Digital Commons Network^™

Machine Learning Approximations To Predict Epigenetic Age Acceleration In Stroke Patients, Isabel Fernández-Pérez, Joan Jiménez-Balado, Uxue Lazcano, Eva Giralt-Steinhauer, Lucía Rey Álvarez, Elisa Cuadrado-Godia, Ana Rodríguez-Campello, Adrià Macias-Gómez, Antoni Suárez-Pérez, Anna Revert-Barberá, Isabel Estragués-Gázquez, Carolina Soriano-Tarraga, Jaume Roquer, Angel Ois, Jordi Jiménez-Conde

2020-Current year OA Pubs

Age acceleration (Age-A) is a useful tool that is able to predict a broad range of health outcomes. It is necessary to determine DNA methylation levels to estimate it, and it is known that Age-A is influenced by environmental, lifestyle, and vascular risk factors (VRF). The aim of this study is to estimate the contribution of these easily measurable factors to Age-A in patients with cerebrovascular disease (CVD), using different machine learning (ML) approximations, and try to find a more accessible model able to predict Age-A. We studied a CVD cohort of 952 patients with information about VRF, lifestyle habits, …

Automatic Diagnosis Of Late-Life Depression By 3d Convolutional Neural Networks And Cross-Sample Entropy Analysis From Resting-State Fmri, Chemin Lin, Shwu-Hua Lee, Chih-Mao Huang, Guan-Yen Chen, Wei Chang, Ho-Ling Liu, Shu-Hang Ng, Tatia Mei-Chun Lee, Shun-Chi Wu

Faculty, Staff and Student Publications

Resting-state fMRI has been widely used in investigating the pathophysiology of late-life depression (LLD). Unlike the conventional linear approach, cross-sample entropy (CSE) analysis shows the nonlinear property in fMRI signals between brain regions. Moreover, recent advances in deep learning, such as convolutional neural networks (CNNs), provide a timely application for understanding LLD. Accurate and prompt diagnosis is essential in LLD; hence, this study aimed to combine CNN and CSE analysis to discriminate LLD patients and non-depressed comparison older adults based on brain resting-state fMRI signals. Seventy-seven older adults, including 49 patients and 28 comparison older adults, were included for fMRI …

Optimized Decision Support For Selection Of Transoral Robotic Surgery Or (Chemo)Radiation Therapy Based On Posttreatment Swallowing Toxicity, Mehdi Hemmati, Carly Barbon, Abdallah S R Mohamed, Lisanne V Van Dijk, Amy C Moreno, Neil D Gross, Ryan P Goepfert, Stephen Y Lai, Katherine A Hutcheson, Andrew J Schaefer, Clifton D Fuller, Md Anderson Head And Neck Cancer Symptom Working Group Affiliations Expand

Faculty, Staff and Student Publications

BACKGROUND: A primary goal in transoral robotic surgery (TORS) for oropharyngeal squamous cell cancer (OPSCC) survivors is to optimize swallowing function. However, the uncertainty in the outcomes of TORS including postoperative residual positive margin (PM) and extranodal extension (ENE), may necessitate adjuvant therapy, which may cause significant swallowing toxicity to survivors.

METHODS: A secondary analysis was performed on a prospective registry data with low- to intermediate-risk human papillomavirus-related OPSCC possibly resectable by TORS. Decision trees were developed to model the uncertainties in TORS compared with definitive radiation therapy (RT) and chemoradiation therapy (CRT). Swallowing toxicities were measured by Dynamic Imaging …

The Orf7a Protein Of Sars-Cov-2 Initiates Autophagy And Limits Autophagosome-Lysosome Fusion Via Degradation Of Snap29 To Promote Virus Replication, Peili Hou, Xuefeng Wang, Hongmei Wang, Tiecheng Wang, Zhangping Yu, Chunqing Xu, Yudong Zhao, Wenqi Wang, Yong Zhao, Fengyun Chu, Huasong Chang, Hongchao Zhu, Jiahui Lu, Fuzhen Zhang, Xue Liang, Xingyu Li, Song Wang, Yuwei Gao, Hongbin He

