Digital Commons Network^™

Neural Upscaling From Residue-Level Protein Structure Networks To Atomistic Structures, Vy T. Duong, Elizabeth M. Diessner, Gianmarc Grazioli, Rachel W. Martin, Carter T. Butts

Faculty Research, Scholarly, and Creative Activity

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly com-pressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from …

Vte And Anticoagulation In Menstruating Women, Ida Micaily, Bethany T. Samuelson Bannow

Department of Medicine Faculty Papers

Women of childbearing potential have a high prevalence of venous thromboembolism (VTE) due to high estrogen states, such as pregnancy and the use of estrogen-containing contraceptives. Abnormal uterine bleeding (AUB) affects up to two-thirds of menstruating women on anticoagulation (AC), and can severely impair a woman's quality of life. Rates of heavy menstrual bleeding (HMB) and other forms of AUB including inter-menstrual and postmenopausal bleeding are consistently underreported in the original clinical trials utilizing AC. VTE can occur at any time in a woman's life, and the aim of this review article is to discuss the current landscape of literature …

Moral Encroachment And The Epistemic Impermissibility Of (Some) Microaggressions, Javiera Perez Gomez

Philosophy Faculty Research and Publications

A recent flurry of philosophical research on microaggression suggests that there are various practical and moral reasons why microaggression may be objectionable, including that it can be offensive, cause epistemic harms, express demeaning messages about certain members of our society, and help to reproduce an oppressive social order. Yet little attention has been given to the question of whether microaggression is also epistemically objectionable. This paper aims to further our understanding of microaggression by appealing to recent work on moral encroachment—the idea that knowledge is sensitive to the moral stakes of believing—to argue that microaggression can be irrational in a …

Spatial Proximity Matters: A Study On Collaboration, Arianna Salazar Miranda, Matthew Claudel

Geography Faculty Publications and Presentations

As scientific research becomes increasingly cross-disciplinary, many universities seek to support collaborative activity through new buildings and institutions. This study examines the impacts of spatial proximity on collaboration at MIT from 2005 to 2015. By exploiting a shift in the location of researchers due to building renovations, we evaluate how discrete changes in physical proximity affect the likelihood that researchers co-author. The findings suggest that moving researchers into the same building increases their propensity to collaborate, with the effect plateauing five years after the move. The effects are large when compared to the average rate of collaboration among pairs of …

Are Vaccine Lotteries Worth The Money?, Christopher Robertson, K. Aleks Schaefer, Daniel Scheitrum

Faculty Scholarship

This research evaluates the effects of the twelve statewide vaccine lottery schemes that were announced as of June 7, 2021 on state vaccination rates. We construct a dataset that matches information on the timing and location of these lotteries with daily, county-level data from the U.S. Centers for Disease Control (CDC) on the cumulative number of people who have received at least one dose of an emergency-authorized Covid-19 vaccine. We find that 10 of the 12 statewide lotteries studied (i.e., all but Arkansas and California) generated a positive, statistically significant, and economically meaningful impact on vaccine uptake after thirty days. …

A Brief History Of Nearly Ev-Erything - The Rise And Rise Of Extracellular Vesicles, Yvonne Couch, Edit I Buzàs, Dolores Di Vizio, Yong Song Gho, Paul Harrison, Andrew F Hill, Jan Lötvall, Graça Raposo, Philip D Stahl, Clotilde Théry, Kenneth W Witwer, David R F Carter

2020-Current year OA Pubs

Extracellular vesicles (EVs) are small cargo-bearing vesicles released by cells into the extracellular space. The field of EVs has grown exponentially over the past two decades; this growth follows the realisation that EVs are not simply a waste disposal system as had originally been suggested by some, but also a complex cell-to-cell communication mechanism. Indeed, EVs have been shown to transfer functional cargo between cells and can influence several biological processes. These small biological particles are also deregulated in disease. As we approach the 75th anniversary of the first experiments in which EVs were unknowingly isolated, it seems right to …

