Digital Commons Network^™

A Patient-Specific Infrared Imaging Technique For Adjunctive Breast Cancer Screening: A Clinical And Simulation - Based Approach, Alyssa Owens

Theses

Breast cancer is currently the most prevalent form of cancer in women with over 266,000 new diagnoses every year. The various methods used for breast cancer screening range in accuracy and cost, however there is no easily reproducible, reliable, low-cost screening method currently available for detecting cancer in breasts, especially with dense tissue. Steady-state Infrared Imaging (IRI) is unaffected by tissue density and has the potential to detect tumors in the breast by measuring and capturing the thermal profile on the breast surface induced by increased blood perfusion and metabolic activity in a rapidly growing malignant tumor. The current work …

Employing Optical Flow On Convolutional Recurrent Structures For Deepfake Detection, Akash Chintha

Theses

Deepfakes, or artificially generated audiovisual renderings, can be used to defame a public figure or influence public opinion. With the recent discovery of generative adversarial networks, an attacker using a normal desktop computer fitted with an off-the-shelf graphics processing unit can make renditions realistic enough to easily fool a human observer. Detecting deepfakes is thus becoming vital for reporters, social networks, and the general public. Preliminary research introduced simple, yet surprisingly efficient digital forensic methods for visual deepfake detection. These methods combined convolutional latent representations with bidirectional recurrent structures and entropy-based cost functions. The latent representations for the video are …

Biological Control Of Fusarium Wilt In Date Palm (Phoenix Dactylifera L.) In The United Arab Emirates By Endophytic Actinobacteria, Aisha Abdullah Darwish Shambeh Alblooshi

Theses

Date palm trees suffer from many various serious diseases, including sudden decline syndrome (SDS). External symptoms were characterized by whitening on one side of the rachis, progressing from the base to the apex of the leaf until the whole leaf dies; while the internal disease symptoms included reddish roots and highly coloured vascular bundles causing wilting and death of the tree. Although three Fusarium spp. (F. oxysporum, F. proliferatum and F. solani) were isolated from diseased root samples, the fungal pathogen F. solani was associated with SDS on date palm in the United Arab Emirates (UAE). Fusarium spp. were identified …

Biological Control Of Sudden Decline Disease Of Date Palm (Phoenix Dactylifera L.) In The United Arab Emirates, Khawla Juma Saif Zeail Alwahshi

Theses

Date palm orchards suffer from serious diseases, including sudden decline syndrome (SDS). The fungal pathogen Fusarium solani was associated with SDS on date palm in the United Arab Emirates (UAE). Application of Cidely® Top (difenoconazole and cyflufenamid) significantly inhibited the fungal mycelial growth In vitro and reduced SDS development on date palm seedlings pre-inoculated with F. solani under greenhouse conditions. This is the first report confirming that the chemical fungicide Cidely® Top is strongly effective against SDS on date palm. Fungal pathogens not only inhibit plant growth directly but also induce the plant to synthesize stress ethylene. Much of the …

Self-Supervised Video Representation Learning By Recurrent Networks And Frame Order Prediction, Sai Shashidhar Nagabandi

Theses

The success of deep learning models in challenging tasks of computer vision and natural language processing depend on good vector representations of data. For example, learning efficient and salient video representations is one of the fundamental steps for many tasks like action recognition and next frame prediction. Most methods in deep learning rely on large datasets like ImageNet or MSCOCO for training, which is expensive and time consuming to collect. Some of the earlier works in video representation learning relied on encoder-decoder style networks in an unsupervised fashion, which would take in a few frames at a time. Research in …

Deep Learning For Quantitative Motion Tracking Based On Optical Coherence Tomography, Peter Abdelmalak

Theses

Optical coherence tomography (OCT) is a cross-sectional imaging modality based on low coherence light interferometry. OCT has been widely used in diagnostic ophthalmology and has found applications in other biomedical fields such as cancer detection and surgical guidance.

