Physical Sciences and Mathematics Commons^™

Continuous And Discrete Models For Optimal Harvesting In Fisheries, Nagham Abbas Al Qubbanchee

Masters Theses

"This work focuses on the logistic growth model, where the Gordon-Schaefer model is considered in continuous time. We view the Gordon-Schaefer model as a bioeconomic equation involved in the fishing business, considering biological rates, carrying capacity, and total marginal costs and revenues. In [25], the authors illustrate the analytical solution of the Schaefer model using the integration by parts method and two theorems. The theorems have many assumptions with many different strategies. Due to the nature of the problem, the optimal control system involves many equations and functions, such as the second root of the equation. We concentrate on Theorem …

Forearc Erosion In Response To Megathrust Plate Coupling Along The Wairarapa Coastline, New Zealand, Chantel E. Jensen

WWU Graduate School Collection

How the subduction zone earthquake cycle contributes to uplift, erosion, and permanent deformation of the overlying forearc remains largely unknown. The Hikurangi subduction zone (HSZ), along the east coast of the North Island of New Zealand, provides a unique location to examine the effects of subduction coupling on forearc deformation over multiple millennia. There, the Wairarapa coastline runs parallel to the HSZ and spans a transitional boundary between locked and freely slipping portions of the plate interface. Using digital topographic analysis and catchment-averaged erosion rates from ¹⁰Be in fluvial sands, I examined the geomorphology of the HSZ forearc to …

To Erupt Or Not To Erupt? That Is The Question: Extremely High Levels Of Background Seismicity And Lack Of Eruptivity From 2003-2019 At Gareloi Volcano, Aleutian Islands, Alaska, Kiana Tamarie Harris

WWU Graduate School Collection

Mount Gareloi, one of the westernmost volcanoes in the Aleutian arc, has not erupted since 1989, yet it continuously exhibits extremely high levels of background seismicity. Hundreds of volcanic earthquakes are recorded per day on the island since seismometer installation in 2003. I analyzed and classified seismic data collected from 2003-2019 to explore the geophysical processes causing this consistent seismicity with no subsequent eruptive activity. Analysis of waveform and corresponding spectra indicate the vast majority of Gareloi earthquakes are characterized by frequencies between 1 and 5 Hz, which are typical of long-period (LP) events, and these events are particularly dominant …

Blood Replacement Therapy By Generation Of Polymeric Recombinant Hemoglobin Using “Click Chemistry” And Circular Tandem Repeat Proteins, Johanna Hamilton Urbach

WWU Graduate School Collection

Our work with hemoglobin-based oxygen carriers (HBOCs) is focused on developing a hemoglobin (Hb) polymer that can be used as a blood replacement in critical care at an affordable cost. For medical use, the Hb must be polymeric since cell-free Hb has multiple adverse side effects when it is not encapsulated in a red blood cell. These include kidney damage and heme-induced toxicity, which is due to cell-free Hb’s ability to extravasate. Challenges in making HBOCs, that have been observed in the past, are low protein expression yields and heterogeneity in polymeric Hb products produced by chemical crosslinking. In conducting …

Covalent Modifications As Targets And Means For Research In Intrinsically Disordered Proteins, Derek Mccaffery

WWU Graduate School Collection

A reported 33% of eukaryotic proteins are predicted to contain intrinsically disordered regions (IDRs) over 30 residues in length. IDRs are regions of protein which natively exist in an unfolded conformation. Due to their highly dynamic nature, many common methods of inquiry such as crystallography and NMR can be thwarted. As a result, valuable analysis such as probing function, dynamics and binding interfaces are unable to be performed. To minimize these problems, researchers typically study shorter IDRs. We probed fragments of plant protein villin 4 (VLN4) for covalent modifications to explore its regulation and degradation. Disordered regions of proteins have …

Methane Emissions In Port Susan Bay: The Missing Link In Carbon Accounting, Rachel S. Yonemura

WWU Graduate School Collection

Coastal wetlands have the ability to sequester large amounts of “blue carbon” in sediments that would otherwise act as a harmful greenhouse gas in the atmosphere. The recently restored marsh in Port Susan Bay, Washington sequesters 231gC m^-2 yr^-1 and accretes 2.75cm of sediment per year. While this restored marsh stores nearly twice as much carbon as the nearby natural marsh, it can also emit methane, a potent greenhouse gas that has the potential to outweigh the benefits of carbon storage. It is critical to measure these emissions to determine if this site is a net source or …

