Physical Sciences and Mathematics Commons^™

Preferential Fish Consumption Based On Omega-3 Fatty Acids And Mercury Concentrations For Maximum Health Benefits, Katrina Smith

Honors Theses

The regular consumption of seafood offers a variety of protective effects, including the reduction of the risk of cardiovascular disease and stroke, due to the presence of omega-3 fatty acids in fish. These protective effects may be diminished by the contamination of seafood by mercury. Mercury increases the risk of cardiovascular problems and impedes neurological development. The objective of this project was to determine the fish species that are appropriate for consumption based on low levels of mercury and recommended intake levels of omega-3 fatty acids. Species that are high in omega-3s and low in mercury include salmon, trout and …

Catalytic Decomposition Of Peroxynitrite And Superoxide By Nafion Films Modified With Iron And Manganese Porphyrin, Amanda Stull, Victor Sarpong

Honors Theses

Nafion films alone and modified with inert electrolytes and metalloporphyrins were tested in their effectiveness of decomposition of aqueous peroxynitrite (PN) and superoxide. Films that were modified with a cationic manganese porphyrin, which has been shown to be responsible for catalytic decomposition of superoxide ion, were found to be most effective. Peroxynitrite was generated in solution by the decomposition of 3-morpholinosydnonimime (SIN-1) that generates nitric oxide and superoxide ion, which rapidly combine to form peroxynitrite. The tyrosine analogue 4-hydroxyphenylacetic (4-HPA) was used to trap the PN in pH 7.00 PBS buffer and was its nitrated product was detected by observing …

Uv Irradiation On Bacteriophage Survival, Sherri Tomlinson

Honors Theses

Bacteriophage is of great interest because of its potential role in controlling bacterial populations in our environment. UV exposure has a damaging effect on the virus decreasing lytic ability. This study set out to test the effects of UV radiation, in amounts comparable to local environmental conditions, on bacteriophage T2. The virus was placed in a Petri dish in a PBS medium and exposed to UV radiation at 365nm. The irradiated virus was allowed to infect E. coli and plated. The plaques formed were counted to determine lytic activity of the virus with respect to UV irradiation. The results showed …

Solid-State Memcapacitive System With Negative And Diverging Capacitance, J. Martinez-Rincon, M. Di Ventra, Yuriy V. Pershin Dr

Faculty Publications

We suggest a possible realization of a solid-state memory capacitive (memcapacitive) system. Our approach relies on the slow polarization rate of a medium between plates of a regular capacitor. To achieve this goal, we consider a multilayer structure embedded in a capacitor. The multilayer structure is formed by metallic layers separated by an insulator so that nonlinear electronic transport (tunneling) between the layers can occur. The suggested memcapacitor shows hysteretic charge-voltage and capacitance-voltage curves, and both negative and diverging capacitance within certain ranges of the field. This proposal can be easily realized experimentally and indicates the possibility of information storage …

The Hydro-Ecology Of Everyday Life: Assessing The Social And Environmental Determinants Of Water Use In The Portland Region, Vivek Shandas

Systems Science Friday Noon Seminar Series

Driven in part by the imminent threats of population growth and climate destabilization, recent studies suggest that urban areas face severe water scarcity, with some areas in Australia and the United States already instituting moratoria on water use. While water managers traditionally avoid such crises by developing demand forecasts based on population estimates, technological developments, and weather predictions, their analysis are often at a regional scale with aggregate measures of water consumption. To date, there exists limited empirical evidence about how urban spatial structure and concomitant socio-demographic and temperature characteristics mutually interact to affect water demand at the scale of …

Ferroelectricity In Strain-Free Srtio3 Thin Films, Dmitri A. Tenne

Physics Faculty Publications and Presentations

Biaxial strain is known to induce ferroelectricity in thin films of nominally non-ferroelectric materials such as SrTiO₃. However, even strain-free SrTiO₃ films and the paraelectric phase of strained films exhibit bulk frequency-dependent polarization hysteresis loops on the nanoscale at room temperature, and stable switchable domains at 50 K. By a direct comparison of the strained and strain-free SrTiO₃ films using dielectric, ferroelectric, Raman, nonlinear optical and nanoscale piezoelectric property measurements, we conclude that SrTiO₃ films and bulk crystals are relaxor ferroelectrics, and the role of strain is to stabilize longer-range correlation of preexisting nanopolar regions, …

