C. elegans is a commonly used genetic model organism due to the ease of genetic screens, transgenesis, and microscopy. Here, I describe methods that improve transgenesis in C. elegans and the development of a genetic screen to identify genes involved in the piRNA pathway. Transgenesis is commonly used for most laboratories that utilize C. elegans and improvements are therefore likely to facilitate research across many research areas. In the first chapter, I characterized a pan-muscular promoter that drives fluorophore expression to help identify C. elegans transgenesis. This promoter is an improved co-injection marker as it drives bright fluorescence with low toxicity and high efficiency. In the second chapter, I study piRNAs which are a large class of non-coding RNA that play important roles in protecting the genome from transposable elements in most animals. The study of piRNAs has mostly focused on their function in the germline, but recent evidence suggests functions in somatic cells such as neurons. To identify genes involved in the piRNA pathway in C. elegans, I performed a chemical genetic screen. I identified one mutant with a somatic phenotype and six mutants with a germline phenotype. I have focused on the germline and sequenced two strains and identified candidate genes involved in the piRNA pathway. Future work will focus on validating and identifying the remaining mutants.

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Indiana University-Purdue University Indianapolis (IUPUI) / Chlamydia trachomatis is an obligate intracellular bacterial pathogen that can infect the eyes, genital tract, and disseminate to lymph nodes in humans. Many C. trachomatis infections are clinically asymptomatic and can become chronic if left untreated. When humans are infected with C. trachomatis, a cytokine that is produced is interferon-gamma (IFN-γ). In vitro, IFN-γ stimulates expression of the host enzyme indoleamine 2,3-dioxygenase. This enzyme converts free intracellular tryptophan to N-formylkynurenine. Tryptophan starvation induces C. trachomatis to enter a viable-but-nonculturable state termed persistence, which has been proposed to play a key role in chronic Chlamydial disease. To circumvent host induced tryptophan depletion, urogenital strains of C. trachomatis encode a functional tryptophan synthase (TS). TS synthesizes tryptophan from indole and serine, allowing Chlamydia to reactivate from persistence. Transcriptomic analysis revealed C. trachomatis differentially regulates hundreds of genes in response to tryptophan starvation. However, genes that mediate entry, survival, and reactivation from persistence remain largely unknown. Using a forward genetic screen, we identified six Susceptible to IFN-γ mediated Persistence (Sip) mutants that have diminished capacities to reactivate from persistence with indole. Mapping the deleterious persistence alleles in three of the Sip mutants revealed that only one of the mutants had a mutation in TS. The two other Sip mutants mapped had mutations in CTL0225, a putative integral membrane protein, and CTL0694, a putative oxidoreductase. Neither of these genes plays a known role in tryptophan synthesis. However, amino acid (AA) competitive inhibition assays suggest that CTL0225 may be involved in the transport of leucine, isoleucine, valine, cysteine, alanine, and serine. Additionally, metabolomics analysis indicates that all free amino acids are depleted in response to IFN-γ, making this amino acid transporter essential during persistence. Taken together we have identified two new chlamydial persistence genes that may play a role in chronic chlamydial disease.

People are nomadic; traveling from place to place. As a user travels, he may need access to his digital information, including his data, applications, and settings. A convenient way to supply this access is to have the user carry that digital information in a portable computer such as a laptop or smart phone. As Moore's Law continues to operate, devices such as smart phones can easily perform the computing necessary for a user's work. Unfortunately, the amount of data a human can receive and convey through such devices is limited. To receive more information humans require more screen real estate. To transmit more information humans need rich input devices like mice and full-sized keyboards. To allow users to carry their digital information in a small device while maintaining opportunities for rich input, this research takes the approach of allowing users to carry a small portable device and then annex screens, keyboards, and mice whenever those devices are available in a user's environment. This research pursued the "carry it with you" paradigm first by building an ideal annexing framework which helps maximize the screen real estate while minimizing the resources—RAM, CPU, and wireless radio—consumed on the personal device. The resource consumption is demonstrated through a comparison with existing remote rendering technologies. Next, a privacy-aware framework was added to the annexing framework to help protect the user's sensitive data from damage and theft when he annexes a potentially malicious device. A framework like this has not existed before, and this research shows how the user's sensitive data is protected by this framework. Third, legacy machines and software are allowed to participate in the carry-it-with-you experience by scraping pixels from the user's existing applications and transmitting those pixels to an annexed display. Finally, when a user encounters a display space he does not own, but which he needs to control (e.g. by preventing anyone else from annexing it simultaneously, or by constraining each user to a different section of the display space), rather than forcing the user to learn and use control software supplied by the display, the user can bring his own control software and use it to enforce the user's desired control paradigm. This dissertation shows the carry-it-with-you paradigm is a powerful potential avenue which allows users to confidently use display spaces with varying configurations in an assortment of environments.

