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Articles 19921 - 19950 of 302451

Full-Text Articles in Physical Sciences and Mathematics

Quantumeyes: Towards A Better Interpretability Of Quantum Circuits, Shaolun Ruan, Yong Wang, Paul Robert Griffin, Qiang Guan Jan 2023

Quantumeyes: Towards A Better Interpretability Of Quantum Circuits, Shaolun Ruan, Yong Wang, Paul Robert Griffin, Qiang Guan

Research Collection School Of Computing and Information Systems

Quantum computing offers significant speedup compared to classical computing, which has led to a growing interest among users in learning and applying quantum computing across various applications. However, quantum circuits, which are fundamental for implementing quantum algorithms, can be challenging for users to understand due to their underlying logic, such as the temporal evolution of quantum states and the effect of quantum amplitudes on the probability of basis quantum states. To fill this research gap, we propose , an interactive visual analytics system to enhance the interpretability of quantum circuits through both global and local levels. For the global-level analysis, …

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Automatic Detection And Analysis Towards Malicious Behavior In Iot Malware, Sen Li, Mengmeng Ge, Ruitao Feng, Xiaohong Li, Kwok Yan Lam Jan 2023

Automatic Detection And Analysis Towards Malicious Behavior In Iot Malware, Sen Li, Mengmeng Ge, Ruitao Feng, Xiaohong Li, Kwok Yan Lam

Research Collection School Of Computing and Information Systems

Our society is rapidly moving towards the digital age, which has led to a sharp increase in IoT networks and devices. This growth requires more network security professionals, who are focused on protecting IoT systems. One crucial task is to analyze malicious software to gain a deeper understanding of its functionalities and response methods. However, malware analysis is a complex process that requires the use of various analysis tools, including advanced reverse engineering techniques. For beginners, parsing complex binary data can be particularly challenging as they may be strange with these tools and the basic principles of analysis. Even for …

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Claimdistiller: Scientific Claim Extraction With Supervised Contrastive Learning, Xin Wei, Md Reshad Ul Hoque, Jian Wu, Jiang Li Jan 2023

Claimdistiller: Scientific Claim Extraction With Supervised Contrastive Learning, Xin Wei, Md Reshad Ul Hoque, Jian Wu, Jiang Li

Computer Science Faculty Publications

The growth of scientific papers in the past decades calls for effective claim extraction tools to automatically and accurately locate key claims from unstructured text. Such claims will benefit content-wise aggregated exploration of scientific knowledge beyond the metadata level. One challenge of building such a model is how to effectively use limited labeled training data. In this paper, we compared transfer learning and contrastive learning frameworks in terms of performance, time and training data size. We found contrastive learning has better performance at a lower cost of data across all models. Our contrastive-learning-based model ClaimDistiller has the highest performance, boosting …

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An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He Jan 2023

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

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Deeppatent2: A Large-Scale Benchmarking Corpus For Technical Drawing Understanding, Kehinde Ajayi, Xin Wei, Martin Gryder, Winston Shields, Jian Wu, Shawn M. Jones, Michal Kucer, Diane Oyen Jan 2023

Deeppatent2: A Large-Scale Benchmarking Corpus For Technical Drawing Understanding, Kehinde Ajayi, Xin Wei, Martin Gryder, Winston Shields, Jian Wu, Shawn M. Jones, Michal Kucer, Diane Oyen

Computer Science Faculty Publications

Recent advances in computer vision (CV) and natural language processing have been driven by exploiting big data on practical applications. However, these research fields are still limited by the sheer volume, versatility, and diversity of the available datasets. CV tasks, such as image captioning, which has primarily been carried out on natural images, still struggle to produce accurate and meaningful captions on sketched images often included in scientific and technical documents. The advancement of other tasks such as 3D reconstruction from 2D images requires larger datasets with multiple viewpoints. We introduce DeepPatent2, a large-scale dataset, providing more than 2.7 million …

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Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu Jan 2023

Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu

Computer Science Faculty Publications

We describe our experience porting FUN3D’s CUDA-optimized kernels to Intel oneAPI SYCL.We faced several challenges, including foremost the suboptimal performance of the oneAPI code on Intel’s new data center GPU. Suboptimal performance of the oneAPI code was due primarily to high register spills, memory latency, and poor vectorization. We addressed these issues by implementing the kernels using Intel oneAPI’s Explicit SIMD SYCL extension (ESIMD) API. The ESIMD API enables the writing of explicitly vectorized kernel code, gives more precise control over register usage and prefetching, and better handles thread divergence compared to SYCL. The ESIMD code outperforms the optimized SYCL …

