Digital Commons Network^™

Extending Existing Models To Capture Vegetation Response To Extreme Weather Events: The Modextreme Project, Gianni Bellocchi, Francisco J. Villalobos, Marcello Donatelli, Ole B. Christensen, Oscar Rojas, Roberto Confalonieri, Ioannis N. Athanasiadis, Irina Carpusca, Claudio O. Stöckle

International Congress on Environmental Modelling and Software

Extreme weather events are combinations of meteorological drivers that exceed certain thresholds and occur with low frequency, negatively impacting human living conditions and economic systems including agriculture. The three-year European project MODEXTREME (started on November 1st, 2013) aims at improving the predictive capability of biophysical crop and grassland simulation models under extreme weather conditions (mainly high/low temperatures and water deficit/excess). Existing modelling solutions can be improved with re-usable software libraries to capture extreme weather impacts. Estimates from existing and new modelling solutions will be compared on a variety of datasets and evaluated with respect to medium-term trajectories of future climate …

Predicting Impact Of Natural Calamities In Era Of Big Data And Data Science, Carol K. Joseph, Sunil Kakade

International Congress on Environmental Modelling and Software

Every year thousands of lives and millions of dollars are lost during natural catastrophic events. Data scientists have recognized the value of employing data mining techniques for evaluating these events to assist in understanding trends, predicting future disasters, and assessing vulnerability of populations. The goal of such analysis is to prepare governments for emergency response and relief efforts as well as to formulate strategies for future disaster mitigation. In addition, increasing pressures from a growing world population further emphasize the need for governments to seek viable solutions for balancing human needs with environmental constraints. Identifying populations vulnerable to environmental calamities …

Graph Clustering Based On Social Network Community Detection Algorithms, Enrique Campbell, David Ayala-Cabrera, Joaquín Izquierdo, Rafael Pérez-García

International Congress on Environmental Modelling and Software

Graph network clustering has been an important field of investigation in recent years with a wide spectrum of applications, including environmental, genetic and engineering studies. There are two main types of applications; their suitability depends of the modeling context. Cases where the number of subdivisions is a priori known are tackled with different techniques than those where such number is not clearly evident. The second falls within the field of community detection, which has been broadly studied by social network scientists. Traditionally, community detection in graphs has been tackled by means of hierarchical clustering, which groups nodes based on their …

A Modeling Framework For Oceanic Basins Under Double Exposure, Christian Mullon, Gorka Merino, Jose Fernandez, William Cheung, Manuel Barange

International Congress on Environmental Modelling and Software

Oceans stand under double exposure to global warming and of economic globalization. This generates anxieties and contributes to the need for specific governance. A first expression lies in the needs for integrated representations allowing a collaborative development of scenarios. Main challenge here lies in finding, in these representations, a balance between realism and abstraction admissible by all participants.

In this talk, we present modeling framework that has been designed to build scenarios about the possible futures of an oceanic basin. The principle lies in using a network model in which nodes correspond to fish stocks, specialized fleets, farming systems, trade …

Tissue Specific Isolation Of Nucleosomes In Caenorhabditis Elegans, Hyrum Shumway, Dr. Steven Johnson

Journal of Undergraduate Research

Hershey and Chase proved DNA to be the genetic material of life in 1952. The structure of DNA largely eluded investigators until Watson and Crick discovered it a year later. These two landmark experiments laid a foundation so that questions in transcription, translation, gene regulation, and inheritance could be answered.

Using Genetic Algorithms To Fit Species And Habitat Parameters For Modelling The Effect Of Climate Change On Species Distributions With Stochastic Patch Occupancy Models, Gary Polhill, Alessandro Gimona

International Congress on Environmental Modelling and Software

Standard approaches to modelling the effect of climate change on species distributions model a direct link between climatic and other biophysical variables and species occupancy. Though these provide a reasonable estimate for the effects of climate change on species distributions in the future, there are a number of issues with these approaches that fail to account for dynamic landscape interactions. For example, the mass occupancy effect means that species may be observed in unsuitable habitat patches surrounding a well-populated area of highly suitable patches. Conversely, a highly suitable area may be too disconnected from other suitable patches to allow long-term …

Modelling Spatial Relationships Between Ecosystem Services And Agricultural Production In An Agent- Based Model, Changxing Dong, Mark Brady, Yann Clough, Ullrika Sahlin, Christoph Sahrbacher, Martin Stjernman