Cost And Accuracy Comparisons In Medical Testing Using Sequential Testing Strategies, Anwar Ahmed

Theses and Dissertations

The practice of sequential testing is followed by the evaluation of accuracy, but often not by the evaluation of cost. This research described and compared three sequential testing strategies: believe the negative (BN), believe the positive (BP) and believe the extreme (BE), the latter being a less-examined strategy. All three strategies were used to combine results of two medical tests to diagnose a disease or medical condition. Descriptions of these strategies were provided in terms of accuracy (using the maximum receiver operating curve or MROC) and cost of testing (defined as the proportion of subjects who need 2 tests to …

Band Reduction For Hyperspectral Imagery Processing, Stefan Robila

Department of Computer Science Faculty Scholarship and Creative Works

Feature reduction denotes the group of techniques that reduce high dimensional data to a smaller set of components. In remote sensing feature reduction is a preprocessing step to many algorithms intended as a way to reduce the computational complexity and get a better data representation. Reduction can be done by either identifying bands from the original subset (selection), or by employing various transforms that produce new features (extraction). Research has noted challenges in both directions. In feature selection, identifying an "ideal" spectral band subset is a hard problem as the number of bands is increasingly large, rendering any exhaustive search …

Geochemistry (Δ13c, Δ15n, 13c Nmr) And Residence Times ( 14c And Osl) Of Soil Organic Matter From Red-Brown Earths Of South Australia: Implications For Soil Genesis, Evelyn Krull, Erick Bestland, Jan Skjemstad, Jeffrey Parr, A Mee

Jeffrey Parr

Soil forming processes important to the development of Red-Brown Earths (duplex soils) in southeastern Australia have been investigated by a combination of techniques, including isotopic (δ13C, δ15N, 14C), spectroscopic (13C NMR, MIR), optically stimulated luminescence dating (OSL) and phytolith analyses. A distinct increase in clay content, corresponding changes in the abundance of major elements, as well as changes in organic chemistry (13C NMR), stable isotope trends (δ13C, δ15N), and phytolith abundance, are apparent in the transition from the very sandy A horizon to the clayey B horizon in three soil profiles from the Coonawarra–Padthaway region of South Australia. These structural …

Dynamic Computational Model Suggests That Cellular Citizenship Is Fundamental For Selective Tumor Apoptosis, Megan Olsen, Nava Siegelmann-Danieli, Hava Siegelmann

Hava Siegelmann

Computational models in the field of cancer research have focused primarily on estimates of biological events based on laboratory generated data. We introduce a novel in-silico technology that takes us to the next level of prediction models and facilitates innovative solutions through the mathematical system. The model's building blocks are cells defined phenotypically as normal or tumor, with biological processes translated into equations describing the life protocols of the cells in a quantitative and stochastic manner. The essentials of communication in a society composed of normal and tumor cells are explored to reveal “protocols” for selective tumor eradication. Results consistently …

The Use Of Propensity Scores To Assess The Generalizability Of Results From Randomized Trials, Elizabeth A. Stuart, Stephen R. Cole, Catherine P. Bradshaw, Philip J. Leaf

Johns Hopkins University, Dept. of Biostatistics Working Papers

Randomized trials remain the most accepted design for estimating the effects of interventions, but they do not necessarily answer a question of primary interest: Will the program be effective in a target population in which it may be implemented? In other words,are the results generalizable? There has been very little statistical research on how to assess the generalizability, or "external validity," of randomized trials. We propose the use of propensity-score-based metrics to quantify the similarity of the participants in a randomized trial and a target population. In this setting the propensity score model predicts participation in the randomized trial, given …

Interview With Jeff Luebbers, Us Forest Service, 2010 (Audio), Jeff Luebbers

All Sustainability History Project Oral Histories

Interview of Jeff Luebbers by Chelsea Saurman on May 13th, 2010.