In the Laboratory of Biophotonics Imaging and Sensing at New Jersey Institute of Technology, we developed a unique needle OCT imager based on a single fiber probe for breast cancer imaging. The needle OCT imager with sub-millimeter diameter can be inserted into tissue for minimally invasive in situ breast imaging. OCT imaging provides spatial resolution similar to histology and has the potential …

Enhanced Removal Of Perfluorooctanoic Acid (Pfoa) Via Microwave-Fenton-Reactive Membrane Filtration, Fangzhou Liu

Theses

Perfluorooctanoic Acid (PFOA), one of the common per- and poly fluorinated alkylated substances (PFASs), is increasingly detected in the environment due to the diverse industrial applications and high resistance to degradation processes. This study evaluated degradation of PFOA in microwave-assistant catalytic membrane filtration, a process that integrates microwave catalytic reactions into a ceramic membrane filtration. First, water permeation of the pristine and catalyst-coated membranes were examined under the influence of microwave irradiation to analyse the impacts of the coating layer and water temperature increase on permeate flux, which were well interpreted by three models. Then, the PFOA removal was first …

Model-Based Deep Siamese Autoencoder For Clustering Single Cell Rna-Seq Data, Zixia Meng

Theses

In the biological field, the smallest unit of organisms in most biological systems is the single cell, and the classification of cells is an everlasting problem. A central task for analysis of single-cell RNA-seq data is to identify and characterize novel cell types. Currently, there are several classical methods, such as K-means algorithm, spectral clustering, and Gaussian Mixture Models (GMMs), which are widely used to cluster the cells. Furthermore, typical dimensional reduction methods such as PCA, t-SNE, and ZIDA have been introduced to overcome “the curse of dimensionality”. A more recent method scDeepCluster has demonstrated improved and promising performances in …

Spectral 3d Reconstruction Based On Macroscopic Oct Imaging, Xingyu Zhou

Theses

Various optical technologies have been utilized to improve art conservation by art conservators, such as laser triangulation, stereophotogrammetry, structured light, laser scanner and time of flight sensors. These methods have been deployed to capture the 3D or surface topography information of sculptures and architectures. Optical coherence tomography (OCT) has introduced new imaging methods to study the surface features and subsurface structures of delicate cultural heritage objects. However, despite its higher spatial resolution, the field of view (FOV) of OCT severely limits the size of the scanning area and does not allow macroscopic examination. To solve this issue, we develop and …

Analysis Of Gameplay Strategies In Hearthstone: A Data Science Approach, Connor W. Watson

Theses

In recent years, games have been a popular test bed for AI research, and the presence of Collectible Card Games (CCGs) in that space is still increasing. One such CCG for both competitive/casual play and AI research is Hearthstone, a two-player adversarial game where players seeks to implement one of several gameplay strategies to defeat their opponent and decrease all of their Health points to zero. Although some open source simulators exist, some of their methodologies for simulated agents create opponents with a relatively low skill level. Using evolutionary algorithms, this thesis seeks to evolve agents with a higher skill …

An Information Theoretic Approach To Assess Perceived Audio Quality Using Eeg With Reduced Number Of Electrodes, Sansit Das

Theses

Electroencephalograph(EEG) is a process mainly used in medical and research fields to study the electrical activities in a brain. In this technique, 128 or 256 electrodes are attached to the scalp and the electrical activities of the human brain is recorded with the help of a software. In the global scenario, the EEG responses are studied and analysed to acknowledge any disorders in the brain, such as epilepsy or head injury.

