Physical Sciences and Mathematics Commons^™

Investigate Genomic 3d Structure Using Deep Neural Network, Yan Zhang

Theses and Dissertations

The 3D structures of the chromosomes play fundamental roles in essential cellular functions, e.g., gene regulation, gene expression, evolution and Hi-C technique provides the interaction density between loci on chromosomes. In this dissertation, we developed multiple algorithms, focusing the deep learning approach, to study the Hi-C datasets and the genomic 3D structures.

Building 3D structure of the genome one of the most critical purpose of the Hi-C technique. Recently, several approaches have been developed to reconstruct the 3D model of the chromosomes from HiC data. However, all of the methods are based on a particular mathematical model and lack of …

Fluorescence Polarization Measurements To Probe Alignment Of A Bithiophene Dye In One-Dimensional Channels Of Self-Assembled Phenylethynylene Bis-Urea Macrocycle Crystals, Preecha Kittikhunnatham

Theses and Dissertations

This thesis describes the use of polarized fluorescence microscopy to directly probe guest molecule orientation in bis-urea macrocycle crystals. These macrocycles assemble to afford one-dimensional (1D) microchannels ∼9 Å in diameter that have previously been shown to exhibit normal Fickian diffusion and induce selective reactivity among the confined guest molecules. In the present work, we take advantage of the quasi-1D morphology of fiber-like microcrystals with the extended dimension corresponding to the channel axis to measure excitation and emission polarization values for a bithiophene guest. Guest fluorescence is shown to be polarized along the fiber axis with emission polarization values up …

Metal-Organic Frameworks: A Versatile Platform For Light Harvesting And Energy Transfer, Derek E. Williams

Theses and Dissertations

The global energy demand is undoubtedly rising at an alarming rate, and as a result, humanity faces the problem of finding alternative energy supplies. Approximately 80 percent of the world’s energy currently comes from fossil fuels, and only a small fraction, 10 percent, from renewable energy sources. The study of energy transfer (ET) processes is a rapidly developing area of interest due to the necessity for more efficient photovoltaic devices, which are crucial to meet the growing energy demand. A promising approach to further advance organic photovoltaics is to precisely arrange many lightharvesting chromophores (e.g., porphyrin derivatives), attainable through a …

Sustainable Polymeric Materials Derived From Plant Oils: From Synthesis To Applications, Xinzhou Zhang

Theses and Dissertations

In this thesis, monomers and polymers derived from high oleic soybean oil are investigated. The properties of these monomers and polymeric materials are characterized and discussed. Chapter 1 describes an overall background of bio-based resources, monomers, polymers, and their potential impact on society. The overall objective of my research is described. Chapter 2 outlines a new large-scale preparation of a soybean based monomer and the use of this monomer in thermoplastic elastomers. The synthetic procedures and characterizations of the monomers and polymers are discussed. In Chapter 3, potential applications of soybean oil monomers in both supramolecular polymers and poly(phosphoester)s are …

Targeting Aberrant Glycosylation In Colon And Prostate Cancer With An Improved Synthetic Lectin Array, Tanya Hundal

Theses and Dissertations

Cancers of the colon and prostate, though treatable, necessitate early detection to improve patient outcomes. Current diagnostics, (visual methods or biopsies) besides being invasive, are subjective towards interpretation, thus decreasing accuracy. Alternatively, blood-based tests involving measuring of specific biomarkers (like CEA and PSA for colon and prostate cancers, respectively) are associated with high false-positive rates and are more useful for monitoring post-treatment patient health, thus driving efforts to identify better screening and diagnostic techniques.

