Digital Commons Network^™

Flexible Fitting Of Alphafold2-Predicted Models To Cryo-Em Density Maps Using Elastic Network Models: A Methodological Affirmation, Maytha Alshammari, Jing He, Willy Wriggers

Computer Science Faculty Publications

Motivation: This study investigates the flexible refinement of AlphaFold2 models against corresponding cryo-electron microscopy (cryo-EM) maps using normal modes derived from elastic network models (ENMs) as basis functions for displacement. AlphaFold2 generally predicts highly accurate structures, but 18 of the 137 models of isolated chains exhibit a TM-score below 0.80. We achieved a significant improvement in four of these deviating structures and used them to systematically optimize the parameters of the ENM motion model.

Results: We successfully refined four AlphaFold2 models with notable discrepancies: lipid-preserved respiratory supercomplex (TM-score increased from 0.52 to 0.69), flagellar L-ring protein (TM-score increased from 0.53 …

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Programs And Courses Catalog 2024-2025, University Of Northern Iowa

UNI Programs and Courses Catalogs

Contents:

Academic Calendar ... 5
General Information ... 7
The University and Its Programs ... 7
Academic Structure ... 9
Admission Requirements ... 16
Enrollment and Registration Procedures ... 21
Fees and Financial Aid ... 22
Student Life ... 28
University Facilities and Educational Services ... 33
The Fine and Performing Arts at UNI ... 39
Academic Regulations ... 44
Undergraduate Information and Degree Requirements ... 61
Graduate Information, Admission, Academic Regulations, and Degree Requirements ... 91
List of Programs by Department ... 120
Department of Accounting ... 127
Department of Applied Engineering & Technical Management ... 129
Department of …

Community Engagement Newsletter, January 2024, University Of Northern Iowa. Office Of Community Engagement.

Community Engagement Newsletter

Contents:

--- Calling all Service-Learning Courses for Designation
--- Engaged Scholars Initiative hosted by National Campus Compact
--- HUD + Higher Ed Engagement Network
--- Spring Volunteer Fair
--- Community Engagement Celebration Day
--- Certified Nonprofit Professional Credential (CNP)
--- UNI Engaged Podcast

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

A-Disetrac Advanced Analytic Dashboard For Distributed Eye Tracking, Yasasi Abeysinghe, Bhanuka Mahanama, Gavindya Jayawardena, Yasith Jayawardena, Mohan Sunkara, Andrew T. Duchowski, Vikas Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Understanding how individuals focus and perform visual searches during collaborative tasks can help improve user engagement. Eye tracking measures provide informative cues for such understanding. This article presents A-DisETrac, an advanced analytic dashboard for distributed eye tracking. It uses off-the-shelf eye trackers to monitor multiple users in parallel, compute both traditional and advanced gaze measures in real-time, and display them on an interactive dashboard. Using two pilot studies, the system was evaluated in terms of user experience and utility, and compared with existing work. Moreover, the system was used to study how advanced gaze measures such as ambient-focal coefficient K …

Autonomous Strike Uavs In Support Of Homeland Security Missions: Challenges And Preliminary Solutions, Meshari Aljohani, Ravi Mukkamala, Stephan Olariu

Computer Science Faculty Publications

Unmanned Aerial Vehicles (UAVs) are becoming crucial tools in modern homeland security applications, primarily because of their cost-effectiveness, risk reduction, and ability to perform a wider range of activities. This study focuses on the use of autonomous UAVs to conduct, as part of homeland security applications, strike missions against high-value terrorist targets. Owing to developments in ledger technology, smart contracts, and machine learning, activities formerly carried out by professionals or remotely flown UAVs are now feasible. Our study provides the first in-depth analysis of the challenges and preliminary solutions for the successful implementation of an autonomous UAV mission. Specifically, we …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

Can Large Language Models Discern Evidence For Scientific Hypotheses? Case Studies In The Social Sciences, Sai Koneru, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Hypothesis formulation and testing are central to empirical research. A strong hypothesis is a best guess based on existing evidence and informed by a comprehensive view of relevant literature. However, with exponential increase in the number of scientific articles published annually, manual aggregation and synthesis of evidence related to a given hypothesis is a challenge. Our work explores the ability of current large language models (LLMs) to discern evidence in support or refute of specific hypotheses based on the text of scientific abstracts. We share a novel dataset for the task of scientific hypothesis evidencing using community-driven annotations of studies …

