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Articles 1 - 10 of 10
Full-Text Articles in Life Sciences
Polya Db3: A Database Cataloging Polyadenation Sites(Pas) Across Different Species And Their Conservation, Ram Mohan Nambiar
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
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 …
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
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
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
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 …
Hypoxic And Viral Contributions To The Etiopathogenesis Of Schizophrenia: A Whole Transcriptome Analysis, Kathryn A. Gorski
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
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 …
Development Of Multi-Class Analytical Methods For Agrochemical Contaminants, Sarah Tuck
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
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
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 …