Abnormal glycosylation of integral membrane and secreted glycoproteins is known to take place at the onset of many diseases, including cancer, and presents as the over, …

Mouse Mesenchymal Progenitor Cells Expressing Adipogenic And Osteogenic Transcription Factors Suppress The Macrophage Inflammatory Response, Jodi F. Evans Ph.D., Natalie Fernandez, Heather Renna, Lauren Mchugh, Katie Mazolkova, William Crugnola

Faculty Works: BCES (1999-2023)

Mesenchymal progenitor cell characteristics that can identify progenitor populations with specific functions in immunity are actively being investigated. Progenitors from bone marrow and adipose tissue regulate the macrophage (MΦ) inflammatory response by promoting the switch froman inflammatory to an anti-inflammatory phenotype.Conversely,mesenchymal progenitors fromthe mouse aorta (mAo) support and contribute to the MΦ response under inflammatory conditions.We used cell lines with purported opposing immune-regulatory function, a bonemarrow derivedmesenchymal progenitor cell line (D1) and amouse aorta derived mesenchymal progenitor cell line (mAo). Their interaction and regulation of the MΦ cell response to the inflammatory mediator, lipopolysaccharide (LPS), was examined by coculture. As …

Cd105 Deficieny In Mouse Aorta-Derived Mesenchymal Stem Cells Promotes An Enhanced Inflammatory Response To Lipolysaccharide., Jodi F. Evans Ph.D., Joseph Granata, Hugo Sanchez, Philip Loeschinger, Anthony Goez

Faculty Works: BCES (1999-2023)

Mesenchymal stem cells (MSCs) are being widely studied for their ability to regulate macrophage cell responses. Previous works have demonstrated that mouse aorta-derived MSC (mAo-MSC) support the macrophage inflammatory response. mAo-MSC have been characterized phenotypically for MSC-associated surface antigens and express CD90 and CD105 but do not express CD73. CD105, also known as endoglin, is a coreceptor in the TGFβ superfamily of receptors. Mouse adipose-derived MSC lacking CD105 have an increased capacity to regulate T-cells by reducing their proliferation while elevated CD105 expression is consistently associated with inflammatory disease. Therefore, we hypothesized that suppression of CD105 in mAo-MSC will reduce …

The Stress Of Public Speaking Increases Cortisol Levels In Undergraduates: Is Increased Preparation Really The Best Remedy?, Jodi F. Evans Ph.D., Erin Clinton, Grace Cookson, Stephanie Brown, Daniel Woods

Faculty Works: BCES (1999-2023)

Perceived stress is prevalent among the undergraduate population. When this stress persists, it has the potential to lead to mental health illnesses. Recent research shows 85% of students experience overwhelming anxiety from academic pressures. Physiologically, during stressful events, cortisol levels rise in the body which disrupts homeostasis. The anticipation prior to a class presentation, a form of public speaking, is a common source of perceived stress among undergraduates. The focus of this experiment was to determine if there is a correlation between factors such as increased preparedness, sleep, level of understanding, perceived anxiety and physiological stress parameters. Twenty-eight student volunteers …

Functional And Mechanistic Insight Into The Role Of Atg9a In Autophagy, Vajira Kaushalya Weerasekara

Theses and Dissertations

The bulk degradative process of macroautophagy requires the dynamic growth of autophagosomes, which carry cellular contents to the lysosome for recycling. Atg9A, a multi-pass transmembrane protein, is an apical regulator of autophagosome growth, yet its regulatory mechanism remains unclear. Our work suggests that hypoxia (low glucose and oxygen) triggers a rearrangement of the small adapter protein 14-3-3ζ interactome. Our data suggest that the localization of mammalian Atg9A to autophagosomes requires phosphorylation on the C terminus of Atg9A at S761, which creates a 14-3-3z docking site. Under basal conditions, this phosphorylation is maintained at a low level and is dependent on …

"I Can Physically Feel The Difference": Exploring Physicalizations Of Running Data, Zann Benjamin Anderson

Theses and Dissertations

We explore user interactions with concrete physical visualizations—physicalizations—of personal experiential data. We conducted three user studies involving physicalizations of data gathered while trail running—a sport in which participants are largely more focused on the experience than the exercise itself. In two qualitative studies, we asked trail runners to give us a GPS path from a "significant run" and then prepared a 3D physicalization featuring the path overlaid as a raised line on the corresponding real-world terrain. In the first, physicalizations had a significant impact in helping participants recall memories of their experiences, and participants shared many stories. In a follow-up …

Energy Rebound As A Potential Threat To A Low-Carbon Future: Findings From A New Exergy-Based National-Level Rebound Approach, Paul E. Brockway, Harry Saunders, Matthew K. Heun, Timothy J. Foxon

