Digital Commons Network^™

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, …

Deep Convolutional Networks Without Learning The Classifier Layer, Zhongchao Qian

Theses

Deep convolutional neural networks (CNNs) are effective and popularly used in a wide variety of computer vision tasks, especially in image classification. Conventionally, they consist of a series of convolutional and pooling layers followed by one or more fully connected (FC) layers to produce the final output in image classification tasks. This design descends from traditional image classification machine learning models which use engineered feature extractors followed by a classifier, before the widespread application of deep CNNs. While this has been successful, in models trained for classifying datasets with a large number of categories, the fully connected layers often account …

Speculative Fashion: A Spacesuit For Life Outside Earth, Lauren Miyoko Furushima

Theses

When Earth is no longer able to house living creatures, humans will need a new environment to inhabit. Space tourism companies are already looking toward building civilizations in outer space. In accordance, humans will need space wear that is able to support their bodies for long periods of time, therefore supporting life outside of Earth. NASA’s white spacesuits protect astronauts but are hard to move in and costly to manufacture. As designers, it is vital to envision different solutions for spacesuits because it will soon become our normal clothing. The importance of designing for future space travel for everyone may …

Toy Design For Children With Autism Spectrum Disorder Based On Existing Therapeutic Training Methods, Ye Wang

Theses

Children with Autism Spectrum Disorder (ASD) behave in different ways from other children as well as face enormous problems in their daily life. Previous research has found that physical treatment not only improves their body functions, but also benefits their mental development. Play therapy is a very effective way to help children with ASD since playing is the way children express themselves. However, after field research and benchmarking, I found that there are few toys helping them with their developmental coordination, which is necessary especially for children with ASD. In this paper, I have designed a series of devices for …

Comparison Of Statistical Models For Imputation Of Missing Data In Clinical Trials, Vaishnavi Purandare

Theses

Missing data is an integral part of clinical trials and its analysis. This study discusses the downsides of having missing values in clinical data, traditional methods used to resolve this issue and some techniques which can be implemented to remedy the same.

The data used for the study is simulated from Theophylline data from Pinheiro and Bates (1995). The simulated data measures the Theophylline drug concentration in the body of 10 Subjects over 24 hours. There are three cases considered with increasing number of randomly created missing values for the Concentration variable. Subsets are created to fit linear and quadratic …

Magnolia Twilight, Qin Zhou

Theses

A village girl, Yulan (19), goes to Shanghai and her life changes completely.

Yulan runs out from a small village in Yunnan, because her family only cares about her brother, and the culture in that town is that boys are always superior to girls. The boy next door from hometown, Jinxian Fang (26), takes care of Yulan. Yulan wants to be independent and moves out, and she has a roommate Mulan (26). Mulan is the kind of female that Yulan wants to become.

Yulan finds out Jinxian has some secret business, and he seems cheats on her. After the suggestion …

Crafting Adversarial Examples Using Particle Swarm Optimization, Rayan Mosli

Theses

Machine learning models have been found to be vulnerable to adversarial attacks that apply small perturbations to input samples to get them misclassified. Attacks that search for and apply the perturbations are performed in both white-box and black-box settings, depending on the information available to the attacker about the target. For black-box attacks, the attacker can only query the target with specially crafted inputs and observing the outputs returned by the model. These outputs are used to guide the perturbations and create adversarial examples that are then misclassified.

Current black-box attacks on API-based malware classifiers rely solely on feature insertion …

Design And Production Of 3d Animation Short Film “The Blue Battery”, Xianyu Liao

Theses

he Blue Battery is a character animation short film telling a story of a robot pursuing freedom in a totalitarian environment. The idea of the film expresses reflection and vigilance against totalitarianism. During World War II, Nazism prevailed in Europe, the extreme abuse of power by the ruling class led to a large number of people suffering from war. After the war, the Soviet Republic gradually moved toward totalitarianism and eventually died out. In these past countries, political scientists have found that violence and secret police often exist. Especially the control of thought, the fanaticism of personal worship, and the …

Shared Kitchen Design For Rental Spaces And Frequent Moving Populations, Qian Liu

Theses

With the frequency of population migration and moving increasing across the world, more people are living in shared rental places. It’s been reported that 17.2 % of people in China move across cities annually and about 15% of the population moves in the US and Korea annually (UNFPA, Statistics Korea, 2019).