Faculty, Staff and Student Publications

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is closely related to various cellular aspects associated with autophagy. However, how SARS-CoV-2 mediates the subversion of the macroautophagy/autophagy pathway remains largely unclear. In this study, we demonstrate that overexpression of the SARS-CoV-2 ORF7a protein activates LC3-II and leads to the accumulation of autophagosomes in multiple cell lines, while knockdown of the viral ORF7a gene via shRNAs targeting ORF7a sgRNA during SARS-CoV-2 infection decreased autophagy levels. Mechanistically, the ORF7a protein initiates autophagy via the AKT-MTOR-ULK1-mediated pathway, but ORF7a limits the progression of autophagic flux by activating CASP3 (caspase 3) to cleave the …

Essays On Entrepreneurship, Yoshiko Oka

Dissertations, Theses, and Capstone Projects

This dissertation explores the determinants of successful entrepreneurship and entrepreneurial entry. It consists of three chapters.

Chapter 1 estimates the effect of regional concentrations of related industrial firms and business owners' cognitive and non-cognitive traits on their business survival. Using data from the National Longitudinal Survey of Youth 1979 and the County Business Patterns, I find that incorporated businesses that operate in a location where similar businesses are clustered together have a significantly higher chance of survival. However, the effect of location appears to be insignificant for unincorporated businesses. On the other hand, the results show that businesses that are …

Three Essays On Substructural Approaches To Semantic Paradoxes, Brian C. Porter

Dissertations, Theses, and Capstone Projects

This thesis consists of three papers on substructural approaches to semantic paradoxes. The first paper introduces a formal system, based on a nontransitive substructural logic, which has exactly the valid and antivalid inferences of classical logic at every level of (meta)inference, but which I argue is still not classical logic. In the second essay, I introduce infinite-premise versions of several semantic paradoxes, and show that noncontractive substructural approaches do not solve these paradoxes. In the third essay, I introduce an infinite metainferential hierarchy of validity curry paradoxes, and argue that providing a uniform solution to the paradoxes in this hierarchy …

Resource Management In Mobile Edge Computing For Compute-Intensive Application, Xiaojie Zhang

Dissertations, Theses, and Capstone Projects

With current and future mobile applications (e.g., healthcare, connected vehicles, and smart grids) becoming increasingly compute-intensive for many mission-critical use cases, the energy and computing capacities of embedded mobile devices are proving to be insufficient to handle all in-device computation. To address the energy and computing shortages of mobile devices, mobile edge computing (MEC) has emerged as a major distributed computing paradigm. Compared to traditional cloud-based computing, MEC integrates network control, distributed computing, and storage to customizable, fast, reliable, and secure edge services that are closer to the user and data sites. However, the diversity of applications and a variety …

Unlocking Potential: The School-To-Prison Pipeline For Students With Disabilities, Navena F. Chaitoo

Dissertations, Theses, and Capstone Projects

This research uses quasi-experimental, matched sampling to examine the school-to-prison pipeline for students with disabilities using data from the National Longitudinal Study of Adolescent to Adult Health. This study presents novel insights into an at-risk group that has faced disproportionate rates of school discipline and incarceration. The study finds school suspension to be associated with future involvement in the criminal legal system and lower educational attainment. Disability was not found to mediate the relationship between suspension and future involvement in the criminal legal system or the relationship between suspension and academic outcomes. However, disability was found to be a statistically …

A Stronger Strong Schottky Lemma For Euclidean Buildings, Michael E. Ferguson

Dissertations, Theses, and Capstone Projects

We provide a criterion for two hyperbolic isometries of a Euclidean building to generate a free group of rank two. In particular, we extend the application of a Strong Schottky Lemma to buildings given by Alperin, Farb and Noskov. We then use this extension to obtain an infinite family of matrices that generate a free group of rank two. In doing so, we also introduce an algorithm that terminates in finite time if the lemma is applicable for pairs of certain kinds of matrices acting on the Euclidean building for the special linear group over certain discretely valued fields.

