Digital Commons Network^™

Deep Learning-Based Automatic Classification Of Ischemic Stroke Subtype Using Diffusion-Weighted Images, Wi-Sun Ryu, Dawid Schellingerhout, Hoyoun Lee, Keon-Joo Lee, Chi Kyung Kim, Beom Joon Kim, Jong-Won Chung, Jae-Sung Lim, Joon-Tae Kim, Dae-Hyun Kim, Jae-Kwan Cha, Leonard Sunwoo, Dongmin Kim, Sang-Il Suh, Oh Young Bang, Hee-Joon Bae, Dong-Eog Kim

Faculty, Staff and Student Publications

Background and purpose: Accurate classification of ischemic stroke subtype is important for effective secondary prevention of stroke. We used diffusion-weighted image (DWI) and atrial fibrillation (AF) data to train a deep learning algorithm to classify stroke subtype.

Methods: Model development was done in 2,988 patients with ischemic stroke from three centers by using U-net for infarct segmentation and EfficientNetV2 for subtype classification. Experienced neurologists (n=5) determined subtypes for external test datasets, while establishing a consensus for clinical trial datasets. Automatically segmented infarcts were fed into the model (DWI-only algorithm). Subsequently, another model was trained, with AF included as a categorical …

Investigation Of Inherited Noncoding Genetic Variation Impacting The Pharmacogenomics Of Childhood Acute Lymphoblastic Leukemia Treatment, Kashi Raj Bhattarai, Robert J Mobley, Kelly R Barnett, Daniel C Ferguson, Baranda S Hansen, Jonathan D Diedrich, Brennan P Bergeron, Satoshi Yoshimura, Wenjian Yang, Kristine R Crews, Christopher S Manring, Elias Jabbour, Elisabeth Paietta, Mark R Litzow, Steven M Kornblau, Wendy Stock, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Cheng Cheng, Shondra M Pruett-Miller, Mary V Relling, Jun J Yang, William E Evans, Daniel Savic

Faculty, Staff and Student Publications

Defining genetic factors impacting chemotherapy failure can help to better predict response and identify drug resistance mechanisms. However, there is limited understanding of the contribution of inherited noncoding genetic variation on inter-individual differences in chemotherapy response in childhood acute lymphoblastic leukemia (ALL). Here we map inherited noncoding variants associated with treatment outcome and/or chemotherapeutic drug resistance to ALL cis-regulatory elements and investigate their gene regulatory potential and target gene connectivity using massively parallel reporter assays and three-dimensional chromatin looping assays, respectively. We identify 54 variants with transcriptional effects and high-confidence gene connectivity. Additionally, functional interrogation of the top variant, rs1247117, …

Proteomics For Optimizing Therapy In Acute Myeloid Leukemia: Venetoclax Plus Hypomethylating Agents Versus Conventional Chemotherapy, Eduardo Sabino De Camargo Magalhães, Stefan Edward Hubner, Brandon Douglas Brown, Yihua Qiu, Steven Mitchell Kornblau

Faculty, Staff and Student Publications

The use of Hypomethylating agents combined with Venetoclax (VH) for the treatment of Acute Myeloid Leukemia (AML) has greatly improved outcomes in recent years. However not all patients benefit from the VH regimen and a way to rationally select between VH and Conventional Chemotherapy (CC) for individual AML patients is needed. Here, we developed a proteomic-based triaging strategy using Reverse-phase Protein Arrays (RPPA) to optimize therapy selection. We evaluated the expression of 411 proteins in 810 newly diagnosed adult AML patients, identifying 109 prognostic proteins, that divided into five patient expression profiles, which are useful for optimizing therapy selection. Furthermore, …

Automated, High-Throughput Platform To Generate A High-Reliability, Comprehensive Rectal Cancer Database, Neal Bhutiani, Mahmoud M G Yousef, Abdelrahman Yousef, Mohammad Zeineddine, Mark Knafl, Olivia Ratliff, Uditha P Fernando, Anastasia Turin, Fadl A Zeineddine, Jeff Jin, Kristin Alfaro-Munoz, Drew Goldstein, George J Chang, Scott Kopetz, John Paul Shen, Abhineet Uppal