With high residential mobility, connections and social networks are constantly cut off (Wang, 2019). In the long-term, people who move frequently become less committed or tied to their surroundings; they invest less effort on interaction and preservation or their environment behaviors. It has been reported that water and waste …

Dog Days On The Chaparral, Hugo Teixeira

Theses

Dog Days on the Chaparral is an installation comprised of three photographic sculptures made in response to the question “where are you from?” Although I define myself as both Portuguese and American, as someone who immigrated as a child, my identification as either ebbs and flows. The work embodies this slipperiness—a complicated emotional geography—in fabricated sculptures which collage images of two landscapes, the California chaparral and Portuguese montado, as proxies for these two homes and identities. I employ vernacular building materials and tools, such as lumber, engineered wood, common fasteners, house paint and steel clamps to create a literal and …

Cruces, Carlos Mario Tobon Franco

Theses

Cruces is a multimedia installation depicting immigrant conditions and experiences throughout landscapes, Latinx communities, and borderlands. Made during the last two years, it is constructed as a multivocal ethnography of immigrants with varying legal statuses, countries of origin, and stages in their journey. The imagery, sounds, and narratives are composed of the distributed yet relational geographies of immigrants’ experience and the pieces are structured to highlight the constitutive elements of human mobilities, such as trains, rivers and immigration hubs, as well as the natural obstacles they face in their perilous transit, such as forests and deserts.

The fieldwork was carried …

Reducing Global Demand On Conflict Minerals In Consumer Electronics And Lithium-Ion Batteries, Mosunmola Odulate

Theses

Advances in technology have led to increasing demand for more sophisticated electronic products, which, in turn, induces demand for raw materials essential for product performance. A class of such materials is mined in places in the world that are politically unstable – they are called Conflict Minerals (CMs) because profits from their mining and trade support human rights violations in their places of origin. They include Tantalum, Tin, Tungsten, and Gold (3TG). To reduce global reliance on 3TG, government policies from local and international communities are the only works in place, but what is still unclear is their efficacy towards …

Because The Sun Hath Looked Upon Me, Granville Carroll

Theses

"Because the Sun Hath Looked Upon Me" is a photographic project examining identity construction on an individual, society, and cosmological level. It is a response to racial limitations and judgements thrust upon the African diaspora. I reimagine my identity through Afrofuturism by intersecting cosmology, philosophy, and spirituality. Using digital technology, I composite photographs to create new landscapes and self-portraits. The landscapes are my vision of the promised land; the ground references the physical world, the sky becomes a canvas for projection and imagination, and the horizon acts as a symbol for the liminal space between the physical and ethereal. The …

In Praise Of Shadows, Jiageng Lin

Theses

In Praise of Shadows is a body of work that explores and pushes the boundaries and meanings of photographic materials, apparatus, and perception. This project started with the desire to challenge the traditional view of photography as a purely representational medium and reveal its hidden processes. Photographs have always been something to look through; what is shown in the image area matters. In Praise of Shadows utilizes basic photographic elements, camera, paper, and photo-sensitive materials as subjects to challenge the perception of photography as simply something to look through. Each work in In Praise of Shadows exhibits varying characteristics that …

Kaizen Programming With Enhanced Feature Discovery: An Automated Approach To Feature Selection And Feature Discovery For Prediction Models, John Stelmack

Theses

Feature selection (FS) is the process of finding an ideal set of features for a prediction model from a set of candidate features. A key step in designing a prediction model is reducing the size of the input feature set while increasing its usefulness. This reduces the complexity of a model, making the model run more quickly while allowing one to explain the usefulness of each individual feature more easily. Despite the desire to determine an ideal feature set, the process of FS can be time consuming and yield mixed results. FS is often partially automated with the use of …

You Know That Feeling You Get Right After You Vomit? Yeah, I Want To Feel That., Jin Chan

