Physical Sciences and Mathematics Commons^™

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

Creating A Community Hub For Natural History Education In The Methow Valley And Beyond, Mary Kiesau

WWU Graduate School Collection

I created and integrated three different methods of natural history education for my final project of my Masters of Education in Environmental Education in order to further establish myself as a professional educator, communicator and naturalist, and to create ways for people who live in or have an affinity for the Methow Valley to be more observant, informed and connected with the natural world. Building on previous graduate coursework as well as professional work as an environmental educator and photographer, I created a new natural history education website and Facebook page with a wide variety of online resources, while also …

Development Of 2d And 3d Conductive Biomaterial Composites For Use As Electromechanical Actuators, Sean Severt

WWU Graduate School Collection

Flexible and conductive biocompatible materials are attractive candidates for a wide range of biomedical applications including implantable electrodes, tissue engineering, and controlled drug delivery. Here we demonstrated that chemical and electrochemical polymerization techniques can be combined to create highly versatile silk-conducting polymer (silk-CP) composites with enhanced conductivity and electrochemical stability. Interpenetrating silk-CP composites were first generated via in situ deposition of polypyrrole during chemical polymerization of pyrrole. These composites were sufficiently conductive to serve as working electrodes for electropolymerization, allowing an additional layer of CP to be deposited on the surface. This two-step technique expanded the range of available polymers …

A Holocene Glaciolacustrine Record Of The Lyman Glacier And Implications For Glacier Fluctuations In The North Cascades, Washington, Harold N. Wershow

WWU Graduate School Collection

The Holocene glacial history of the North Cascades is poorly understood, in part because most existing records rely on moraine remnants and are therefore discontinuous. To develop a more complete record of Holocene fluctuations of North Cascades glaciers, we collected and analyzed glaciolacustrine sediments (i.e., rock flour) deposited over the past ~7800 years in Lyman Lake by the upstream Lyman Glacier. We combined these results with equilibrium-line altitude (ELA) reconstructions and glacier-climate modeling to quantify the climatic conditions that drove these fluctuations. Finally, we compared the Lyman Glacier’s continuous fluctuation record to existing glacier and climate records of the North …

Effects Of Zostera Marina Roots And Leaf Detritus On The Concentration And Distribution Of Pore-Water Sulfide In Marine Sediments, Alexandra G. (Alexandra Garcia) Simpson

WWU Graduate School Collection

Sulfide toxicity is implicated in seagrass declines worldwide. Studies examining the relationship between seagrass presence and sulfide concentrations have yielded conflicting results. Interpretation of the seagrass-sulfide relationship is complicated due to the opposing effects of the root system which can increase sulfide oxidation and the burial of organic matter from the plant itself which can increase sulfide production. To quantify the impact of eelgrass leaf detritus and the Zostera marina rhizosphere on pore-water sulfide concentrations, field samples of pore-water sulfide were collected in areas with and without eelgrass. To decouple the effects of live versus dead eelgrass tissue, laboratory studies …

Emergent Wetland Plant Biophysical Characteristics Associated With Wave Attenuation And Sediment Retention, Chad D. Stellern

WWU Graduate School Collection

Estuarine wetlands have proven a cost-effective buffer against coastal hazards because they reduce erosive wave energy and enable sediment retention by producing hydraulic friction. Human modifications to coastal hydrology and sediment transport have resulted in loss of wetlands and associated protection. Our study area, the Stillaguamish Delta has experienced a 55% loss in wetlands and significant marsh retreat (Grossman and Curran (in review)). We quantified vegetation characteristics (spatial, vertical and, seasonal) that effect wave attenuation using image analysis, remote sensing and, in-situ measurements. We produced a sediment budget for the northern region and evaluate suspended sediment dynamics. Our elasticity and …

A High Performance Ceramic-Polymer Separator For Lithium Batteries, Jitendra Kumar, Padmakar Kichambare, Amarendra K. Rai, Rabi Bhattacharya, Stanley J. Rodrigues, Guru Subramanyam