Recent studies performed by researchers, have focused on analysing these electrical activities to access perceived audio quality from users by using information theoretic approaches, such as mutual information. Experiments …

A Recent (2020) Comparative Analysis Of Genome Aligners Shows Hisat2 And Bwa Are Among The Best Tools, Ryan J. Musich

Theses

Genome aligners are an important tool in bioinformatics research as they can be used to detect gene variants to create higher crop yields, detect abnormal gene production in cancer cell lines, or identify weaknesses in a newly discovered pathogen. Aligners work by taking sequenced DNA or RNA and mapping these reads to their corresponding location in a reference genome. Although beneficial as a tool, choosing which aligner to use for a project is often a difficult decision due to the large number of tools available and each one claiming to be the best at what it does. The goal of …

The Infratemporal Fossa: Visual Communication & 2d Animation To Present Anatomical Forms, Gwendolyn Fuller

Theses

Gross Anatomy is the study of human organs and tissues that are visible to the naked eye. It is a keystone class intended for medical students, where they can gain hands-on knowledge of human anatomy by dissecting each region of a human cadaver. The class consists of a lecture, where the instructor will discuss a specific anatomical region, and a subsequent lab, where the students will then dissect that region of the cadaver. The goal for lecture is to present an anatomical region to the students with the intention of aiding them to identify the structures later in lab. Most …

An Analysis Of The Components Of Terrorism, Rhianna Hayes

Theses

Terrorism is a complex topic to study. There is no consensus on what the word terrorism means, and there is even less consensus on why groups of people go out of their way to use terrorism as a form of political expression. Various analyses and studies have been conducted to attempt to explain this complex topic. Many of these studies have drawn from criminal justice research to apply criminological theories as an explanation for terrorism. The application of criminological theories provides one baseline for people to attempt to understand terrorism. At first glance, it may seem that criminological theories will …

The B Respirator Respiratory Protection For The Bearded Man, Joseph R. Allgeier

Theses

The news today is filled with stories of respiratory illnesses. The health risks to people are everywhere. Dangerous health situations are created by nature and they are also man made. One thing stands between people and breathing contaminated air and that is a variety of different types of dust masks and respirators. Unfortunately, a huge portion of our population has been left out of this protective solution since most affordable respirators rely on seal created by skin contact. Men with beards or facial hair that interfere with this seal must choose between faulty protection or no protection at all. “Just …

Ar Comic Chat, Dylan Bowald

Theses

Live speech transcription and captioning are important for the accessibility of deaf and hard of hearing individuals, especially in situations with no visible ASL translators. If live captioning is available at all, it is typically rendered in the style of closed captions on a display such as a phone screen or TV and away from the real conversation. This can potentially divide the focus of the viewer and detract from the experience. This paper proposes an investigation into an alternative, Augmented Reality driven approach to the display of these captions, using deep neural networks to compute, track and associate deep …

Gait Generation For Damaged Hexapods Using Genetic Algorithm, Justin Kon

Theses

This paper discusses the design and implementation of a Genetic Algorithm for the generation of gaits compensating for system damage on the joint level of a hexapod system. The hexapod base used for this algorithm consists of six three degree of freedom legs on a rectangular body. The purpose of this algorithm is to generate a gait such that when N motors become inoperable, as detected by the robot’s internal software, the system is able to continue moving about its environment. While algorithms like this have been implemented before, the generated gaits are a sequence of discrete foot positions. This …

Elucidating The Effect Of Temperature And Concentration On The Rotational Diffusion Of Yb– Crystallin To Elucidate Inter-Protein Interactions, Olivia Fraser

Theses

γB – crystallin is a 21 kDa protein found in the lens of the bovine eye, existing without turnover. It shares 76% sequence identity with a human lens protein, γD – crystallin, with a structural RMSD of 0.8 Å by Dali (174 residues, Cα atoms only). Damages to and abnormalities on crystallin proteins can lead to phase separation and aggregation in the lens, resulting from aberrant inter-protein interactions, which can lead to partial or total blindness by cataract. The purpose of this work is to elucidate global inter-protein interactions of wild-type γB – crystallin by T1 and T2 relaxation NMR …

Application Of Biochar As An Additive To Enhance Biomethane Potential In Anaerobic Digestion, Cecilia B. Frias Flores

