Physical Sciences and Mathematics Commons^™

Tfa Inference: Using Mathematical Modeling Of Gene Expression Data To Infer The Activity Of Transcription Factors, Cynthia Ma

McKelvey School of Engineering Theses & Dissertations

Transcription factors (TFs) are a set of proteins that play a key role in the information processing system that enables a cell to respond to changes in internal and external state. By binding near a gene in a cell’s DNA, a TF can influence that gene’s expression level, triggering the appropriate increase or decrease in production levels of proteins that are needed to handle stressors like a change in nutrient availability or damage to the cell’s internal structures. Transcription factor activity (TFA) is a measure of how much effect a TF has on its target genes in a given sample …

Development Of The Assessment Of Clinical Prediction Model Transportability (Apt) Checklist, Sean Chonghwan Yu

McKelvey School of Engineering Theses & Dissertations

Clinical Prediction Models (CPM) have long been used for Clinical Decision Support (CDS) initially based on simple clinical scoring systems, and increasingly based on complex machine learning models relying on large-scale Electronic Health Record (EHR) data. External implementation – or the application of CPMs on sites where it was not originally developed – is valuable as it reduces the need for redundant de novo CPM development, enables CPM usage by low resource organizations, facilitates external validation studies, and encourages collaborative development of CPMs. Further, adoption of externally developed CPMs has been facilitated by ongoing interoperability efforts in standards, policy, and …

Machine Learning And Scalable Informatics Methods To Predict Disease Status From Multimodal Biomedical Data, Hossein Mohammadian Foroushani

McKelvey School of Engineering Theses & Dissertations

Biological understanding of complex diseases such as stroke and obesity is critical for the advancement of medicine. Further knowledge discovery can provide effective biomarkers to improve disease diagnosis and prognosis, identify driver mutations, predict individual genetic susceptibility for early prevention and effective disease management, and facilitate development of personalized drugs. Stroke is the second leading cause of death and long-term disability in the world. Thus, stroke management is a time-sensitive emergency. The initial hours after stroke onset map the trajectory of subsequent neurologic complications. Cerebral edema develops hours to days after acute ischemic stroke and may result in midline shift …

Development Of Intravital Microscopy For Brain Imaging With Improved Spatiotemporal Coverage And Contrast, Yifeng Zhou

McKelvey School of Engineering Theses & Dissertations

Capitalizing on the Brownian motion of red blood cells, the distinct optical absorption spectra of oxy-hemoglobin and deoxy-hemoglobin, and the blood flow-induced signal decorrelation, multi-parametric photoacoustic microscopy (PAM) is capable of quantifying concentration of hemoglobin (CHb), blood oxygen saturation (sO2), and hemodynamics at the microscopic level via statistical, spectroscopic, and correlation analyses. Multi-parametric PAM has found broad biomedical applications. In fact, there are still much room to further improve the performance and imaging capability of multi-parametric PAM to meet the ever-increasing demanding requirements of biomedical research. To date, there are two main obstacles that prevent multi-parametric PAM from being more …

Disjoint And Simultaneously Hypercyclic Pseudo-Shifts, Nurhan Çolakoğlu, Özgür Martin, Rebecca Sanders

Mathematical and Statistical Science Faculty Research and Publications

We characterize disjoint and simultaneously hypercyclic tuples of unilateral pseudo-shift operators on ℓ^p(ℕ) . As a consequence, complementing the results of Bernal and Jung, we give a characterization for simultaneously hypercyclic tuples of unilateral weighted shifts. We also give characterizations for unilateral pseudo-shifts that satisfy the Disjoint and Simultaneous Hypercyclicity Criterions. Contrary to the disjoint hypercyclicity case, tuples of weighted shifts turn out to be simultaneously hypercyclic if and only if they satisfy the Simultaneous Hypercyclicity Criterion.

Human-Centered Machine Learning: Algorithm Design And Human Behavior, Wei Tang

McKelvey School of Engineering Theses & Dissertations

Machine learning is increasingly engaged in a large number of important daily decisions and has great potential to reshape various sectors of our modern society. To fully realize this potential, it is important to understand the role that humans play in the design of machine learning algorithms and investigate the impacts of the algorithm on humans.