The interview index is available for download.

Light-Induced Self-Synchronizing Flow Patterns, Elad Greenfield, Carmel Rotschild, Alexander Szameit, Jonathan Nemirovsky, Ramy El-Ganainy, Demetrios N. Christodoulides, Meirav Saraf, Efrat Lifshitz, Mordechai Segev

Ramy El-Ganainy

In this paper, we present the observation of light-induced self-synchronizing flow patterns in a light–fluid system. A light beam induces local flow patterns in a fluid, which oscillate periodically or chaotically in time. The oscillations within different regions of the fluid interact with each other through heat- and surface-tension-induced fluid waves, and they become synchronized. We demonstrate optical control over the state of synchronization and over the temporal correlation between different parts of the flow field. Finally, we provide a model to elucidate these results and we suggest further ideas on light controlling flow and vice versa.

Comparison Of Viscous Damping In Unsaturated Soils, Compression And Shear, Paul Michaels

Paul Michaels

Geophysical down-hole surveys can be used to measure the small strain dynamic properties of soils by the effects these properties have on wave propagation. The relevant effects include amplitude decay (corrected for beam divergence) and velocity dispersion. In this paper, down-hole data collected during the GeoInstitute's Denver 2000 field day are presented and analyzed as a Kelvin-Voigt solid. Findings for these unsaturated soils include viscous damping and stiffness which differ significantly for shear and compressional waves. A strong viscous damping is observed in compression, but weak damping is presented in shear. Lumped parameter constitutive models are discussed which mathematically represent …

Local Surface Water Policy Under Conditions Of Climate Change, Elizabeth Brabec, Elisabeth Hamin, Chingwen Cheng

Elizabeth Brabec

Climate change means two things for local stormwater managers – that storm events will become more severe, and rainfall will, in many instances, become more erratic, causing enhanced periods of drought and flood. Two approaches are needed to deal with the eventualities: mitigation and adaptation.

While urbanization increases stormwater runoff and decreases the lag time of stormwater discharge, there is also a resulting lack of infiltration and reduction in evapotranspiration (Brunke and Gonser 1997). Stormwater detention, retention and infiltration have attempted to compensate, resulting in the concentrated point location infiltration of stormwater, which replenishes groundwater and baseflow. Equally important to …

Effect Of Anions On The Iron Release Pathways Of Human Serum Transferrin, Rashmi Subhash Chander Sharma

Dissertations

Transferrin, the serum iron transport protein in humans, is used to transport 30-40 mg of iron per day through blood. The accessibility of transferrin makes it an attractive target for iron cheating therapeutic agents used in the treatment of iron overload. There is an ongoing search for ligands which can accelerate the rate of iron release, as the currently approved drug DFO has a very slow rate for iron removal. Previous studies have shown that anions can accelerate the rate of iron release. Studies on the effect of anions on the rates of iron release from C-terminal monoferric transferrin at …

Thermodynamics Of Modified Theories Of Gravity, Aric Hackebill

Theses and Dissertations

Einstein’s equations are derived by following Jacobson’s thermodynamic method. It is seen that a family of possible field equations exist which satisfy the thermodynamic argument. Modified theories of gravity are addressed as possible candidates for replacing dark matter as an explanation for anomalous cosmological phenomena. Many of the proposed modified theories are not powerful enough to explain the currently observed phenomena and are rejected as viable theories of gravity. A surviving candidate, TeVeS, is further analyzed under the aforementioned thermodynamic argument to check for its consistency with thermodynamics.

On Building An Index Advisor For Semantic Web Queries, Lubomir Stanchev, Grant Weddell

Computer Science and Software Engineering

Current optimization techniques for answering queries over Semantic Web data use realization to precalculate the individuals associated with every concept in the given ontology. However, this technique does not take into account the type of queries, written for example in nRQL or SPARQL-DL, that will arrive at the system. In this paper we propose how this additional knowledge can be used to create query-specific indices. We include experimental results that show how our approach can be used to improve the performance of the Pellet query engine for the popular LUBM benchmark.