Tire-Wear-Particle Leachate Toxicity To Americamysis Bahia: Analysis Of Sublethal And Molecular Effects, Karrin Leazer

WWU Graduate School Collection

Tire-wear particles (TWPs) are considered among the largest contributors of microplastics to the environment. They are subject to break-down due to environmental weathering, which allows for potentially toxic chemicals to be released from and sorbed onto the particles. In this study, leachate generated from “weathered” and “un-weathered” TWPs were used for sublethal toxicity tests with Americamysis bahia. Organisms were exposed for 2, 4, and 6 days and the effects endpoints included changes in respiration rate and molecular responses (i.e., changes in the abundance of transcripts after 4 days of exposure). A threshold for stimulated respiration rate was detected for weathered …

Bioaccumulation Of Metals In Whatcom County Estuaries By Native Tidal Plants, Margaret Critchlow

WWU Graduate School Collection

Estuaries are unique environments which provide many needed ecosystem services, but are threatened by anthropogenic activities. Contamination with metals represents a significant concern, as even small amounts can persist in the soil and affect biological functions. Phytoremediation, or the use of plants to take up contaminants from the soil, is one possible solution. There is a lack of research on estuarine phytoremediators native to the Pacific Northwest, as well as the ultimate fate of these metals following plant senescence. In this study, we evaluated the total metal concentration at three Whatcom County, WA estuaries and sampled four native plant species …

Transport Mechanisms Of Nitrate On The Washington Shelf, Liesl G. Danyluk

WWU Graduate School Collection

Nutrient supply is a fundamental driver of primary productivity, and often a limiting factor for organism growth in both open-ocean and coastal systems. Continental shelves are locations of high primary productivity in the world’s oceans because of high nutrient supply. Understanding the dominant transport mechanisms of nutrients in these locations is paramount to understanding patterns in primary productivity. While there have been extensive studies of nutrient transport and productivity on the Pacific Northwestern coast of the US (Davis et al., 2014, Siedlecki et al., 2015, Ware and Thomson, 2005, Banas et al., 2009), there is renewed interest in understanding these …

Soil Mesofauna And Microbial Community Response To Mixed Biochar And Compost Application In A Skagit Silt Loam, Jameson Goff

WWU Graduate School Collection

I sampled Skagit silt loam soils from a field trial at the WSU NWREC where biochar and compost were added to potato crops in late spring pre-planting. Soil mesofauna were sampled at mid and late-summer, while soil microbes were sampled at late summer exclusively. Soil treatments included mixed biochar and compost, compost-only, and an unamended control. Mesofauna were extracted with Berlese funnels and sorted to functional groups. F:B ratios and total microbial C were determined using microbiometer test kits. To test whether biochar and compost induced changes to soil mesofauna communities, I used permutational ANOVA. Differences in F:B ratios and …

A Mastcam Multispectral Investigation Of Rock Variability In Gale Crater, Mars: Implications For Alteration In The Clay-Sulfate Transition Of Mount Sharp, Alivia Eng

WWU Graduate School Collection

The Mars Science Laboratory Curiosity rover has explored over 650 m of strata since landing in 2012. After leaving Vera Rubin Ridge (VRR), the rover traversed though the phyllosilicate-rich region, Glen Torridon, and the Mg-sulfate-bearing strata that lies above it, with excursions onto the Greenheugh Pediment and Amapari Marker Band. These unique stratigraphic units were investigated using Curiosity's instrument suite which includes the Mast Camera (Mastcam) pair of multispectral imagers. Mastcam’s narrowband filters are sensitive to iron-bearing phases and some hydrated minerals. We used Mastcam spectra, in combination with chemical data from Curiosity’s CheMin, APXS and ChemCam instruments, to assess …

Streaminghub: Interactive Stream Analysis Workflows, Yasith Jayawardana, Vikas G. Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Reusable data/code and reproducible analyses are foundational to quality research. This aspect, however, is often overlooked when designing interactive stream analysis workflows for time-series data (e.g., eye-tracking data). A mechanism to transmit informative metadata alongside data may allow such workflows to intelligently consume data, propagate metadata to downstream tasks, and thereby auto-generate reusable, reproducible analytic outputs with zero supervision. Moreover, a visual programming interface to design, develop, and execute such workflows may allow rapid prototyping for interdisciplinary research. Capitalizing on these ideas, we propose StreamingHub, a framework to build metadata propagating, interactive stream analysis workflows using visual programming. We conduct …

Segmenting Technical Drawing Figures In Us Patents, Md Reshad Ul Hoque, Xin Wei, Muntabir Hasan Choudhury, Kehinde Ajayi, Martin Gryder, Jian Wu, Diane Oyen

