The process of domestication of the chicken had knowingly and unknowingly employed genetics to achieve human perceived changes in economic traits such as growth and egg production. These changes sometimes resulted in negative side effects, such as a physiological delay in sexual maturity observed in a line of White Plymouth Rock chickens selected for low body weight. These chickens plateaued after about 30 generations of selection possibly due to a conflict between survival/reproduction and the selection for slow growth. Yet, the even smaller red junglefowl seem to be free of such physiological barriers. Here, data are presented for reproductive, growth, and behavioral traits for the Richardson strain of red junglefowl, a line of White Plymouth Rock chickens that has undergone 57 generations of selection for 8-week body weight and their F1 and F2 reciprocal crosses. While exploring the physical and genetic differences between domestic chickens, as well as the genetic basis for the striking differences in growth patterns between the two lines, observed was plasticity and considerable residual genetic variation which likely facilitated the adaptability of the chicken to a broad range of husbandry practices. Differences in growth patterns implied additive and non- additive genetic variation and modifications in resource allocation strategies during domestication. / PHD / The use of intensive genetic selection and heterosis in breeding programs since the end of World War II has contributed to poultry industry achievements of high economic production. This has come about through increased feed efficiency, greater processing yield, shorter generation intervals, and improvements in growth rates of commercial populations. However, with these improvements there has been a 50% decrease in genetic diversity in commercial pure lines in comparison to their ancestors. This change has been attributed to the limited number of commercial primary breeders and increased inbreeding. Animals in populations that have been through intense selection for high and efficient production may be more at risk for physiological, and immunological issues. This dissertation addresses the relationship between the junglefowl and the domestic chicken with regard to these issues through a three-generation quantitative and molecular analysis.

Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. HGT is a mechanism that plays a significant role in prokaryotic evolution and leads to biodiversity in nature. One of the important components of HGT is the genomic island (GI) which is a subsequence of the genome created by HGT. This research aims to identify the structures of the prokaryotic GIs that have a fundamental role in the adoption of prokaryotes and the impact of the species on the environment. Previous computational biology research has focused on developing tools that detect GIs in prokaryotic genomes, while there is little research investigating GI structure. This research introduces a novel idea that has not yet been addressed intensively, which is identifying additional structures of the GIs in prokaryotes. There are two main directions in this research used to study the prokaryotic GIs structure from each different perspective. In the first direction, the aim is to investigate GI patterns and the existence of biological connections across bacterial phyla in terms of GIs on a large scale. This direction mainly aims to pursue the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families across many species. A pattern is a sequence of protein families that is found to frequently occur in the genomes of a number of species. Here the large data set available from the IslandViewer4 database and protein families from the Pfam database have been combined. Furthermore, implementing a comprehensive strategy to identify patterns that makes use of HMMER, BLAST, and MUSCLE; also implement Python programs that link the analysis into a single pipeline. Research results demonstrate that related GIs often exist in multiple species that are not evolutionarily related and indeed may be from multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages through their GIs. A connection is an HGT relation represented as a pattern that exists in a phage and a number of prokaryotic species. These discovered connections suggest quite broad HGT connections across the bacterial kingdom and its associated phages. In addition, these connections provide the basis for additional analysis of the breadth of HGT and the identification of individual HGT events that span bacterial phyla. Moreover, these patterns can suggest the basis for discovering the specific patterns in pathogenic GIs that could play a crucial role in antibiotic resistance. The second direction aims to identify the structure of the GIs in terms of their location within the genome. Prokaryotic GIs have been analyzed according to the genome structure that they are located in, whether it be a circular or a linear genome. The analysis is performed to study the GIs' location in relation to the oriC, investigating the nature of the distances between the GIs, and determining the distribution of GIs in the genome. The analysis has been performed on all of the GIs in the data set. Moreover, the GIs in one genome from each species and the GIs of the most frequent species are in the data set, in order to avoid bias. Overall, the results showed that there are preferable sites for the GIs in the genome. In the linear genomes, they are usually located in the origin of replication area and terminus, and in the circular genomes they are located in the terminus. / Doctor of Philosophy / Prokaryotes are one of the most abundant species on earth that play an essential role in naturally shaping the planet and its life. This research aims to identify the structure of a component in these species that has a fundamental role in the adoption of prokaryotes and the impact of the species on the environment. This component is a part of the genome named the genomic island (GI). This dissertation aims to identify the structure of the GIs in two different ways that have not yet been addressed extensively. The first direction aims to discover patterns in the GIs and then use them to bring to light biological connections between prokaryotic and bacteriophages. In this direction, a comprehensive strategy has been utilized to identify patterns and connections. This strategy uses several tools such as BLAST, HMMER, and MUSCLE. Furthermore, Python programs that link the analysis into a single pipeline have been implemented. In the second direction, an investigation has been performed to understand the nature of the GIs' locations within the genome. This direction addresses three different analysis techniques to achieve its target. The three analyses are studying the GIs' location in relation to the origin of replication, investigating the nature of the distances between the GIs, and discovering the location distribution of GIs in the genome. The analysis is performed on linear genomes and circular genomes separately. In each group of GIs, the data set has been utilized to see the results from different perspectives. The overall analysis in both directions relived several findings. In the first direction, the discovered patterns merit deep investigation based on the possibility that they are related to diseases. In addition, in prokaryotic genomes, there are specific sites where the GIs can be frequently seen that need further search to understand the relation between the GIs' location and the content of the GI in terms of proteins.