Theses

You Know that Feeling You Get Right After You Vomit? Yeah, I Want to Feel That is an ongoing collection of photographic and sculptural components existing as found object mixedmedia such as oranges, wood, flowers, and inkjet prints held by T-pins. Through a surrealistic indulgence of abjection and uncanniness, with an implied bodily violence, this series of work comes to an understanding of time, identity, and existing between social boundaries creating a push and pull to define “in-betweenness”. This contradiction causes a psychic dissonance, or a mental contradiction of belonging; to exist in-between is to exist uncannily. “In-betweenness” is represented …

Tiny Furious Circles, Ann M. Herrington

Theses

I have had time to live and time to reflect on that living. What I have found is that certain things present themselves, over and over, wearing different skins. And though they look different, there is a certain whiff of familiarity that activates the soul’s hindbrain and pulls you close. That’s how it has been for me. Because of this — my failure to learn the first time; my need to see a thing from all its sides; my constant picking at the half-healed — certain themes repeat. And because they have come to me at different times in many …

The Vulnerability Of Chronic Stress: Implications For Feeling Like Giving Up, Miranda Jany

Theses

The feeling of learned helplessness has been associated with prolonged stress and trauma. Additionally, many previous studies have examined the relationship between stress and decreased feelings of control, such as self-efficacy and locus of control. However, these forms of control have been primarily self-reported. The present study aimed to investigate the relationships among learned helplessness, chronic stressors, and self-agency using a computer-based task. We also measured heart rate variability (HRV) during the self-agency task to assess psychophysiological correlates of these variables. Seventy-four participants completed a series of questionnaires that were used to assess lifelong stressors (e.g., exposure to natural disasters, …

Influences Of Salvinorin A And Sex Differences On Depressive- And Anxiety-Like Behaviors In A Chronic Mild Stress Paradigm, Sarah Mitchell

Theses

Kappa opioid receptors are colocalized with dopamine receptors and are frequently associated with depression, anxiety, stress, and drug use and abuse. KOR antagonism has widely been considered anti-depressive and anxiolytic in animal models while agonism is pro-depressive and anxiogenic. However, recent findings suggest that SalvA, a natural kappa agonist derived from a plant in the mint family, can reduce depressive- and anxiety-like behavior in rats. The current study investigated the effects of chronic mild stress on behavior, attenuation by SalvA, and sex differences. 52 Long-Evans rats, 26 males and 26 females, were exposed to six weeks of CMS. Animals received …

Polarization Engineering For Deep-Ultraviolet Light-Emitting Diodes, Cheng Liu

Theses

The new Coronavirus or Covid-19 has already became a world-wide pandemic. As of April 22nd, 2020, there are more than 2593129 confirmed case and 179725 total deaths. To fight against the Coronavirus, tremendous efforts have been made for slowing down the spread, such as social distancing. Recently, deep-ultraviolet (DUV) light-emitting diodes (LEDs) are demonstrated to be super effective to deactivate the virus/bacteria. In addition, the outstanding properties such as long life-time, compact size and environmental-friendly from DUV LEDs make them ideal for protecting people from the Coronavirus. However, all AlGaN-based DUV LEDs suffers from low external quantum efficiency issue. Among …

Effects Of Prior Land Use, Carbon Availability, And Hydrology On Nitrogen Cycling In Created Freshwater Wetlands, Michael Mcgowan

Theses

Freshwater wetlands are a critical feature of the landscape, providing important ecosystem services such as nutrient removal. However, created wetlands often fail to meet functional performance criteria, frequently due to shortcomings in management of key functional drivers, especially hydrology and soil quality. In natural wetlands, hydrology, carbon (C) and nitrogen (N) availability play an important role in nutrient cycling. However, controls on the relative importance of denitrification and N fixation, and release of the greenhouse gas nitrous oxide (N2O ) are poorly understood in created wetlands. The tradeoff between these processes and the mechanisms for improved management are are imperative …

Meaning In The Noise: Neural Signal Variability In Major Depressive Disorder, Sally M. Pessin

Theses

Clinical research has revealed aberrant activity and connectivity in default mode (DMN), frontoparietal (FPN), and salience (SN) network regions in major depressive disorder (MDD). Recent functional magnetic resonance imaging (fMRI) studies suggest that variability in brain activity, or blood oxygen level-dependent (BOLD) signal variability, may be an important novel predictor of psychopathology. However, to our knowledge, no studies have yet determined the relationship between resting-state BOLD signal variability and MDD nor applied BOLD signal variability features to the classification of MDD history using machine learning (ML). Thus, the current study had three aims: (i) to investigate the differences …