Faculty, Staff and Student Publications

Purpose: Dynamic operations platforms allow for cross-platform data extraction, integration, and analysis, although application of these platforms to large-scale oncology enterprises has not been described. This study presents a pipeline for automated, high-fidelity extraction, integration, and validation of cross-platform oncology data in patients undergoing treatment for rectal cancer at a single, high-volume institution.

Methods: A dynamic operations platform was used to identify patients with rectal cancer treated at MD Anderson Cancer Center between 2016 and 2022 who had magnetic resonance imaging (MRI) imaging and preoperative treatment details available in the electronic health record (EHR). Demographic, clinicopathologic, tumor mutation, radiographic, and …

Genomic Landscape Of Lynch Syndrome Colorectal Neoplasia Identifies Shared Mutated Neoantigens For Immunoprevention, Ana M Bolivar, Fahriye Duzagac, Nan Deng, Laura Reyes-Uribe, Kyle Chang, Wenhui Wu, Charles M Bowen, Melissa W Taggart, Selvi Thirumurthi, Patrick M Lynch, Y Nancy You, Jesus Rodriguez-Pascual, Steven M Lipkin, Scott Kopetz, Paul Scheet, Gregory A Lizee, Alexandre Reuben, Krishna M Sinha, Eduardo Vilar

Faculty, Staff and Student Publications

Background & aims: Lynch syndrome (LS) carriers develop mismatch repair-deficient neoplasia with high neoantigen (neoAg) rates. No detailed information on targetable neoAgs from LS precancers exists, which is crucial for vaccine development and immune-interception strategies. We report a focused somatic mutation and frameshift-neoAg landscape of microsatellite loci from colorectal polyps without malignant potential (PWOMP), precancers, and early-stage cancers in LS carriers.

Methods: We generated paired whole-exome and transcriptomic sequencing data from 8 colorectal PWOMP, 41 precancers, 8 advanced precancers, and 12 early-stage cancers of 43 LS carriers. A computational pipeline was developed to predict, rank, and prioritize the top 100 …

Cross-Vendor Multiparametric Mapping Of The Human Brain Using 3d-Qalas: A Multicenter And Multivendor Study, Shohei Fujita, Borjan Gagoski, Ken-Pin Hwang, Akifumi Hagiwara, Marcel Warntjes, Issei Fukunaga, Wataru Uchida, Yuya Saito, Towa Sekine, Rina Tachibana, Tomoya Muroi, Toshiya Akatsu, Akihiro Kasahara, Ryo Sato, Tsuyoshi Ueyama, Christina Andica, Koji Kamagata, Shiori Amemiya, Hidemasa Takao, Yasunobu Hoshino, Yuji Tomizawa, Kazumasa Yokoyama, Berkin Bilgic, Nobutaka Hattori, Osamu Abe, Shigeki Aoki

Faculty, Staff and Student Publications

Purpose: To evaluate a vendor-agnostic multiparametric mapping scheme based on 3D quantification using an interleaved Look-Locker acquisition sequence with a T2 preparation pulse (3D-QALAS) for whole-brain T1, T2, and proton density (PD) mapping.