Dark Patterns are a variety of different software designs that are used to manipulate and mislead the users of an application or service. These patterns range from making it harder to end a subscription service, adding additional charges to a purchase, or having the user give out data or personal information. With how widespread and varied dark patterns are, it led to us creating a way to detect and warn users of different dark patterns. In this study, we created Dark Pattern Detector, a Chrome extension that would help users detect and understand three different dark patterns: Hidden Costs, Disguised Ads, and Sneak into Basket. This extension was made to detect each of these patterns on any web page while not requiring any information from the user or their data. Study participants installed the extension and completed a series of tasks given to them that would occur on different websites containing the previous dark patterns. After completing the tasks, the users were surveyed to give feedback on what they thought of the extension and what suggestions for change they had. In the study, we had 40 participants and we found that 50% of the users were completely unfamiliar with dark patterns and that 77.5% have used extensions before. For the five tasks, each one had a majority of the participants successfully complete them. Finally, when asked about what they thought, the majority of the participants gave positive feedback claiming that they found the extension useful, interesting, and a good idea. Many participants also gave useful feedback about what changes or additions they would like to see. With our results, we can help users have a better understanding of dark patterns and have created a baseline for any future research done on dark pattern knowledge and detection. / Master of Science / Dark patterns are designs on the internet that websites use to trick its users. They may be used to hide advertisements, make the user spend more time or money on their website or more. Our goal was to create a way to help protect anyone on the internet and their information. For this study, we created a program called Dark Pattern Detector that would help the users see different dark patterns that appeared on websites. A study was conducted that had the participants use our program and give us feedback on what they thought of it as well as data on how well it worked. Out of the 40 participants, we found that half the users were unfamiliar with what dark patterns were. Once they completed the study, we saw that the majority of users were able to complete tasks while using our program and gave positive feedback. Seeing the positive feedback and results from our study, we believe that we can help users not get tricked by these patterns and help forward future research on Dark Patterns.

Background: Dietary patterns that include recommended servings of fruits, vegetables, whole grains, dietary fiber, and dairy, combined with regular physical activity and frequent breakfast consumption are optimal choices for weight loss or weight maintenance over time. College students are at an increased risk for weight gain due to environmental and behavioral changes that are associated with decreased dietary quality and physical inactivity. Preventing weight gain in college students may have a profound impact on prevalence of overweight or obesity later in life. Objective: To examine associations between weight change and dietary patterns in college students. Design: A longitudinal observational study. Dietary intake and physical activity were self-reported on seven-day food records and compared to dietary guidelines for compliance with recommendations. Subjects/Setting: Data from 80 students enrolled in a fall semester introductory nutrition course at a large state university were analyzed in the fall and spring semester . Main outcome measures: Daily servings of total fruit (fruit and juice), total vegetables (fried and non-fried), dairy (regular and low-fat), whole grains, and dietary fiber, breakfast consumption, body weight changes and physical activity. Statistical Analysis Performed: Associations between diet quality and weight change were analyzed using Chi-square analysis. Weight change was analyzed by diet quality and breakfast consumption using t-test and by metabolic equivalents (METHRS/day) using one-way analysis of variance (ANOVA) (p<0.05). Significant associations were analyzed by Pearson's correlation (two-sided, p<0.05). Results: Weight and body mass index (BMI kg/m2) were significantly higher compared to baseline. The majority of students did not meet recommendations for daily servings of fruit, vegetable, dairy, whole grains, and dietary fiber. Higher diet quality was significantly associated with more frequent breakfast consumption and students who maintained or lost weight reported significantly higher intakes of total fruit, low-fat dairy and whole grains. Conclusion: Failure to meet dietary guidelines resulting in lower diet quality was distinctive of this population and was associated with significant changes in body weight over one academic year. Applications: Educational interventions aimed at improving diet quality may inhibit weight gain commonly seen in college students. / Master of Science