University Faculty Publications and Creative Works

150 years ago, Stanley Jevons introduced the concept of energy rebound: that anticipated energy efficiency savings may be "taken back" by behavioural responses. This is an important issue today because, if energy rebound is significant, this would hamper the effectiveness of energy efficiency policies aimed at reducing energy use and associated carbon emissions. However, empirical studies which estimate national energy rebound are rare and, perhaps as a result, rebound is largely ignored in energy-economy models and associated policy. A significant difficulty lies in the components of energy rebound assessed in empirical studies: most examine direct and indirect rebound in the …

Outsourcing Or Efficiency? Investigating The Decline In Final Energy Consumption In The Uk Productive Sectors, Lukas Hardt, John Barrett, Paul E. Brockway, Timothy J. Foxon, Matthew K. Heun

University Faculty Publications and Creative Works

Over the past two decades reductions in the final energy consumption of the productive sectors (industry, public administration, commercial services and agriculture), have made important contributions to overall reductions in UK final energy consumption. This study investigates the drivers of the reductions in final energy consumption in the UK productive sectors between 1997 and 2013 using a decomposition analysis that incorporates two novel approaches. Firstly, it uses results from a multi-regional input-output model to investigate how much of the structural change in the economy has been driven by outsourcing production overseas. Secondly, it utilises energy conversion chain analysis to determine …

A Survey Of Butterfly Diagrams For Knots And Links, Mark Ronnenberg

Dissertations and Theses @ UNI

A “butterfly diagram” is a representation of a knot as a kind of graph on the sphere. This generalization of Thurston’s construction of the Borromean rings was introduced by Hilden, Montesinos, Tejada, and Toro to study the bridge number of knots. In this paper, we study various properties of butterfly diagrams for knots and links. We prove basic some combinatorial results about butterflies and explore properties of butterflies for classes of links, especially torus links. The Wirtinger presentation for the knot group will be adapted to butterfly diagrams, and we translate the Reidemeister moves for knot diagrams into so-called “butterfly …

Rules And Mechanisms For Efficient Two-Stage Learning In Neural Circuits, Tiberiu Teşileanu, Bence Ölveczky, Vijay Balasubramanian

Publications and Research

Trial-and-error learning requires evaluating variable actions and reinforcing successful variants. In songbirds, vocal exploration is induced by LMAN, the output of a basal ganglia-related circuit that also contributes a corrective bias to the vocal output. This bias is gradually consolidated in RA, a motor cortex analogue downstream of LMAN. We develop a new model of such two-stage learning. Using stochastic gradient descent, we derive how the activity in ‘tutor’ circuits (e.g., LMAN) should match plasticity mechanisms in ‘student’ circuits (e.g., RA) to achieve efficient learning. We further describe a reinforcement learning framework through which the tutor can build its teaching …

Bulk Viscous Corrections To Screening And Damping In Qcd At High Temperatures, Qianqian Du, Adrian Dumitru, Yun Guo, Michael Strickland

Publications and Research

Non-equilibrium corrections to the distribution functions of quarks and gluons in a hot and dense QCD medium modify the “hard thermal loops” (HTL). The HTLs determine the retarded, advanced, and symmetric (time-ordered) propagators for gluons with soft momenta as well as the Debye screening and Landau damping mass scales. We compute such corrections to a thermal as well as to a non-thermal fixed point. The screening and damping mass scales are sensitive to the bulk pressure and hence to (pseudo-) critical dynamical scaling of the bulk viscosity in the vicinity of a second-order critical point. This could be reflected in …

Nature Of Magnetic Ordering In Cobalt‐Based Spinels, Subhash Thota, Sobhit Singh

Faculty & Staff Scholarship

In this chapter, the nature of magnetic ordering in cobalt‐based spinels Co3O4, Co2SnO4, Co2TiO4, and Co2MnO4 is reviewed, and some new results that have not been reported before are presented. A systematic comparative analysis of various results available in the literature is presented with a focus on how occupation of the different cations on the A‐ and B‐sites and their electronic states affect the magnetic properties. This chapter specifically focuses on the issues related to (i) surface and finite‐size effects in pure Co3O4, (ii) magnetic‐compensation effect, (iii) co‐existence of ferrimagnetism and spin‐glass‐like ordering, (iv) giant coercivity (HC) and exchange bias …

