Physical Sciences and Mathematics Commons^™

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Department of Computer Electronics and Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Designed Synthesis Of Halogenated Borazine-Linked Polymers And Their Applications In Gas Storage And Separation, Thomas Reich

Theses and Dissertations

The synthesis of highly porous organic polymers with predefined porosity has attracted considerable attention due to their potential in a wide range of applications. Of particular interest in porous organic polymers is their potential use in automotive applications as well as separation processes whereby advancements could result in a reduction in carbon dioxide emissions and the production of natural gas in a more economically friendly manner. Along these pursuits, seven borazine-linked polymers (BLPs) have been synthesized through the introduction of p-phenylenediamine, 1,3,5-tris-(4-aminophenyl)benzene, benzidine, or tetra-(4-aminophenyl)methane with boron tribromide or boron trichloride followed by the thermolysis reaction of the resulting in …

Two-Dimensional Electron Gas At Oxide Interfaces, Karolina Janicka

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

Extraordinary phenomena can occur at the interface between two oxide materials. A spectacular example is a formation of a two-dimensional electron gas (2DEG) at the SrTiO₃/LaAlO₃ interface. In this dissertation the properties of the 2DEG are investigated from first principles.

The spatial extent of the 2DEG formed at the SrTiO₃/LaAlO₃ n-type interface is studied. It is shown that the confinement of the 2DEG is controlled by metal induced gap states formed in the band gap of SrTiO₃. The confinement width is then determined by the attenuation length of the metal induced gap …

Development And Optimization Of Organic Based Monoliths For Use In Affinity Chromatography, Erika L. Pfaunmiller

Department of Chemistry: Dissertations, Theses, and Student Research

Affinity chromatography is an important and useful tool for studying biological interactions, such as the binding of an antibody with an antigen. Monolithic supports offer many advantages over traditional packed bed supports in affinity chromatography, including their ease of preparation, low back pressures and good mass transfer properties. Monoliths can be broken down into two basic categories: organic (polymer) and inorganic (silica) monoliths. There are many varieties of polymer based monoliths; however, a large focus has been on co-polymers of glycidyl methacrylate (a functional monomer) and ethylene dimethacrylate (a cross-linking agent). The solvents of choice for making this type of …

Global Change, Global Trade, And The Next Wave Of Plant Invasions, Bethany A. Bradley, Dana M. Blumenthal, Regan Early, Edwin D. Grosholz, Joshua J. Lawler, Luke P. Miller, Cascade J.B. Sorte, Carla M. D'Antonio, Jeffrey M. Diez, Jeffrey S. Dukes, Ines Ibanez, Julian D. Olden

Faculty Publications, Biological Sciences

Many non-native plants in the US have become problematic invaders of native and managed ecosystems, but a new generation of invasive species may be at our doorstep. Here, we review trends in the horticultural trade and invasion patterns of previously introduced species and show that novel species introductions from emerging horticultural trade partners are likely to rapidly increase invasion risk. At the same time, climate change and water restrictions are increasing demand for new types of species adapted to warm and dry environments. This confluence of forces could expose the US to a range of new invasive species, including many …

Climate Change And Climate Variability: El Salvador – Impacts On Productivity Of Grain Crops And Opportunities For Management And Improvement, P. V. Vara Prasad

INTSORMIL Presentations

1. Climate change and climate variability (past and future).

2. Climate change and variability in El Salvador (climate models).

3. Impact of temperature on grain yield of dry bean, maize and sorghum in El Salvador (crop simulation models).

4. Effects of temperature, drought and/or carbon dioxide: experimental evidence (response of grain sorghum, maize and dry bean).

5. Opportunities for crop management and genetic improvement.

Quantifying Burned Area For North American Forests: Implications For Direct Reduction Of Carbon Stocks, Eric S. Kasischke, Tatiana Loboda, Louis Giglio, Nancy H. F. French, E. E. Hoy, Bernardus De Jong, David Riano

Michigan Tech Research Institute Publications

A synthesis was carried out to analyze information available to quantify fire activity and burned area across North America, including a comparison of different data sources and an assessment of how variations in burned area estimate impact carbon emissions from fires. Data sets maintained by fire management agencies provide the longest record of burned area information. Canada and Alaska have the most well developed data sets consisting of the perimeters of large fires (>200 ha) going back to 1959 and 1950, respectively. A similar data set back to 1980 exists for the Conterminous U.S., but contains data only from …