Purpose: The present investigation was conducted to assess the relationship between television viewing time and cardiorespiratory fitness. Design: Cross-sectional. Setting: Intermountain West. Participants: 302 middle-aged women. Method: TV viewing was assessed using a questionnaire. Cardiorespiratory fitness was measured using a maximal graded treadmill test. Physical activity (PA) was evaluated using Actigraph accelerometers worn over seven consecutive days, while body fat percentage (BF%) was measured using air displacement plethysmography (Bod Pod). Results: (Mean ± SD) age: 40.2 ± 3.0 years. VO2max of the frequent (≥ 3hrs/day) TV group (32.6 ± 6.4) was significantly lower than both the moderate (1-2 hrs/day) (36.2 ± 7.2) and infrequent (<1hr/day) (36.5 ± 6.5) TV groups (F = 8.0, P = 0.0004). The infrequent and moderate groups did not differ significantly from each other. Differences in age, education, BMI, and season of assessment had no influence on the relationship when controlled individually. Adjusting for differences in physical activity (F = 4.2, P = 0.0157) weakened the relationship by 59.4%, and adjusting for differences in BF% (F = 5.0, P = 0.0071) weakened the association by 58.5%, but in both cases, the relationships remained significant. After controlling for both PA and BF% simultaneously (F = 2.9, P = 0.0572), the relationship was weakened by 80.7% and was only borderline significant. Conclusion: Frequent female TV viewers have significantly lower cardiorespiratory fitness levels than moderate or infrequent viewers. This association appears to be largely a function of differences in both PA and BF%.

Background: Movement screens are frequently used to identify abnormal movement patterns that may increase risk of injury and/or hinder performance. However, abnormal patterns are often detected visually based on the observations of a coach or clinician leading to poor inter- and intrarater reliability. In addition, they have been criticized for having poor validity and sensitivity. Quantitative, or data-driven methods can increase objectivity, remove issues related to inter-rater reliability and offer the potential to detect new and important features that may not be observable by the human eye. The combination of motion capture data, pattern recognition and machine learning could provide a quantitative method to better assess movement competency. Purpose: The purpose of this doctoral thesis was to create the foundation for the development of an objective movement screening tool that combines motion capture data, pattern recognition and machine learning. This doctoral thesis is part of a larger project to bring an objective movement screening tool for use in the field to market. Methods: This thesis is comprised of four studies based on a single data collection and a common series of pre-processing steps. Data from 542 athletes were collected by Motus Global, a for-profit biomechanics company, with athletes ranging in competition level from youth to professional and competing in a wide-range of sports. For the first study of this thesis, an online software program was developed to examine the inter- and intra-reliability of a movement screen, with intrareliability being further examined to compare reliability when body-shape was and was not modified. The second study developed the objective movement screen framework that utilized motion capture, pattern recognition and machine learning. Study 3 and 4 assessed different types of input data, classification goals (e.g., skill level and sport played), feature reduction and selection methods, and increasingly complex machine learning algorithms. Results: For Study 1, when looking at inter- and intra-rater reliability of expert assessors during subjective scoring of movements, intra-rater reliability was better than inter-rater reliability. When assessing the effects of body-shape, on average, reliability worsened when body-shape was manipulated. Study 2 provided proof-of-principle that athletes were able to be classified based on skill level using marker-based optical motion capture data, principal component analysis (PCA) and linear discriminant analysis. For Study 3, PCA in combination with linear classifiers outperformed non-linear classifiers when classifying athletes based on skill level; feature selection increased classification rates, and classification rates when using simulated inertial measurement unit data as the input data were on average better than when using marker-based optical motion capture data. In Study 4, athletes were able to be differentiated based on sport played and recurrent neural nets (RNNs) and PCA in combination with traditional linear classifiers were the optimal machine learning algorithms when classifying athletes based on skill level and sport played. Conclusion: This thesis demonstrates that objective methods can differentiate athletes based on desired demographics using motion capture, pattern recognition and machine learning. This thesis is part of a larger project to bring an objective movement screening tool for field-use to market and provides a solid foundation to use in the continued development of an objective movement screening tool.

PURPOSE: Television (TV) viewing remains a popular form of screen time for adults. However, it is important to understand the obesity risks associated with other screens, not only TV, in a changing media landscape. This study aimed to examine the association between energy intake, BMI, and screen time using the data obtained from the AIM-2 wearable camera. METHODS: The AIM-2 device was used by (n=18) participants for seven consecutive days. Three days of images from the device were analyzed for energy intake, and 1 of these days was coded for screen use (i.e., TV, phone, and computer), the number of screens, and screen duration while eating. A preliminary analysis of screen use in relation to BMI and energy intake was conducted. Potential confounders (age, sex, race, ethnicity, marital status, and education level) were considered. RESULTS: Phones were the most used screen type, and TV alone was not watched by any participants. While eating, screens were used 73% of the time. Participants with the highest screen time usage consumed more total energy than those with the lowest screen time usage (p<0,.05). This difference was attenuated when controlling for duration of eating, perhaps suggesting that higher screen time usage may lead to an extended eating duration and, thus, higher intakes of energy. There were no statistically significant associations between any screen time variable (type, duration, or number of screens used) and BMI. Screen time usage was examined during four time periods: before 11:00 am; 11:00 am-2:59 pm; 3:00 pm-7:59 pm; 8:00 pm, and later. There was a statistically significant positive association between higher screen time after 8:00 pm and total daily energy intake (P=0.005). CONCLUSION: Eating while using a screen can be objectively assessed using the AIM-2 device. Our data agree with recent studies showing that phones and computers are used more than TV. While there were no significant associations between any of these screen variables and BMI, data from a single day in this study suggests that those with the highest screen time usage tended to have higher energy intakes. In addition, there was also a statistically significant association between screen time usage while eating later in the evening (after 8:00 pm) and total daily energy intake. These preliminary results should be interpreted with caution due to the small sample size and the availability of only one day of screen use and energy intake. Future studies should examine more than one day and use wearable cameras for objective evaluations of screen use.