Methods: This prospective, multi-institutional study was conducted between September 2021 and February 2022 using five different 3T systems from four prominent MRI vendors. The accuracy of this technique was evaluated using a standardized MRI system phantom. Intra-scanner repeatability and inter-vendor reproducibility of T1, T2, and PD values were evaluated in 10 healthy volunteers (6 men; mean age ± SD, 28.0 ± 5.6 y) who underwent scan-rescan sessions …

Mapping Genotypes To Chromatin Accessibility Profiles In Single Cells, Franco Izzo, Robert M Myers, Saravanan Ganesan, Levan Mekerishvili, Sanjay Kottapalli, Tamara Prieto, Elliot O Eton, Theo Botella, Andrew J Dunbar, Robert L Bowman, Jesus Sotelo, Catherine Potenski, Eleni P Mimitou, Maximilian Stahl, Sebastian El Ghaity-Beckley, Joann Arandela, Ramya Raviram, Daniel C Choi, Ronald Hoffman, Ronan Chaligné, Omar Abdel-Wahab, Peter Smibert, Irene M Ghobrial, Joseph M Scandura, Bridget Marcellino, Ross L Levine, Dan A Landau

Faculty, Staff and Student Publications

In somatic tissue differentiation, chromatin accessibility changes govern priming and precursor commitment towards cellular fates1-3. Therefore, somatic mutations are likely to alter chromatin accessibility patterns, as they disrupt differentiation topologies leading to abnormal clonal outgrowth. However, defining the impact of somatic mutations on the epigenome in human samples is challenging due to admixed mutated and wild-type cells. Here, to chart how somatic mutations disrupt epigenetic landscapes in human clonal outgrowths, we developed genotyping of targeted loci with single-cell chromatin accessibility (GoT-ChA). This high-throughput platform links genotypes to chromatin accessibility at single-cell resolution across thousands of cells within a single assay. …

Raise The Dead, Kendall Cruise

Gandy Dancer Archives

No abstract provided.

Gandy Dancer 12.2, Gandy Dancer

Gandy Dancer Archives

Gandy Dancer is a literary magazine, publishing fiction, poetry, creative nonfiction, and visual art. We invite submissions from student writers and artists at all of the SUNY campuses. Edited by students at SUNY Geneseo, Gandy Dancer is published twice yearly. For more information, visit www.gandydancer.org. Gandy Dancer 12.2 is the twenty-third issue, published Spring 2024.

Lincoln's Carnegie Library: A History Of Community And Philanthropy, Emily Blomstedt

Honors Program: Senior Projects (Public)

Nebraska received 69 Carnegie libraries from the Carnegie foundation between 1899 and 1922. The first and most expensive Nebraska Carnegie library was granted to Lincoln in December 1899, after a fire destroyed Lincoln’s previous library. Lincoln’s main Carnegie library served the community between 1902 and 1960 before it was torn down in 1961 to build the present-day Bennett Martin library. This thesis explores the 60-year history of Lincoln’s Carnegie library, how it connects to national trends surrounding Carnegie libraries, and the role community and philanthropy played in the development of Lincoln’s public library system. These themes are examined through a …

Lululemon Strategic Audit, Tessa Mozingo, Olivia Eno, Molly Mitchell, Connor Morrissey, James Eshleman

Honors Program: Senior Projects (Public)

This case study focuses on lululemon, a prominent athleisure apparel company. Our team conducted an audit of the company revolving around strategic business management principles. Our research used publicly available information that included the company’s website, SEC filings, news articles, lululemon’s annual reports, financial statements, IBIS industry reports, and online sources. The goal of this strategic audit is to develop an understanding of lululemon’s business activities and strategies, collect and analyze both internal and external data, and evaluate lululemon based on strategic management concepts.

In this strategic audit, we conduct internal, external, performance, and competitive analyses and an examination of …

Suicidal Ideation Among Survivors Of Childhood Sexual Abuse: The Role Of Shame And Sexual Grooming, Aysegul Yucel

Student Theses

Childhood Sexual Abuse (CSA) is a global public health issue, with 25% of girls and 5% of boys in the U.S. reporting abuse before the age of 18. While CSA is known to increase the risk of suicidal ideation in later life, the additional psychosocial factors involved are understudied. This study investigates the impact of abuse-related shame and sexual grooming on suicidal ideation in adults with CSA histories. Data from 118 undergraduate students were analyzed using binomial logistic regression and the PROCESS macro to explore direct and indirect effects. Results show that abuse-related shame significantly predicts suicidal ideation and mediates …

