Life Sciences Commons^™

Machine Learning And Network Embedding Methods For Gene Co-Expression Networks, Niloofar Aghaieabiane

Dissertations

High-throughput technologies such as DNA microarrays and RNA-seq are used to measure the expression levels of large numbers of genes simultaneously. To support the extraction of biological knowledge, individual gene expression levels are transformed into Gene Co-expression Networks (GCNs). GCNs are analyzed to discover gene modules. GCN construction and analysis is a well-studied topic, for nearly two decades. While new types of sequencing and the corresponding data are now available, the software package WGCNA and its most recent variants are still widely used, contributing to biological discovery.

The discovery of biologically significant modules of genes from raw expression data is …

Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao

Dissertations

Traumatic brain injury (TBI) in children is a major public health concern worldwide. Attention deficits are among the most common neurocognitive and behavioral consequences in children post-TBI which have significant negative impacts on their educational and social outcomes and compromise the quality of their lives. However, there is a paucity of evidence to guide the optimal treatment strategies of attention deficit related symptoms in children post-TBI due to the lack of understanding regarding its neurobiological substrate. Thus, it is critical to understand the neural mechanisms associated with TBI-induced attention deficits in children so that more refined and tailored strategies can …

Biomechanical And Psychophysical Underpinnings Of Balance Dysfunction In Individuals With Traumatic Brain Injury, Naphtaly Ehrenberg

Dissertations

Falls are a major burden on healthcare infrastructure, especially in older adults and even more so in older individuals that are living in institutions. According to data from the Centers for Disease Control and Prevention (CDC), from 2010 to 2020, unintentional falls were the leading cause of nonfatal emergency department visits for all age groups except among individuals from 15-24 years of age, where unintentional falls ranked a very close second to being unintentionally struck by or against. Among older individuals living in the community, approximately 30-35% fall at least once in a given year, and around three times as …

Continuum Modeling Of Active Nematics Via Data-Driven Equation Discovery, Connor Robertson

Dissertations

Data-driven modeling seeks to extract a parsimonious model for a physical system directly from measurement data. One of the most interpretable of these methods is Sparse Identification of Nonlinear Dynamics (SINDy), which selects a relatively sparse linear combination of model terms from a large set of (possibly nonlinear) candidates via optimization. This technique has shown promise for synthetic data generated by numerical simulations but the application of the techniques to real data is less developed. This dissertation applies SINDy to video data from a bio-inspired system of mictrotubule-motor protein assemblies, an example of nonequilibrium dynamics that has posed a significant …

Deep Hybrid Modeling Of Neuronal Dynamics Using Generative Adversarial Networks, Soheil Saghafi

Dissertations

Mechanistic modeling and machine learning methods are powerful techniques for approximating biological systems and making accurate predictions from data. However, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. This dissertation constructs Deep Hybrid Models that address these shortcomings by combining deep learning with mechanistic modeling. In particular, this dissertation uses Generative Adversarial Networks (GANs) to provide an inverse mapping of data to mechanistic models and identifies the distributions of mechanistic model parameters coherent to the data.

Chapter 1 provides background information on …

Development Of Non-Viral Nano-Carriers For Gene Delivery And Covid-19 Vaccines, Zhongyu Li

Dissertations

Gene therapy is one of the most promising medical fields with the potential to effectively advance the treatment of difficult diseases by producing therapeutic proteins or repairing defective gene sequences. However, gene therapy presents severe challenges in delivery including renal clearance, phagocytosis, enzymatic degradation, protein absorption, and cellular internalization barriers, which have been barriers for translation into the clinic. Naked nucleic acids, with their intrinsic negative charge, electrostatically repulse the anionic cell membrane, preventing cellular uptake. Also, they are considered foreign genetic material when introduced into the body and are rapidly cleared by the reticuloendothelial system or degraded by nucleases, …

Development Of Novel Nanocarbon Based Materials And Membranes With Enhanced Biocidal Capabilities For Clean Water Generation, Indrani Gupta