Dynamics In Designed Elastins And Enzymes, Jonathan M. Preston

Dissertations, Theses, and Capstone Projects

In this dissertation I present experimental results on the structure and dynamics of elastin, an elastomeric extracellular component in vertebrates that, in mammals, provides structure and elasticity to the circulatory system, lungs, skin and joints. These experiments, using a set of designed elastin like proteins with properties analogous to the natural protein, show that elastin is highly disordered and connect this disorder to its mechanism of assembly and elasticity. In addition, I also present preliminary work on imparting flexibility into a set of computationally designed metalloenzymes to broaden the range of catalytic activities they perform.

Salty: A Diffractive Inquiry Of Visceral Knowing And Embodied Aesthetics, Mei Ling Chua

Dissertations, Theses, and Capstone Projects

This dissertation takes a diffractive, onto-epistemological approach to everyday practices with salt in order to articulate an expanded understanding of meaning making and knowledge production. This research reckons with and challenges dominant modes of knowing that engage a Cartesian perspective to situate knowing as the exclusive domain of the mind in both form and topic of inquiry. This research acts simultaneously as both a direct practice of and metacognition about knowledge production by examining 1. the embodied (including sensory and emotional aspects) and 2. the relational (including interpersonal and socio-cultural) dimensions of experience as visceral knowing. This articulation of …

Synthesis And Analysis Of Novel Troponoid-Based Chemical Probes, Alex Berkowitz

Dissertations, Theses, and Capstone Projects

Troponoids are a class of non-benzenoid aromatic species featuring a cycloheptatrienone ring and varying degrees of oxygenation. These scaffolds have proven ubiquitous amongst natural products, and have displayed promise as therapeutic agents against a variety of diseases. Herein, we will describe our efforts towards furthering troponoids as potential pharmaceuticals. In Chapter 1, we outline a kojic acid-derived oxidopyrylium cycloaddition/ring-opening method developed in our lab to generate ahydroxytropolones (aHTs). This route was successfully adapted to synthesize a small library of lipophilic aHTs that were proven to be effective against herpes simplex virus-1 (HSV-1) replication, while providing further insight into the mechanism …

One-Loop Corrections To Dihadron Production In Dis At Small X, Filip Bergabo

Dissertations, Theses, and Capstone Projects

We calculate the one-loop corrections to dihadron production in Deep Inelastic Scattering (DIS) at small x using the Color Glass Condensate formalism. We show that all UV and soft singularities cancel while the collinear divergences are absorbed into quark and anti quark-hadron fragmentation functions. Rapidity divergences lead to JIMWLK evolution of dipoles and quadrupoles describing multiple-scatterings of the quark anti-quark dipole on the target proton/nucleus. The resulting cross section is finite and can be used for phenomenological studies of dihadron angular correlations at small x in a future Electron-Ion Collider (EIC).

Beam-Based Target Alignment For Mu2e, Helenka Casler

Dissertations, Theses, and Capstone Projects

The Mu2e Experiment is a precision experiment at Fermi National Accelerator Laboratory, searching for charged lepton flavor violation (CLFV) in the conversion of a muon to an electron in the presence of an atomic nucleus. In order to achieve the expected single-event sensitivity of 3 × 10^-17 , Mu2e will require an intense muon beam, generated via pion decay. These pions are the product of a proton beam striking a radiatively-cooled tungsten target. In order to maximize pion production and prevent target failure, the beam will have to be aligned with the target center to within 0.5 mm. The …

It Has Always Been The “Business Model”: Racism And Sexism In Creative Arts Therapy Higher Education, Yasmine J. Awais

Dissertations, Theses, and Capstone Projects

Part of the Neoliberal drive is to privatize the structure and operation of public and private organizations and institutions. Managerialism has shaped higher education since the mid to late 1970s through a focus on productivity, efficiency, accountability, and standardization. Workers employed in social service organizations and universities have employed strategies for managing organizations based on the neoliberal business philosophy for the last 40 years. This research examines the impact of managerialism in higher education through the experience of faculty teaching in creative arts therapy master’s professional programs. During 2021, twenty-three faculty of color and white faculty who identified as women …

Analyzing Relationships With Machine Learning, Oscar Ko

Dissertations, Theses, and Capstone Projects

Procedurally, this project aims to take a dataset, analyze it, and offer insights to the audience in an easy-to-digest format. Conceptually, this project will seek to explore questions like: “Do couples that meet through online dating or dating apps have higher or lower quality relationships?”, “Can any features in this dataset help predict how a subject would rate their relationship quality?”, and “What other insights can I derive from using machine learning for exploratory analysis?” The intended audience for this project is anyone interested in romantic relationships or machine learning.