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Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis Jan 2023

Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis

Computer Science Faculty Publications

This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete …

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Dial "N" For Nxdomain: The Scale, Origin, And Security Implications Of Dns Queries To Non-Existent Domains, Gunnan Liu, Lin Jin, Shuai Hao, Yubao Zhang, Daiping Liu, Angelos Stavrou, Haining Wang Jan 2023

Dial "N" For Nxdomain: The Scale, Origin, And Security Implications Of Dns Queries To Non-Existent Domains, Gunnan Liu, Lin Jin, Shuai Hao, Yubao Zhang, Daiping Liu, Angelos Stavrou, Haining Wang

Computer Science Faculty Publications

Non-Existent Domain (NXDomain) is one type of the Domain Name System (DNS) error responses, indicating that the queried domain name does not exist and cannot be resolved. Unfortunately, little research has focused on understanding why and how NXDomain responses are generated, utilized, and exploited. In this paper, we conduct the first comprehensive and systematic study on NXDomain by investigating its scale, origin, and security implications. Utilizing a large-scale passive DNS database, we identify 146,363,745,785 NXDomains queried by DNS users between 2014 and 2022. Within these 146 billion NXDomains, 91 million of them hold historic WHOIS records, of which 5.3 million …

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Toward A Generative Modeling Analysis Of Clas Exclusive 2𝜋 Photoproduction, T. Alghamdi, Y. Alanazi, M. Battaglieri, Ł. Bibrzycki, A. V. Golda, A. N. Hiller Blin, E. L. Isupov, Y. Li, L. Marsicano, W. Melnitchouk, V. I. Mokeev, G. Montaña, A. Pilloni, N. Sato, A. P. Szczepaniak, T. Vittorini Jan 2023

Toward A Generative Modeling Analysis Of Clas Exclusive 2𝜋 Photoproduction, T. Alghamdi, Y. Alanazi, M. Battaglieri, Ł. Bibrzycki, A. V. Golda, A. N. Hiller Blin, E. L. Isupov, Y. Li, L. Marsicano, W. Melnitchouk, V. I. Mokeev, G. Montaña, A. Pilloni, N. Sato, A. P. Szczepaniak, T. Vittorini

Computer Science Faculty Publications

AI-supported algorithms, particularly generative models, have been successfully used in a variety of different contexts. This work employs a generative modeling approach to unfold detector effects specifically tailored for exclusive reactions that involve multiparticle final states. Our study demonstrates the preservation of correlations between kinematic variables in a multidimensional phase space. We perform a full closure test on two-pion photoproduction pseudodata generated with a realistic model in the kinematics of the Jefferson Lab CLAS g11 experiment. The overlap of different reaction mechanisms leading to the same final state associated with the CLAS detector’s nontrivial effects represents an ideal test case …

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A Hybrid Deep Learning Approach For Crude Oil Price Prediction, Hind Aldabagh, Xianrong Zheng, Ravi Mukkamala Jan 2023

A Hybrid Deep Learning Approach For Crude Oil Price Prediction, Hind Aldabagh, Xianrong Zheng, Ravi Mukkamala

Computer Science Faculty Publications

Crude oil is one of the world’s most important commodities. Its price can affect the global economy, as well as the economies of importing and exporting countries. As a result, forecasting the price of crude oil is essential for investors. However, crude oil price tends to fluctuate considerably during significant world events, such as the COVID-19 pandemic and geopolitical conflicts. In this paper, we propose a deep learning model for forecasting the crude oil price of one-step and multi-step ahead. The model extracts important features that impact crude oil prices and uses them to predict future prices. The prediction model …

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Charged Track Reconstruction With Artificial Intelligence For Clas12, Gagik Gavalian, Polykarpos Thomadakis, Angelos Angelopoulos, Nikos Chrisochoides Jan 2023

Charged Track Reconstruction With Artificial Intelligence For Clas12, Gagik Gavalian, Polykarpos Thomadakis, Angelos Angelopoulos, Nikos Chrisochoides