Detection Of Deficiencies And Data Analysis Of Bridge Members With Deep Convolutional Neural Networks, Bennett Jackson

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Concrete cracks and structural steel corrosion are two of the most common defects in bridges. Quantifying and classifying these defects provide bridge inspectors and engineers with valuable data for assessing deterioration levels. However, the bridge inspection process is typically a subjective, time intensive, and tedious task, as defects can be overlooked or in locations not easily accessible. Previous studies have investigated deep learning-based inspection methods, implementing popular models such as Mask R-CNN and U-Net. The architectures of these models offer certain advantages depending on the required task. This thesis aims to evaluate and compare Mask R-CNN and U-Net regarding their …

Grading Climate Action Plans In The Midwest, Megan Baker

Department of Environmental Studies: Undergraduate Student Theses

As agreed upon by international climate scientists, decarbonization in the American Midwest is critical to keeping the planet below the 1.5C increase in global temperature from pre-industrial levels. However, most previous research that evaluates climate action plans (CAPs) to find their weaknesses and provide policy recommendations neglects this crucial region of the United States. To fill this gap, this paper replicates Deetjen et al.’s (2018) review of CAPs in 29 US cities by applying their CAP rubric to 11 Midwestern cities. The results of both quantitative analysis were used to analyze the differences in plans in the Midwest versus the …

Dynamic Impact Testing And Numerical Analysis Of Non-Proprietary Astm F2656-20 M50 Anti-Ram Barrier Components, Weston Kelley

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

In a post-9/11 world, hostile actors are using vehicles as weapons to inflict civilian casualties. Pedestrians, vulnerable road users, military personnel, and police may be targeted using a vehicle as a weapon. The United States Department of Defense (DoD) also utilizes Entry Control Facilities (ECFs) which are carefully designed transportation corridors to manage how threat vehicles are able to access military facilities. In 2004, DoD started to upgrade all ECFs using both passive and active barriers. Many anti-ram vehicle barriers were evaluated according to the criteria established in ASTM F2656, but to date few options are available which are (1) …

How Gender Affirming Care Affects The Current Sex Estimation Standards In Forensic Anthropology: A Preliminary Study, Dakota Taylor

Department of Anthropology: Theses and Student Research

Current sex estimation standards in forensic anthropology are based on individuals whose gender matches their biological/osteological sex, also known as Cisgendered individuals. Recently, transgender individuals have started to become more common in the forensic context due to the increase in hate crimes and violence. This research builds upon past research done on how facial feminization surgery can affect both visual and metric methods, where it was found that forensic anthropologists should rely on the visual methods if they suspect someone to be transgender due to it being more accurate and being able to clearly state the scars left on the …

Numerical Variations In The Thoracic And Lumbar Vertebrae Within The John A. Williams Skeletal Collection, Western Carolina University, Cullowhee, Nc (Usa), Leanna Annette Sanford

Department of Anthropology: Theses and Student Research

This research is on how human variation can lead to the identification of remains based on skeletal variation. The data were collected by performing a morphoscopic trait study of the John A. Williams (J.A.W.) Documented Human Skeletal Collection at Western Carolina University in Cullowhee, NC (USA). Morphoscopic traits are nonmetric traits, visually identified using the knowledge of osteology. The study was performed to study variation of the vertebral column, specifically focusing on morphoscopic traits of the thoracic and lumbar vertebrae. The focus of this research is centralized on the presence of numerical variations in the vertebral column such as eleven …

The Kruger Collection Reimagined: A Case Study In 3d Scanning And Interactive Exhibit Design, Annissa Davis

Department of Anthropology: Theses and Student Research

This thesis examines the use of 3D modeling in museum exhibition to create exploratory exhibits that facilitate unique relationships between the visitors and the collection beyond what is provided by the collection’s in person counterparts. Typical use of 3D modeling in museums is currently often representative rather than exploratory. By employing a Digital Humanities lens to approach the development of a digital exhibition utilizing 3D technology and interactive elements created in a video game engine (Unity), this thesis project evaluates these potential new relationships. Using the Eloise Kruger Collection of Miniatures as a case study, the following text details the …