Investigation Of Water Vapor Transport In Membrane Mass Exchangers For Hvac Applications, Nathan Demario

Theses

Vapor compression systems have dominated the HVAC area for close to 100 years. These systems require significant amounts of energy to complete the compression cycle and the refrigerants used are known contributors to global warming. As a result, new innovations are being sought and a membrane-based system, the subject of this thesis, is one such technology. Water selective membrane materials offer a promising alternative to vapor compression for dehumidification of building air. For HVAC systems, process air pressure drop constrains flow path design in a membrane-based approach. The transport resistance for water vapor from air flow channels is experimentally investigated …

Detecting Malicious Websites Using Machine Learning, Saeed Ahmad Al Tamimi

Theses

The growing use of the internet resulted in emerging of new websites every day (Total number of Websites - Internet Live Stats, 2020). Web surfing has become important for everyone regardless of their occupation, age or location. However, as the use of the internet is increasing so is the vulnerability to malware attacks through malicious websites (Softpedia, 2016). Identifying and dealing with such malicious website has been quite difficult in the past as it is quite challenging to separate good websites from bad websites. However, by using machine learning algorithms on large datasets it is now possible to detect such …

Whispering Messengers: Everyone Has A Bunny, Tracy Shih-Tung Cheng

Theses

How can I connect people through my art? My research focuses on the “bonds” of relations. The intent is for my art to become a bond to connect people. Compared to just walking around and staring at the artwork, I believe that experience with touch and play can impact audiences more directly.

The idea of my work is based on the experience of passing notes to exchange messages When I was a student I wrote notes to friends, then folded the note to create an origami form before passing them to the recipient. The origami from transformed the note into …

Supererogation And Moral Reasons, Justin B. Yee

Theses

This paper is about the paradox of supererogation and why supererogation is morally optional. I argue that supererogation is morally optional because it is supported by both moral reasons and nonmoral reasons. I understand moral reasons to be agent-neutral reasons that apply to everybody while nonmoral reasons are agent-relative reasons that don’t apply to everybody. By understanding supererogation in this way, I have rejected the common assumption that what makes supererogation supererogatory is moral. Instead I argue that the source of supererogation is nonmoral. One important upshot to this is that unlike those who claim that the source of supererogation …

The Public’S Reaction, Over Time, To The Findings Of The Warren Report, Adam T. Fry

Theses

Abstract

From the moment President Kennedy was shot, the public had difficulty accepting Lee Harvey Oswald as the lone assassin, and spoke in terms of conspiracy. Polling data indicated that while Oswald may have participated in the plot, the majority believed others were also involved. Examining the public’s response to the vocal critics of the Warren Commission, the findings of both the Church Committee and the House Select Committee on Assassinations (HSCA), and the release of pertinent documents as a result of the Kennedy Assassination Records Collection Act, an image of an unconvinced public is seen. Evidence of this can …

Do Hardworking Role Models Lower Implicit Gender-Science Bias?, Christina Garasky

Theses

Prior research has demonstrated that implicit gender-science biases discourage women from pursuing careers in science, technology, engineering, and math (STEM). Gender-science biases promote the belief that women cannot be successful in STEM, which can affect women's sense of belonging and commitment to STEM. While women scientists serving as role models benefit women in STEM by decreasing implicit gender-science biases and increasing perceived belonging and performance in STEM, the influence of role model qualities on implicit bias has not been widely explored. The current study examined the influence role model qualities (hardworking, gifted) have on implicit gender-science bias. The research also …

A Social Game Design To Solve Young Peoples’ Loneliness Problem, Jiaxi Yuan

Theses

This project’s topic is helping solve young people’s loneliness problem. According to my research, young people are more likely to feel lonely than old people. Because young people need to work or study in other cities or countries, they have always been apart from their families and friends. Although loneliness is not a mental illness, it does have negative effects on young people’s mental health.

Therefore, I designed a warm and healing social game to help to solve young people’s loneliness problems. After the user research, I defined the major functions of this social game. The functions of this social …