Computer Science Faculty Publications

In this paper, we present the results of charged particle track reconstruction in CLAS12 using artificial intelligence. In our approach, we use neural networks working together to identify tracks based on the raw signals in the Drift Chambers. A Convolutional Auto-Encoder is used to de-noise raw data by removing the hits that do not satisfy the patterns for tracks, and second Multi-Layer Perceptron is used to identify tracks from combinations of clusters in the drift chambers. Our method increases the tracking efficiency by 50% for multi-particle final states already conducted experiments. The de-noising results indicate that future experiments can run …

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Application Of Mixture Models For Doubly Inflated Count Data, Monika Arora, N. Rao Chaganty Jan 2023

Application Of Mixture Models For Doubly Inflated Count Data, Monika Arora, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

In health and social science and other fields where count data analysis is important, zero-inflated models have been employed when the frequency of zero count is high (inflated). Due to multiple reasons, there are scenarios in which an additional count value of k > 0 occurs with high frequency. The zero- and k-inflated Poisson distribution model (ZkIP) is more appropriate for such situations. The ZkIP model is a mixture distribution with three components: degenerate distributions at 0 and k count and a Poisson distribution. In this article, we propose an alternative and computationally fast expectation–maximization (EM) algorithm to obtain the parameter …

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Deep Learning-Based Classification Of Chaotic Systems Over Phase Portraits, Sezgi̇n Kaçar, Süleyman Uzun, Burak Aricioğlu Jan 2023

Deep Learning-Based Classification Of Chaotic Systems Over Phase Portraits, Sezgi̇n Kaçar, Süleyman Uzun, Burak Aricioğlu

Turkish Journal of Electrical Engineering and Computer Sciences

This study performed a deep learning-based classification of chaotic systems over their phase portraits. To the best of the authors' knowledge, such classification studies over phase portraits have not been conducted in the literature. To that end, a dataset consisting of the phase portraits of the most known two chaotic systems, namely Lorenz and Chen, is generated for different values of the parameters, initial conditions, step size, and time length. Then, a classification with high accuracy is carried out employing transfer learning methods. The transfer learning methods used in the study are SqueezeNet, VGG-19, AlexNet, ResNet50, ResNet101, DenseNet201, ShuffleNet, and …

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An Effective Hilbert-Huang Transform-Based Approach For Dynamic Eccentricity Fault Diagnosis In Double-Rotor Double-Sided Stator Structure Axial Flux Permanent Magnet Generator Under Various Load And Speed Conditions, Makan Torabi, Yousef Alinejad Beromi Jan 2023

An Effective Hilbert-Huang Transform-Based Approach For Dynamic Eccentricity Fault Diagnosis In Double-Rotor Double-Sided Stator Structure Axial Flux Permanent Magnet Generator Under Various Load And Speed Conditions, Makan Torabi, Yousef Alinejad Beromi

Turkish Journal of Electrical Engineering and Computer Sciences

Eccentricity fault in double-sided axial flux permanent magnet generator is very difficult to be detected as the fault generated variations in terminal electrical parameters are very weak and chaotic, especially at the initial stages of the fault occurrence. In addition, one of the most important problems in any fault diagnosis approach is the investigation of load and speed variation on the proposed indices. To overcome the aforementioned difficulty and problems, this paper adopts a novelty detection algorithm based on Hilbert-Huang transform (HHT) which is a time-frequency signal analysis approach based on empirical mode decomposition and the Hilbert transform. It is …

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Early Diagnosis Of Pancreatic Cancer By Machine Learning Methods Using Urine Biomarker Combinations, İrem Acer, Firat Orhan Bulucu, Semra İçer, Fatma Lati̇foğlu Jan 2023

Early Diagnosis Of Pancreatic Cancer By Machine Learning Methods Using Urine Biomarker Combinations, İrem Acer, Firat Orhan Bulucu, Semra İçer, Fatma Lati̇foğlu

Turkish Journal of Electrical Engineering and Computer Sciences

The most common type of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC), which accounts for the vast majority of pancreatic cancers. The five-year survival rate for PDAC due to late diagnosis is 9%. Early diagnosed PDAC patients survive longer than patients diagnosed at a more advanced stage. Biomarkers can play an essential role in the early detection of PDAC to assist the health professional. Machine learning and deep learning methods are used with biomarkers obtained in recent studies for diagnostic purposes. In order to increase the survival rates of PDAC patients, early diagnosis of the disease with a noninvasive test …