Model Comparisons For Estimating Carbon Emissions From North American Wildland Fire, Nancy H. F. French, Willam J. De Groot, Liza K. Jenkins, Brendan M. Rogers, Ernesto Alvarado, Brian Amiro, Bernardus De Jong, Scott Goetz, Elizabeth Hoy, Edward Hyer, Robert Keane, B. E. Law, Donald Mckenzie, Steven G. Mcnulty, Roger Ottmar, Diego R. Perez-Salicrup, James Randerson, Kevin M. Robertson, Merritt Turetsky

Michigan Tech Research Institute Publications

Research activities focused on estimating the direct emissions of carbon from wildland fires across North America are reviewed as part of the North American Carbon Program disturbance synthesis. A comparison of methods to estimate the loss of carbon from the terrestrial biosphere to the atmosphere from wildland fires is presented. Published studies on emissions from recent and historic time periods and five specific cases are summarized, and new emissions estimates are made using contemporary methods for a set of specific fire events. Results from as many as six terrestrial models are compared. We find that methods generally produce similar results …

Vulnerability Of High Latitude Soil Organic Carbon In North America To Disturbance, Guido Grosse, Jennifer Harden, Merritt Turetsky, David A. Mcguire, Philip Camill, Charles Tarnocai, Steve Frolking, Edward A.G. Schuur, Torre Jorgenson, Sergei Marchenko, Vladimir Romanovsky, Kimberly P. Wickland, Nancy H. F. French, Mark Waldrop, Laura Bourgeau-Chavez, Robert G. Striegl

Michigan Tech Research Institute Publications

This synthesis addresses the vulnerability of the North American high-latitude soil organic carbon (SOC) pool to climate change. Disturbances caused by climate warming in arctic, subarctic, and boreal environments can result in significant redistribution of C among major reservoirs with potential global impacts. We divide the current northern high-latitude SOC pools into (1) near-surface soils where SOC is affected by seasonal freeze-thaw processes and changes in moisture status, and (2) deeper permafrost and peatland strata down to several tens of meters depth where SOC is usually not affected by short-term changes. We address key factors (permafrost, vegetation, hydrology, paleoenvironmental history) …

Adaptive Management Of Bull Trout Populations In The Lemhi Basin, Andrew J. Tyre, James T. Peterson, Sarah J. Converse, Tiffany Bogich, Damien Miller, Max Post Van Der Burg, Carmen Thomas, Ralph Thompson, Jeri Wood, Donna C. Brewer, Michael C. Runge

School of Natural Resources: Faculty Publications

The bull trout Salvelinus confluentus, a stream-living salmonid distributed in drainages of the northwestern United States, is listed as threatened under the Endangered Species Act because of rangewide declines. One proposed recovery action is the reconnection of tributaries in the Lemhi Basin. Past water use policies in this core area disconnected headwater spawning sites from downstream habitat and have led to the loss of migratory life history forms. We developed an adaptive management framework to analyze which types of streams should be prioritized for reconnection under a proposed Habitat Conservation Plan. We developed a Stochastic Dynamic Program that identified optimal …

Characterizing The Performance Of Ecosystem Models Across Time Scales: A Spectral Analysis Of The North American Carbon Program Site-Level Synthesis, Michael C. Dietze, Rodrigo Vargas, Andrew D. Richardson, Paul C. Stoy, Alan G. Barr, Ryan S. Anderson, M. Altaf Arain, Ian T. Baker, T. Andrew Black, Jing M. Chen, Philippe Ciais, Lawrence B. Flanagan, Christopher M. Gough, Robert F. Grant, David Hollinger, R. Cesar Izaurralde, Christopher J. Kucharik, Peter Lafleur, Shugang Liu, Erandathie Lokupitiya, Yiqi Luo, J. William Munger, Changhui Peng, Benjamin Poulter, David T. Price, Daniel M. Ricciuto, William J. Riley, Alok Kumar Sahoo, Kevin Schaefer, Andrew E. Suyker, Hanqin Tian, Christina Tonitto, Hans Verbeeck, Shashi B. Verma, Weifeng Wang, Ensheng Weng