The dataset is from a Stanford University survey, “How Couples …

Nanoscale Imaging Of Electrocatalytic Nanomaterials By High-Resolution Scanning Electrochemical Microscopy, Xiang Wang

Dissertations, Theses, and Capstone Projects

Numerous insights of the structure–electrochemical activity relationship of nanocatalysts have been obtained by using macroscopic electrochemical measurements over the last several decades. However, signals measured by large electrodes are inevitably averaged out of many nanocatalysts, non-uniformed sizes, uneven morphologies, and multiple crystallographic facets. Over the last ten years, Scanning Electrochemical Microscopy (SECM) has advanced electrochemical measurements toward micro- to nanoscale level at a high spatial resolution. The advantages of using nanoelectrode in SECM include fast mass transfer of reactive species, dominated radial diffusion pattern, small double layer capacitance and small RC constant. In this thesis, high-resolution SECM is applied to …

Revealing The Three-Dimensional Magnetic Texture With Machine Learning Models, Shihua Zhao

Dissertations, Theses, and Capstone Projects

Revealing three-dimensional (3D) magnetic textures with vector field electron tomography (VFET) is essential in studying novel magnetic materials with topologically protected spin textures potentially being used in the next-generation semiconductor industry. In this dissertation, we use machine learning (ML) models to reconstruct 3D magnetic textures from electron holography (EH) data.

We can feed the EH data, a series of two-dimensional (2D) phasemaps, into a neural network (NN) architecture directly or feed the EH data into a conventional VFET and then feed the reconstructed results into a NN. Thus, perceptive NN, either a simple convolutional neural network (CNN) or Unet architecture, …

E Pluribus Unum: Prospective Acceptability Benchmarking From The Contouring Collaborative For Consensus In Radiation Oncology Crowdsourced Initiative For Multiobserver Segmentation, Diana Lin, Kareem A Wahid, Benjamin E Nelms, Renjie He, Mohammed A Naser, Simon Duke, Michael V Sherer, John P Christodouleas, Abdallah S R Mohamed, Michael Cislo, James D Murphy, Clifton D Fuller, Erin F Gillespie

Faculty, Staff and Student Publications

Purpose: Contouring Collaborative for Consensus in Radiation Oncology (C3RO) is a crowdsourced challenge engaging radiation oncologists across various expertise levels in segmentation. An obstacle to artificial intelligence (AI) development is the paucity of multiexpert datasets; consequently, we sought to characterize whether aggregate segmentations generated from multiple nonexperts could meet or exceed recognized expert agreement.

Approach: Participants who contoured ≥1 region of interest (ROI) for the breast, sarcoma, head and neck (H&N), gynecologic (GYN), or gastrointestinal (GI) cases were identified as a nonexpert or recognized expert. Cohort-specific ROIs were combined into single simultaneous truth and performance level estimation (STAPLE) consensus segmentations. …

Biosynthesis Of Chlorophyll And Other Isoprenoids In The Plastid Of Red Grape Berry Skins, António Teixeira, Henrique Noronha, Sarah Frusciante, Gianfranco Diretto, Hernâni Gerós

Faculty, Staff and Student Publications

Despite current knowledge showing that fruits like tomato and grape berries accumulate different components of the light reactions and Calvin cycle, the role of green tissues in fruits is not yet fully understood. In mature tomato fruits, chlorophylls are degraded and replaced by carotenoids through the conversion of chloroplasts in chromoplasts, while in red grape berries, chloroplasts persist at maturity and chlorophylls are masked by anthocyanins. To study isoprenoid and lipid metabolism in grape skin chloroplasts, metabolites of enriched organelle fractions were analyzed by high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS) and the expression of key genes was evaluated by real-time …