Animal Crossing As A @Digitalaltar, Lillyanne Pham

Animal Crossing as a @DigitalAltar

Lillyanne Pham, Maria Mejia, Gavrielle Thompson, Bea Yeh, Maria Mayorya, Chanel Matsunami Govreau, virtual care lab , Roz Crews, Candace Avalos

For Fall 2021 Art & Social Practice History at Portland State University, I explored the social simulation game Animal Crossing: New Horizons (ACNH) as a digital altar. I asked How do social simulation games provide a dream space, a neighborhood btwn IRL and URL relationships? How is online gardening similar to sanctuary making, altar making? My co-conspirators offered me Fuck Tom Nook. In other words, should we build an altar in a capitalist, escapist, and colonialist dystopia? This project …

The Impact Of Light Intensity On The Subjective Complaints Of Librarians And Users: An Investigation Of An Academic Library, Tri Niswati Utami, Retno Sayekti, Triana Santi

Library Philosophy and Practice (e-journal)

The objective of this study is to analyze the impact of light intensity on the subjective complaints of librarians and visitiors at an academic library. This research applied both quantitative and qualitative techniques on 696 visitors and librarians. The result suggests that the effects of light intensity include eyestrain, reading difficulty, dizziness, shoulder and back pains, as well as impaired concentration. Also, the frequency of reading and working impacted the subjective complaints. Furthermore, the intensity as well as the frequency of reading and working greatly influenced the subjective complaints. Based on the qualitative analysis, the development of light concepts and …

Timber Constructed: Towards An Alternative Material History, Laila Seewang, Irina Davidovici

School of Architecture Faculty Publication and Presentations

Editorial:

This issue of Architectural Theory Review proposes an alternative intellectual history of timber architecture. It foregrounds the relationships that tie the natural resource to the cultural artefact, its processing into construction material and, with it, the production of associated disciplinary expertise. The essays explore the spatial and symbolic possibilities of timber in historical and contemporary discourse by highlighting its simultaneity as cultural artefact, material commodity, environmental resource, and structural element. Thus, the material’s appearance and representation are positioned within perennial oscillations between globalism and locality, natural and man-made, industry and craft, innovation and tradition, material and ideology, modernity and …

Voltage And Frequency Control In Ac Islanded Microgrid, Hamad Mohammad Al Sharif

Theses

Microgrids are described as linking many power sources (renewable energy and traditional sources) to meet the load consumption in real-time. Because renewable energy sources are intermittent, battery storage systems are required, typically used as a backup system. An energy management strategy (EMS) is required to govern power flows across the entire microgrid. In recent research, various methods have been proposed for controlling the micro-grids, especially voltage and frequency control. This study introduces a microgrid system, an overview of local control in the microgrid, and an efficient EMS for effective microgrid operations using three smart controllers for optimal microgrid stability. We …

A Pipeline For Enhanced Multimodal 2d Imaging Of Concrete Structures, Sina Mehdinia, Thomas Schumacher, Xubo Song, Eric A. Wan

Civil and Environmental Engineering Faculty Publications and Presentations

We present an imaging pipeline to achieve enhanced images of the interior of concrete from ground penetrating radar (GPR) and ultrasonic echo array (UEA) measurements. This work lays the foundation for an advanced yet practical imaging tool to assess concrete structures. Specifically, we propose an enhanced two-dimensional (2D) total focusing method (XTFM) to reconstruct images from raw GPR and UEA data. The proposed XTFM algorithm integrates total focusing method (TFM) and synthetic aperture focusing technique (SAFT) concepts to post-process large independent and interelement measurements from both modalities in a computationally efficient way. Furthermore, we introduce a novel 2D image fusion …

An Examination Of Environmental Applications For Uncooled Thermal Infrared Remote Sensing Instruments, Cody M. Webber