School of Natural Resources: Faculty Publications

Ecosystem models are important tools for diagnosing the carbon cycle and projecting its behavior across space and time. Despite the fact that ecosystems respond to drivers at multiple time scales, most assessments of model performance do not discriminate different time scales. Spectral methods, such as wavelet analyses, present an alternative approach that enables the identification of the dominant time scales contributing to model performance in the frequency domain. In this study we used wavelet analyses to synthesize the performance of 21 ecosystem models at 9 eddy covariance towers as part of the North American Carbon Program’s site-level intercomparison. This study …

Heritable Choice Of Colony Size In Cliff Swallows: Does Experience Trump Genetics In Older Birds?, Erin A. Roche, Charles R. Brown, Mary Bomberger Brown

School of Natural Resources: Faculty Publications

The variation in breeding colony size seen in populations of most colonial birds may reflect heritable choices made by individuals that are phenotypically specialized for particular social environments. Although a few studies have reported evidence for genetically based choice of group sizes in birds, we know relatively little about the extent to which animals potentially rely on experience versus innate preferences in deciding how many conspecifics to settle with at different times of their lives. We conducted a cross-fostering experiment in 1997–1998 on cliff swallows, Petrochelidon pyrrhonota, in southwestern Nebraska, USA, in which some individuals were reared in colonies …

Second-Order Subdifferential Calculus With Applications To Tilt Stability In Optimization, Boris S. Mordukhovich, R T. Rockafellar

Mathematics Research Reports

The paper concerns the second-order generalized differentiation theory of variational analysis and new applications of this theory to some problems of constrained optimization in finitedimensional spaces. The main attention is paid to the so-called (full and partial) second-order subdifferentials of extended-real-valued functions, which are dual-type constructions generated by coderivatives of first-order sub differential mappings. We develop an extended second-order subdifferential calculus and analyze the basic second-order qualification condition ensuring the fulfillment of the principal secondorder chain rule for strongly and fully amenable compositions. The calculus results obtained in this way and computing the second-order subdifferentials for piecewise linear-quadratic functions and …

Organ-Distribution Of The Metabolite 2-Aminothiazoline-4-Carboxylic Acid In A Rat Model Following Cyanide Exposure, Ilona Petrikovics, David E. Thompson, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

The reaction of cyanide (CN⁻) with cystine to produce 2-aminothiazoline-4-carboxylic acid (ATCA) is one of the independent detoxification pathways of cyanide in biological systems. In this report, in vivo production of ATCA and its distributions in plasma and organs were studied after a subcutaneous sublethal dose of 4 mg/kg body weight potassium cyanide (KCN) administration to rats. At this sublethal dose of KCN, ATCA concentration was not significantly increased in the plasma samples, however, it was found significantly increased in liver samples. These results suggested that ATCA might not be a good diagnostic biomarker in plasma for sublethal …

Chilling A Hot Planet: Many Solutions, No Answers, Singapore Management University

Perspectives@SMU

If there was a report card on how the world is doing on issues related to climate change, it would read a resounding 'F'. Consider the figures. It took about 12,500 years between the last glacial age and today for global temperatures to rise six degrees Celsius. Yet in this century alone – despite heightened awareness of the need to arrest the ever-increasing levels of greenhouse gas emission – temperatures have risen up to four degrees Celsius.

Mobile Phone Graph Evolution: Findings, Model And Interpretation, Siyuan Liu, Lei Li, Christos Faloutsos, Lionel M. Ni

LARC Research Publications

What are the features of mobile phone graph along the time? How to model these features? What are the interpretation for the evolutional graph generation process? To answer the above challenging problems, we analyze a massive who-call-whom networks as long as a year, gathered from records of two large mobile phone communication networks both with 2 million users and 2 billion of calls. We examine the calling behavior distribution at multiple time scales (e.g. day, week, month and quarter), and find that the distribution is not only skewed with a heavy tail, but also changing at different time scales. How …

A Distributed Approach For Fault Mitigation In Large Scale Distributed Systems, Mina Jung

Electrical Engineering and Computer Science - Dissertations

In a large scale real-time distributed system, a large number of components and the time criticality of tasks can contribute to complex situations. Providing predictable and reliable service is a paramount interest in such a system. For example, a single point failure in an electric grid system may lead to a widespread power outage like the Northeast Blackout of 2003. System design and implementation address fault avoidance and mitigation. However, not all faults and failures can be removed during these phases, and therefore run-time fault avoidance and mitigation are needed during the operation. Timing constraints and predictability of the system …

