total of eighteen people responded to the external validation survey. They held the positions of principal investigator, consultant or post-doctoral fellow, and all but one had a graduate degree (Ph.D. or M.Sc.). Participants came from four countries (Australia, Canada, Israel, and the United States). Those contacted directly came from nine institutions (3 Australian, 2 Canadian and 4 American). The institutions of those who responded to the listserv messages is not known, as this was not asked.

3. RESULTS
The initial interviews generated descriptions of twenty individual processes for applying bioinformatics information retrieval in the context of the functional analysis of a gene sequence. Common characteristics of the individual processes include a step-wise approach using multiple bioinformatics resources (up to 10 steps with 20-30 different resources). The information obtained from each step is integrated with that from other steps, to generate a picture of the putative function of the gene product. No one

Figure 1. Data flow diagram of the bioinformatics analysis protocol for the functional analysis of a gene 4

Table 1. Steps Included in the Protocol for the Functional Analysis of a Gene Sequence

particular structures or functions. The analysis relies on the presence of well characterized motifs within the reference databases. Step 6 - Multiple Alignment is done hand-in hand with homology searching. Once similar sequences have been identified, multiple alignment lines them up, and identifies the regions of similarity. These regions that have been conserved among different genes are likely to also have functional similarity. Step 7 - Phylogenetic Analysis expands on homology searching and multiple alignment by predicting the evolutionary relationship among similar sequences. The analysis is premised on the theory that the more closely related sequences are to one another, the more likely they are to share similar function. The Multiple Alignment Path is sequential, with the output data from one step serving as the input data for the next. The alternate choice at Step 5 is the Domain/Motif Path. This path is subdivided at the second major decision point, Step 8 - Multi-step vs. One-step Domain/Motif Analysis. Both of these approaches involve the analysis of portions (domains) of the sequence. The Multi-Step Domain/Motif Path uses multiple steps and resources to conduct the analysis, while the One-Step Domain/Motif Path uses resources that are able to do the same analysis in a single step. Steps 9-12 (Step 9 - Domain/motif Analysis, Step 10 Transmembrane Region Analysis, Step 11 - Cellular Localization, and Step 12 - Secondary Structure Analysis) each compare the novel sequence to a reference database, searching for patterns (motifs) that are known to be characteristic of a specific structure or function. Step 9 - Domain/motif analysis is a general domain/motif search, not limited to any specific type of motif. The next three steps relate to specific motifs, with correspondingly specialized resources. Step 10 - Transmembrane Region Analysis searches for domains characteristic of a membrane spanning protein (e.g., alternating hydrophobic and hydrophilic regions). Step 11 - Cellular Localization analyzes the C-terminal end of the protein sequence for characteristic signal peptide sequences. This gives an indication of where the protein product is located in the cell. Step 12 Secondary Structure Analysis identifies sequence patterns characteristic of secondary structure elements. Secondary structure refers to the first level of structural conformation, consisting of alpha helices and beta sheets. While these structures are not directly related to function, the finding of certain structural elements can be predictive of a particular structural feature, which in turn would relate to function. Step 13 - Threader Analysis bases the analysis not only on sequence identity or similarity, but also on the chemical characteristics of each amino acid residue in the sequence. If two amino acids have similar chemical properties, then they may behave similarly; therefore protein sequences that are similar at the chemical (although not the sequence) level may also share similar function. In the data flow diagram, these five steps are shown in parallel, since they all share common input data the novel amino acid sequence. Each of the five steps has its own particular type of output data (e.g., a hydrophobicity plot from Step 10 Transmembrane Region Analysis or a secondary structure profile from Step 12 - Secondary Structure Analysis). None of these

Step 1 - Contig Assembly

Description Obtains the full length of a sequence, either by searching for it, or by putting smaller pieces of sequence together Predicts the open reading frame Converts nucleic acid sequence to amino acid sequence Looks for similar sequences Choice between multiple alignment path or domain/motif path Compares two or more sequences to identify and align areas of sequence identity Suggests the evolutionary relationship between genes Choice between one-step and multistep approach to domain/motif analysis Looks for sequence patterns characteristic of known structures or functions Identifies regions of sequence likely to form transmembrane regions Predicts the location in the cell of the protein produced by the gene Identifies secondary structure elements (e.g., alpha-helix, beta-sheet) elements that form the basis of the three-dimensional structure of the protein Finds similarity based on chemical characteristics of each sequence component (amino acid), rather than on sequence alone Identifies characteristics (chemical, structural and functional) of the putative protein