Dissertations

Water scarcity is one of the major challenges facing humanity today, driven by population growth, economic development, and dietary shifts towards more water-intensive animal products. To address this issue, efficient water resource management and recycling of wastewater are essential. However, around 80% of wastewater globally is discharged into water bodies without treatment, posing a risk to ecosystems and human health. Pathogens, or harmful microorganisms, are a primary cause of water impairment and the transmission of waterborne diseases, leading to increased mortality rates. Traditional methods of treating pathogens involve the use of radiation or chemical disinfectants. Nonetheless, these methods have drawbacks, …

Field Observations And An Herbarium Study To Understand Plant Reproductive Phenology In Areas Surrounding The Mississippi River, Caitlyn Marie Sims

Student Theses and Dissertations

Plant phenology – the timing of cyclical phases during development – is sensitive to environmental and climatic factors. This thesis focuses on two main factors driving plant reproductive phenology, inundation from flooding and temperature. In Chapter 2, I examine phenological shifts of six taxa along the elevation gradient of a Lower Mississippi River island in response to flood regime. Analyses showed that five out of six taxa responded to flooding, such that their mature fruiting onset, peak, and/or cessation events were shifted in association with elevation, but only two taxa had all three phenological events shifted. Additionally, the total reproductive …

Habitat Occupancy And Use For Bat Species Of Concern On The Buffalo National River, James W. Gore

Student Theses and Dissertations

Populations of several North American bat species have been in decline for several years. Much of this decline is attributed to white-nose syndrome (WNS). To better understand the effects of WNS by increasing our understanding of the bats’ foraging habits, I used bat calls collected by National Park Service personnel on the Buffalo National River, Arkansas, and estimated the bats’ foraging habitat occupancy and relative use. I determined that 1.) a false-positive occupancy model is valid for occupancy estimation when using multiple acoustic bat-id programs; 2.) as of 2016, the progression of WNS had yet to affect bat occupancy on …

Economic Analysis Of Fortified Food Products In India: Evidence From Heckman Selection Model, Ramanjeet Singh Toor

Student Theses and Dissertations

Food fortification refers to the addition of nutrients and minerals to food. About 70% of the people in India are suffering from a deficiency of nutrients and minerals. The main objective of this study is to examine the critical economic and demographic characteristics related to the consumption of fortified products and to investigate their effects on expenditures in India using survey data published on Qualtrics. We utilized the Heckman selection model to estimate different parameters for choice and consumption processes with controlling non-random samples. Our results show that sociodemographic characteristics such as marital status, income, age, education, gender, and the …

They Shrank The Futures Contracts! Mini Futures Contracts: What They Are And How To Use Them, Fabio Mattos

Cornhusker Economics

Mini futures contracts (or e-mini, since they are traded electronically) were first developed in the late 1990s based on futures contracts that already existed. The main characteristic of mini contracts is that they represent a fraction of standard-size contracts. For example, the first mini contract was launched in 1997 and based on the S&P500 futures contract. The size of the standard futures contract is $250 times the value of the S&P500 index, while the size of the mini futures contract is $50 times the value of the S&P500 index. If the index is at 4,200 points, the total value of …

A Foundational Population Genetics Investigation Of The Sexual Systems Of Solanum (Solanaceae) In The Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit From Increased Genetic Admixture Via Obligate Outcrossing, Jason T. Cantley, Ingrid E. Jordon-Thaden, Morgan Roche, Daniel S. Hayes, Stephamie Kate, Christopher T. Martine

Faculty Journal Articles

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor—including sexual system—that influences …

The Role Of Trees In Reducing The Urban Heat Island Effect On The New Jersey Institute Of Technology Campus, Newark, Nj, Dahlia Mansour

Theses

Every year, an estimated 12.3 million tons of glass are generated in the United States. Of all glass generated, only 3.1 million tons are recycled. Despite the near endless recyclability of glass waste, recycling rates in the United States remain low. This is primarily due to the lack of color separation and presence of non-recyclable materials associated with single-stream curbside collection used in many municipalities throughout the country. These factors make recycled glass unusable for many glass bottle manufacturers, causing the majority of glass placed in a recycling bin to eventually be landfilled. The purpose of this research is to …

Ergodic Characterization Of Nonergodic Anomalous Diffusion Processes, Madhur Mangalam, Ralf Metzler, Damian G. Kelty-Stephen