Theses

Advancements in system design for thermal instruments require assessment of potential environmental applications and appropriate data processing techniques. A novel multi-band thermal imaging system was proposed by DRS Leonardo for the National Aeronautics and Space Administration Earth Science Technology Office Instrument Incubator Program, for which these criteria were assessed. The Multi-Band Uncooled Radiometer Imager (MURI) is a six spectral channel instrument designed to collect images in the thermal infrared, specifically in the range of 7.5 to 12.5 μm. The work detailed in this thesis characterizes the ability of a thermal imager with an uncooled microbolometer focal plane array to provide …

Heat Patrl: Network-Agnostic Cyber Attack Campaign Triage With Pseudo-Active Transfer Learning, Stephen Frank Moskal

Theses

SOC (Security Operation Center) analysts historically struggled to keep up with the growing sophistication and daily prevalence of cyber attackers. To aid in the detection of cyber threats, many tools like IDS’s (Intrusion Detection Systems) are utilized to monitor cyber threats on a network. However, a common problem with these tools is the volume of the logs generated is extreme and does not stop, further increasing the chance for an adversary to go unnoticed until it’s too late. Typically, the initial evidence of an attack is not an isolated event but a part of a larger attack campaign describing prior …

Modeling The Speed And Timing Of American Sign Language To Generate Realistic Animations, Sedeeq Al-Khazraji

Theses

While there are many Deaf or Hard of Hearing (DHH) individuals with excellent reading literacy, there are also some DHH individuals who have lower English literacy. American Sign Language (ASL) is not simply a method of representing English sentences. It is possible for an individual to be fluent in ASL, while having limited fluency in English. To overcome this barrier, we aim to make it easier to generate ASL animations for websites, through the use of motion-capture data recorded from human signers to build different predictive models for ASL animations; our goal is to automate this aspect of animation synthesis …

Among Us, Kaixin Chen

Theses

The networked society provides an extremely complex environment where we are free to swim, and to sink. In this thesis, I used different materials and forms to visualize this concept. The final work is a series of human faces floating from the water surface with steady gaze. Affected by the background of my sculpture and oil painting, I explored how to combine the two, and drew a 3D portrait, then completely transformed from two-dimensional to three-dimensional, and produced a set of installations with repeated face elements. With the experience and emotional response to working three-dimensionally, I once again returned to …

Neural Network Models For Tcp - Syn Flood Denial Of Service Attack Detection With Source And Destination Anonymization, Sahil Anande

Theses

The Internet has become a necessity in today's digital world, and making it secure is a pressing concern. Hackers are investing ever-increasing efforts to compromise Internet nodes with novel techniques. According to Forbes, every minute, $ 2,900,000 is lost to cybercrime. A common cyber-attack is Denial of Service (DoS) or Distributed Denial of Service (DDoS) attacks, which may bring a network to a standstill, and unless mitigated, network services could be halted for an extended period. The attack can occur at any layer of the OSI model. This thesis focuses on SYN Flood DoS/DDoS attacks, also known as TCP Flood …

Dysregulation Of Mir-21-Associated Mirna Regulatory Networks By Chronic Ethanol Consumption Impairs Liver Regeneration., Austin Parrish, Ankita Srivastava, Egle Juskeviciute, Jan B Hoek, Rajanikanth Vadigepalli

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Impaired liver regeneration has been considered as a hallmark of progression of alcohol-associated liver disease. Our previous studies demonstrated that in vivo inhibition of the microRNA (miRNA) miR21 can restore regenerative capacity of the liver in chronic ethanol-fed animals. The present study focuses on the role of microRNA regulatory networks that are likely to mediate the miR-21 action. Rats were chronically fed an ethanol-enriched diet along with pair-fed control animals and treated with AM21 (anti-miR-21), a locked nucleic acid antisense to miR-21. Partial hepatectomy (PHx) was performed and miRNA expression profiling over the course of liver regeneration was assessed. Our …