2 - ORF Prediction 3 - Translation 4 - Homology Searching 5 - Decision Point 1 6 - Multiple Alignment 7 - Phylogenetic Analysis 8 - Decision Point 2 9 - Domain/motif Analysis 10 -Transmembrane Region Analysis 11 - Cellular Localization 12 - Secondary Structure Analysis

13 - Threader

14 - Protein Profile

Step 5 - Multiple Alignment Path vs. Domain/Motif Path defines the first of the two major decision points in the protocol. The two alternate pathways at this point are named for their respective first steps. The Multiple Alignment Path focuses subsequent analysis on the intact sequence, and compares it with other, intact sequences. The goal is to compare similar sequences, and to base the prediction of function on the similarities to other, known proteins. This approach relies on the presence of related sequences in repository databases. The Domain/Motif Path is based on the analysis of fragments (domains) of the novel sequence, rather than the complete sequence. The goal is to identify patterns within the novel sequence which match domains or motifs associated with

outputs serve as inputs for subsequent steps instead, all are considered together in the analysis of the putative function of the gene. Step 6 - Multiple alignment compares two or more sequences to identify and align areas of sequence identity Why? must have two or more sequences known or suspected to be related helpful if at least some have been characterized but not essential areas of identity may be functionally significant if conserved within a protein family or through evolution useful if moderate homology (30-50%) found, indicating that there are some areas of high homology in the sequences useful if common areas fall within known domain/motif regions Tools CLUSTALW Entrez Input amino acid sequence for each protein of interest (typically in FASTA format) Output graphical representation of the alignment of the sequences with the areas of identity highlighted text file of the alignment, which can be viewed with corresponding viewing tools gaps may have been introduced into the sequences in order to permit alignment these are also indicated Interpretation conserved residues are more likely to have some functional significance flags region for more detailed analysis ID region as a domain, even if that particular sequence has not previously been characterized Are conserved residues known to be associated with a particular function? (i.e., Are some of the proteins in the alignment already characterized?). If so, then that function is likely in the novel protein Next steps analyze conserved regions in more detail phylogenetic analysis go to the lab to test/verify the putative function Caveats not all "conserved" regions are of importance - some may be artifacts of the alignment process Step 14 - Protein Profile Analysis has the same objective as the five steps of the Multi-Step Domain/Motif Path, but accomplishes the analysis in a single step. The bioinformatics resources that are used for Protein Profile Analysis do information retrieval at various levels, identifying possible structural and functional motifs, as well as chemical and physical characteristics of the protein. This step also has the novel amino acid sequence as its input, and generates a profile of the protein as output. The three pathways in the protocol merge at the point of predicting the putative function of the novel gene, and conclude with testing the putative function in the laboratory. The steps are arranged in the diagram with respect to the flow of data. In some parts (Steps 1-4 and 6-7), the data flow matches the order in which an individual would manually conduct the analysis. The steps would be done in sequence, with the output data from one step serving as the input data for the next. However, in the case of Steps 9-13, the data flow and the manual analysis do not match. From a data flow perspective, these five steps are viewed in parallel; all have the same input, and the output from each is analyzed at a single point. However, an individual doing this analysis manually would conduct each analysis in order. This is due to the limitations of not being able to manually conduct multiple analyses at once, short of running several computers. With the objective of automating the process, the sequential arrangement of Steps 9-13 is an artifact, and the parallel approach is a better reflection of the process. In addition to the relationship among the steps shown in the flowchart, the protocol also includes considerable detail for each step. For the twelve analytical steps (1-4, 6-7, 9-14), the following information is detailed: the rationale for the analysis, the bioinformatics resources used, the data input and output, how the results should be interpreted, what steps should be followed next, and any caveats to consider in doing the analysis or applying the results. An example of the detail (for Step 6 - Multiple Alignment) is shown in Figure 2. The protocol also includes detail for Steps 5 and 8, the two major decision points. These describe the type of information that would be obtained by doing the analysis, and the reasons for choosing one path over another.

