Digital Commons Network^™

The Extracellular Contractile Injection System Is Enriched In Environmental Microbes And Associates With Numerous Toxins, Alexander Martin Geller, Inbal Pollin, David Zlotkin, Aleks Danov, Nimrod Nachmias, William B. Andreopoulos, Keren Shemesh, Asaf Levy

Faculty Research, Scholarly, and Creative Activity

The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that evolved from a bacteriophage tail. Four eCISs have previously been shown to mediate interactions between bacteria and their invertebrate hosts. Here, we identify eCIS loci in 1,249 bacterial and archaeal genomes and reveal an enrichment of these loci in environmental microbes and their apparent absence from mammalian pathogens. We show that 13 eCIS-associated toxin genes from diverse microbes can inhibit the growth of bacteria and/or yeast. We identify immunity genes that protect bacteria from self-intoxication, further supporting an antibacterial role for some eCISs. We also identify previously undescribed eCIS …

Deep Underground Neutrino Experiment (Dune) Near Detector Conceptual Design Report, A. Abed Abud, B. Abi, R. Acciarri, M. A. Acero, G. Adamov, D. Adams, M. Adinolfi, A. Aduszkiewicz, Z. Ahmad, J. Ahmed, T. Alion, S. Alonso Monsalve, M. Alrashed, C. Alt, A. Alton, P. Amedo, A. Hatzikoutelis, For Full Author List, See Comments Below

Faculty Research, Scholarly, and Creative Activity

The Deep Underground Neutrino Experiment (DUNE) is an international, world-class experiment aimed at exploring fundamental questions about the universe that are at the forefront of astrophysics and particle physics research. DUNE will study questions pertaining to the preponderance of matter over antimatter in the early universe, the dynamics of supernovae, the subtleties of neutrino interaction physics, and a number of beyond the Standard Model topics accessible in a powerful neutrino beam. A critical component of the DUNE physics program involves the study of changes in a powerful beam of neutrinos, i.e., neutrino oscillations, as the neutrinos propagate a long distance. …

Adaptive Laboratory Evolution Of Β-Caryophyllene Producing Saccharomyces Cerevisiae, Avinash Godara, Katy C. Kao

Faculty Research, Scholarly, and Creative Activity

Background: β-Caryophyllene is a plant terpenoid with therapeutic and biofuel properties. Production of terpenoids through microbial cells is a potentially sustainable alternative for production. Adaptive laboratory evolution is a complementary technique to metabolic engineering for strain improvement, if the product-of-interest is coupled with growth. Here we use a combination of pathway engineering and adaptive laboratory evolution to improve the production of β-caryophyllene, an extracellular product, by leveraging the antioxidant potential of the compound. Results: Using oxidative stress as selective pressure, we developed an adaptive laboratory evolution that worked to evolve an engineered β-caryophyllene producing yeast strain for improved production within …

Fuel Load, Stand Structure, And Understory Species Composition Following Prescribed Fire In An Old-Growth Coast Redwood (Sequoia Sempervirens) Forest, David Cowman, Will Russell

Faculty Research, Scholarly, and Creative Activity

Background: With the prevalence of catastrophic wildfire increasing in response to widespread fire suppression and climate change, land managers have sought methods to increase the resiliency of landscapes to fire. The application of prescribed burning in ecosystems adapted to fire can reduce fuel load and fire potential while minimizing impacts to the ecosystem as a whole. Coast redwood forests have historically experienced fire from both natural and anthropogenic sources, and are likely to respond favorably to its reintroduction. Results: Random sampling was conducted in three burned sites and in three unburned sites, in an old-growth coast redwood (Sequoia sempervirens [D. …

Comparative Egg Attendance Patterns Of Incubating Polar Petrels, Scott A. Shaffer, Pierre Blévin, Christophe Barbraud, Olivier Chastel, Henri Weimerskirch

Faculty Research, Scholarly, and Creative Activity

Background: The internal environment of eggs in most birds is regulated by transferring heat energy through contact incubation, maintaining nest microclimate, and frequent egg turning by the incubating parent on its nest. However, we lack information about egg attendance patterns in birds that breed in polar environments where variations in life history are expected to influence incubation behavior. Moreover, crevice/burrow nesting petrels in high-latitude regions are known for periodically leaving their egg unattended (hereafter ‘egg neglect’), but there is little reporting on the internal condition of unattended eggs. At Dumont d’Urville Station, Antarctica, we studied the incubation behavior of 24 …