Electrical and Computer Engineering Faculty Publications

A three-layered (ceramic-polymer-ceramic) hybrid separator was prepared by coating ceramic electrolyte [lithium aluminum germanium phosphate (LAGP)] over both sides of polyethylene (PE) polymer membrane using electron beam physical vapor deposition (EB-PVD) technique. Ionic conductivities of membranes were evaluated after soaking PE and LAGP/PE/LAGP membranes in a 1 Molar (1M) lithium hexafluroarsenate (LiAsF₆) electrolyte in ethylene carbonate (EC), dimethyl carbonate (DMC) and ethylmethyl carbonate (EMC) in volume ratio (1:1:1). Scanning electron microscopy (SEM) and X-ray diffraction (XRD) techniques were employed to evaluate morphology and structure of the separators before and after cycling performance tests to better understand structure-property correlation. …

Echo Behavior In Large Populations Of Chemical Oscillators, Tianran Chen, Mark R. Tinsley, Edward Ott, Kenneth Showalter

Faculty & Staff Scholarship

Experimental and theoretical studies are reported, for the first time, on the observation and characterization of echo phenomena in oscillatory chemical reactions. Populations of uncoupled and coupled oscillators are globally perturbed. The macroscopic response to this perturbation dies out with time: At some time τ after the perturbation (where τ is long enough that the response has died out), the system is again perturbed, and the initial response to this second perturbation again dies out. Echoes can potentially appear as responses that arise at 2τ,3τ,... after the first perturbation. The phase-resetting character of the chemical oscillators allows a detailed analysis, …

Human Shields And Redistribution Of Prey Species Complicate The Utility Of Protected Areas As Ecological Baselines, Wesley Sarmento

Graduate Student Theses, Dissertations, & Professional Papers

A key goal of protected areas is the conservation of biodiversity, an aim that garners increasing public support through positive experiences. Increasing visitation, however, can come at the cost of reduced ecological integrity. A fundamental conundrum is that if parks are to serve as our most pristine places, then we must understand how our presence alters species interactions. Species redistributing closer to people is of growing management concern both in and out of national parks because of 1) human safety, 2) animal health, and 3) ecological consequences. Across parks drivers of distributional change are often dissimilar, and include movement to …

Synthesis Of Satellite Microwave Observations For Monitoring Global Land-Atmosphere Co2 Exchange, Lucas Alan Jones

Graduate Student Theses, Dissertations, & Professional Papers

This dissertation describes the estimation, error quantification, and incorporation of land surface information from microwave satellite remote sensing for modeling global ecosystem land-atmosphere net CO₂ exchange. Retrieval algorithms were developed for estimating soil moisture, surface water, surface temperature, and vegetation phenology from microwave imagery timeseries. Soil moisture retrievals were merged with model-based soil moisture estimates and incorporated into a light-use efficiency model for vegetation productivity coupled to a soil decomposition model. Results, including state and uncertainty estimates, were evaluated with a global eddy covariance flux tower network and other independent global model- and remote-sensing based products.

Hydraulic Conductivity As A Proxy For Drainage System Connectivity In A Subglacial Hydrology Model, Jacob Z. Downs

Graduate Student Theses, Dissertations, & Professional Papers

The link between subglacial hydrology and basal sliding has prompted work on basal hydrology models with water pressure and storage as prognostic variables. We find that a commonly used model of distributed drainage through linked cavities underpredicts winter water pressure when compared to borehole observations from Issunguata Sermia in Western Central Greenland. Possible causes for this discrepancy including unrealistic model inputs or unconstrained parameters are investigated through a series of modeling experiments on both synthetic and realistic ice sheet geometries. We find that conductivity acts as a proxy for the connectivity of the linked cavity system and should therefore change …

Investigating The Influence Of Offline Friendship On Twitter Networking Behaviors, Young Soo Kim, Felicia Natali, Feida Zhu, Ee-Peng Lim

Research Collection School Of Computing and Information Systems

We investigate the influence of offline friendship in three specific areas of Twitter networking behaviors: (a) network structure, (b) Twitter content and (c) interaction on Twitter. We observe some interesting findings through the empirical analysis of 2193 pairs of users who are online friends. When these pairs of users know each other offline, they are more likely to (1) respond to the online gesture of friendship from their friend, (2) share mutual online friends, (3) distribute and gather information in their friend’s Twitter network, (4) pay attention to their friend’s tweets, (5) post tweets that might be of interest to …