Journal Articles

Anomalous diffusion in various complex systems abounds in nature and spans multiple space and time scales. Canonical characterization techniques that rely upon mean squared displacement break down for nonergodic processes, making it challenging to characterize anomalous diffusion from an individual time-series measurement. Nonergodicity reigns when the time-averaged mean square displacement differs from the ensemble-averaged mean squared displacement even in the limit of long measurement series. In these cases, the typical theoretical results for ensemble averages cannot be used to understand and interpret data acquired from time averages. The difficulty then lies in obtaining statistical descriptors of the measured diffusion process …

Utilizing Natural Language Processing For Automated Clinical Text Review: Identification Of Care Preference Documentation In Patients’ Discharge Summaries, Saksham Arora

Computer Science Senior Theses

Improving patient-centered care necessitates accurate documentation of care preferences, a crucial aspect often underrepresented in administrative data. Most studies apply care documentation to specific patient populations, rather than more appropriately broad population of `seriously ill' patients. This paper addresses this gap by leveraging transformer-based machine learning models, exhibiting an improvement over traditional keyword-based search methods in identifying care preference documentation.

In order to capture a broad spectrum of seriously ill patients, we matched decedent patients to non-decedent counterparts by utilizing a propensity score matching, accounting for important variables like age, gender, primary diagnoses and commodities. We trained and fine-tuned Bio_ClinicalBERT …

Coordination Rigidity In The Gait, Posture, And Speech Of Persons With Parkinson’S Disease, Dobromir Dotov, Valérie Cochen De Cock, Valérie Driss, Benoît Brady, Simone Dalla Bella

Journal Articles

Parkinson’s disease (PD) is associated with reduced coordination abilities. These can result either in random or rigid patterns of movement. The latter, described here as coordination rigidity (CR), have been studied less often. We explored whether CR was present in gait, quiet stance, and speech—tasks involving coordination among multiple joints and muscles. Kinematic and voice recordings were used to compute measures describing the dynamics of systems with multiple degrees of freedom and nonlinear interactions. After clinical evaluation, patients with moderate stage PD were compared against matched healthy participants. In the PD group, gait dynamics was associated with decreased dynamic divergence—lower …

Hrd Effects On First-Line Adjuvant Chemotherapy And Parpi Maintenance Therapy In Chinese Ovarian Cancer Patients, Lei Li, Yu Gu, Mengpei Zhang, Xiaohua Shi, Zhe Li, Xinyun Xu, Tianqi Sun, Yu Dong, Chao Xue, Xiaoru Zhu, Ran Lv, Kai Jiao, Xuwo Ji, Li-Juan Wang, Yang Zhang, Zhiyong Liang, Ying Jin, Rutie Yin, Ming Wu, Han Liang

Faculty, Staff and Student Publications

Homologous recombination deficiency (HRD) testing has been approved by FDA for selecting epithelial ovarian cancer (EOC) patients who may benefit from the first-line poly (ADP-ribose) polymerase inhibitor (PARPi) maintenance therapy. However, the effects of HRD on the clinical outcomes of first-line chemotherapy and first-line PARPi maintenance therapy have not been rigorously evaluated in Chinese EOC patients. Here, we developed an HRD assay and applied it to two large retrospectively collected Chinese EOC patient cohorts. In the first-line adjuvant chemotherapy cohort (FACT, N = 380), HRD status significantly improved PFS (median, 15.6 months vs. 9.4 months; HR, 0.688; 95% CI, 0.526-0.899; …

Diverse Murine Vaccinations Reveal Distinct Antibody Classes To Target Fusion Peptide And Variation In Peptide Length To Improve Hiv Neutralization, Mallika Sastry, Anita Changela, Jason Gorman, Kai Xu, Gwo-Yu Chuang, Chen-Hsiang Shen, Cheng Cheng, Hui Geng, Sijy O'Dell, Li Ou, Reda Rawi, Mateo Reveiz, Guillaume B E Stewart-Jones, Shuishu Wang, Baoshan Zhang, Tongqing Zhou, Andrea Biju, Michael Chambers, Xuejun Chen, Angela R Corrigan, Bob C Lin, Mark K Louder, Krisha Mckee, Alexandra F Nazzari, Adam S Olia, Danealle K Parchment, Edward K Sarfo, Tyler Stephens, Jonathan Stuckey, Yaroslav Tsybovsky, Raffaello Verardi, Yiran Wang, Cheng-Yan Zheng, Yuling Chen, Nicole A Doria-Rose, Adrian B Mcdermott, John R Mascola, Peter D Kwong