Towards the understanding of such interactions between humans and algorithms, this dissertation takes a human-centric perspective and focuses on investigating the interplay between human behavior and algorithm design. Accounting for the roles of humans in algorithm design creates unique challenges. For example, humans might …

Scheduling For High Throughput And Small Latency In Parallel And Distributed Systems, Zhe Wang

McKelvey School of Engineering Theses & Dissertations

Parallel and distributed systems are pervasive, such as web services, clouds, and cyber-physical systems. We often desire high throughput and small latency in the parallel and distributed system. However, since the system is distributed and the input is online, scheduling for high throughput while keeping the latency small is often challenging. In this dissertation, we developed scheduling algorithms, policies, and mechanisms to approach high throughput with small latency in various parallel and distributed applications. First, we developed AMCilk runtime system for running multi-programmed parallel jobs on many-processor machines. When running parallel jobs, the allocation of processors to the parallel jobs …

Modeling, Analysis, And Simulation To Reveal The Mechanisms Of Ciliary Beating, Louis Woodhams

McKelvey School of Engineering Theses & Dissertations

Cilia are microscopic cellular appendages that help us breathe by clearing our airways, maintain the health of our central nervous system by circulating cerebrospinal fluid, and allow us to reproduce by transporting eggs and propelling sperm cells. Cilia even determine the asymmetry of our internal organs during embryonic development. However, the mechanisms underlying ciliary beating are not fully understood. Questions remain as to how arrays of the motor protein dynein generate the propulsive waveforms observed in cilia and how structural elements within the cilium and its connection to the cell deform during beating. In the current work, mathematical modeling, analysis, …

Design And Analysis Of Strategic Behavior In Networks, Sixie Yu

McKelvey School of Engineering Theses & Dissertations

Networks permeate every aspect of our social and professional life.A networked system with strategic individuals can represent a variety of real-world scenarios with socioeconomic origins. In such a system, the individuals' utilities are interdependent---one individual's decision influences the decisions of others and vice versa. In order to gain insights into the system, the highly complicated interactions necessitate some level of abstraction. To capture the otherwise complex interactions, I use a game theoretic model called Networked Public Goods (NPG) game. I develop a computational framework based on NPGs to understand strategic individuals' behavior in networked systems. The framework consists of three …

Model-Based Deep Learning For Computational Imaging, Xiaojian Xu

McKelvey School of Engineering Theses & Dissertations

This dissertation addresses model-based deep learning for computational imaging. The motivation of our work is driven by the increasing interests in the combination of imaging model, which provides data-consistency guarantees to the observed measurements, and deep learning, which provides advanced prior modeling driven by data. Following this idea, we develop multiple algorithms by integrating the classical model-based optimization and modern deep learning to enable efficient and reliable imaging. We demonstrate the performance of our algorithms by validating their performance on various imaging applications and providing rigorous theoretical analysis.

The dissertation evaluates and extends three general frameworks, plug-and-play priors (PnP), regularized …

Geometric Algorithms For Modeling Plant Roots From Images, Dan Zeng

McKelvey School of Engineering Theses & Dissertations

Roots, considered as the ”hidden half of the plant”, are essential to a plant’s health and pro- ductivity. Understanding root architecture has the potential to enhance efforts towards im- proving crop yield. In this dissertation we develop geometric approaches to non-destructively characterize the full architecture of the root system from 3D imaging while making com- putational advances in topological optimization. First, we develop a global optimization algorithm to remove topological noise, with applications in both root imaging and com- puter graphics. Second, we use our topology simplification algorithm, other methods from computer graphics, and customized algorithms to develop a high-throughput …

Spatio-Temporal Changes In Vegetation In The Last Two Decades (2001–2020) In The Beijing–Tianjin–Hebei Region, Yuan Zou, Wei Chen, Siliang Li, Tiejun Wang, Le Yu, Min Xu, Ramesh P. Singh, Cong-Qiang Liu

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In terrestrial ecosystems, vegetation is sensitive to climate change and human activities. Its spatial-temporal changes also affect the ecological and social environment. In this paper, we considered the Beijing–Tianjin–Hebei region to study the spatio-temporal vegetation patterns. The detailed analysis of a moderate-resolution imaging spectroradiometer (MODIS) data were carried out through the Google Earth Engine (GEE) platform. Our results show a slow and tortuous upward trend in the average leaf area index (LAI) in the study region for the periods 2001–2020. Specifically, Beijing had the highest LAI value, with an average of 1.64 over twenty years, followed by Hebei (1.30) and …

Investigation Of Basal Imnaha Basalt Flows And Their Relationship To The Picture Gorge Basalt Of The Columbia River Basalt Group, Luke James Fredenberg