A Theoretical Framework For The Ecological Role Of Three-Dimensional Structural Diversity, Elizabeth A. Larue, Robert T. Fahey, Brandon C. Alveshere, Jeff W. Atkins, Parth Bhatt, Brian Buma, Anping Chen, Stella Cousins, Jessica M. Elliott, Andrew J. Elmore, Christopher R. Hakkenberg, Brady S. Hardiman, Jeremy S. Johnson, Daniel M. Kashian, Anil Koirala, Monica Papeş, Jamille B. St Hilaire, Thilina D. Surasinghe, Jenny Zambrano, Lu Zhai, Songlin Fei

Michigan Tech Publications, Part 1

The three-dimensional (3D) physical aspects of ecosystems are intrinsically linked to ecological processes. Here, we describe structural diversity as the volumetric capacity, physical arrangement, and identity/traits of biotic components in an ecosystem. Despite being recognized in earlier ecological studies, structural diversity has been largely overlooked due to an absence of not only a theoretical foundation but also effective measurement tools. We present a framework for conceptualizing structural diversity and suggest how to facilitate its broader incorporation into ecological theory and practice. We also discuss how the interplay of genetic and environmental factors underpin structural diversity, allowing for a potentially unique …

Selectively Modified Lactose And N-Acetyllactosamine Analogs At Three Key Positions To Afford Effective Galectin-3 Ligands †, Shuay Abdullayev, Priyanka Dipak Kadav, Purnima Bandyopadhyay, Francisco Javier Medrano, Gabriel A. Rabinovich, Tarun K. Dam, Antonio Romero, René Roy

Michigan Tech Publications, Part 1

Galectins constitute a family of galactose-binding lectins overly expressed in the tumor microenvironment as well as in innate and adaptive immune cells, in inflammatory diseases. Lactose ((β-D-galactopyranosyl)-(1→4)-β-D-glucopyranose, Lac) and N-Acetyllactosamine (2-acetamido-2-deoxy-4-O-β-D-galactopyranosyl-D-glucopyranose, LacNAc) have been widely exploited as ligands for a wide range of galectins, sometimes with modest selectivity. Even though several chemical modifications at single positions of the sugar rings have been applied to these ligands, very few examples combined the simultaneous modifications at key positions known to increase both affinity and selectivity. We report herein combined modifications at the anomeric position, C-2, and O-3′ of each of the two …

A Catalog Of The Highest-Energy Cosmic Rays Recorded During Phase I Of Operation Of The Pierre Auger Observatory, A. Abdul Halim, P. Abreu, M. Aglietta, I. Allekotte, P. Allison, K. Almeida Cheminant, J. Chirinos, B. Fick, D. Nitz, I. Norwood, A. Puyleart, Et Al.

Michigan Tech Publications, Part 1

A catalog containing details of the highest-energy cosmic rays recorded through the detection of extensive air showers at the Pierre Auger Observatory is presented with the aim of opening the data to detailed examination. Descriptions of the 100 showers created by the highest-energy particles recorded between 2004 January 1 and 2020 December 31 are given for cosmic rays that have energies in the range 78-166 EeV. Details are also given on a further nine very energetic events that have been used in the calibration procedure adopted to determine the energy of each primary. A sky plot of the arrival directions …

The Effects Of Robot Voices And Appearances On Users' Emotion Recognition And Subjective Perception, Sangjin Ko, Jaclyn A. Barnes, Jiayuan Dong, Chung Hyuk Park, Ayanna Howard, Myounghoon Jeon

Michigan Tech Publications, Part 1

As the influence of social robots in people's daily lives grows, research on understanding people's perception of robots including sociability, trust, acceptance, and preference becomes more pervasive. Research has considered visual, vocal, or tactile cues to express robots' emotions, whereas little research has provided a holistic view in examining the interactions among different factors influencing emotion perception. We investigated multiple facets of user perception on robots during a conversational task by varying the robots' voice types, appearances, and emotions. In our experiment, 20 participants interacted with two robots having four different voice types. While participants were reading fairy tales to …