Glaciovolcanic Megapillows Of Undirhliðar, Reykjanes Peninsula, Southwestern Iceland, Rachel Heineman

Honors Papers

At Undirhliðar tindar on the Reykjanes Peninsula, southwestern Iceland, megapillows are among the features formed during a series of ridge-building glaciovolcanic eruptions. Mapping of the northeastern 3 km of the ridge and petrographic and geochemical analysis of the megapillow outcrops occurring throughout this area demonstrate their role in the multi-stage construction of the ridge modeled by Pollock et al. (2014). The outcrops exhibit radial jointing, bands of vesicles and glassy rims, they occur in high relief surrounded by basalt breccia resembling pillow rubble, and are composed of plagioclase-phyric olivine basalt with plagioclase-rich groundmass. They occur in multiple pillow lava units …

Experimental Biomechanics Of Trinucleid Fringe Pits (Trilobita), Kirk Pearson

Honors Papers

The morphometric uniqueness of the trinucleid family of fossil arthropods, known as the trilobites, has led to a considerable amount of attention in paleontology literature. In particular, the distinctive hourglass-shaped pits that dot their anterior have been the subject of debate for over a century. Though anatomically well understood, their function remains unknown. Many proposals have been suggested, including its use as a sieve for filter-feeding, a strong shield for defense, and a sensory mechanism to compensate for their blindness. Despite the wide range of speculations, no study has attempted to model these hypotheses experimentally. Flume experiments and mechanical strength …

Electron Correlations In An Excited State Of A Quantum Dot In A Uniform Magnetic Field, Marlina Slamet, Viraht Sahni

Publications and Research

Electron correlations in a two-electron two-dimensional ‘artificial atom’ or quantum dot (with harmonic confining potential) in the presence of a uniform magnetic field in an excited singlet state are studied via quantal density functional theory (QDFT). QDFT allows for the separation of the electron correlations due to the Pauli exclusion principle and Coulomb repulsion, as well as the determination of the contribution of these correlations to the kinetic energy. The QDFT mapping is from the excited state of the quantum dot to one of noninteracting fermions in their ground state possessing the same basic variables of the density and physical …

Generalization Of The Schrödinger Theory Of Electrons, Viraht Sahni

Publications and Research

The Schrödinger theory for a system of electrons in the presence of both a static and time-dependent electromagnetic field is generalized so as to exhibit the intrinsic self-consistent nature of the corresponding Schrödinger equations. This is accomplished by proving that the Hamiltonian in the stationary-state and time-dependent cases {\hat{H}; \hat{H}(t)} are exactly known functionals of the corresponding wave functions {\Psi; \Psi(t)}, i.e. \hat{H} = \hat{H}[\Psi] and \hat{H}(t) = \hat{H}[\Psi(t)]. Thus, the Schrödinger equations may be written as \hat{H}[\Psi]\Psi = E[\Psi]\Psi and \hat{H}[\Psi(t)]\Psi(t) = i\partial\Psi(t)/\partial t. As a consequence the eiegenfunctions and energy eigenvalues {\Psi; E} of the stationary-state equation, and …

Multi-Instrument Comparison And Compilation Of Non-Methane Organic Gas Emissions From Biomass Burning And Implications For Smoke-Derived Secondary Organic Aerosol Precursors, Lindsay E. Hatch, Robert J. Yokelson, Chelsea E. Stockwell, Patrick R. Veres, Isobel J. Simpson, Donald R. Blake, John J. Orlando, Kelley C. Barsanti

Civil and Environmental Engineering Faculty Publications and Presentations

Multiple trace-gas instruments were deployed during the fourth Fire Lab at Missoula Experiment (FLAME-4), including the first application of proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOFMS) and comprehensive two-dimensional gas chromatography-time-offlight mass spectrometry (GC X GC-TOFMS) for laboratory biomass burning (BB) measurements. Open-path Fourier transform infrared spectroscopy (OP-FTIR) was also deployed, as well as whole-air sampling (WAS) with one-dimensional gas chromatography-mass spectrometry (GCMS) analysis. This combination of instruments provided an unprecedented level of detection and chemical speciation. The chemical composition and emission factors (EFs) determined by these four analytical techniques were compared for four representative fuels. The results demonstrate that the instruments …