Dissertations and Theses

The lower American Bar flows (AB 1 and 2) of the Imnaha Basalt have previously been observed as being chemically similar to those of the Picture Gorge Basalt (PGB). Previous age data separate eruption of the Imnaha and Picture Gorge Basalts by approximately 1.5 Ma, precluding the possibility of a genetic link between the two basalt units. New age data for the Picture Gorge Basalt has expanded the eruptive timeframe and the earliest flows coincide with the eruption of the Imnaha Basalt, making it possible that the lower American Bar flows of the Imnaha Basalt and the Picture Gorge Basalt …

Air Quality Impacts From Mineral Dust, Fireworks, And Urban Pollution Revealed By Trace Element Chemistry And Strontium Isotopes Ratios In The Wasatch Front, Utah, Usa, Micah J. Marcy

Theses and Dissertations

Airborne particulate matter (PM) in urban areas is derived from a combination of natural and anthropogenic sources. To identify PM sources and their effects on air quality, we collected PM using active filter samplers over a two-year period in the urban Wasatch Front, northern Utah, an area affected by multiple pollution sources. Filters from active samplers and other PM samples were analyzed for major and trace element concentrations and 87Sr/86Sr ratios. We identified wind-blown mineral dust from dry lake beds, winter inversions, and fireworks as primary PM sources affecting air quality in the Wasatch Front. Dust contributes Al, Be, Ca, …

On The Thom Isomorphism For Groupoid-Equivariant Representable K-Theory, Zachary J. Garvey

Dartmouth College Ph.D Dissertations

This thesis proves a general Thom Isomorphism in groupoid-equivariant KK-theory. Through formalizing a certain pushforward functor, we contextualize the Thom isomorphism to groupoid-equivariant representable K-theory with various support conditions. Additionally, we explicitly verify that a Thom class, determined by pullback of the Bott element via a generalized groupoid homomorphism, coincides with a Thom class defined via equivariant spinor bundles and Clifford multiplication. The tools developed in this thesis are then used to generalize a particularly interesting equivalence of two Thom isomorphisms on TX, for a Riemannian G-manifold X.

Towards Fast Weak Adversarial Training To Solve High Dimensional Parabolic Partial Differential Equations Using Xnode-Wan, Paul Valsecchi Oliva, Yue Wu, Cuiyu He, Hao Ni

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

Due to the curse of dimensionality, solving high dimensional parabolic partial differential equations (PDEs) has been a challenging problem for decades. Recently, a weak adversarial network (WAN) proposed in Zang et al. (2020)[17] offered a flexible and computationally efficient approach to tackle this problem defined on arbitrary domains by leveraging the weak solution. WAN reformulates the PDE problem as a generative adversarial network, where the weak solution (primal network) and the test function (adversarial network) are parameterized by the multi-layer deep neural networks (DNNs). However, it is not yet clear whether DNNs are the most effective model for the parabolic …

Unplanned Dilution Prediction In Open Stope Mining: Developing New Design Charts Using Artificial Neural Network Classifier, Sultan Korigov, Amoussou Coffi Adoko, Fhatuwani Sengani

Journal of Sustainable Mining

Minimizing dilution is essential in open stope mine design as excessive unplanned dilution can compromise the operation's profitability. One of the main challenges associated with the empirical dilution graph method used to design open stopes is how to determine the boundary of the dilution zones objectively. Hence, this paper explores the implementation of machine learning classifiers to bridge this gap in the conventional dilution graph method. Stope performance data consisting of the stope dilution (unplanned dilution), the modified stability number, and the hydraulic radius were compiled from a mine located in Kazakhstan. First, the conventional dilution graph methods were used …

Avist: A Benchmark For Visual Object Tracking In Adverse Visibility, Mubashir Noman, Wafa Al Ghallabi, Daniya Najiha, Christoph Mayer, Hisham Cholakkal, Salman Khan, Luc Van Gool, Fahad Shahbaz Khan

Computer Vision Faculty Publications

One of the key factors behind the recent success in visual tracking is the availability of dedicated benchmarks. While being greatly benefiting to the tracking research, existing benchmarks do not pose the same difficulty as before with recent trackers achieving higher performance mainly due to (i) the introduction of more sophisticated transformers-based methods and (ii) the lack of diverse scenarios with adverse visibility such as, severe weather conditions, camouflage and imaging effects. We introduce AVisT, a dedicated benchmark for visual tracking in diverse scenarios with adverse visibility. AVisT comprises 120 challenging sequences with 80k annotated frames, spanning 18 diverse scenarios …