4. DISCUSSION
The systematized approach described in this protocol pulls together a myriad of individual analyses and forms the potential for a semiautomated (and potentially fully automated) process. It has documented a complex process that has previously been within the realm of oral tradition. It also provides a foundation for an information retrieval system to make the process explicit and approachable by laboratory scientists. One element of the protocol is the linking of data flow among the various analyses. By documenting how data flows and is manipulated and transformed through the process, this provides a basis for the partial, and potential full automation of the protocol. It may be possible to enter a novel DNA sequence, and have an information system process and analyze that sequence to generate the final output data that currently takes several steps to generate. The factors that currently limit the full automation of the process

Figure 2. Detail for Step 6 - Multiple Alignment

are likely to be minimized in the future. Among these are an absence of clearly defined, empirically tested parameters (such as those that exist as part of clinical decision trees in medicine) for making decisions about results. Automation is also limited by the current state of the art in bioinformatics, with, for example, databases containing sequence data that may be erroneous. Bioinformatics research typically focuses on one particular algorithm or type of analysis, but the application of bioinformatics analysis to solve a laboratory problem involves multiple analyses. The protocol described here shifts the focus towards both the user and the task. The task-orientation links together the twelve different analyses that can be applied to the functional analysis of a gene sequence. The explicitly integrated approach helps to mitigate the challenge currently facing scientists, that of knowing what information to look for, and where and how to obtain it. Likewise, the user-focus is also important. The value of an information retrieval system is in its ability to provide the information required by those using it. The system should be designed to be responsive to the needs of the users, rather than the other way around. Since human decision-making remains an integral part of the protocol, the detailed description for each step provides as much information as possible to guide, direct and support the decision-making process. The details of each step also provide the link between the bioinforamtics analysis and the laboratory, by specifying how the information obtained at each step can be applied to interpreting the biological problem. Finally, the validation of the protocol reinforces its applicability beyond the original group of participants. Both cohorts of participants (interview and validation test) felt that the protocol would be applicable in both their own and other research contexts, supporting the intention of developing the protocol for use in other research settings. What remains is to develop and test the effectiveness of an information retrieval system based on the protocol.

contributions of her supervisor, Dr. Elaine G. Toms, Faculty of Management, Dalhousie University, and committee members Dr. Joan M. Cherry, Faculty of Information Studies, University of Toronto, and Dr. Chris W.V. Hogue, Department of Biochemistry, University of Toronto. This research was partially funded by a Natural Sciences and Engineering Research Council (Canada) grant held by E. G. Toms.

7. REFERENCES
[1] And rade, M. (Ed.). Bioinform atics and Gen omes: Current perspectives. Horizo n Scientific Press, W ymondham, (200 3). [2] Annett, J., K. D. Duncan, R. B. Stammers, and M. J. Gra y, Task Analysis. H.M.S.O., Londo n, (1971). [3] Bartlett, J. C., Understanding how experts use bioinformatics resources. Proceedings of the 29th Annual Canadian Association for Information Science Conference, 297-306, (2001). [4] Bartlett, J. C., and E. G. Toms, Capturing and modeling the research process of bioinformatics experts: and integrated information behavior and task analysis approach, Journal of the American Society for Information Science and Technology. (2004). in press. [5] Baxevanis, A. D., and D. B. Davison, eds., Current Protocols in Bioinformatics, Wiley (2002).[On-line]. [6] Butler, D. Are you ready for the revolution? Nature, 409, 758-60 (2001). [7] Hackos, J. T., and J. C. Redish, User and Task Analysis for Interface Design, Wiley, New Y ork (1998). [8] Hersh, W., and J. Pentecost, A task-oriented approach to information retrieval evaluation, Journal of the American Society for Information Science, 47(1), 50-56 (1996). [9] Kirwan, B ., and L. K. Ainsworth, eds., A G uide to Task Analysis, Taylor and Francis, London (1992 ). [10] Marchio nini, G., Informa tion S eekin g in E lectron ic Environ ments, Cambridge University Press, Cambridge (1995). [11] Vakkari, P ., Task-based informatio n searc hing, Annual Review of Information Science and Technology, 37, 413-464 (2003). [12] Vicente, K . J., Cognitive Work Analysis: Toward Safe, Prod uctive an d He alth Co mputer-Ba sed Work, Lawrence Erlbaum A ssociates, Mahwa h, NJ (1999 ).

5. CONCLUSIONS
This research has resulted in the development of a task-based and user-oriented protocol describing the application of bioinformatics information search and retrieval to the problem of functionally analyzing a gene sequence. The protocol forms the foundation for an information retrieval system that will support the functional analysis of a gene sequence. The task-based approach links the use of multiple analyses and resources into an integrated process that relates directly to a scientific problem. The user-focus complements and enhances research into the development and refinement of bioinformatics resources, and provides an approach to making these resources more easily accessible to laboratory scientists.

6. ACKNOWLEDGEMENTS
This work was conducted as part of the author's dissertation research. She would like to acknowledge the advice and