Childhood (ages 2-9 years) and adolescence (ages 10-19 years) make up important periods of human life. Food preferences and dietary behaviors are developing during this time, and health status can impact noncommunicable disease (NCD) risk in adulthood. Many of the behaviors associated with developing NCD are modifiable and include dietary behaviors. Globally, children and adolescents are impacted by NCD, and obesity prevalence is growing among this population. One of the recommendations for combating obesity is to promote the consumption of healthy foods and beverages and the reduction of sugar-sweetened beverage intake. In order to assess beverage patterns, the Healthy Beverage Index (HBI) was created for adults. This tool provides a score from 0-100, with higher scores indicating better adherence to evidence-based beverage recommendations. Because many beverage recommendations for children and adolescents differ from those for adults, the purpose of this thesis was to develop the HBI for U.S. Children and Adolescents (HBI-CA). National Health and Nutrition Examination Survey (NHANES) data was used to calculate HBI-CA scores among a sample of U.S. children and adolescents. The HBI-CA resulted in scores similar to the adult HBI and provides a reference of beverage pattern quality in this population. Significant differences in scores were found among males and females and certain races. Evaluation of the HBI-CA demonstrated its construct validity and reliability. The HBI-CA still needs to undergo predictive validity tests. Overall, the HBI-CA provides a method to assess beverage pattern quality in clinical, public health, and research settings for this important population. / Master of Science / Children (ages 2-9 years) and adolescents (ages 10-19 years) makeup an important population for the implementation of dietary interventions because they are still developing their food preferences and dietary behaviors. The rise of obesity among these age groups indicates that their dietary behaviors may not be aligned with recommendations. Beverages can easily be overlooked as a dietary component, but they currently constitute a large portion of daily energy intake. In order to assess beverage pattern quality in this population, the Healthy Beverage Index for U.S. Children and Adolescents (HBI-CA) was developed based on the HBI for adults. This tool provides a score from 0-100, with higher scores indicating better adherence to evidence-based beverage recommendations. The HBI-CA also provides a resource of comprehensive beverage recommendations for these age groups, which was previously limited in the literature. National Health and Nutrition Examination Survey (NHANES) data was used to calculate HBICA scores among a sample of U.S. children and adolescents. The HBI-CA resulted in scores similar to the adult HBI and provides a reference of beverage pattern quality in this population. Significant differences in scores were found among males and females and certain races. Evaluation of the HBI-CA demonstrated its ability to reliably and consistently measure beverage pattern quality. Future evaluation of the HBI-CA should include examination of the relationship between HBI-CA scores and dietary-related health outcomes. Overall, the HBI-CA provides a method to assess beverage pattern quality in clinical, public health, and research settings for this important population.

Master of Architecture / This thesis explores the transformative potential of designing spaces that prioritize healing, connection, and mindfulness, especially for those with post-traumatic stress disorder (PTSD). It uses intentional design choices like natural light, wood, water, and granite to create a relaxing and grounding environment. Geometric Islamic patterns are incorporated to enhance visual appeal and provide a sense of order. By prioritizing healing, connection, and mindfulness, we can create spaces that alleviate PTSD symptoms and empower individuals on their journey towards healing and well-being.

Yes / Within river systems, the process of bed-forming is intricate, dynamic and is shaped by different factors. Hydraulic forces exerted by water flow play a crucial role, forming the bed substrate over time. Additionally, the presence of vegetation within the riverbed and along its banks introduces further complexity, as the interaction between plants and hydrodynamics can alter sediment transport patterns and riverbed morphology. The movement of both suspended particles and bedload materials within the water column contributes to the ongoing riverbed landscape evolution. The primary aim of this editorial collection is to assemble an extensive range of research methodologies aimed to inform engineering practices pertinent to river management. Through an exhaustive exploration of various topics, including water quality indexing, erosion and sedimentation patterns, influence of vegetation, hydrological modelling for understanding flow dynamics, and identification of critical hydraulic parameters with the utilisation of both analytical and experimental modelling techniques, this paper endeavours to provide valuable insights derived from rigorous research efforts. By synthesising and presenting these findings, we offer a resource that can effectively guide future endeavours in river engineering and related disciplines.