A Spanner In The Works: Human–Elephant Conflict Complicates The Food–Water–Energy Nexus In Drylands Of Africa, Bruce Schulte, Mwangi Githiru, Urbanus Mutwiwa, Simon Kasaine

Biology Faculty Publications

The two major conservation issues for drylands of Africa are habitat loss or degradation and habitat fragmentation, largely fromagriculture, charcoal production, and infrastructural development. A key question for management is how these landscapes can retain their critical ecological functions and services, while simultaneously supporting resilient livelihoods. It is a clear nexus question involving food (agriculture), water, and energy (fuelwood), which is complicated by human–wildlife conflicts. While these could appear disparate issues, they are closely connected in dryland forest landscapes of Africa where elephants occur close to areas of human habitation. For instance, crop failure, whether due to weather or wildlife …

Surry County, Virginia - Shoreline Inventory Report: Methods And Guidelines, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Carl Hershner

Reports

No abstract provided.

Summary Tables: 2017 Hanover County, Virginia Shoreline Inventory Report, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Resistivity, Magnetic Susceptibility And Sediment Characterization Of The York River Estuary In Support Of The Empirical Investigation Of The Factors Influencing Marine Applications Of Emi (Year 2 Of Serdp Project Mr-2409) Final Report., Grace M. Massey, Carl T. Friedrichs

Reports

Vessel and personnel support was provided for a series of cruises to three salinity regimes along the York River. Data and samples from a standard suite of hydrographic and sedimentological measurements, as well as electrical resistivity and magnetic susceptibility, were collected and analyzed for each location. These cruises provided opportunities to obtain information that is being used to quantify the unique marine contributions to the early time TEM noise, including conductivity variations in the water and variability in bottom sediment properties in real marine environments, for use in the parallel modeling and electromagnetic-induction sensor work ongoing in the same project. …

Wonderful Wetlands: Why Do We Need Them And What Can They Do For Us? Subjects: Environmental Science, Marine/Ocean Science, Life Science/Biology Grades: 9-12, Amanda Knobloch

Reports

This lesson plan introduces students to a variety of different types of wetlands and how they function in the coastal environment. Students will work through activities that illustrate the economic importance of wetlands and the services wetlands provide, as well as building conceptual models of wetlands to illustrate these points.

Plastic As A Habitat For Bacteria And Human Pathogens. Subjects: Life Science / Biology Grades: 6-8, Amanda Laverty

Reports

This lesson plan invites 7th grade life science students to investigate marine plastic pollution as a habitat for bacteria and human pathogens. Students will examine the hazards of marine plastic pollution and learn about current science. They will have the opportunity to use data to create graphs and discuss patterns.

The Watershed Game: Land Use & Water Quality. Subjects: Environmental Science, Marine/Ocean Science, Life Science/Biology Grades: 9-12, Shanna Williamson

Reports

This lesson plan is a hands-on activity that allows students to explore how water and nutrients are transported from a watershed with three different land cover types and eventually ends up in a nearby stream.

Earthquakes, Glaciers, And Sediments, Oh My! Subjects: Earth Science, Environmental Science, Life Science/Biology Grades: 9-12, Elisabeth Clyne

Reports

This lesson plan is developed for 9th grade earth science classrooms, but can be scaled up or down. Students will explore how marine sediments serve as a history book for geologic activity. They will collect mock cores and developing conclusions about earth history.

How Green Is It? Learning Light And Electromagnetic Spectrum Properties By Measuring Algae. Subjects: Physical Science, Chemistry, Environmental Science, Life Science Grades: 9-12, Alice Besterman

Reports

This lesson plan allows students to apply knowledge of light absorption and reflectance to reveal information about an invasive species in the environment. Students will incorporate art and quantitative analysis to form and test a hypothesis through plotting provided data, interpreting graphs, and answering discussion questions that require deeper thinking.