Species And Population Specific Gene Expression In Blood Transcriptomes Of Marine Turtles, Shreya M. Banerjee, Jamie Adkins Stoll, Camryn D. Allen, Jennifer M. Lynch, Heather S. Harris, Lauren Kenyon, Richard E. Connon, Eleanor J. Sterling, Eugenia Naro-Maciel, Kathryn Mcfadden, Margaret M. Lamont, James Benge, Nadia B. Fernandez, Jeffrey A. Seminoff, Scott R. Benson, Rebecca L. Lewison, Tomoharu Eguchi, For Full Author List, See Comments Below

Faculty Research, Scholarly, and Creative Activity

Background: Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms’ responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. Results: We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys …

Supervision Of A Self-Driving Vehicle Unmasks Latent Sleepiness Relative To Manually Controlled Driving, Erin E. Flynn-Evans, Lily R. Wong, Yukiyo Kuriyagawa, Nikhil Gowda, Patrick F. Cravalho, Sean Pradhan, Nathan H. Feick, Nicholas G. Bathurst, Zachary L. Glaros, Theerawit Wilaiprasitporn, Kanika Bansal, Javier O. Garcia, Cassie J. Hilditch

Faculty Research, Scholarly, and Creative Activity

Human error has been implicated as a causal factor in a large proportion of road accidents. Automated driving systems purport to mitigate this risk, but self-driving systems that allow a driver to entirely disengage from the driving task also require the driver to monitor the environment and take control when necessary. Given that sleep loss impairs monitoring performance and there is a high prevalence of sleep deficiency in modern society, we hypothesized that supervising a self-driving vehicle would unmask latent sleepiness compared to manually controlled driving among individuals following their typical sleep schedules. We found that participants felt sleepier, had …

Potential Health And Economic Impacts Of Dexamethasone Treatment For Patients With Covid-19, Ricardo Águas, Adam Mahdi, Rima Shretta, Peter Horby, Martin Landray, Lisa White, Fatima Arifi, Chynar Zhumalieva, Inke N.D. Lubis, Antoninho Benjamin Monteiro, Ainura Moldokmatova, Siyu Chen, Aida Estebesova, Mofakhar Hussain, Dipti Lata, Emmanuel A. Bakare, Michael Klein, For Full Author List, See Comments Below

Faculty Research, Scholarly, and Creative Activity

Dexamethasone can reduce mortality in hospitalised COVID-19 patients needing oxygen and ventilation by 18% and 36%, respectively. Here, we estimate the potential number of lives saved and life years gained if this treatment were to be rolled out in the UK and globally, as well as the cost-effectiveness of implementing this intervention. Assuming SARS-CoV-2 exposure levels of 5% to 15%, we estimate that, for the UK, approximately 12,000 (4,250 - 27,000) lives could be saved between July and December 2020. Assuming that dexamethasone has a similar effect size in settings where access to oxygen therapies is limited, this would translate …

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 …

The Human Connectome Project: A Retrospective, Jennifer Stine Elam, Matthew F. Glasser, Michael P. Harms, Gregory C. Burgess, Sandra W. Curtiss, Michael R. Hodge, Eileen A. Cler, Daniel M. Marcus, Deanna M. Barch, David C. Van Essen, Et Al.

2020-Current year OA Pubs

The Human Connectome Project (HCP) was launched in 2010 as an ambitious effort to accelerate advances in human neuroimaging, particularly for measures of brain connectivity; apply these advances to study a large number of healthy young adults; and freely share the data and tools with the scientific community. NIH awarded grants to two consortia; this retrospective focuses on the "WU-Minn-Ox" HCP consortium centered at Washington University, the University of Minnesota, and University of Oxford. In just over 6 years, the WU-Minn-Ox consortium succeeded in its core objectives by: 1) improving MR scanner hardware, pulse sequence design, and image reconstruction methods, …

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 …

Enhancing Permanency In Children And Families (Epic): A Child Welfare Intervention For Parental Substance Abuse, Bridget Freisthler, Kathryn Maguire-Jack, Susan Yoon, Elinam Dellor, Jennifer Price Wolf

Faculty Research, Scholarly, and Creative Activity

Background: Across Ohio, parental substance abuse has contributed to a marked increase in the number of children in foster care. Children exposed to parental substance use have a higher likelihood of physical abuse and neglect, and consequently a variety of physical, psychological and cognitive problems. The Enhancing Permanency in Children and Families (EPIC) program is a collaborative effort between the Ohio State University College of Social Work, two county offices of the Ohio Department of Job and Family Services, two juvenile courts and local behavioral health agencies. The goal of EPIC is to use three evidence-based and evidence-informed practices to …

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 …