Land Cover Mapping And Change Analysis At The Tensleep Preserve In Wyoming, Tyler Richard Grupa

All Graduate Theses, Dissertations, and Other Capstone Projects

Mapping land cover and land cover change are important, especially for land managers who protect natural lands and generate restoration projects. Accurate land cover assessment of rangelands can be difficult because the spectral difference between plant species may be minimal. The goal of this research is to map the land cover in the Tensleep Preserve and highlight change that has occurred over the past twenty-three years using the Feature Analyst extension. The land cover change map will highlight significant changes and Feature Analyst will accurately identify different land covers using historical aerial photographs and ground truthing data collected in 2013. …

Early Detection Of Mountain Pine Beetle Damage In Ponderosa Pine Forests Of The Black Hills Using Hyperspectral And Worldview-2 Data, Kyle Edward Mullen

All Graduate Theses, Dissertations, and Other Capstone Projects

A leading cause for mortality in the pine forests of western North America, the mountain pine beetle, has impacted over 400,000 acres of ponderosa pine forest in the Black Hills of South Dakota since 1996. Methods aimed at earlier detection, prior to visual manifestation of a mountain pine beetle damage in the tree crown, have not been successful because of the overlap and variability of spectral response between the initial stages of attack (green-attacked) and non-attacked tree crowns. Needle-level reflectance spectra was measured from green-attack and non-attack ponderosa pine trees in early spring following an infestation and analyzed using a …

Leveraging Heritrix And The Wayback Machine On A Corporate Intranet: A Case Study On Improving Corporate Archives, Justin F. Brunelle, Krista Ferrante, Eliot Wilczek, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

In this work, we present a case study in which we investigate using open-source, web-scale web archiving tools (i.e., Heritrix and the Wayback Machine installed on the MITRE Intranet) to automatically archive a corporate Intranet. We use this case study to outline the challenges of Intranet web archiving, identify situations in which the open source tools are not well suited for the needs of the corporate archivists, and make recommendations for future corporate archivists wishing to use such tools. We performed a crawl of 143,268 URIs (125 GB and 25 hours) to demonstrate that the crawlers are easy to set …

A Hybrid Algorithm Based On Optimal Quadratic Spline Collocation And Parareal Deferred Correction For Parabolic Pdes, Jun Liu, Yan Wang, Rongjian Li

Computer Science Faculty Publications

Parareal is a kind of time parallel numerical methods for time-dependent systems. In this paper, we consider a general linear parabolic PDE, use optimal quadratic spline collocation (QSC) method for the space discretization, and proceed with the parareal technique on the time domain. Meanwhile, deferred correction technique is also used to improve the accuracy during the iterations. In fact, the optimal QSC method is a correction of general QSC method. Along the temporal direction we embed the iterations of deferred correction into parareal to construct a hybrid method, parareal deferred correction (PDC) method. The error estimation is presented and the …

Interactively Cutting And Constraining Vertices In Meshes Using Augmented Matrices, Yu-Hong Yeung, Jessica Crouch, Alex Pothen

Computer Science Faculty Publications

We present a finite-element solution method that is well suited for interactive simulations of cutting meshes in the regime of linear elastic models. Our approach features fast updates to the solution of the stiffness system of equations to account for real-time changes in mesh connectivity and boundary conditions. Updates are accomplished by augmenting the stiffness matrix to keep it consistent with changes to the underlying model, without refactoring the matrix at each step of cutting. The initial stiffness matrix and its Cholesky factors are used to implicitly form and solve a Schur complement system using an iterative solver. As changes …

Experimental Apparatus For Quantum Pumping With A Bose-Einstein Condensate., Megan K. Ivory

Dissertations, Theses, and Masters Projects

No abstract provided.