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The Effects Of The Dielectric Substrate Thickness And The Loss Tangent On The Absorption Spectrum: A Comprehensive Study Considering The Resonance Type, The Ground Plane Coupling, And The Characterization Setup, Umut Köse, Evren Ekmekçi̇ Jan 2023

The Effects Of The Dielectric Substrate Thickness And The Loss Tangent On The Absorption Spectrum: A Comprehensive Study Considering The Resonance Type, The Ground Plane Coupling, And The Characterization Setup, Umut Köse, Evren Ekmekçi̇

Turkish Journal of Electrical Engineering and Computer Sciences

In this study, the effects of dielectric substrate thickness and the dielectric loss tangent on the absorption spectrum are investigated parametrically in S-band. The study has been conducted on two different absorber topologies, one is closed ring resonator (CRR) and the other is composed of a split ring resonator (SRR), to observe the effects on both LC - and dipole-type resonances. The studies on the substrate thickness have been performed both numerically and experimentally, whereas the studies on the dielectric loss tangent have been performed numerically. The results agree with the literature such that the substrate thickness has significant effects …

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Variational Autoencoder-Based Anomaly Detection In Time Series Data For Inventory Record Inaccuracy, Hali̇l Arğun, Sadetti̇n Emre Alpteki̇n Jan 2023

Variational Autoencoder-Based Anomaly Detection In Time Series Data For Inventory Record Inaccuracy, Hali̇l Arğun, Sadetti̇n Emre Alpteki̇n

Turkish Journal of Electrical Engineering and Computer Sciences

Retail companies monitor inventory stock levels regularly and manage them based on forecasted sales to sustain their market position. Inventory accuracy, defined as the difference between the warehouse stock records and the actual inventory, is critical for preventing stockouts and shortages. The root causes of inventory inaccuracy are the employee or customer theft, product damage or spoilage, and wrong shipments. In this paper, we aim at detecting inaccurate stocks of one of Turkey's largest supermarket chain using the variational autoencoder (VAE), which is an unsupervised learning method. Based on the findings, we showed that VAE is able to model the …

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Binary Text Classification Using Genetic Programming With Crossover-Based Oversampling For Imbalanced Datasets, Mona Aljero, Nazi̇fe Di̇mi̇li̇ler Jan 2023

Binary Text Classification Using Genetic Programming With Crossover-Based Oversampling For Imbalanced Datasets, Mona Aljero, Nazi̇fe Di̇mi̇li̇ler

Turkish Journal of Electrical Engineering and Computer Sciences

It is well known that classifiers trained using imbalanced datasets usually have a bias toward the majority class. In this context, classification models can present a high classification performance overall and for the majority class, even when the performance for the minority class is significantly lower. This paper presents a genetic programming (GP) model with a crossover-based oversampling technique for oversampling the imbalanced dataset for binary text classification. The aim of this study is to apply an oversampling technique to solve the imbalanced issue and improve the performance of the GP model that employed the proposed technique. The proposed technique …

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A Robust Model For Spot Virtual Machine Bidding In The Cloud Market Using Information Gap Decision Theory (Igdt), Mona Naghdehforoushha, Mehdi Dehghan Takht Fooladi, Mohammed Hossein Rezvani, Mohammad Mehdi Gilanian Sadeghi Jan 2023

A Robust Model For Spot Virtual Machine Bidding In The Cloud Market Using Information Gap Decision Theory (Igdt), Mona Naghdehforoushha, Mehdi Dehghan Takht Fooladi, Mohammed Hossein Rezvani, Mohammad Mehdi Gilanian Sadeghi

Turkish Journal of Electrical Engineering and Computer Sciences

The spot market is one of the most common cloud markets where cloud providers, such as Amazon EC2, rent their surplus computing resources at lower prices in the form of spot virtual machines (SVMs). In this market, which is often managed through an auction mechanism, users seek optimal bidding strategies for renting SVMs to minimize cost and risk. Uncertainty in the price of SVMs and their low availability/reliability is a challenging issue to bid on the user side. In this paper, we present a robust model for minimizing the cost of executing tasks by considering the uncertainty of the price …

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A New Approach To Linear Displacement Measurements Based On Hall Effect Sensors, İsmai̇l Yari̇çi̇, Yavuz Öztürk Jan 2023

A New Approach To Linear Displacement Measurements Based On Hall Effect Sensors, İsmai̇l Yari̇çi̇, Yavuz Öztürk

