Physical Sciences and Mathematics Commons^™

Polya Db3: A Database Cataloging Polyadenation Sites(Pas) Across Different Species And Their Conservation, Ram Mohan Nambiar

Theses

Polyadenation is an important process occurring in the messenger RNA that involves cleavage of 3 end nascent mRNAs and addition of poly(A) tails. For this thesis,I present PolyA DB3 ,a database cataloging cleavage and polyadenylation sites (PASs) in several genomes specifically for human,mouse,rat and chicken. This database is based on deep sequencing data. PASs are mapped by the 3’ region extraction and deep sequencing (3’READS) method, ensuring unequivocal PAS identification. Large volume of data based on diverse biological samples is used to increase PAS coverage and provide PAS usage information. Strand-specific RNA-seq data were used to extend annotated 3’ ends …

A Parallelized Implementation Of Cut-And-Solve And A Streamlined Mixed-Integer Linear Programming Model For Finding Genetic Patterns Optimally Associated With Complex Diseases, Michael Yip-Hin Chan

Theses

With the advent of genetic sequencing, there was much hope of finding the inherited elements underlying complex diseases, such as late-onset Alzheimer’s disease (AD), but it has been a challenge to fully uncover the necessary information hidden in the data. A likely contributor to this failure is the fact that the pathogenesis of most complex diseases does not involve single markers working alone, but patterns of genetic markers interacting additively or epistatically. But as we move upwards beyond patterns of size two, it quickly becomes computationally infeasible to examine all combinations in the solution space. A common solution to solving …

Lc-Ms/Ms Based Analysis Of Vitamins B3 And B6 In Healthy And Obese Emirati Population, Ghada Rashad Mohamed Shafiek Ibrahim

Theses

Water-soluble vitamins like Vitamin B3, B6, and B9 are of utmost importance in human health and disease, as they are involved in numerous critical metabolic reactions. Not surprisingly, deficiencies of these vitamins have been linked to various disease states. For example, Vitamin B6 deficiency has been related to many diseases in humans especially in women with type 1 diabetes and in patients with systemic inflammation, liver disease, rheumatoid arthritis, and those infected with HIV. Similarly, derivatives of Vitamin B9 (such as folates), are needed to synthesize, repair, and methylate DNA as well as to act as a cofactor in certain …

Mathematical Modeling Of Corona Virus In The United Arab Emirates, Alya Saif Ahmad Alshehhi

Theses

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a viral in-fectious disease that can be transmitted to humans through interaction with infected ani-mals or humans. The Middle East respiratory syndrome (MERS) is still one of the main public health concerns in the Gulf region including United Arab Emirates. The fact that diseases have been imported into other parts of the world show the possibility of has a MERS pandemic. In this work, we are aiming to study a mathematical model of the MERS transmission among the UAE population and camels. The goal is to determine what are the paths of …

The Use Of Bacteriophages To Control Legionella Spp. In Environmental Water Samples, Naama Abdulla Ali Al-Kaabi

Theses

Legionnaires' disease is a potentially fatal form of pneumonia which can affect human, but principally affects those who are susceptible and predisposed to infection due to old age, illness, immunosuppressed and patients at risk. Legionnaires' disease is caused by Gram-negative rod bacteria called Legionella pneumophila. An estimation of 8,000 to 18,000 are actually confirmed cases of Legionnaires' disease per year in the USA. In the UAE, there has been an increase in the number of cases of Legionnaires’ disease which are associated with recent travel to Dubai. Incidents doubled between October 2016 and August 2017. Legionella pneumophila is found …

Habitat Preferences Of Blue Marlin (Makaira Nigricans) And Black Marlin (Istiompax Indica) In The Eastern Pacific Ocean, Nima Farchadi, Michael G. Hinton, Andrew R. Thompson, Zhi-Yong Yin