Computer Science Faculty Publications

Image segmentation is the core computer vision problem for identifying objects within a scene. Segmentation is a challenging task because the prediction for each pixel label requires contextual information. Most recent research deals with the segmentation of natural images rather than drawings. However, there is very little research on sketched image segmentation. In this study, we introduce heuristic (point-shooting) and deep learning-based methods (U-Net, HR-Net, MedT, DETR) to segment technical drawings in US patent documents. Our proposed methods on the US Patent dataset achieved over 90% accuracy where transformer performs well with 97% segmentation accuracy, which is promising and computationally …

Lithofacies Characterization Of Marine Shelf Shale And Implicaitons On Depositional Conditions And Processes On The Continental Shelf — A Case Study Of The Upper-Cretaceous Tuscaloosa Marine Shale In Louisiana And Mississippi, U.S.A., Efren Mendez Jr

Masters Theses

"The Upper Cretaceous Tuscaloosa Marine Shale (TMS) is an unconventional shale reservoir deposited on the continental shelf of the northern Gulf of Mexico Basin. Previous studies have focused on sequence stratigraphy, thermal modeling, and well-log correlations. However, a limited understanding of the stratigraphic heterogeneity of the TMS is yet to be studied. This study aims to characterize the stratigraphic heterogeneity of the TMS using core, petrographic, and well-log analyses to better understand the depositional conditions and processes that occur on the continental shelf. The TMS has been classified into four lithofacies of very fine sands – coarse silts (LF1), medium-fine …

Adsorption Of Arsenic Onto River Sediments, Leticia Augusta Dos Santos Ferreira

Masters Theses

“Previous studies have noted the relationship between shallow groundwater rich in sodium (Na) and bicarbonate (HCO₃) and elevated levels of dissolved arsenic. However, most experimental work on arsenic adsorption in the presence of HCO₃ and differing Na/Ca ratios has proven difficult to extrapolate to natural systems because of differences in tested mineral compositions and component concentrations. In this study, I performed a series of adsorption experiments using river sediments to evaluate the influence of HCO₃ and monovalent/divalent cations on the extent of arsenic adsorption onto natural sediment in groundwater.

Batch adsorption (kinetics, equilibrium, and metal loading) …

M-Cubes: An Efficient And Portable Implementation Of Multi-Dimensional Integration For Gpus, Ioannis Sakiotis, Kamesh Arumugam, Marc Paterno, Desh Ranjan, Balŝa Terzić, Mohammad Zubair

Computer Science Faculty Publications

The task of multi-dimensional numerical integration is frequently encountered in physics and other scientific fields, e.g., in modeling the effects of systematic uncertainties in physical systems and in Bayesian parameter estimation. Multi-dimensional integration is often time-prohibitive on CPUs. Efficient implementation on many-core architectures is challenging as the workload across the integration space cannot be predicted a priori. We propose m-Cubes, a novel implementation of the well-known Vegas algorithm for execution on GPUs. Vegas transforms integration variables followed by calculation of a Monte Carlo integral estimate using adaptive partitioning of the resulting space. mCubes improves performance on GPUs by maintaining relatively …

Camouflaged Poisoning Attack On Graph Neural Networks, Chao Jiang, Yi He, Richard Chapman, Hongyi Wu

Computer Science Faculty Publications

Graph neural networks (GNNs) have enabled the automation of many web applications that entail node classification on graphs, such as scam detection in social media and event prediction in service networks. Nevertheless, recent studies revealed that the GNNs are vulnerable to adversarial attacks, where feeding GNNs with poisoned data at training time can lead them to yield catastrophically devastative test accuracy. This finding heats up the frontier of attacks and defenses against GNNs. However, the prior studies mainly posit that the adversaries can enjoy free access to manipulate the original graph, while obtaining such access could be too costly in …

Spaghetti Tracer: A Framework For Tracing Semiregular Filamentous Densities In 3d Tomograms, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D …

Loss Of Acta2 In Cardiac Fibroblasts Does Not Prevent The Myofibroblast Differentiation Or Affect The Cardiac Repair After Myocardial Infarction, Yuxia Li, Chaoyang Li, Qianglin Liu, Leshan Wang, Adam X. Bao, Jangwook P. Jung, Sanjeev Dodlapati, Jingwen Sun, Peidong Gao, Xujia Zhang, Joseph Francis, Jeffery D. Molkentin, Xing Fu