Green Intellectual Capital And Green Supply Chain Performance: Does Big Data Analytics Capabilities Matter?, Ayman Wael Al-Khatib, Ahmed Shuhaiber

All Works

In light of global environmental concerns growing, environmental awareness within firms has become more important than before, and many scholars and researchers have argued the importance of environmental management in promoting sustainable organizational performance, especially in the context of supply chains. Thus, the current study aimed at identifying the impact of the components of green intellectual capital (green human capital, green structural capital, green relational capital) on green supply chain performance in the manufacturing sector in Jordan, as well as identifying the moderating role of big data analytics capabilities. To achieve this aim, we developed a conceptual model of Structural …

Mathematical Models Yield Insights Into Cnns: Applications In Natural Image Restoration And Population Genetics, Ryan Cecil

Electronic Theses and Dissertations

Due to a rise in computational power, machine learning (ML) methods have become the state-of-the-art in a variety of fields. Known to be black-box approaches, however, these methods are oftentimes not well understood. In this work, we utilize our understanding of model-based approaches to derive insights into Convolutional Neural Networks (CNNs). In the field of Natural Image Restoration, we focus on the image denoising problem. Recent work have demonstrated the potential of mathematically motivated CNN architectures that learn both `geometric' and nonlinear higher order features and corresponding regularizers. We extend this work by showing that not only can geometric features …

Synthesis And Physicochemical Characterization Of Noncentrosymmetric Quaternary Sulfides With Potential Nonlinear Optical Applications, Andrew J. Craig

Electronic Theses and Dissertations

In this work, several new quaternary sulfides were synthesized and investigated for their potential applications in optics. Chapter 1 provides an overview of nonlinear optical (NLO) materials in general, including their applications, ideal characteristics, current deficiencies, and strategies for the discovery of new candidate NLO materials, particularly those for use in the infrared (IR). Two families of compounds are investigated in this work, including Ln₃LiTS₇ (3-1-1-7) compounds and I₄-II-IV₂-VI₇ (4-1-2-7) diamond-like semiconductors (DLSs). All products were synthesized via traditional high-temperature, solid-state synthesis and their structures were solved and refined through single crystal …

Theory Of Aqueous Solvation: Uninterrupted, Cyclic Hydrogen-Bonding Essential For Accurate Keto-Enol Energies And Grotthuss Tautomerism Of Acetone, Mark Recznik

Electronic Theses and Dissertations

Keto-enol tautomerization (KET) is a fundamental process impacting a range of molecular phenomena in organic and biochemistry. However, the accurate computation of solution-phase KET energies remains a challenge, even for prototypical acetone.

In Part I, keto-enol tautomers of acetone were incorporated into solvent clusters that interact via uninterrupted, cyclic hydrogen-bonding (UCHB) networks. An empirical model was created to predict accurate KET energies, E_taut, of simple carbonyl compounds. Based on the availability of experimental data and structural simplicity, acetone was selected as a prototype. A discrete-continuum strategy was employed – accounting simultaneously for local noncovalent interactions and bulk-phase effects …

Assessing The Risk Of Land Subsidence In The Lower Limpopo River Basin, Mozambique With Remote Sensing, Gabriella Zuccolotto

Electronic Theses and Dissertations

Land subsidence is a threat to coastal cities around the world. In the lower Limpopo River Basin, the presence of compaction-prone alluvial sediments, groundwater use, and reports of saltwater intrusion suggest that subsidence could be occurring. Using interferometric synthetic aperture radar (InSAR) from Sentinel-1, combined with in-situ sea level and river height measurements, this study aims to determine if land subsidence could contribute to increased saltwater intrusion. InSAR results indicate that subsidence in the lower Limpopo River valley has occurred at an average rate of -2.98 cm/yr based on data from the dry seasons (May to October) of 2017-2021. River …

Using Heritage Sites At Bahariya Oasis On The Tourism Urban Development, Medhat Ahmed Shabaan Samra

Mansoura Engineering Journal

Throughout the tourism planning process for the Bahariya Oasis area, the current study aims to prepare this area to become an applicable model that converts the values of cultural heritage resources into economic values within the tourism industry and the establishment of tourism projects in this area. The Bahariya Oasis area is characterized by many Valuable regions that have not been included on the tourism map by the Egyptian government. To achieve those objectives, the researcher adopted the 'Analytic-Descriptive Approach', as it is suitable for this study throughout reviewing the literature related to the research subject, describing the current situation, …

Geochronology Of Cambrian Sedimentary And Volcanic Rocks In The Illinois Basin: Defining The Illinois Aulacogen, Jared T. Freiburg, David H. Malone, Matthew Huisman