Theses

Overexploitation and climate change can reduce the abundance and shift the spatial distribution of marine species. Determining the habitat suitability of a mobile pelagic species, such as Makaira nigricans (BUM) and Istiompax indica (BLM), can help describe their spatiotemporal distribution patterns over a broad spatial scale, which is a crucial need for fisheries management. Using 14 years (1997-2010) of Inter-American Tropical Tuna Commission (IATTC) catch data from purse-seine vessels in the eastern Pacific Ocean (EPO), we modeled the dynamic habitat suitability of BUM and BLM in response to environmental variables within the EPO using a species distribution model (MaxEnt) with …

The Effects Of Density Gradients On The Distribution And Behavior Of Copepods, Connor Cayson

Theses

Observations of fine-scale behavioral dynamics of zooplankton may shed insight into much larger-scale ecosystem patterns and phenomena. Some zooplankton, such as copepods, are known to aggregate near density gradients; however, it is not clear the extent to which density gradients alone affect copepod distribution and behavior, since these gradients are often associated with phytoplankton layers. In this study, we investigated the behavior of Calanus pacificus in response to salinity gradients through laboratory experiments observed with high-resolution video and analyzed using computational techniques. Image data were collected using two cameras recording continuously for a duration of 30 minutes or more, allowing …

Bubble Stream Production By Belugas (Delphinapterus Leucas), Megan Slack

Theses

Bubble stream production in belugas has been poorly characterized and its function is not well understood. I examined behavioral states when producing bubble streams (“bubbling”), and when bubbling calls, to determine whether bubbling was significantly associated with a particular call category or behavioral state. Using 19 hours of video and audio recordings collected over a two-day period, I quantified bubble streams of a 4-month old calf and an unrelated adult female housed together. Based on the overall activity budgets and pool of vocalizations for both animals, I calculated the expected counts of bubble streams with and without vocalizations, assuming that …

Detecting And Characterizing Self Hiding Behavior In Android Applications, Raina Samuel

Theses

Applications (apps) that conceal their activities are fundamentally deceptive; app marketplaces and end-users should treat such apps as suspicious. However, due to its nature and intent, activity concealing is not disclosed up-front, which puts users at risk. This study focuses on characterization and detection of such techniques, e.g., hiding the app or removing traces, known as 'self hiding' (SH) behavior. SH behavior has not been studied per se - rather it has been reported on only as a byproduct of malware investigations. This gap is addressed via a study and suite of static analyses targeted at SH in Android apps. …

Hypoxic And Viral Contributions To The Etiopathogenesis Of Schizophrenia: A Whole Transcriptome Analysis, Kathryn A. Gorski

Theses

Schizophrenia is a mental illness with a complex and as of yet unclear etiology. It is highly heritable and has a strong polygenic character, however, studies examining the genetics of schizophrenia have not sufficiently explained all variability in its prevalence. Environmental causes are theorized to have a non trivial contribution to the pathoetiology of schizophrenia, including interactions with genetic components, but these mechanisms remain unclear. Analyzing schizophrenia dysfunction using transcriptomic approaches is a paradigm still in its infancy, and fewer studies still have examined non neurological contributions to schizophrenia pathology with next generation sequencing technologies. This pilot study uses several …

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …

Social Media: On Tech-Caves, Virtual Panopticism, And The Science Fiction-Like State In Which We Unwittingly Find Ourselves, Michael Major

Theses

Making use of three historic philosophical thought experiments, this paper blends psychological perspectives with philosophical reasoning to show how social media is corrupting our perception of reality, the result of which is ultimately detrimental to society as a whole. This is accomplished by first using Plato’s “Allegory of the Cave” to analyze and discuss the ways in which social media is limiting humanity’s access to real knowledge. Next, Michel Foucault’s analysis of punishment in its social context, Discipline and Punish, is used to discuss the ways in which social media is adversely affecting our behavior. Finally, Robert Nozick’s “Experience …

Evaluation Of Vaporization Enthalpies And Vapor Pressures Of Various Aroma And Pharmacologically Active Compounds By Correlation Gas Chromatography, Daniel Simmons

Theses

Scientists in the pharmaceutical, food, and aroma industries can benefit from reliable thermochemical data. Vaporization enthalpy and vapor pressure data are not available for all compounds. Furthermore, some literature data is conflicting. The goal of this work was to use a method called correlation gas chromatography (CGC) to generate reliable vaporization enthalpy data in instances where other experimental methods are not applicable. Vapor pressures of the targets were also calculated in cases where the required literature data on the standards used in this technique were available.