Turkish Journal of Electrical Engineering and Computer Sciences

Since displacement is a vital variable to be considered in many industrial applications, displacement sensing devices have been extensively studied both theoretically and experimentally. There have been also many studies on Hall effect-based displacement measurement, but for many systems linearity still remains a problem. This paper discusses different approaches to calculate the magnetic field due to a cylindrical permanent magnet and proposes a new setup geometry with 2-Hall effect sensors and a permanent magnet between them to overcome the linearity problems. Furthermore, theoretical and experimental studies of the discussed displacement sensor were presented by focusing on the linear range and …

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Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly Jan 2023

Deep Learning-Based Technique For The Perception Of The Cervical Cancer, Aya Haraz, Hossam El-Din Moustafa, Abeer Twakol Khaleel, Ahmed H. Eltanboly

Mansoura Engineering Journal

In third-world countries, cervical cancer is the most prevalent and leading cause of death. It is affected by a variety of factors, including smoking, poor nutritional status, immunological inadequacy, and prolonged use of contraception. The Pap smear test, which is intended to prevent cervical cancer, finds preneoplastic changes in cervical epithelial cells. This study framework classified cervical cancer cells from Pap smears into five specified cell types using machine learning-based classification algorithms. The SIPaKMeD database is used in this investigation. This public dataset, which was manually cropped from 966 cluster cell images taken from Pap smear slides, has 4045 isolated …

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Not Your Typical Tower Of Sauron: Solutions For Fermi Questions, September 2023, John Adam Jan 2023

Not Your Typical Tower Of Sauron: Solutions For Fermi Questions, September 2023, John Adam

Mathematics & Statistics Faculty Publications

The picture is of the tapering Chester Shot Tower, located in Chester, England. It was built in 1799 for the manufacture of lead shot for use in the Napoleonic Wars. Molten lead was poured through a sieve at the top of the tower, with the tiny droplets forming perfect spheres during the fall; these were then cooled in a vat of water at the base. This process was less labor-intensive than an earlier method using molds. It is the oldest of the three remaining shot towers in the UK. Using the parked van at the base, estimate (i) the height …

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A Conceptual Framework For Managed Aquifer Recharge In The Columbia River Basalts Of The Lower Yakima River Basin, Bethany Kharrazi Jan 2023

A Conceptual Framework For Managed Aquifer Recharge In The Columbia River Basalts Of The Lower Yakima River Basin, Bethany Kharrazi

All Master's Theses

In the Yakima River Basin in south-central Washington, increasing demands for water, overallocation of surface water, and a changing climate are leading to a loss of water storage and increasing water deficits in drought years. A warming climate has reduced snowpack in the Cascade Range, a vital reservoir for the irrigated agricultural industry which supports the basin’s economy. Managed aquifer recharge (MAR) is a sustainable and cost-effective approach for securing water supply by storing water underground for recovery during drought. Diminishing groundwater levels in regional basalt aquifers over the last several decades suggest there is significant storage available for intentional …

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Does Sediment Supply Impact The Threshold For Initial Sediment Motion In Natural, Gravel Bedded Streams?, Emily Loucks Jan 2023

Does Sediment Supply Impact The Threshold For Initial Sediment Motion In Natural, Gravel Bedded Streams?, Emily Loucks

WWU Graduate School Collection

Sediment transport in river channels control channel morphology, streamflow, and benthic ecosystems. Predicting sediment transport rates through a channel is required for sediment management for stream restoration and aquatic habitat assessment. The critical Shields stress (τ*c), is a dimensionless parameter used in sediment transport models that characterizes the river bed surface shear stress required to initiate sediment motion. The τ*c is typically assumed constant in transport models, yet compilations of field data have shown that τ*c can vary wildly, causing sediment transport models to over- or under-predict fluxes by an order of magnitude or more. Understanding …

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Paleomagnetic Determination Of Vertical Axis Block Rotation Near The Doty Fault In Southwestern Washington, Charles Linneman Jan 2023

Paleomagnetic Determination Of Vertical Axis Block Rotation Near The Doty Fault In Southwestern Washington, Charles Linneman