International Congress on Environmental Modelling and Software

The collective impacts of farmers’ land management decisions on above ground ecosystem services (ES) and their implications for agriculture are poorly understood. Managing habitat to provide ES is costly but at the same time it can support higher yields through, e.g., pollination or natural pest control. Due to the mobility of ES-providers (bees, natural enemies) farmers providing habitat might also benefit their neighbours, creating interdependencies among their decisions. Interdependencies among farmers’ land-use decisions and the flow of ES in space can be considered by integrating agent-based modelling and evidence-based ES models. Such integration requires a trade-off between the land-use details …

Supporting Environmental Modelling With Taverna Workflows, Web Services And Desktop Grid Technology, Ferenc Horváth, Péter Ittzés, Dóra Ittzés, Zoltán Barcza, Laura Dobor, Dóra Hidy, Attila Marosi, Alex Hardisty

International Congress on Environmental Modelling and Software

Ecosystem functioning, climate change, and multiple interactions among biogeochemical cycles, climate system, site conditions and land use options are leading-edge topics in recent environmental modelling. Terrestrial ecosystem models are widely used to support carbon sequestration and ecosystem studies under various ecological circumstances. Our team uses the Biome-BGC model (Numerical Terradynamic Simulation Group, University of Montana), and develops an improved model version of it, called Biome-BGC MuSo. Both the original and the improved model estimate the ecosystem scale storage and fluxes of energy, carbon, nitrogen and water, controlled by various physical and biological processes on a daily time-scale. Web services were …

Activated Sludge With Total Solids Retention: Modified-Asm1 Modelling And Simulation, Cheikh Fall, Anabel Jimenez-Zarate, Ericka Millan-Lagunas, Yves Comeau

International Congress on Environmental Modelling and Software

There are many new strategies put forward for minimizing excess sludge generation in biological wastewater treatment. Some of them were developed within the context of dynamic activated sludge modelling (ASM). A number of means can be used to eliminate the traditional waste activated sludge flow and the build-up of inert solids in the aeration tanks. This includes the use of fine screens to remove the inert particulate organic fraction (X_I), hydrocyclones to lower the inorganic suspended solids (ISS), and different kinds of on-line digesters to further biodegrade the endogenous residues (X_P), via the return activated sludge …

The Qmra Wiki: A Social Media Tool For Interdisciplinary And Interagency Collaboration For Quantitative Microbial Risk Assessment, Jade Mitchell, Mark H. Weir, Wietske Van Osch, Joan Rose

International Congress on Environmental Modelling and Software

This study presents a web-based social media system that supports quantitative microbial risk assessment (QMRA) and collaboration among interdisciplinary scientists and interagency stakeholders, namely the QMRA wiki. The QMRA wiki is intended to aid the development of risk assessments by providing a collection of raw data, models and calculators as well as a platform for exchange and cross-fertilization between the QMRA community and its stakeholders. The wiki is organized around the exploration of the QMRA paradigm including the following five components: hazard identification, dose-response assessment, exposure assessment, risk characterization and risk management. Additionally, the wiki houses a number of case …

Sensitivity And Uncertainty Analysis Of A Plant-Wide Model For Carbon And Energy Footprint Of Wastewater Treatment Plants, Giorgio Mannina, Alida Cosenza, Riccardo Gori, Reza Sobhani, Manel Garrido, Diego Rosso

International Congress on Environmental Modelling and Software

This paper presents the sensitivity and uncertainty analysis of a mathematical model for Greenhouse gas (GHG) and energy consumption assessment from wastewater treatment plants (WWTPs). The model is able to simultaneously describe the main biological and physical-chemical processes in WWTP. Specifically, the mathematical model includes the main processes of the water and sludge lines influencing the methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) emissions. Further, the process energy demand and the energy recovery are also taken into account. The main objective of this paper is to analyze the key factors and sources …

Defining The Spatiotemporal Surveillance Space For Alien Species' Invasions Using Approximate Bayesian Computation, Grant Hamilton, Rune Rasmussen, Jana Mullerova, Jan Pergl, Petr Pysek

International Congress on Environmental Modelling and Software

The spatiotemporal dynamics of an alien species invasion across a real landscape are typically complex. While surveillance is an essential part of a management response, planning surveillance in space and time present a difficult challenge due to this complexity. We show here a method for determining the highest probability sites for occupancy across a landscape at an arbitrary point in the future, based on occupancy data from a single slice in time. We apply to the method to the invasion of Giant Hogweed, a serious weed in the Czech republic and throughout Europe.