Faculty, Staff and Student Publications

While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could neutralize ~30% of HIV-1 strains. To explore the ability of the murine immune system to generate cross-clade neutralizing antibodies and to investigate how higher breadth and potency might be achieved, we tested 17 prime-boost regimens that utilized diverse fusion peptide-carrier conjugates and HIV-1 envelope trimers with different fusion peptides. We observed priming in mice with fusion peptide-carrier conjugates of variable peptide length to elicit higher neutralizing responses, a result we …

Dissociation Protocols Used For Sarcoma Tissues Bias The Transcriptome Observed In Single-Cell And Single-Nucleus Rna Sequencing, Danh D Truong, Salah-Eddine Lamhamedi-Cherradi, Robert W Porter, Sandhya Krishnan, Jyothishmathi Swaminathan, Amber Gibson, Alexander J Lazar, J Andrew Livingston, Vidya Gopalakrishnan, Nancy Gordon, Najat C Daw, Nicholas E Navin, Richard Gorlick, Joseph A Ludwig

Faculty, Staff and Student Publications

BACKGROUND: Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to …

Dietary Changes Among Normal And High Blood Pressure Adolescents During The Covid-19 Pandemic, Bernadette Victoria, Ratu Ayu Dewi Sartika, Rizti Millva Putri

Kesmas

The COVID-19 pandemic has significantly impacted adolescents' unhealthy eating habits and sedentary lifestyles, leading to an increase in blood pressure and obesity rate. High blood pressure among adolescents is an early indicator of adult hypertension, but this condition has received less attention recently. Therefore, this study aimed to determine the differences in dietary changes among high school students with normal and high blood pressure before and during the COVID-19 pandemic in West Lampung District, Indonesia. A cross-sectional design was used, and the sample population consisted of 167 students aged 14-19 years. The results showed that 43 participants had elevated blood …

Effect Of Local Culture-Based Nutrition Education On Compliance With Iron And Folic Acid Supplementation In Female Adolescent, Anita Rahmiwati, Kusharisupeni Djokosujono, Tri Krianto, Diah Mulyawati Utari, Ratna Djuwita, Asih Setiarini, Besral Besral, Dadang Hikmah Purnama, Cesilia Meti Dwiriani, Nana Mulyana

Kesmas

The non-compliance of female adolescents with the consumption of iron and folic acid supplementation (IFAS) poses a challenge to reducing the incidence of anemia. Therefore, this study aimed to determine the effect of nutrition education using the local culture-based approach on the level of knowledge and attitudes regarding awareness, interest, evaluation, trial, and adoption dimensions, as well as compliance of female adolescents in consuming IFAS. The intervention was conducted using a quantitative quasi-experimental design approach. The sample comprised 68 and 58 senior high school girls in the control and intervention groups. The intervention group received IFAS and local culture-based nutrition …

Heritable Aortic Root Aneurysms, Maral Ouzounian, Scott A Lemaire, Dianna M Milewicz

Faculty, Staff and Student Publications

No abstract provided.

The Evaluation Of Carbon Benefits Produced By Urban Street Trees, Hanyu Wang

Theses

Urban tree service and urban forestry are important fields that focus on the care and management of trees in urban areas. Urban trees provide numerous benefits around all aspect, including carbon storage, improving air and water qualities. Carbon storage refers to the process of removing carbon dioxide (CO2) from the atmosphere and storing it in various reservoirs, and in this case, in trees and forests.

i-Tree is a suite of software tools developed by the United States Forest Service that provides a range of resources for assessing and managing forests. i-Tree Eco is one of the more used tools from …

The Influence Of Environmental Tax And Technology On Different Air Pollution Emissions In Oecd Countries, Malak Ali Assaf