Weak Shear Study Of Galaxy Clusters By Simulated Gravitational Lensing, David Raymond Coss

Dissertations

Gravitational lensing has been simulated for numerical galaxy clusters in order to characterize the effects of substructure and shape variations of dark matter halos on the weak lensing properties of clusters. In order to analyze realistic galaxy clusters, 6 high-resolution Adaptive Refinement Tree N-body simulations of clusters with hydrodynamics are used, in addition to a simulation of one group undergoing a merger. For each cluster, the three-dimensional particle distribution is projected perpendicular to three orthogonal lines of sight, providing 21 projected mass density maps. The clusters have representative concentration and mass values for clusters in the concordance cosmology. Two gravitational …

Scalable Probabilistic Databases With Factor Graphs And Mcmc, Michael Wick, Andrew Mccallum, Gerome Miklau

Gerome Miklau

Probabilistic databases play a crucial role in the management and understanding of uncertain data. However, incorporating probabilities into the semantics of incomplete databases has posed many challenges, forcing systems to sacrifice modeling power, scalability, or restrict the class of relational algebra formula under which they are closed. We propose an alternative approach where the underlying relational database always represents a single world, and an external factor graph encodes a distribution over possible worlds; Markov chain Monte Carlo (MCMC) inference is then used to recover this uncertainty to a desired level of fidelity. Our approach allows the efficient evaluation of arbitrary …

Powerful Snp Set Analysis For Case-Control Genome Wide Association Studies, Michael C. Wu, Peter Kraft, Michael P. Epstein, Deanne M. Taylor, Stephen J. Chanock, David J. Hunter, Xihong Lin

Harvard University Biostatistics Working Paper Series

No abstract provided.

Asymptotic Properties Of The Sequential Empirical Roc And Ppv Curves, Joseph S. Koopmeiners, Ziding Feng

UW Biostatistics Working Paper Series

The receiver operating characteristic (ROC) curve, the positive predictive value (PPV) curve and the negative predictive value (NPV) curve are three common measures of performance for a diagnostic biomarker. The independent increments covariance structure assumption is common in the group sequential study design literature. Showing that summary measures of the ROC, PPV and NPV curves have an independent increments covariance structure will provide the theoretical foundation for designing group sequential diagnostic biomarker studies. The ROC, PPV and NPV curves are often estimated empirically to avoid assumptions about the distributional form of the biomarkers. In this paper we derive asymptotic theory …

Scalable Probabilistic Databases With Factor Graphs And Mcmc, Michael Wick, Andrew Mccallum, Gerome Miklau

Andrew McCallum

Probabilistic databases play a crucial role in the management and understanding of uncertain data. However, incorporating probabilities into the semantics of incomplete databases has posed many challenges, forcing systems to sacrifice modeling power, scalability, or restrict the class of relational algebra formula under which they are closed. We propose an alternative approach where the underlying relational database always represents a single world, and an external factor graph encodes a distribution over possible worlds; Markov chain Monte Carlo (MCMC) inference is then used to recover this uncertainty to a desired level of fidelity. Our approach allows the efficient evaluation of arbitrary …

Ultrafast Optical Study Of Small Gold Monolayer Protected Clusters: A Closer Look At Emission, S. Hei Yau, O. Varnavski, John D. Gilbertson, Bert D. Chandler, G. Ramakrishna, T. Goodson

Chemistry Faculty Research

Monolayer-protected metal nanoclusters (MPCs) were investigated to probe their fundamental excitation and emission properties. In particular, gold MPCs were probed by steady-state and time-resolved spectroscopic measurements; the results were used to examine the mechanism of emission in relation to the excited states in these systems. In steady-state measurements, the photoluminescence of gold clusters in the range of 25 to 140 atoms was considerably stronger relative to larger particle analogues. The increase in emission efficiency (for Au₂₅, Au₅₅, and Au₁₄₀ on the order of 10^-5) over bulk gold may arise from a different mechanism …