Citrate Binding To The Membrane Protein Proteorhodopsin, Farhana F. Syed

Chemistry - Dissertations

Proteorhodopsin (pR) is an intrinsic membrane protein with an important role in solar-energy storage of the biosphere. Earlier work in our lab has shown that polyhistidine-tagged pR can be purified by means of selective precipitation with citrate under specific conditions, as can a number of mutants based on this His₆-tagged pR. Purification of a heterologously-expressed trans-membrane protein by a simple salt such as citrate is novel. However, such a phenomenon leads to several questions: How does citrate cause pR precipitation? Does the polyhistidine-tag assist in such a precipitation? Is this precipitation pH-specific? Does citrate affect the function of …

The Design And Construction Of A Green Laser And Fabry-Perot Cavity System For Jefferson Lab's Hall A Compton Polarimeter, Abdurahim Rakhman

Physics - Dissertations

A high finesse Fabry-Perot cavity with a frequency doubled green laser (CW, 532 nm) have been built and installed in Hall A of Jefferson Lab for high precision Compton polarimetry project in spring of 2010. It provides a high intensity circularly polarized photon target for measuring the polarization of electron beam with energies from 1.0 GeV to 11.0 GeV in a nondestructive manner. The IR beam (CW, 1064 nm) from a Ytterbium doped fiber laser amplifier seeded by a Nd:YAG narrow linewidth NPRO laser is frequency doubled in by a single-pass Periodically Poled Lithium Niobate (PPMgLN) crystal. The maximum achieved …

Manuscript Content: Where Does It Belong?, Christopher N. Jacques

The Prairie Naturalist

One of the most common issues we address during content editing of papers for The Prairie Naturalist (journal) is the appropriate placement of content in the text body. Based on my experience with the editorial process, content placement also is one of the issues that authors are most resistant to suggestions or do not fully understand why we are so persistent about it (Thompson 2010). One of the primary objectives of scientific writing is to concisely and accurately disseminate information. Scientific papers are structured to help both the author and reader accomplish this objective. The material that belongs in each …

An Extension Of The Rishon Model, Paul Finkler

Paul Finkler Papers

We present an extension of the Rishon Model of Harari, et. al. [1] [2] [3] In that model, the first generation leptons and quarks are each made from three rishons of two varieties, T and V as follows: v_e = V V V , e⁺ = T T T , d = T V V , and u = T T V . In addition to the original rishons and their anti-rishons T and V , we introduce the dark rishon X and its anti-rishon X; all have spin 1/2.

An exciting possibility that emerges from this idea …

Environmental Influences On Juvenile Fish Abundances In A River-Dominated Coastal System, Laure Carassou, Brian Dzwonkowski, Frank J. Hernandez, Jr., Sean P. Powers, William M. Graham, Kyeong Park, John Mareska

University Faculty and Staff Publications

We investigated the influence of climatic and environmental factors on variations in juvenile abundances of marine fishes in a river-dominated coastal system of the north-central Gulf of Mexico, where an elevated primary productivity sustains fisheries of high economic importance. Fish were collected monthly with an otter trawl at three stations near Mobile Bay from 1982 to 2007. Fish sizes were used to isolate juvenile stages within the data set, and monthly patterns in juvenile fish abundance and size were then used to identify seasonal peaks for each species. The average numbers of juvenile fish collected during these seasonal peaks in …

Comparison Of Fish Communities In Recently Constructed Side-Channel Chutes With The Main Stem Missouri River, Kasey Whiteman, Vincent H. Travnichek, Darrick L. Garner, Brandon Eder, Kirk Steffensen

The Prairie Naturalist

Two United States Army Corp of Engineers- (USACE) funded projects were conducted from 2006 to 2008 along the Missouri River to monitor fish communities in recently constructed side-channel chutes and to monitor pallid sturgeon (Scaphirhynchus albus) and the associated fish assemblage in the main stem Missouri River. Data from both monitoring projects were compared to evaluate fish assemblages among four mitigated habitats (e.g., constructed side-channel chutes) and the main-stem Missouri River. Chutes had a greater overall number of species (n = 59) and higher species richness (Margalef’s index = 5.81), but richness was not different (F1, 4 = …