Stem Signatures Associating Sox2 Antibody Helps To Define Diagnosis And Prognosis Prediction With Esophageal Cancer, Zi-Yang Peng, Qing-Shi Wang, Kai Li, Si-Si Chen, Xiang Li, Guo-Dong Xiao, Shou-Ching Tang, Hong Ren, Zhe Wang, Xin Sun

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Background: esophageal cancer is one of the deadliest diseases worldwide. Due to the ineffectual screening methods referring to early diagnosis, most people have lost their chance of radical resection when diagnosed with esophageal cancer. This aim of this study was designed to evaluate the latent values of the stem signatures-associated autoantibodies (AABS) in predicting the early diagnosis, and particularly seeking the precise predictive outcomes with sensitive SOX2. We also studied the potential immunotherapeutic targets and prospective long-term prognosis predicators of esophageal cancer.

Methods: The serum concentrations of selective antibodies were quantitated by enzyme-linked immunosorbent assay (ELISA), and a total of …

A Practical Extension To The Ab/Ba Design, My T.A Nguyen

Electronic Theses and Dissertations

In this work, we take a close look at a general extension to the traditional AB/BA
crossover design that is commonly used in clinical trials to determine the effectiveness
of new candidate drugs. While the traditional crossover design requires each patient
in the study to be measured on both treatment A and treatment B, we consider the
possibility of additional measurements being available on each patient. This produces
designs such as the AABB/BBAA design which has been used in previous studies.
A general test statistic will be derived to test for treatment effects as well as its
corresponding power function …

Soil Gypsum Content Analysis Of The Proposed Road Route Extension Of Fm 2185 In The Gypsum Plain, Culberson County, Texas, Chikaodili Ohakawa

Electronic Theses and Dissertations

Soils serve as the underlying substrate on which foundations for most structures are built. The properties of a soil type are therefore an important consideration in building engineered structures. Gypsic soils are problematic for construction of such structures. One of the main problems with gypsic soils is dissolution. Gypsum (CaSO₄·2H₂O) in soils dissolves easily creating voids which can be detrimental to the integrity of engineering structures. To mitigate this, it is important to determine the amount of gypsum present in soils, before construction is initiated.

In this study, three methods were employed in the determination of …

Preferred Rendering Of Memory Colors, Anku Manderna Anku

Theses

With the rise in high quality displays and cameras following the mainstream adoption of smartphones, image quality has become an essential aspect of engaging and attracting consumers. In the case of smartphones, the bar raises with release of every new generation. There are many factors affecting image quality such as sharpness, image noise or non-uniformity, and geometric distortion, but it is fair to say that color plays a vital role in the perceived quality of an image. Colors not only spark emotions and engage a user but also decide the likability of a certain image. Over the past few years …

Continuous Variable Quantum Compilation Analysis, Federico Rueda

Theses

Over the last few years quantum computers have rose to prominence as a solution for increasing computing power and tackling problems intractable by classical computers. Classical computers have struggled to meet the ever-increasing demand for data processing and modeling. Thus, quantum computers would meet the demand for heavy computing tasks that classical computers could never achieve. Today there exist two promising quantum technologies that have the potential to prove quantum supremacy in the near future: super-conducting qubits and Continuous Variable (CV) model. Out of the two, superconducting qubits have been at the forefront of quantum computing research. NISQ (Noise intermediate-scale …

The Use Of Reverse Vending Machine (Rvm) For Less Plastic In Dubai, Sarah Obaid Al Shamsi

Theses

Plastic pollution is affecting negatively on the environment, it affects trees, animals, marine life, and even humans. One of the most common plastic types is plastic bags, it is widely spread due its special characteristics such as light weigh, and cheap price. In Dubai City, plastic bags are widely used especially in the supermarkets, with the increase in the population of Dubai, the number of plastic bags will increase and the impacts will be more appearance. Dubai City is a leading city in the region for its ability to change and adapt with new strategies that serves the citizen and …