CGC involves making a standard cocktail that includes a mixture of standards and one …

Sustainability Of Sprinkler- Irrigated Horticulture On Sandy Soils At Binningup - Swan Coastal Plain, W.A., Eric Law

Theses

The sustainability of sprinkler-irrigated vegetable crops in the Binningup–Myalup area of south-western Australia was investigated. The main crops are carrots, potatoes and onions. The crops are grown throughout the year in sandy soils and require large volumes of sprinkler irrigation during the summer growing period and little during winter. The irrigation water is extracted from the underlying superficial aquifer.

The combination of water with a relatively high salt content, evaporation between the sprinkler and the ground, and subsequent high evapotranspiration, leads to escalating soil water salinity during summer. At Binningup, the necessary horticultural practice of daily watering in summer to …

Sub-Wavelength Gratings For Long Wavelength Sensing, Brian Hogan

Theses

This Ph.D. thesis is concerned with the design and use of guided mode resonance (GMR) reflectors for applications in optical absorption sensing at wavelengths around 10 μm. These grating based reflectors comprise appropriately designed optical nanostructures which resonantly reflect a wide range of incident wavelengths. Because of the periodic modulation of the refractive index in the grating layer, the guided modes which exist in this region leak out of the waveguide and arc more appropriately termed leaky or quasi guided modes. Resonant reflection occurs when phase matching of the incident light and these leaky modes cancels any transmitted light. The …

Development Of Multi-Class Analytical Methods For Agrochemical Contaminants, Sarah Tuck

Theses

In this project, cost-effective multi-class analytical methods were developed to detect a range of antiparasitic, feed additive and pesticide substances in foodstuffs of animal origin. These substances have the potential to enter the food chain through their occurrence as residues either through the animals themselves or other routes e.g. contamination. To ensure the continued safety of food destined for human consumption regulatory control limits have been established for permitted levels of these residues in foods of animal origin. Despite these controls the continued monitoring of foodstuffs is necessary to ensure these limits are not breached and that substances are not …

Predicting Energy And Water Consumption On Dairy Farms Through Statistical Analysis And Machine-Learning Methods, Philip Shine

Theses

With the abolishment of milking quotas across all European Union member states in April 2015, dairy farmers must adjust their farming practises to minimise milk production costs to adequately prepare for potential periods of reduced revenue. Milk production is an intense energy and water consuming process. Coupled with challenging European greenhouse gas reduction targets and legislation regarding the prevention of groundwater pollution and deterioration, increasing the production of milk in Ireland must be met with the sustainable consumption of on-farm energy and direct water resources, to ensure the future monetary and environmental sustainability of Ireland’s dairy industry. Thus, this body …

The Use Of Machine Learning To Detect Suckling In Pre-Weaned Calves, Sukumar Katamreddy

Theses

The weaning of cattle is a process which is known to be labour intensive and to have stressful effects on both cow and calf Common methods used in the weaning process include the temporary removal of a mother from the calf and manual observation and intervention. Early and speedy weaning is known to have a number of benefits, including health benefits for both cow and calf, additional weight gains for the calves as well as reduced labour and feed requirements. The process known as Two-Stage Weaning is recognised to be an effective low-stress approach to weaning in which the calf …

Passive Planar Terahertz Retroreflectors, Dhruvkumar Desai

Theses

As the application of the Terahertz (THz) band (0.1 - 10 THz) is investigated in various settings, wireless communication stands out as an important frontier to explore. The benefits of increased bandwidth and data rates it promises will only be realized if new technology is developed to support it. Specifically, since THz wireless communication links are typically line-of-sight (LoS), the LoS can be blocked by moving obstacles, thereby requiring alternative link paths. One proposed solution for indoor wireless communications involves systems of steerable antennas, reflective "wallpaper", and steerable mirrors which would redirect THz beams around a blocking obstacle.

As an …