Computer Science Faculty Publications

In response to myocardial infarction (MI), quiescent cardiac fibroblasts differentiate into myofibroblasts mediating tissue repair. One of the most widely accepted markers of myofibroblast differentiation is the expression of Acta2 which encodes smooth muscle alpha-actin (SMαA) that is assembled into stress fibers. However, the requirement of Acta2/SMαA in the myofibroblast differentiation of cardiac fibroblasts and its role in post-MI cardiac repair remained unknown. To answer these questions, we generated a tamoxifen-inducible cardiac fibroblast-specific Acta2 knockout mouse line. Surprisingly, mice that lacked Acta2 in cardiac fibroblasts had a normal post-MI survival rate. Moreover, Acta2 deletion did …

Github Discussions: An Exploratory Study Of Early Adoption, Hideaki Hata, Nicole Novielli, Sebastian Baltes, Raula Kula, Christoph Treude

Research Collection School Of Computing and Information Systems

Discussions is a new feature of GitHub for asking questions or discussing topics outside of specific Issues or Pull Requests. Before being available to all projects in December 2020, it had been tested on selected open source software projects. To understand how developers use this novel feature, how they perceive it, and how it impacts the development processes, we conducted a mixed-methods study based on early adopters of GitHub discussions from January until July 2020. We found that: (1) errors, unexpected behavior, and code reviews are prevalent discussion categories; (2) there is a positive relationship between project member involvement and …

Github Repositories With Links To Academic Papers: Public Access, Traceability, And Evolution, Supatsara Wattanakriengkrai, Bodin Chinthanet, Hideaki Hata, Raula Kula, Christoph Treude, Jin Guo, Kenichi Matsumoto

Research Collection School Of Computing and Information Systems

Traceability between published scientific breakthroughs and their implementation is essential, especially in the case of open-source scientific software which implements bleeding-edge science in its code. However, aligning the link between GitHub repositories and academic papers can prove difficult, and the current practice of establishing and maintaining such links remains unknown. This paper investigates the role of academic paper references contained in these repositories. We conduct a large-scale study of 20 thousand GitHub repositories that make references to academic papers. We use a mixed-methods approach to identify public access, traceability and evolutionary aspects of the links. Although referencing a paper is …

Lidar-Landsat Covariance For Predicting Canopy Fuels, Margaret D. Epstein

Graduate Student Theses, Dissertations, & Professional Papers

Managing wildfires in the western United States is becoming increasingly complex. Visualizing and quantifying canopy structures allows fire managers to both plan for fire and track recovery. Light detecting and ranging, or LiDAR can measure forests in three dimensions, but has limited spatial and temporal coverage. LiDAR-Landsat covariance uses machine learning to fill in the spatial and temporal gaps of LiDAR coverage with supplemental Landsat imagery. However, in order to capture real forest dynamics, a model needs to be stable enough to detect long term trends, sensitive to episodic disturbance, and general enough to work on multiple landcovers. The purpose …

Hydrogeomorphic Response Of Steep Streams Following Severe Wildfire In The Western Cascades, Oregon, David Matthew Busby

Graduate Student Theses, Dissertations, & Professional Papers

Severe wildfire may alter the morphologic resilience of steep mountain streams by increasing peak discharges, elevating inputs of sediment and wood into channels, and increasing susceptibility to landslides and debris flows. In the Pacific Northwest, where mean annual precipitation is high and mean fire return intervals range from decades to centuries, understanding of steep stream response to fire is limited. In 2020, the Western Cascade Range, Oregon, experienced wildfire of historic magnitude and severity. The objective of this study was to evaluate the hydrologic and geomorphic response of steep streams to the 2020 fires. I assessed streamflow, instream wood, and …

Action-Centric Relation Transformer Network For Video Question Answering, Jipeng Zhang, Jie Shao, Rui Cao, Lianli Gao, Xing Xu, Heng Tao Shen

Research Collection School Of Computing and Information Systems

Video question answering (VideoQA) has emerged as a popular research topic in recent years. Enormous efforts have been devoted to developing more effective fusion strategies and better intra-modal feature preparation. To explore these issues further, we identify two key problems. (1) Current works take almost no account of introducing action of interest in video representation. Additionally, there exists insufficient labeling data on where the action of interest is in many datasets. However, questions in VideoQA are usually action-centric. (2) Frame-to-frame relations, which can provide useful temporal attributes (e.g., state transition, action counting), lack relevant research. Based on these observations, we …

M2lens: Visualizing And Explaining Multimodal Models For Sentiment Analysis, Xingbo Wang, Jianben He, Zhihua Jin, Muqiao Yang, Yong Wang, Huamin Qu