Faculty Publications-- Geography, Geology, and the Environment

The Wabash #1 well, drilled for the Wabash CarbonSAFE Project and located in Vigo County, Indiana, USA, was drilled in early 2020 as a stratigraphic test well to characterize and evaluate the basal Cambrian Mt. Simon Sandstone for carbon dioxide storage (TD=8750 ft; 2667 m). The Wabash #1 well is located along the eastern flank of a newly interpreted Cambrian aulacogen that occurs in western Indiana and eastern Illinois. Here we present 938 new detrital zircon U-Pb ages (LA-ICPMS) from early Cambrian sandstones sampled near the base of the well. A basalt lava flow was penetrated at ~8530 ft (2600 …

Bot-Mgat: A Transfer Learning Model Based On A Multi-View Graph Attention Network To Detect Social Bots, Eiman Alothali, Motamen Salih, Kadhim Hayawi, Hany Alashwal

All Works

Twitter, as a popular social network, has been targeted by different bot attacks. Detecting social bots is a challenging task, due to their evolving capacity to avoid detection. Extensive research efforts have proposed different techniques and approaches to solving this problem. Due to the scarcity of recently updated labeled data, the performance of detection systems degrades when exposed to a new dataset. Therefore, semi-supervised learning (SSL) techniques can improve performance, using both labeled and unlabeled examples. In this paper, we propose a framework based on the multi-view graph attention mechanism using a transfer learning (TL) approach, to predict social bots. …

Lc-Ms/Tof Characterization And Stability Study Of Artesunate In Different Solvent Systems, Kogila Oke, Amos Mugweru

College of Science & Mathematics Departmental Research

Artemisinin (ART) is a sesquiterpene lactone and a popular malaria drug used in many parts of the world. Artesunate (ARTS) is a semi-synthetic derivative of ART with improved pharmacokinetic properties. However, the half-life of ARTS is less than an hour in vivo. The analysis of this drug in vitro in different solvent systems using LC-MS/TOF showed a solvent-driven breakdown. ARTS breakdown formed several derivatives, including dihydroartemisinin (DHA), artemether (ARTM) and DHA-dimer among others, at different rates in different solvent composition systems. The change in temperature from room temperature to physiological temperature (37 °C) was found to enhance the rate of …

Lc-Ms/Tof Characterization And Stability Study Of Artesunate In Different Solvent Systems, Kogila Oke, Amos Mugweru

College of Science & Mathematics Departmental Research

Artemisinin (ART) is a sesquiterpene lactone and a popular malaria drug used in many parts of the world. Artesunate (ARTS) is a semi-synthetic derivative of ART with improved pharmacokinetic properties. However, the half-life of ARTS is less than an hour in vivo. The analysis of this drug in vitro in different solvent systems using LC-MS/TOF showed a solvent-driven breakdown. ARTS breakdown formed several derivatives, including dihydroartemisinin (DHA), artemether (ARTM) and DHA-dimer among others, at different rates in different solvent composition systems. The change in temperature from room temperature to physiological temperature (37 °C) was found to enhance the rate of …

Design And Surface Modification Of Noble Metal-Based Nanocatalysts, Xuchun Wang

Electronic Thesis and Dissertation Repository

This thesis investigates approaches to modifying the surface structure of noble metal-based nanocatalysts. Noble metal-based nanocatalysts, such as Pt and Pd, play a significant role in heterogeneous catalysis due to their capabilities in activating the cleavage or formation of chemical bonds, but still suffer from the high-cost issue and unsatisfied catalytic performance due to too strong or too weak adsorption of intermediates. Considering the surface specificity of heterogeneous catalysis, Bi, a cheap metal, was used to modify the surface of Pt- and Pd-based nanocatalysts. This thesis aims to unveil the role of Bi in improving their catalytic performance from both …

Geomechanical Modeling Of A Fault During Fluid Injection, Charles Kw Hulls

Electronic Thesis and Dissertation Repository

The injection of fluid into rock masses as a part of industrial processes, such as hydraulic fracturing, can lead to an increase in seismic activity. The movement of the injected fluid and resulting stresses can be simulated and analyzed. One aspect of this analysis is the predicted rate of seismic activity, obtained via the Dietrich rate-and-state law and the Coulomb Failure Stress. This work produces simulations for two fracturing scenarios in the Duvernay Shale region. Model parameters, such as layer permeability and timing of fault slip, are varied to determine their impact on the model results. The simulated results show …