Theses

Energy and useful materials can be produced by applying biological and thermal conversion processes such as anaerobic digestion and pyrolysis. Agricultural and industrial wastes seem to be the most attractive substrates since they are essentially unlimited resources. Pyrolysis has been used mostly for the conversion of biomass to bio-crude and biochar, a stable form of nearly pure carbon that has application in many agricultural and environmental applications. There is a widespread literature describing use of biochar as an additive to stabilize the anaerobic digestion process. We studied the effects that biochar has on the biomethane potential (BMP) during anaerobic digestion …

Detecting Performance Regression Inducing Code Changes Using Static And Dynamic Metrics, Hiten Gupta

Theses

Performance regression testing is a cost-intensive task as it delays the system development. The process, if performed in Iterations, significantly slows down the developer’s pace. Hence, it is essential to execute the performance tests only on the new commit and not the whole system, as regression is induced by a newly made change to the system. This work presents a novel contribution to the detection of performance regression inducing code changes to solve the optimization problem. In this study, we combine the static and dynamic metrics as features to train classifiers to predict the performance regression if introduced by the …

Identifying Performance Regression From The Commit Phase Utilizing Machine Learning Techniques, Max Mendelson

Theses

Over the lifespan of a software application, it is inevitable that changes to the source code will be made that causes unintended slowdowns in functionality. These slowdowns are referred to as performance regression. Typically projects who are particularly concerned about performance have performance testing that are run to identify if a performance regression is introduced into the code. This is difficult however due to how time consuming and resource intensive running performance tests are when trying to simulate a realistic scenario.

The study of De Oliveira et. al. (Perphecy) [4] suggests a technique to predict the likelihood that a commit …

Modular Synthesis Of Dual- And Tri-Modal Targeted Molecular Imaging Agents, Nicholas C. Schug

Theses

There are few reported methods for combining two or three different imaging dyes, metals, or dye-metal combinations, followed by the conjugation of a disease- targeting group to enable the use a given imaging system for multiple imaging applications. Previously, peptides have been used as scaffolds for dyes and metals used in diagnostic techniques such as optical molecular imaging (OMI), positron emission tomography (PET), and magnetic resonance imaging (MRI). The aim of this project was to reassemble peptide-based imaging agents through a modular method by coupling together modules comprised of amino acids with imaging agents attached to their side chains to …

Breathing Pacer Device For Stress And Anxiety Relief, Maria Grazia Guerrero Bejarano

Theses

Stress and stress-related physical and mental diseases are increasing and affecting more people every day. There have been many approaches to try to solve this issue. Many of them are based on the idea that meditation and mindfulness breathing could improve these conditions. The problem is that not everyone can achieve those levels of meditation for that to work. Another issue is that those solutions are relying on a particular way of breathing to help all.

In contrast, this project developed under research that shows that the amount of CO₂ in a person's exhaled breath could be an indicator of …

The Effect Of Β-Caryophyllene On Isoproterenol-Induced Myocardial Infarction, Farah M. Jamal Laham

Theses

Cannabinoid type 2 receptors (CB2), a key member of the endocannabinoid system have recently emerged as a crucial therapeutic target for cardiovascular diseases (CVDs). Downregulation of CB2 receptors has been witnessed in various cancers, neurological and cardiovascular disorders. Thus, the activation of CB2 receptors may protect against ISO-induced myocardial infarction (MI) in rats. The present study investigates the cardioprotective effect of a selective cannabinoid type 2 receptor agonist β-caryophyllene (BCP), a dietary phytocannabinoid, and a natural bicyclic sesquiterpene against isoproterenol (ISO)-induced MI in rats. Male albino Wistar rats were pre-and co-treated with β-caryophyllene (50 mg/kg, orally) twice daily for 10 …

Correlating Direct And Indirect Executive Functioning Measures And Language Skills Of Children With Autism, Emily Claire Wagner