The Effect Of Recovery On Modeling Inactivation Of Bacillus Spores On Hvac Filters, Bharathi Murali, Jade Mitchell

International Congress on Environmental Modelling and Software

The ability of microorganisms to persist on fomite surfaces is an important component in modeling their spread in physical environment. For example, Bacillus anthracis (Ba) spores have been found to be extremely resistant to inactivation, environmental stresses, and stable over decades. Modeling the inactivation of spores could form an integral element for estimating the exposure and the subsequent health risks posed by them. However, there is a knowledge gap in the quantification of recovery of Bacillus spores on porous surfaces, which may have a significant effect on the quantification of their persistence in the environment. Our work investigates the recovery …

A Model Of Grammatical Category Acquisition Using Adaptation And Selection, Sarah Zitting Cluff

Theses and Dissertations

By the later preschool years, most children have a knowledge of the grammatical categories of their native language and are capable of expanding this knowledge to novel words. To model this accomplishment, researchers have created a variety of explicit, testable models or algorithms. These have had partial but promising success in extracting grammatical word categories from transcriptions of caregiver input to young children. Additional insight into children's learning of the grammatical categories of words might be gained from evolutionary computing algorithms, which apply principles of evolutionary biology such as variation, adaptive change, self-regulation, and inheritance to computational models. The current …

Vaccination Perceptions Of School Employees In A Rural School District, Janelle L. B. Macintosh

Faculty Publications

Background: There continues to be a need for increases in adult vaccination rates, especially among those working in environments which may easily become communicable disease outbreak centers, such as school employees in the school environment. The purpose of this study was to evaluate why rural Utah school employees were non-compliant with the influenza and measles, mumps, and rubella (MMR) vaccines, as well as to identify their view on mandatory vaccination policies.

Methods: A questionnaire was distributed to all school employees in a rural Utah school district. Data analysis included frequencies and measures of central tendency and dispersion for quantitative items …

Facies Analysis, Sequence Stratigraphy And Paleogeography Of The Middle Jurassic (Callovian) Entrada Sandstone: Traps, Tectonics, And Analog, George R. Jennings Iii

Theses and Dissertations

The late Middle Jurassic (Callovian) Entrada Sandstone has been divided into two general facies associations consisting primarily of eolian sandstones in eastern Utah and "muddy" redbeds in central Utah. Sedimentary structures within the redbed portion are explained by the interfingering of inland sabkha, alluvial, and eolian depositional systems. A complete succession from the most basinward facies to the most terrestrial facies in the Entrada Sandstone consists of inland sabkha facies overlain by either alluvial or eolian facies. Where both alluvial and eolian facies interfinger, alluvial facies overlain by eolian facies is considered a normal succession. Sequence boundaries, often identified by …

Characterization Of The Granule-Bound Starch Synthase I Gene In Chenopodium, Douglass C. Brown

Theses and Dissertations

Chenopodium L. is a relatively under-studied genus that includes the cultivated seed crop quinoa (Chenopodium quinoa Willd.). Quinoa is an allotetraploid (2n=4x=36, AABB genomes) that is cultivated by subsistence farmers and commercial growers in the Andean regions of South America. Approximately 60% of a quinoa seed is starch, a glucose polymer that is an important carbohydrate energy source in the human diet. Seed starch is normally comprised of amylose and amylopectin in a 1:3 ratio, but starches with different amylose:amylopectin ratios have different properties and potential uses. The accumulation of the amylose fraction of starch is controlled by a single …

Patterns Of Student Curricular Experience In Psychology As Predictors Of Performance On The Ets Major Field Test, Jason J. Van Der Horst

Theses and Dissertations

The purpose of this dissertation is to evaluate the relationship between student performance and their performance on the Major Field Test (MFT). The MFT purports to adequately assess student mastery and achievement in the college major, in this case psychology. The major advantages of the MFT over internally-created instruments are its standardized content, its established national norms, and its connection to the Graduate Record Examination (GRE). The MFT is the most widely used standardized test for learning outcomes assessment within psychology departments. The first hypothesis, that MFT scores are reflective of summary curricular values (i.e. GPA), was not supported when …

Expression Of Osteoarthritis Biomarkers In Temporomandibular Joints Of Mice With And Without Receptor For Advanced Glycation End Products (Rage), Elizabeth Murayama Chavez Matias