Innovations In Publicly Funded Workforce Training Programs, Chris Ackley

School of Professional Studies

This paper explores the aspects of the current public workforce system and detail persistent challenges as well as promising practices in the field from both Rhode Island and other locations. The author will present a series of recommendations for state and local leaders in the field as well as affiliated training providers and nonprofit practitioners. These proposals are designed to strengthen the overall system and create more opportunity for upward mobility, especially among individuals who have historically not had equitable access to postsecondary educational attainment which provides access to economic advancement.

The State Of Special Education In Virginia, Caroline R. Aramini

School of Professional Studies

This capstone research paper discusses the current state of special education in Virginia. Some of the problems faced by the state include a checkered history of noncompliance with federal mandates, cultural hindrances related to special educator attrition and retention, and resource constraints. A history of special education and disability in education in America is provided to better contextualize solutions found in the research. Recommendations are proposed to address deficiencies, including increased economic compensation for special educators and transformation of the school culture through different strategies. These suggestions are designed to improve the current issues and address the problematic patterns displayed …

The Importance Of Framing The Context Of Black/African Americans' Livelihood To Enhance Health Outcomes And Mitigate Health Inequalities, Elvis Gyan

Theses, Dissertations and Culminating Projects

This study investigates the portrayal of Black/African Americans in Health Marriage and Relationship Education (HMRE) programs, which predominantly follow Eurocentric models while examining how social and structural determinants (e.g., community context) influence stress levels, general health, and relationship satisfaction through two main objectives. Firstly, it aims to scrutinize the acknowledgment of biases towards non-Eurocentric communities in published Administration of Children and Families HMRE programs, analyzing 39 research studies. Secondly, it examines the interplay between perceived community context, stress as a mediator, general health, and relationship satisfaction among Black/African Americans across three distinct articles by testing hypothesized process models. Results for …

Iraqi Education Past And Present: The Role Of Policymakers And Their Ideological Background, Hadi T. Pir

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The history of Iraqi education unmistakably illustrates how policymakers have consistently operated within the same worldview since 1920. Despite apparent differences among Iraqis in terms of race, religion, sect, geography, and social and tribal norms, a shared worldview has emerged, which I term the Traditional Iraqi Paradigm (TIP). This shared worldview comprises a set of interconnected postulates. The divergence among Iraqi groups lies not in the postulates themselves but in how they translate these postulates into actions and behaviors. These translations have become historical, institutional, and psychological aspects of reality contributing to the political, social, and educational differences, conflicts, and …

Improving Visual Inspection Skills In Special Education Teachers, George G. Toman

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The Conservative Dual Criteria (CDC) method is known to improve decision-making accuracy in users when interpreting graphed data. The effectiveness of this method with in-service special education teachers, however, has not been investigated. The present study examined the effects of a virtual training package designed to improve the data-based decision-making skills of in-service special education teachers. Specifically, the virtual training consisted of a training video on the CDC method, access to a decision-making guide, and a brief training assessment. Five in-service special education teachers received training in the CDC method via the online learning management system, Canvas. A multiple baseline …

Sun, Thunder, Daugava: Accessible Choral Music From The Latvian Choral Tradition, Paul M. Von Kampen

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

I have been fortunate enough to visit Latvia twice, once in 2009 and again in 2023. With connections made through the global outreach arm of the Lutheran Church Missouri–Synod, I was able to incorporate myself into Latvian culture in ways that may not have been possible had I been a standard tourist. I am grateful to have been invited into the homes of Latvian friends, to have studied in the Jāzeps Vītols Music Academy Library, and to have celebrated both the Jāņi midsummer festival in the Latvian countryside and my twenty-second birthday on the shores of the mighty Daugava River. …