Order Sum Graph Of A Group, Javeria Amreen, Sudev Naduvath

Baghdad Science Journal

The concept of the order sum graph associated with a finite group based on the order of the group and order of group elements is introduced. Some of the properties and characteristics such as size, chromatic number, domination number, diameter, circumference, independence number, clique number, vertex connectivity, spectra, and Laplacian spectra of the order sum graph are determined. Characterizations of the order sum graph to be complete, perfect, etc. are also obtained.

Efficient Approach For Solving (2+1) D- Differential Equations, Luma N. M. Tawfiq, Noor A. Hussein

Baghdad Science Journal

In this article, a new efficient approach is presented to solve a type of partial differential equations, such (2+1)-dimensional differential equations non-linear, and nonhomogeneous. The procedure of the new approach is suggested to solve important types of differential equations and get accurate analytic solutions i.e., exact solutions. The effectiveness of the suggested approach based on its properties compared with other approaches has been used to solve this type of differential equations such as the Adomain decomposition method, homotopy perturbation method, homotopy analysis method, and variation iteration method. The advantage of the present method has been illustrated by some examples.

3-D Packing In Container Using Teaching Learning Based Optimization Algorithm, Linda Fitriyani, Larissa Alva Zerinda, Asri Bekti Pratiwi, Edi Winarko

Baghdad Science Journal

The paper aims to propose Teaching Learning based Optimization (TLBO) algorithm to solve 3-D packing problem in containers. The objective which can be presented in a mathematical model is optimizing the space usage in a container. Besides the interaction effect between students and teacher, this algorithm also observes the learning process between students in the classroom which does not need any control parameters. Thus, TLBO provides the teachers phase and students phase as its main updating process to find the best solution. More precisely, to validate the algorithm effectiveness, it was implemented in three sample cases. There was small data …

Breast Cancer Mri Classification Based On Fractional Entropy Image Enhancement And Deep Feature Extraction, Ali M. Hasan, Asaad F. Qasim, Hamid A. Jalab, Rabha W. Ibrahim

Baghdad Science Journal

Disease diagnosis with computer-aided methods has been extensively studied and applied in diagnosing and monitoring of several chronic diseases. Early detection and risk assessment of breast diseases based on clinical data is helpful for doctors to make early diagnosis and monitor the disease progression. The purpose of this study is to exploit the Convolutional Neural Network (CNN) in discriminating breast MRI scans into pathological and healthy. In this study, a fully automated and efficient deep features extraction algorithm that exploits the spatial information obtained from both T2W-TSE and STIR MRI sequences to discriminate between pathological and healthy breast MRI scans. …

A Quantum Approach To Language Modeling, Constantijn Van Der Poel

Dissertations, Theses, and Capstone Projects

This dissertation consists of six chapters. . . Chapter 1: We introduce language modeling, outline the software used for this thesis, and discuss related work. Chapter 2: We will unpack the transition from classical to quantum probabilities, as well as motivate their use in building a model to understand language-like datasets. Chapter 3: We motivate the Motzkin dataset, the models we will be investigating, as well as the necessary algorithms to do calculations with them. Chapter 4: We investigate our models’ sensitivity to various hyperparameters. Chapter 5: We compare the performance and robustness of the models. Chapter 6: We conclude …

Pronunciation Ambiguities In Japanese Kanji, Wen Zhang

Dissertations, Theses, and Capstone Projects

Japanese writing is a complex system, and a large part of the complexity resides in the use of kanji. A single kanji character in modern Japanese may have multiple pronunciations, either as native vocabulary or as words borrowed from Chinese. This causes a problem for text-to-speech synthesis (TTS) because the system has to predict which pronunciation of each kanji character is appropriate in the context. The problem is called homograph disambiguation. In Japanese TTS technology, the trick in any case is to know which is the right reading, which makes reading Japanese text a challenge. To solve the problem, …