Theses and Dissertations

This thesis will be organized into three chapters discussing the mechanism underlying the onset and progression of osteoarthritis (OA) in the temporomandibular joint (TMJ). Understanding the mechanism of OA development in the TMJ helps in understanding how OA progresses and how to treat this disease. The goal of this investigation is to examine the process of cartilage degeneration and OA biomarker expression in the TMJ to understand their role in TMJ OA onset and development.Chapter one covers mechanisms that are altered in TMJ OA during disease progression. Using animal models with different stressors such as mechanical disturbances, direct injury, and …

Rapid Adaptation Of Dopamine D2 Receptor Responses In The Brain And Blood Following Acute Ethanol, Ryan J. Folsom

Theses and Dissertations

Dopamine (DA) D2 receptor expression parallels DA levels in the brain and these autoreceptors have been shown to be modulated by long-term ethanol exposure. We have previously demonstrated that ventral tegmental area (VTA) GABA neurons also express D2 autoreceptors (D2R), and that DA and D2R agonists markedly enhance the excitability of VTA GABA neurons, opposite to their well-known auto-receptor inhibition of DA neurons. Most importantly, D2R antagonists block ethanol inhibition of VTA GABA neurons and D2R expression in VTA GABA neurons down-regulates with chronic ethanol, as others have shown for whole VTA D2R expression. The aim of this study was …

Examination Of Anabolic Signaling And Muscle Growth With Caffeine Treatment In Overloaded Hindlimb Muscle And Electrically Stimulated Muscle Lacking Liver Kinase B1, Timothy Michael Moore

Theses and Dissertations

Skeletal muscle has the ability to increase in size (hypertrophy) after resistance is placed upon it. This hypertrophy is marked by significant upregulation of the mammalian target of rapamycin (mTOR) and its downstream targets. The upstream kinases, protein kinase B (also known as Akt) and AMP-activated protein kinase (AMPK), are two of the many regulators of the mTOR pathway. Recent studies suggest that the widely consumed neuroactive compound caffeine could potentially inhibit mTOR by acting through Akt and/or AMPK. The purpose of this thesis was to: 1) determine if caffeine can inhibit the mTOR pathway and ultimately attenuate skeletal muscle …

Discovery Of Novel Serum Biomarkers For Diagnosing And Staging Alzheimer's Disease, Dipti Jigar Shah

Theses and Dissertations

Discovery of Novel Serum Biomarkers for Diagnosing and Staging Alzheimer’s DiseaseDipti Jigar ShahDepartment of Chemistry and Biochemistry, BYUDoctor of PhilosophyAlzheimer’s disease (AD) is an untreatable neurologic disease affecting more than 5 million Americans, most over 60 years of age. Protein plaques and neurofibrillary tangles typify AD brain pathology and are thought to cause the progressive dementia and brain shrinkage observed in AD. Currently there are no methods to diagnose the disease at a time before damage becomes irreversible.Biochemical tests for AD using cerebrospinal fluid analysis or neuroimaging are not yet sufficiently sensitive and specific, and they are invasive. This points …

The Effect Of Student Gender On Secondary School Teacher Perceptions Of Social, Emotional, And Behavioral Concerns, Erin Ann Williams

Theses and Dissertations

Students at risk for social, emotional and behavioral concerns (SEBC) are likely to experience a variety of negative outcomes if not identified and provided with appropriate interventions in a timely manner. Males tend to be identified more frequently than females for SEBC (Young, Sabbah, Young, Reiser, & Richardson, 2010), and there are many variables that may contribute to this disproportionate identification. This study specifically examined the influence of student gender on secondary education teachers’ referral decisions for students at risk for SEBC. This study additionally examined the influence of teachers’ prior referral experience, confidence in the mental health services available …

Divalent Copper Compounds As Inhibitory Agents Of Influenza A, Nathan Allan Gordon

Theses and Dissertations

Influenza A virus (IAV) exhibits a high mutation frequency. Mutations in primary viral targets such as hemagglutinin, neuraminidase, and the proton channel M2 have afforded IAV with substantial drug resistance to previously effective drugs such as oseltamivir and amantadine (AMT) along with their analogs. One of the main drug-resistant alterations in the M2 protein that has become ubiquitous is the mutation S31N. Divalent copper has previously been suggested to have anti-IAV properties using in vitro assays involving Xenopus oocytes and SSNMR. In this work, the EC₅₀ of AMT, two AMT analogs, CuCl₂ · 2H₂O, and four …