Sm And Dy Interaction With Dissolved Organic Matter (Dom) In Freshwater Measured By Ion-Selective Electrode And Fluorescence Quenching Analytical Techniques, Alexandra Carvajal

Theses and Dissertations (Comprehensive)

With the increased demand for lanthanide metals in various industries, companies are looking into mining of these metals in Northern Canada. The release of these metals into the environment may have adverse effect on aquatic ecosystems; thus, it is important to understand potential toxicological effects of lanthanides on aquatic organisms. One way to predict these effects is by using a Biotic Ligand Model (BLM). Although incorporation of lanthanides into the model will require a substantial amount of future research, initial studies into speciation and toxicity can provide a useful basis for future reference. There are two main objectives to this …

Epr Paradox, Nonlocality, And Entanglement In Multi-Qubit Systems, Raja Emlik

Theses and Dissertations (Comprehensive)

Bell inequalities were formulated by John Bell to test the possible violation of local realistic theories by quantum mechanical systems. It was shown that entangled quantu-m states of multiple particles violate various Bell’s inequalities. This proved that quan-tum mechanics allows correlations between spatially separated systems that have no classical analogue. The main focus of this work is to investigate genuine multiqubit non-locality in families of entangled 3 and 4-qubit pure states by studying a Bell-type inequality that is violated only if all qubits are non-locally correlated. We numerically study the relationship between entanglement and violation of the Svetlichny Bell-type inequality. …

Comparing The Regio- And Enantioselectivity Of Inverting Versus Retaining Epoxide Hydrolases, Mark A. Aliwalas

Theses and Dissertations (Comprehensive)

Epoxide hydrolases (EHs) are enzymes that catalyze the ring opening of an epoxide, yielding a vicinal diol. This exciting class of enzymes is often associated with natural product and small molecule biosynthesis. One interesting class of natural products that epoxide hydrolases are involved in the biosynthesis of is the enediynes. Previously, 5 enediyne-associated epoxide hydrolases have been characterized, revealing an inverting-versus-retaining paradigm for enediyne epoxide hydrolases. The work described herein sets the table for future studies involving the probing of the α/β-epoxide hydrolase mechanism for styrene oxide. Kinetic and regioselectivity characterization of the enediyne-associated CynF and SghF has determined that …

Choosing A Repository Platform: Open Source Vs. Hosted Solutions, Hillary Corbett, Jimmy Ghaphery, Lauren Work, Sam Byrd

VCU Libraries Faculty and Staff Publications

Discusses selection of a locally hosted, open-source system (DSpace/Fedora) versus a cloud-hosted, proprietary system (Digital Commons), it is important to note that these examples are merely illustrative. Libraries have a range of choices for repository software that includes open source and proprietary in any number of support environments, and exemplary repositories are flourishing on a variety of systems, both open source and proprietary. This chapter focuses on the differences between proprietary and open-source solutions, but also demonstrates how and why libraries choose a repository system. In writing about this process, we realized that it was important to acknowledge that there …

On Shelf-Slope Water Mass Exchanges Near Washington Canyon And Norfolk Canyon In The Mid-Atlantic Bight, Haixing Wang

Dissertations, Theses, and Masters Projects

The physical exchanges between shelf and slope water masses are important drivers of biological productivity in the shelfbreak region of the Mid-Atlantic Bight (MAB). Based on two ocean glider surveys that were conducted in Autumn 2013, and concurrent wind and satellite based sea surface height observations, this study investigates the dynamic mechanisms of wind, surface height variation, water column hydrographic structure, and canyon topography in driving shelf-slope water mass exchanges across the shelfbreak near Norfolk Canyon and Washington Canyon in the MAB. Over the outer shelf, sea surface height variation and wind are important drivers of cross-shelfbreak transport through geostrophic …

Gis Data: City Of Chesapeake Shoreline Management Model, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, David Stanhope, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Data

The Shoreline Management Model is a GIS spatial model that determines appropriate shoreline best management practices using available spatial data and decision tree logic. Available shoreline conditions used in the model include the presence or absence of tidal marshes, beaches, and forested riparian buffers, bank vegetation cover, bank height, wave exposure (fetch), nearshore water depth, and proximity of coastal development to the shoreline. The model output for shoreline best management practices is displayed in the locality Comprehensive Map Viewer. One GIS shapefile is developed that describes two arcs or lines representing practices in the upland area and practices at the …