BAU Journal - Creative Sustainable Development

Although countries continuously employ taxation and technological measures to control air pollution in the Organization for Economic Co-operation and Development, the results of these practices should be evaluated to determine whether they reach their intended outcomes. This study used panel autoregressive distributed lag model to establish how environmental taxes and technology affects the emission of air pollutants (nitrogen oxides, Carbon dioxide, and particulate matter 2.5). Using secondary data present in the OECD Database and The World Bank, EViews panel was derived to create 3 model in which each of the three variables would be sufficiently explained by environmental tax, abatement …

Evidence On The Impact Of Corruption On Economic Growth: A Systematic Literature Review, Nour Mohamad Fayad

BAU Journal - Creative Sustainable Development

The relationship between corruption and economic growth is complex and has been extensively studied. Till recent days it is still one of the most genuine political challenges that all countries face. Even though anti-corruption measures have improved, they still lack consistency and clarity. Accordingly, this paper reviews the extant literature on this issue, by examining 66 research papers on the impact of corruption on economic growth. The study was aided by analysis of the theme Corruption and economic growth identified in the present literature. Impact of Corruption on economic growth has been tested in multiple studies utilizing time series, panel, …

Towards Urban Biodiversity: Simulating Design Parameters For Wildlife-Inclusive Green Infrastrcuture, Alisa Abdulghany, Baher Farahat

BAU Journal - Creative Sustainable Development

As of 2021, more than half of the global population resides in urban areas. This resulted in an overwhelming footprint affecting species habitat areas leading to biodiversity loss. By definition, urban biodiversity is the diversity of living things within the urban realm. By providing chances for habitat as part of new developments, preserving on-site habitats, and attempting to connect with the local ecosystems, we can help promote biodiversity. Green infrastructure (GI), which includes all semi-natural areas in the urban context, can serve as a vessel for biodiversity. Therefore, the problem can be defined by the urban footprint that expands on …

Discussing Different Images Of Pharmaceutical Company, Roula Afif Bou Assi, Ola Bazaza

BAU Journal - Creative Sustainable Development

Every organization is a complex, non-linear, and dynamic system. Gareth Morgan discussed eight different metaphors where they can be useful devices to create mental images to clarify and interpret our organizations. These eight metaphors are: machine, organism, brain, culture, political, flux and transformation, psychic prisons and instruments of domination. This combination of metaphors helps us understand our organization, analyze the structure, the leadership style (NAGY, December 2014). In this paper I will discuss the different metaphors of a pharmaceutical company (X). It is a growing pharmaceutical company, where reading and analyzing the different metaphors will definitely help them to prepare …

Dissociation Between Conscious And Unconscious Processes As A Criterion For Sentience, Ivan Ivanchei, Nicolas Coucke, Axel Cleeremans

Animal Sentience

Based on the literature on human consciousness, we suggest that to demonstrate sentience in a system, one needs to demonstrate both conscious and unconscious processing in the system. Major theories of consciousness require the existence of both conscious and unconscious processes. Contrasting effects of conscious and unconscious processes have been successfully used in human studies and have begun being applied in animal sentience research as well.

Plant Sentience: Getting To The Roots Of The Problem, Krzysztof Dolega, Savannah Siekierski, Axel Cleeremans

Animal Sentience

Segundo-Ortin’s (2023) target article invites us to consider the possibility that plants can experience subjectively felt states. We discuss this speculation on the basis of the functional neurobiology of consciousness. We suggest that demonstrating plant sentience would require that we identify not only behaviors analogous to those exhibited by sentient creatures, but also the functional analogues of the mechanisms causing such behaviors. The lack of clear evidence for any kind of integration between self-states, self-movement, environmental states, memory, or affective communication within plants suggests that plant sentience remains an admittedly fascinating, but ultimately merely provocative speculation.

Understanding Irrigation Water Optimization, Burdette Barker, Matt Yost, Jody Gale, Mark Nelson

All Current Publications

Irrigation is applied to much of the cropped area of Utah to support crop production. Limited water resources and competing demand for those resources make irrigation water conservation, irrigation water optimization, and efficient use of irrigation water important components of overall water resource management. It is well known in Utah that optimal irrigation use is even more critical during drought conditions. However, optimization practices change the quantity, quality, and timing of water flows. It is important to consider the possible hydrologic impact of irrigation practice changes and the desired outcome of an optimization practice to avoid implementing a practice that …