Analysis Of Nucleosome Mobility, Fragility, And Recovery: From Embryonic Stem Cells To Invitrosomes, Ashley Nicolle Wright

Theses and Dissertations

Several factors direct the placement of specific nucleosomes, which in turn have the ability to regulate DNA accessibility. These factors include, but are not limited to, nucleotide sequence preference, nucleotide modifications, the type of histones present within the nucleosome, and the presence of additional transcription factor or chromatin remodelers. A combination of these and other factors are responsible for tightly controlled efficient transcription within the eukaryotic cell. In order to contribute to the understanding of these complicated processes, three separate hypothesis-driven investigations were carried out. First, we looked into nucleosome positioning and phasing within closely related cells lines. Second, we …

Cathy Trask, Monstrosity, And Gender-Based Fears In John Steinbeck’S East Of Eden, Claire Warnick

Theses and Dissertations

In recent years, the concept of monstrosity has received renewed attention by literary critics. Much of this criticism has focused on horror texts and other texts that depict supernatural monsters. However, the way that monster theory explores the connection between specific cultures and their monsters illuminates not only our understanding of horror texts, but also our understanding of any significant cultural artwork. Applying monster theory to non-horror texts is a useful and productive way to more fully understand the cultural fears of a society. One text that is particularly fruitful to explore in this context is John Steinbeck’s 1952 novel, …

The Impact Of Relationship Functioning On Cortisol In Married Couples: A Dyadic Exploration Of Sleep As A Potential Mediator, Benjamin D. Clark

Theses and Dissertations

Relationship functioning in couples has been linked to numerous health outcomes. The purpose of this study was to examine the association between 1) marital functioning and sleep dimensions, 2) marital functioning and cortisol, and 3) sleep dimensions and cortisol. The sample consisted of 108 heterosexual, married couples and was part of a larger marital intervention study. As predicted, poor marital functioning was related to negative sleep outcomes. However, these effects were only significant for wives. There was also evidence to suggest that poor marital functioning was associated with increased cortisol levels in husbands. These effects were independent of age and …

Use Of Remote Sensing To Assess Changes In Wetland Plant Communities Over An 18-Year Period: A Case Study From The Bear River Migratory Bird Refuge, Great Salt Lake, Utah, Melina Santos Vanderlinder, Christopher M. U. Neale, David E. Rosenberg, Karin M. Kettenring

Western North American Naturalist

Successfully managing wetlands requires monitoring changes in plant community composition. We used remote sensing techniques to document the replacement of desirable native wetland vegetation with invasive species in response to catastrophic flood disturbance in the 1980s and to evaluate wetland vegetation management between 1998 and 2010. We conducted our study at the Bear River Migratory Bird Refuge wetlands, which are located on the northeastern arm of the Great Salt Lake in northern Utah. We acquired high-resolution airborne multispectral imagery of the refuge in 1992 and 2010 to quantify changes in vegetation cover over time. We produced classified vegetation maps for …

Phylogeography Of The Scaled Quail In The American Southwest, Damon Williford, Randy W. Deyoung, Rodney L. Honeycutt, Leonard A. Brennan, Fidel Hernández

Western North American Naturalist

We used sequences from the mitochondrial control region to examine the phylogeography and historical demography of the Scaled Quail and to determine whether the geographic distributions of mtDNA genealogy were concordant with the distribution of the subspecies. Overall, the Scaled Quail exhibited lower haplotype and nucleotide diversity than other quail species. The highest levels of haplotype diversity were found in 3 Texas counties: Dimmit, La Salle, and Hudspeth. The Scaled Quail exhibited no phylogeographic structure among its 16 haplotypes, and the patterns of genetic variation were not congruent with potential geographic barriers or current subspecies taxonomy. The geographic distribution of …

Temperature Does Not Affect The Timing Of First Nest Departure In Orange-Crowned Warblers, Jessica J. Ims, Helen R. Sofaer, T. Scott Sillett, Cameron K. Ghalambor

Western North American Naturalist

Organisms often respond to variation in temperature by altering their behavior, but the sensitivity of each behavioral trait depends on the degree to which temperature affects its costs and benefits. Here, we tested whether a little-studied trait, the timing of the first nest departure in the morning, varied in response to ambient temperature at sunrise, sunrise time, and nesting stage (incubation vs. nestling) in female Orange-crowned Warblers breeding on Santa Catalina Island, California. We found that the time of first nest departure was significantly correlated with sunrise time but was not affected by ambient temperature at sunrise. Compared with the …