WWU Graduate School Collection

In this paper I present the results of paleomagnetically derived vertical axis rotations (VARs) of sites in two different flows of the Columbia River Basalt (CRB) – the 16 Ma Sentinel Bluffs member of the Grande Ronde flow and the 12 Ma Pomona Member of the Packsack Lookout – near the Doty fault in southwestern Washington. In two field seasons, I collected 99 cores from 14 sites, 11 in the Grande Ronde flow and three in the Pomona member flow. Of the 227 specimens that I demagnetized, 212 had well-defined magnetic directions. Positive fold and reversal tests results confirm the …

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Glacial Loss And Threatened Fish: The Future Of Mount Rainier’S Cold-Water Bull Trout Habitats, Kathleen C. Ewen Jan 2023

Glacial Loss And Threatened Fish: The Future Of Mount Rainier’S Cold-Water Bull Trout Habitats, Kathleen C. Ewen

WWU Graduate School Collection

Glaciers play a key ecological role in the river systems that they support. Cold-water reaches supplied by glacial ice serve as critical habitats for aquatic organisms that rely on specific thermal ranges to survive. Federally threatened Bull Trout (Salvelinus confluentus) require very cold temperatures, like those found in glacial systems, to complete their life cycles. However, glaciers are retreating due to climate change and are expected to continue diminishing throughout this century. Decreased glacial extent could result in warmer stream temperatures downstream from glaciers and, depending on the magnitude of stream temperature increase, cold-water habitats relied upon by Bull Trout …

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Structural, Mutational, And Kinetic Characterization Of Ura4, An Isocytosine Deaminase, Ashlee Hoffman Jan 2023

Structural, Mutational, And Kinetic Characterization Of Ura4, An Isocytosine Deaminase, Ashlee Hoffman

WWU Graduate School Collection

Cytosine Deaminases (CD) are a class of enzymes found in prokaryotes and fungi that have been studied in the past due to their ability to deaminate the prodrug 5-fluorocytosine (5-FC) producing 5-fluorouracil (5-FU). 5-FU is a common anti-cancer drug that can inhibit DNA synthesis leading to cancer cell death. 5-fluorocytosine can interact with digestive bacteria leading to unwanted side effects for cancer patients. Isocytosine Deaminases (ICD) are enzymes that are of interest in the treatment of cancers using Gene Directed Enzyme Prodrug Therapy (GDEPT). ICDs can deaminate the prodrug 5-fluoroisocytosine (5-FIC) also producing the drug 5-FU.  5-FIC will likely not …

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Evaluating Leaf Trait Variation In High Elevation Bristlecone Pine (Pinus Longaeva) Under Increasing Water Stress: Insights From Needle Length, Stomatal Density, And Cambial Growth, Audrey Salerno Jan 2023

Evaluating Leaf Trait Variation In High Elevation Bristlecone Pine (Pinus Longaeva) Under Increasing Water Stress: Insights From Needle Length, Stomatal Density, And Cambial Growth, Audrey Salerno

WWU Graduate School Collection

Increasing aridification caused by climate change is altering growth patterns in trees. There is revived attention on how foliar traits respond to climate and the relationship of these traits to ring width. Bristlecone pine (Pinus longaeva, DK Bailey), a long-lived conifer found at high elevations in the cool and dry intermountain west of America, is used in paleoclimate reconstructions by measurement of their annually resolvable tree rings. The species also has annually datable needles retained on their branches for an average of 45 years making it the ideal subject for research on foliar trait and growth relationships under …

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Quantifying Channel Change Following Post-Fire Debris Flows In A Steep, Coastal Stream, Big Sur, California, Telemak Olsen Jan 2023

Quantifying Channel Change Following Post-Fire Debris Flows In A Steep, Coastal Stream, Big Sur, California, Telemak Olsen

WWU Graduate School Collection

Debris flows commonly occur following wildfire in steep landscapes, introducing large volumes of sediment to downstream fluvial systems. Fire-related sediment supply perturbations impact channel morphology, and importantly, fragile aquatic and riparian ecosystems downstream of disturbance. The Big Creek watershed drains 57 km2 of steep chaparral and coast redwood forest along California’s Central Coast. Streams in the Big Creek watershed typically exhibit step-pool/cascade morphology and serve as vital spawning habitat for anadromous Steelhead Trout (Oncorhynchus mykiss). In 2020, 97% of the Big Creek watershed burned in the Dolan Wildfire. In January 2021, an atmospheric river event triggered a series of …

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Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang Jan 2023

Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell …

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