Theses

Executive functioning usually refers to one’s ability to regulate one’s behavior, set goals, be mentally flexible, and understand the consequence of one’s actions. However, certain neurodevelopmental disabilities such as Autism, often can negatively impact executive function processes. Although applied behavior analytic (ABA) treatment is the most recommended intervention for autism treatment practitioners rarely assess or target executive functioning within their treatment planning. The present study assessed the relationship between direct and indirect executive functioning scores and a language assessment used by ABA providers. Thirty-nine children with autism spectrum disorder were administered a variety of scales including the Behavior Rating Inventory …

Anti-Normative Women And Queer Space In Early Modern Drama, Chelsea Brooks

Theses

The most interesting oddity about the Early Modern English stage is the overwhelming presence of the female form despite the obvious lack of female performers. Male actors performed female characters and sometimes those female characters were subversive and tested the boundaries of their constructed heteronormative society. A common comedic trope followed the crossdressed crossgendered heroine, or the boy actor dressed as women dressed as a man. This trope appears in the plays discussed in this thesis: Thomas Heywood’s Fair Maid of the West, Part 1 and John Lyly’s Gallathea. By adapting Michel de Certeau’s concept of space, wherein space …

Up-Regulation Of Sexual Desire In Long-Term Relationships: Self-Report And Electrophysiological Data, Lauri L. Davis

Theses

Diminished sexual desire is a common in long-term relationships yet little research has examined strategies to promote sexual desire within healthy intact couples. This study focused on three regulation strategies: 1) positive reappraisal of the partner, 2) reappraisal of sexual desire decline, and 3) sexual imagery. These regulation strategies were used to test for an increase in sexual desire, infatuation, attachment, and relationship satisfaction for the partner. We additionally examined whether these strategies increased motivated attention to the partner as indicated by the late positive potential (LPP), an event-related potential (ERP) component. Participants (N=25, age=18-32 yrs, 6 men) …

Different Exercise Tendencies Modulate Behavioral And Molecular Changes To Opioid Or Exercise-Induced Reward, Amanda Titus

Theses

Reward changes were observed in rodents with different exercise tendencies by utilizing the conditioned place preference paradigm. Adult male Wistar rats with distinct phenotypes (low volume runners, high volume runners, and wild-type) were given access to a running wheel or an injection of morphine as a rewarding stimulus. There was no difference observed in the strength of conditioned place preference between the rewarding stimuli. Extinction was significantly more effective in low volume runners than high volume runners and wild-type animals, as was observed in the lower percentage of time spent in their assigned conditioning chamber. These findings suggest that low …

Deepmind’S Protein Folding Quality Process Analysis, Amro Oussama Noueihed

Theses

Proteins are the building blocks of life and are responsible for the vast majority of our cellular activity. For decades, the major method of producing acceptable protein structures was laboratory testing. Scientists have been perplexed by how the components of a protein, which are made up of a string of different amino acids, come together to produce a complex twisting and folding pattern. Following that, scientists started developing computer algorithms for predicting protein structure from amino acid sequence. To test the anticipated structural accuracy, data from multiple prediction models were compared with CASP entries in this research. Later, the experiment …

Transcriptomic Analysis And Developmental Neural Transcript Identification In The Brittle Star Ophioplocus Esmarki, Alexandria Shumway

Theses

Ophioplocus esmarki is one species within a family of brittle stars that includes an abbreviated mode of development with a non-feeding, vitellaria larva. This development contrasts with the ancestral mode that produces a feeding, ophiopluteus larva. This project aims to complete functional annotation of the O. esmarki transcriptome, to provide a comparison of gene classification in both the vitellaria and juvenile stages of development, and to identify developmental neural transcripts through ortholog searches, and verify their identify through phylogenetic analysis. During my undergraduate research, Illumina sequencing was performed at the University of Rochester Genomics Center. The samples underwent RNA isolation, …