Synthesis And Biosynthesis Of Polyketide Natural Products, Atahualpa Pinto

Chemistry - Dissertations

Traditionally separate disciplines of a large and broad chemical spectrum, synthetic organic chemistry and biochemistry have found in the last two decades a fertile common ground in the area pertaining to the biosynthesis of natural products. Both disciplines remain indispensable in providing unique solutions on numerous questions populating the field. Our contributions to this interdisciplinary pursuit have been confined to the biosynthesis of polyketides, a therapeutically and structurally diverse class of natural products, where we employed both synthetic chemistry and biochemical techniques to validate complex metabolic processes. One such example pertained to the uncertainty surrounding the regiochemistry of dehydration and …

Bifurcation And Invariant Manifolds Of The Logistic Competition Model, M. Guzowska, Rafael Luís, Saber Elaydi

Mathematics Faculty Research

In this paper we study a new logistic competition model. We will investigate stability and bifurcation of the model. In particular, we compute the invariant manifolds, including the important center manifolds, and study their bifurcation. Saddle-node and period doubling bifurcation route to chaos is exhibited via numerical simulations.

Powersearch: Augmenting Mobile Phone Search Through Personalization, Xiangyu Liu

Computer Science and Computer Engineering Undergraduate Honors Theses

Cell phone has become a fundamental element of people's life. People use it to call each other, browse websites, send text messages, etc. Among all the functionalities, the most important and frequently used is the search functionality. Based on ComScore, in July 2008, Google was estimated to host 235 millions searches per day. However, unlike the search on desktop, the search on cell phone has one critical constrain: battery. Cell phone performing a normal Google search, the battery drains very fast. The reason is that when sending a query to and fetching the results from Google, cell phone keeps communicating …

Webtailor: Internet Service For Salient And Automatic User Interest Profiles, John Anderson

Computer Science and Computer Engineering Undergraduate Honors Theses

Website personalization systems seek to give users unique, tailored content and experiences on the Internet. A key feature of these systems is a user profile that represents each user in a way that distinguishes them from others. In current personalization systems, the data used to create these profiles is extremely limited, which leads to a host of problems and ineffectual personalization. The main goal of this thesis is to improve these personalization systems by addressing their lack of data and its poor quality, breadth, and depth. This is accomplished by analyzing and classifying the content of each user's Internet browsing …

A Cooperative Game Theoretic Approach For Data Replication In Mobile Ad-Hoc Networks, Dan Hirsch, Sanjay Madria

Computer Science Faculty Research & Creative Works

The mobile computing environment provides many benefits such as ubiquitous access to computing but include constraints on resources such as: Available bandwidth and battery life. Replication is a widely recognized method for balancing the demands of storage space with bandwidth and battery life. We propose a novel scheme that seeks to strategically balance these constrained resources through a cooperative game-theoretic approach for replication in a mobile environment. Our replication strategy relies on the cooperation of the nodes within the network to make replica caching decisions which are spatiotemporally local-optimal for the network from an energy and bandwidth conservation standpoint. in …

Thermodynamics And Phase Transitions For The Heisenberg Model On The Pinwheel Distorted Kagome Lattice, Ehsan Khatami, Rajiv Singh, Marcos Rigol

Faculty Publications

We study the Heisenberg model on the pinwheel distorted kagome lattice as observed in the material Rb2Cu3SnF12. Experimentally relevant thermodynamic properties at finite temperatures are computed utilizing numerical linked-cluster expansions. We also develop a Lanczos-based, zero-temperature, numerical linked-cluster expansion to study the approach of the pinwheel distorted lattice to the uniform kagome-lattice Heisenberg model. We find strong evidence for a phase transition before the uniform limit is reached, implying that the ground state of the kagome-lattice Heisenberg model is likely not pinwheel dimerized and is stable to finite pinwheel-dimerizing perturbations.

The Update, December 2011, University Of Northern Iowa. College Of Humanities, Arts And Sciences.

Update

Inside this issue:

-- Two UNI Alums to Graduate with Doctoral Degrees
-- Department News
-- UNI Department of Theatre: Guernica Re-Cap
-- Art High School Scholarship Day
-- Faculty member Awarded Fellowship
-- School of Music Events
-- Student Spotlight: Department of Art: Erlinda Babauta
-- Military Veteran and UNI Alumnus Joins the Center for Teaching and Learning Mathematics
-- UNI Geology Students Explore Heavy Metal: Learning How to Rock!
-- Modern Motives: Influences in Today's Art
-- New U.S.-Brazil Program in Communication Disorders
-- Student Spotlight: Department of Math: Nathan Bradfield