Making Czech Art Song Accessible For Novice Singers, Rachel Jane Sweeney Green

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Czech art song is often overlooked by vocal instructors while assigning music for the novice singer. The repertoire of Czech art song is vast, yet seldom used in vocal studios in America. Though some consider the language difficult, when approached in the correct manner it is easy for a novice to sing in Czech. This document advocates for Czech art song to be assigned and selected for the novice singer. Each chapter serves as a tool to understand and navigate Czech repertoire. The last chapter provides five examples of Czech art song selected because they align with the guidelines of …

Singing While Acting: A Mixed Methods Study Of Classical Singers’ Application Of The Chekhov And Meisner Acting Methods, Amy C. Johnson

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

When considering the minimal acting training incorporated into most voice performance programs, it is understandable why many singers struggle to balance vocal demands with acting demands. Furthermore, the expectations on singers to deliver authentic and nuanced performances are increasing as opera evolves. There is little in-depth understanding of classical singers’ experiences with applying specific acting techniques to their singing. There is also little information about how different acting methods may affect classical singing. This mixed methods collective case study aims to identify the impact of training in a specific acting method on classical singing. The qualitative strand focuses on the …

Occupational Therapy’S Role In Developmental Programming At Early Childhood Education And Childcare Centers: A Qualitative Study, Alexis N. Foehrkolb, Jenna Lenhart, Hayley Woods, Madison Wetzel, Breanna Adkins, Sueann R. Woods

Graduate Student Scholarship

This research study aimed to discover what strategies of developmental programming are integrated into early childhood curriculum, whether occupational therapy had a role in the formation of the guidelines, and the importance of early intervention on child development. A case study with ethnographic methods was used, including observations and interviews, to gain an understanding of how sociocultural phenomena affect rural childcare centers in Morgantown, West Virginia. Data was collected and coded into 14 themes, and then analyzed by student researchers. Results from interview data found that daycare teachers are given the choice to follow provided lesson plans or individualize their …

The Governance Of Director Compensation, Lily Fang, Sterling Huang

Research Collection School Of Accountancy

The average total compensation of directors in U.S.-listed companies was $342,030 in 2020, 5.06 times the median household income. Directors set their own pay, giving rise to potential self-dealing. We argue and document that in the presence of self-dealing, external mechanisms such as legal standards act as effective means of governance. Following a landmark Delaware court ruling that subjected director pay to a more stringent legal standard, Delaware-incorporated firms reduced director compensation relative to non-Delaware firms and experienced positive and non-transient stock price reactions. Our results indicate that proper governance of director compensation enhances firm value.

Do Firms With Technological Capabilities Rush In? Evidence From The Timing Of Licensing Of Stanford Inventions, Young-Choon Kim, Reddi Kotha, Mooweon Rhee

Research Collection Lee Kong Chian School Of Business

This study investigates the influence of licensees’ technological capabilities on the timing of technology licensing in university technology commercialization. Drawing on the appropriation-collaboration tension from the literature on university technology licensing and intellectual property management, we propose that while the licensee’s technological capabilities drive early licensing by averting technological obsolescence, this effect diminishes significantly with an overlap in the technological domain of the focal invention due to expropriation concerns. Cox regression analysis of Stanford University’s invention dataset confirmed our hypotheses. This research reveals that technology licensing experiences delays with the most suitable licensees, namely, those with strong technological capabilities in …

The Regenerative Playbook: Fintech’S Bold Approach To Sustainability, Simon J.D. Schillebeeckx, Ryan Merrill

Research Collection Lee Kong Chian School Of Business

Fintechs are struggling to attract and retain Gen Z and Millennial customers. Research has shown that this demographic is demanding purpose and climate action. As a result, companies are responding by integrating nature-positive actions into fintech activities. Captivating Gen Z and Millennial customers attention with tangible impact, fosters long-term loyalty, retention and business growth.