Population Dynamics Of Gelatinous Zooplankton In The Chesapeake Bay And Sargasso Sea, And Effects On Carbon Export, Joshua Paul Stone

Dissertations, Theses, and Masters Projects

Gelatinous zooplankton (GZ; cnidarians, ctenophores, and pelagic tunicates) periodically are the dominant members of the zooplankton throughout the majority of the world’s oceans. their unique body plans and life cycles allow them to rapidly take advantage of favorable environmental conditions, which has far-ranging consequences for food web dynamics and biogeochemical cycles. GZ populations have been speculated to respond to anthropogenic changes, but few long-term studies exist to test this hypothesis and even fewer have examined the consequent effects on carbon export. I analyzed two long-term time series in the Chesapeake Bay and one in the Sargasso Sea for annual and …

Disorder Effects In Dirac Heterostructures, Martin Alexander Rodriguez-Vega

Dissertations, Theses, and Masters Projects

In this dissertation, we study theoretically heterostructures based on Dirac mate- rials, i.e. materials, such as graphene in which the electrons behave as massless Dirac fermions at low energies. We first examine how the presence of long-range disorder affects the electronic ground state of a double layer graphene heterostruc- ture formed by two graphene layers separated by a thin dielectric film. We then identify the necessary conditions for the formation of an interlayer exciton conden- sate in such a system. We also comment on the effect of long-range disorder on the broken symmetry ground state induced by electron-electron interactions in …

Molecular And Performance Properties Of Poly(Amides & Imides) And The Use Of Graphene Oxide Nano-Particles For Improvement, John-Andrew Samuel Hocker

Dissertations, Theses, and Masters Projects

Macroscopic properties of polymers, and in general all types of materials, are innately related to their molecular structure and intermolecular properties. This dissertation offers insight into how the molecular structure, chain properties, and inter-molecular chain interactions within PA11 can be used to explain and predict improved macro level performance properties; and how the addition of graphene oxide nanosheets enhances the performance properties of PA11 and polyimide(ODA-BTDA) through those same intermolecular interactions. Chapter 3 describes the unexpected result that weak small organic acids at low concentrations hydrolyze a polyamide at rates approximately twice that of a water HCl solution of the …

Expanding The Scope Of Terminal Alkynes In Chemical Biology, Johnathan Charles Maza

Dissertations, Theses, and Masters Projects

The terminal alkyne is one of the most widely used chemical moieties in chemical biology. Thanks to the relative absence of this functional group in biology, it has become a widespread functional handle for a plethora of biorthogonal chemistries. Our group has extended the scope of this functionality by developing a biological variant of the Glaser-Hay coupling, which brings together two terminal alkynes to form a diyne linkage. However, our initial findings revealed that the chemistry is plagued by protein degradation due to a deleterious copper(II) hydroxyl intermediate. Herein we extend the scope of the terimanl alkyne be developing a …

Dye-Sensitized Tio2 Modified With Iron Polypyridyl Catalyst For Photocatalytic Hydrogen Evolution, Wanji Zhang

Dissertations, Theses, and Masters Projects

Artificial Photosynthesis (AP) focuses on finding a way to harness solar energy to generate a chemical fuel. TiO2 semiconductors are of interest to AP research due to its relatively low cost and widespread use as an efficient charge-separating support. This research focuses on the development of a device for photocatalytic hydrogen generation. Our approach utilizes the immobilization of iron polypyridyl catalysts and ruthenium chromophores on TiO2 through stable phosphonic acid anchoring groups.

Finding The Cutpoint Of A Continuous Covariate In A Parametric Survival Analysis Model, Kabita Joshi

Theses and Dissertations

In many clinical studies, continuous variables such as age, blood pressure and cholesterol are measured and analyzed. Often clinicians prefer to categorize these continuous variables into different groups, such as low and high risk groups. The goal of this work is to find the cutpoint of a continuous variable where the transition occurs from low to high risk group. Different methods have been published in literature to find such a cutpoint. We extended the methods of Contal and O’Quigley (1999) which was based on the log-rank test and the methods of Klein and Wu (2004) which was based on the …