Research Collection School Of Computing and Information Systems

Multimodal sentiment analysis aims to recognize people's attitudes from multiple communication channels such as verbal content (i.e., text), voice, and facial expressions. It has become a vibrant and important research topic in natural language processing. Much research focuses on modeling the complex intra- and inter-modal interactions between different communication channels. However, current multimodal models with strong performance are often deep-learning-based techniques and work like black boxes. It is not clear how models utilize multimodal information for sentiment predictions. Despite recent advances in techniques for enhancing the explainability of machine learning models, they often target unimodal scenarios (e.g., images, sentences), and …

Center For Coastal Resources Management Annual Report 2021, Center For Coastal Resources Management

Reports

No abstract provided.

Artificial Intelligence And Machine Learning In Optical Information Processing: Introduction To The Feature Issue, Khan Iftekharuddin, Chrysanthe Preza, Abdul Ahad S. Awwal, Michael E. Zelinski

Electrical & Computer Engineering Faculty Publications

This special feature issue covers the intersection of topical areas in artificial intelligence (AI)/machine learning (ML) and optics. The papers broadly span the current state-of-the-art advances in areas including image recognition, signal and image processing, machine inspection/vision and automotive as well as areas of traditional optical sensing, interferometry and imaging.

"Mystify": A Proactive Moving-Target Defense For A Resilient Sdn Controller In Software Defined Cps, Mohamed Azab, Mohamed Samir, Effat Samir

Electrical & Computer Engineering Faculty Publications

The recent devastating mission Cyber–Physical System (CPS) attacks, failures, and the desperate need to scale and to dynamically adapt to changes, revolutionized traditional CPS to what we name as Software Defined CPS (SD-CPS). SD-CPS embraces the concept of Software Defined (SD) everything where CPS infrastructure is more elastic, dynamically adaptable and online-programmable. However, in SD-CPS, the threat became more immanent, as the long-been physically-protected assets are now programmatically accessible to cyber attackers. In SD-CPSs, a network failure hinders the entire functionality of the system. In this paper, we present MystifY, a spatiotemporal runtime diversification for Moving-Target Defense (MTD) to secure …

Broadband Dielectric Spectroscopic Detection Of Ethanol: A Side-By-Side Comparison Of Zno And Hkust-1 Mofs As Sensing Media, Papa K. Amoah, Zeinab Mohammed Hassan, Pengtao Lin, Engelbert Redel, Helmut Baumgart, Yaw S. Obeng

Electrical & Computer Engineering Faculty Publications

The most common gas sensors are based on chemically induced changes in electrical resistivity and necessarily involve making imperfect electrical contacts to the sensing materials, which introduce errors into the measurements. We leverage thermal- and chemical-induced changes in microwave propagation characteristics (i.e., S-parameters) to compare ZnO and surface-anchored metal-organic-framework (HKUST-1 MOF) thin films as sensing materials for detecting ethanol vapor, a typical volatile organic compound (VOC), at low temperatures. We show that the microwave propagation technique can detect ethanol at relatively low temperatures (<100 >°C), and afford new mechanistic insights that are inaccessible with the traditional dc-resistance-based measurements. In addition, …

Surface Morphologies In A Mars-Analog Ca-Sulfate Salar, High Andes, Northern Chile, Nancy W. Hinman, Michael H. Hofmann, Kimberly Warren-Rhodes, Michael S. Phillips, Nora Noffke, Nathalie A. Cabrol, Guillermo Chong Diaz, Cecilia Demergasso, Cinthya Tebes-Cayo, Oscar Cabestro, Janice L. Bishop, Virginia C. Gulick, David Summers, Pablo Sobron, Michael Mcinenly, Jeffrey Moersch, Constanza Rodriguez, Philippe Sarazzin, Kevin L. Rhodes, Camila Javiera Riffo Contreras, David Wettergreen, Victor Parro

OES Faculty Publications

Salar de Pajonales, a Ca-sulfate salt flat in the Chilean High Andes, showcases the type of polyextreme environment recognized as one of the best terrestrial analogs for early Mars because of its aridity, high solar irradiance, salinity, and oxidation. The surface of the salar represents a natural climate-transition experiment where contemporary lagoons transition into infrequently inundated areas, salt crusts, and lastly dry exposed paleoterraces. These surface features represent different evolutionary stages in the transition from previously wetter climatic conditions to much drier conditions today. These same stages closely mirror the climate transition on Mars from a wetter early Noachian to …