Research suggests that elevated levels of screen time in the evening can negatively impact sleep outcomes (sleep duration, quality, and latency). Yet, there is a lack of evidence exploring if this relationship exists in college students. The purpose of this study is to investigate the relationship between evening screen time use and objectively measured sleep outcomes in US college students. College students (N = 29) junior or senior standing in a Health Sciences major were recruited to participate in this cross-sectional study. Participants wore accelerometers on their wrist for 24hr/day for seven days to capture sleep duration, efficiency, awakenings, and timing. Participants completed a survey regarding their screen time habits and evening usage. Twenty-nine college students (86% female, averaged 21.5 years old, 38% White, 35% Overweight/Obese) provided valid accelerometer data. There were 180 total valid night sleep observations. Average nighttime sleep duration was 433.8 minutes with an average of 22.3 awakenings. The mean sleep efficiency was 87.3%. The average bedtime was 2:26 am, and the average wake time was 8:01 am. The average daily screen time of participants was 419.1 minutes, and after 10:00 pm was 112.2 minutes. Cell phone use before bed was negatively correlated with self-reported sleep duration (r = -0.42; p-value = 0.02), and positively correlated with stimulating screen time content (r = 0.43; p-value = 0.02). Those who napped had a lower daily screen time duration compared to those who did not nap (Mean difference = 91.7 minutes; p-value = 0.05) and had a higher sleep efficiency of 95.8%. Preliminary evidence suggests that a relationship between both evening screen time duration in addition to content, and objectively measured sleep outcomes may exist for US college students. This study provides reliable, objective data of college student sleep that may inform future public health interventions in this population.

The purpose of this study was to determine if a firefighter's fundamental movement patterns can act as predictors for occupational injury and performance during the firefighter academy training. The study consisted of 23 firefighter candidates entering the 16-week firefighter academy training. The firefighter candidates', VO2Max, 1.5 mile-run and Firefighter Physical Conditioning Course and movement patterns were assessed at the on-set of the 16-week training. The firefighter movement patterns were assessed utilizing the Functional Movement Screen, which was designed to identify flaws in fundamental movement patterns. The firefighter candidates were then observed and their injuries documented during the firefighter academy training. The injury results as well as the initial performance tests were then compared to the results obtained by the Functional Movement Screen. There were no significant findings when comparing the Functional Movement Screen to the performance tests. The only significant correlation was with the Functional Movement Screen asymmetry score and the Firefighter Physical Conditioning Course. The relationship between the injuries recorded and Functional Movement Screen scores were inconclusive. The results of this study were unable to determine if a movement-based assessment such as the Functional Movement Screen can be utilized as an injury or performance predictor tool. The findings determined that further research needs to be performed with efforts placed on larger population groups and more emphasis placed on the scoring and analysis criteria used by the movement-based assessment. / Ph. D.

A vast majority of coal and mineral cleaning and upgrading processes involve the addition of water. The water allows the movement of particles throughout the processing plant and the upgrading of the material. When the process is complete the finished product must be dewatered. This is due to storage concerns, in which the water takes up a majority of the space, and high transportation costs, in which no compensation is obtained from the buyer for the shipment of the liquid. Dewatering is accomplished by many devices, with the two most common pieces of equipment being the screen-bowl centrifuge and disk filter. This thesis tests and compares the effect of reagents on dewatering using the screen-bowl centrifuge and disk filter. Coal was obtained from the Upper Banner, Pittsburgh No. 8, Taggart, and Dorchester seams, crushed and ground to the desired size, and run through the dewatering circuits. The results showed that the moisture content of the product can be greatly reduced in the disk filter while being only slightly reduced in the screen-bowl centrifuge. It was also shown that the recovery can be slightly increased in the screen-bowl centrifuge. Overall, with the addition of reagents, the disk filter outperformed the centrifuge in both recovery and moisture content. A model was also developed for the screen-bowl centrifuge. The results from the screen-bowl tests helped in the development of this model. This model can be used to predict the moisture content of the product, the recovery, particle size distribution of the effluent and particle size distribution of the product. The model also predicted how the product moisture and recovery were affected by changing the feed flow rate, feed percent solids, centrifuge speed, and particle size distribution. / Master of Science