Smart Urban Solutions For Low-Income Neighborhoods In Dubai: Hor Al Anz Area As A Case Study, Alaa Yahia Ragab Eleraqi

Theses

The project’s main objective is to study and assess the current situation and future setup of implementing smart solutions technologies, and the main challenges facing the growth in Dubai in general and the Hor Al Anz neighborhood in Dubai in particular. The expected results and outcomes of this study are illustrated in this research report. The project report consists of 5 parts. Part 1 covers the implemented initiatives and presents the problem statement and the historical background of the case study area by showing why did I select the Hor Al Anz neighborhood in Dubai (Figure 1 below). The purpose …

Futuristic Smart Solutions For People Of Determination In Schools And Universities, Luloa Alsayah, Shaikha Abdulrahman, Sanaa Enkeleya

Theses

In this project, future smart solutions for people of determination in schools and universities were discussed. The background was presented on the topic, as the issue of integrating people of determination in schools and then integrating them into society still takes a wide range of societal, family, and institutional attention, and it undoubtedly deserves much attention that befits this dear group in our society. The literature has shown the existence of previous studies and applications similar to those proposed in the project, which sought within the framework of this advanced vision to enable "people of determination" to provide quality services …

Test Naming Failures. An Exploratory Study Of Bad Naming Practices In Test Code, Zachariah Wigent

Theses

Unit tests are a key component during the software development process, helping ensure that a developer's code is functioning as expected. Developers interact with unit tests when trying to understand, maintain, and when updating code. Good test names are essential for making these various processes easier, which is important considering the substantial costs and effort of software maintenance. Despite this, it has been found that the quality of test code is often lacking, specifically when it comes to test names. When a test fails, its name is often the first thing developers will see when trying to fix the failure, …

Predicting Risk Of Readmission In Heart Failure Patients Using Electronic Health Records, Pradumna Suryawanshi

Theses

This thesis research investigates the prediction of readmission risk in heart failure patients using their electronic health record (EHR) data from previous hospitalizations. We examine three primary questions. First, we study the use of attention mechanism in readmission prediction model based on long short-term memory(LSTM) networks and investigate the interpretability it offers regarding the importance of critical time during the visit in readmission prediction. Second given that, generally dataset is curated by combining data from multiple hospitals we investigate model generalization across multiple sites. Finally since in real life scenario model will be trained on past data and used to …

Evaluation Of Neuro-Evolution Algorithms For Tactic Volatility Aware Processes, Aizaz Ul Haq

Theses

Our society is increasingly evolving to rely on computer mechanisms that perform a variety of tasks. From a self-driving car to a satellite in space relaying data from Mars rovers, we need these systems to perform optimally and without failure. One such point of failure these systems can encounter is tactic volatility of an adaptation tactic. Adaptation tactics are defined workflows that allow systems to navigate their environment. Tactic volatility is the variance in the behavior in the attribute of a tactic, such as cost and latency and/or the combination of the two. Current systems consider these tactic attributes to …

Survey And Analysis Of Deepfake Media As It Applies To The New Era Of Disinformation, Jade L. Wise

Theses

The world has become a place where technology and the internet is so integrated into every-day life that people rely on the media and internet access to stay informed and connected. But, that has exposed us to a whole new world of positives and negatives, and the negatives could be catastrophic for our society. It will very soon be very difficult for the average person to distinguish between figment and reality; primarily with video, which has always been seen as a credible form of evidence. Deepfake videos are a prime example of this growing phenomenon. They are videos in which, …

Radio Carbon - Hybrid Documentary Process, Robert Stokes

Theses

Radio Carbon is a documentary made using a methodology for creating conscious digital video projects with a process privileging respect for crew, subject, and environment over the needs of a commercial, or market driven product. The guidelines imposed by this method are fluid, and project-specific in terms of their exact interpretation for each film. This project is meant to demonstrate a production style that allows for work to be made by the participants without a dominating creative force at every stage of production. This is made possible through the introduction of chance operations at several key points along the production …