Five species of stoneflies (Zapada haysi, Plumiperla diversa, Taenionema pacificum, Isoperla petersoni, Arcynopteryx compacta) from the North Slope and Interior of Alaska were examined for seasonal patterns of emergence of adults and growth of nymphs. Generally growth was retarded during the winter in this region, and all species except I. petersoni completed growth prior to January. The life cycles of six stonefly species (Prostoia besametsa, Triznaka signata, Sweltsa coloradensis. Isoperla fulva, Skwala parallela, Claassenia sabulosa) are described from northern New Mexico. In this region growth was generally less retarded during the winter than in Alaska; P. besametsa completed all nymphal growth during late fall and winter. Drumming behavior of a Colorado population of Pteronarcella badia was described using an evolutionary framework to explain the maintenance of signal variation in this species. Laboratory experiments were used to explore the effect of intraspecific and interspecific interactions on spatial partitioning in P. badia and Claassenia sabulosa. P. badia exhibited clumping and distributed itself as the surface area of substrate in low densities; however, in the presence of C. sabulosa its distribution was random and different from available surface area. A field study was used to examine spatial partitioning by three New Mexico stonefly species (I_. fulva, P. besametsa, T. signata) and to ascertain patterns of microdistribution relating to several abiotic and biotic factors. Generally, there was an interaction of the measured abiotic parameters (current, water temperature, time) with nymphal size. Additionally, void space and sample volume were successfully used to compare biotic densities among leaf and mineral substrates, which were higher in leaf packs than in mineral substrates.

Sunlight is a multidimensional phenomenon that influences occupant’s comfort and well-being through its dynamic visual and thermal attributes. Previous studies suggested that the presence of sunlight patterns in space was cheering and visually interesting, which could improve visual comfort and space quality. However, it remains unclear what the attributes of visually interesting sunlight patterns are, and whether their visual interest influences visual comfort. This dissertation aims to answer three main questions: (1) is there a difference in visual interest and mood response among different projected light patterns? (2) How do sunlight patterns of different geometries influence visual interest and visual comfort in offices? And (3) what are the geometrical attributes of sunlight patterns that should be implemented in office spaces? To address these questions, a series of four studies were conducted. The first two studies extended empirical findings on visual interest and mood responses elicited by varying complexities of fractal and non-fractal light patterns projected on walls and floors of an interior space. These two studies determined which patterns to be further examined in Studies 3 and 4, which investigated the visual comfort, visual interest of sunlight patterns, and view quality under three different window conditions in office spaces. The results of studies 1 and 2 suggested that fractal light patterns of medium to medium-high complexity, quantified by the fractal dimension in the range (D=1.5-1.7), were significantly more visually interesting than other patterns. Both studies found that fractal compared to non-fractal light patterns provided a better balance between relaxation and excitement. Study 3 found that the fractal pattern was associated with a significant increase in visual comfort, compared to the striped pattern, though the difference in visual interest between the two patterns was not statistically significant. Study 4 found that the effect of the fractal pattern on visual comfort, visual interest of sunlight patterns, and view quality was dependent on occupant’s view direction and façade orientation. These findings can have implications for the design and control of facade systems to improve occupant’s visual comfort, interest, and view quality in work environments. This dissertation includes both previously published/unpublished and co-authored material. / 2019-01-27

Mining frequent patterns is an important component of many prediction systems. One common usage in web applications is the mining of users' access behavior for the purpose of predicting and hence pre-fetching the web pages that the user is likely to visit. Frequent sequence mining approaches in the literature are often based on the use of an Apriori-like candidate generation strategy, which typically requires numerous scans of the potentially huge sequence database. In this paper we instead introduce a more efficient strategy for discovering frequent patterns in sequence databases that requires only two scans of the database. The first scan obtains support counts for subsequences of length two. The second scan extracts potentially frequent sequences of any length and represents them as a compressed frequent sequences tree structure (FS-tree). Frequent sequence patterns are then mined from the FS-tree. Incremental and interactive mining functionalities are also facilitated by the FS-tree. As part of this work, we developed the FS-Miner, an system that discovers frequent sequences from web log files. The FS-Miner has the ability to adapt to changes in users' behavior over time, in the form of new input sequences, and to respond incrementally without the need to perform full re-computation. Our system also allows the user to change the input parameters (e.g., minimum support and desired pattern size) interactively without requiring full re-computation in most cases. We have tested our system using two different data sets, comparing it against two other algorithms from the literature. Our experimental results show that our system scales up linearly with the size of the input database. Furthermore, it exhibits excellent adaptability to support threshold decreases. We also show that the incremental update capability of the system provides significant performance advantages over full re-computation even for relatively large update sizes.