The Linkset Model For 2^N Contingency Tables, Mikel Aickin

COBRA Preprint Series

Abstract The linkset model is defined for parametrizing the general 2^n contingency table. The linkset parameters are designed to represent latent influences that promote the co-occurrences of binary events beyond that explained by chance. Linkages involving 2 through n binary variables are included in this parametrization. The intent of this process is to elucidate the patterns of linkage, no matter how complex they might be, rather than to fit simplifying models. The relationship between linkset parameters and the natural parameters for a 2n table are derived, and large sample inference methods are provided. Examples are given from medical diagnostics, survival …

Analysis Of Medical Images By Colonies Of Prehending Entities, Rebecca Smith

Theses and Dissertations

The concept of emergent behavior is difficult to define, but can be considered as higher-level activity created by the individual actions of a population of simple agents. A potential means to model such behavior has been previously developed using Alfred North Whitehead's concept of Actual Entities. In computational form, actual entities are agents which evolve over time in response to interactions with their environment via the process of prehension. This occurs within the context of a Colony of Prehending Entities, a framework for implementation of AE concepts. This thesis explores the practical application of this framework in analysis of medical …

Noncommutative Topology And The World’S Simplest Index Theorem, Erik Van Erp

Dartmouth Scholarship

In this article we outline an approach to index theory on the basis of methods of noncommutative topology. We start with an explicit index theorem for second-order differential operators on 3-manifolds that are Fredholm but not elliptic. This low-brow index formula is expressed in terms of winding numbers. We then proceed to show how it is derived as a special case of an index theorem for hypoelliptic operators on contact manifolds. Finally, we discuss the noncommutative topology that is employed in the proof of this theorem. The article is intended to illustrate that noncommutative topology can be a powerful tool …

Intrinsic Contact Geometry Of Protein Dynamics, Yosi Shibberu, Allen Holder, David Cooper

Mathematical Sciences Technical Reports (MSTR)

We introduce a new measure for comparing protein structures that is especially applicable to analysis of molecular dynamics simulation results. The new measure generalizes the widely used root-mean-squared-deviation (RMSD) measure from three dimensional to n-dimensional Euclidean space, where n equals the number of atoms in the protein molecule. The new measure shows that despite significant fluctuations in the three dimensional geometry of the estrogen receptor protein, the protein's intrinsic contact geometry is remarkably stable over nanosecond time scales. The new measure also identifies significant structural changes missed by RMSD for a residue that plays a key biological role in …

A Flare In The Jet Of Pictor A, Herman L. Marshall, Eric S. Perlman

Aerospace, Physics, and Space Science Faculty Publications

A Chandra X-ray imaging observation of the jet in Pictor A showed a feature that appears to be a flare that faded between 2000 and 2002. The feature was not detected in a follow-up observation in 2009. The jet itself is over 150kpc long and about 1 kpc wide, so finding year-long variability is surprising. Assuming a synchrotron origin of the observed high-energy photons and a minimum energy condition for the outflow, the synchrotron loss time of the X-ray emitting electrons is of order 1200 years, which is much longer than the observed variability timescale. This leads to the possibility …

Discovery Of Rotational Braking In The Magnetic Helium-Strong Star Sigma Orionis E, R. H.D. Townsend, M. E. Oksala, David H. Cohen, S. P. Owocki, A. Ud-Doula

Physics & Astronomy Faculty Works

We present new U-band photometry of the magnetic helium-strong star sigma Ori E, obtained over 2004-2009 using the SMARTS 0.9 m telescope at Cerro Tololo Inter-American Observatory. When combined with historical measurements, these data constrain the evolution of the star's 1.19 day rotation period over the past three decades. We are able to rule out a constant period at the p(null) = 0.05% level, and instead find that the data are well described (p(null) = 99.3%) by a period increasing linearly at a rate of 77 ms per year. This corresponds to a characteristic spin-down time of 1.34 Myr, in …