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …

Enhancing Research Productivity: Seamless Integration Of Personal Devices And Hpc Resources With The Cybershuttle Notebook Gateway, Yasith Jayawardana, Dimuthu Wannipurage, Eroma Abeysinghe, Suresh Marru

Computer Science Faculty Publications

Scientists often utilize personal laptops and workstations for initial research stages and turn to high-performance computing (HPC) supercomputers for compute-intensive tasks. However, seamless transitions between these environments are vital for enhancing productivity and accelerating research progress. Our paper presents the Cybershuttle Notebook Gateway, an open-source framework crafted to streamline this transition, optimize resource utilization, and reduce time-to-science for researchers. Leveraging JupyterLab, the framework extends kernel mechanics for seamless provisioning and connection to remote HPC cluster kernels. We delve into its architecture, which separates user authentication, kernel provisioning, and remote file system access. Additionally, we highlight practical capabilities like analyzing network …

Developing A Framework For Personalized Video-Based Quantum Information Science Education, Nikos Chrisochoides, Norou Diawara, Michail Giannakos

Computer Science Faculty Publications

This is a white paper on Workforce Development for Quantum Information Sciences (QIS) led by the Center for Real-Time Computing at Old Dominion University (ODU). We plan to investigate the potential of video lectures in supporting QIS. Specifically, we focus on following four objectives: (a) design a two-course series for both Master-level and PhD students; b) an upgrade of Experimental Lecture System (ELeSy) to test new, innovative, and transformative approaches for inclusive QIS education; c) design and implementation of a mixed-method systematic empirical study on the effects of video learning styles (in-person flipped classroom and voluntary video use) on graduate …

Evaluating Social Media Reach Via Mainstream Media Discourse, Himarsha R. Jayanetti

Computer Science Faculty Publications

This study examines the intersection between social media and mainstream television (TV) news with an aim to understand how social media content amplifies its impact through TV broadcasts. While many studies emphasize social media as a primary platform for information dissemination, they often underestimate its total influence by focusing solely on interactions within the platform. This research examines instances where social media posts gain prominence on TV broadcasts, reaching new audiences and prompting public discourse. By using TV news closed captions, on-screen text recognition, and social media logo detection, we analyze how social media is referenced in TV news. Our …

Abortion And The Extremism Of Bright Line Rules, Teneille R. Brown

Utah Law Faculty Scholarship

Rather than eliding the workability or necessity of bright-line rules in certain domains, this Essay is a rallying cry for epistemic humility regarding what biological criteria can and cannot say. Policymakers sometimes lean on the biosciences to offer “objective” solutions to thorny
moral and legal issues. But descriptive biological data cannot answer normative questions on their own. Cloaking the theoretical, normative scaffolding in biological criteria is a disingenuous but common phenomenon I refer to as the “bio-legal mismatch.”

In this Essay, I discuss various abortion-restrictive statutes and cases to elucidate the problems with the bio-legal mismatch. Specifically, I explore the …

Addressing Unlawful Cyber Operations In Armed Conflict Through Human Rights Bodies Instead Of The International Criminal Court, Zachary R. Orr

Vanderbilt Journal of Transnational Law

Although the ICC-or other similarly-situated international criminal tribunals-could soon see the first cyber war crime prosecution, two glaring issues persist. First, the universe of conduct that could give rise to such a prosecution is limited. Second, heavy reliance on the war crimes framework fails to provide a forum for redress of many harms caused by other unlawful cyber operations in armed conflict. The fragmented nature of international law and its enforcement mechanisms requires solutions that harness the full range of the integrated architecture of the international system. Cyber operations might soon feature at the ICC, but only a fraction of …

Temporary Protection For Ukrainians In The European Union: Why Now And When Again?, Maryellen Fullerton

Vanderbilt Journal of Transnational Law

In 2022, the Russian invasion of Ukraine produced an unprecedented wave of temporary immigration protections throughout the European Union (EU). Within the first few months of the war in Ukraine, over 4 million displaced individuals had registered for temporary protection. EU States distant from Ukraine sheltered hundreds of thousands of displaced families, while Poland and other EU States that border Ukraine sheltered more than 2 million. This groundswell response marked a striking departure from just seven years earlier, when the EU Commission and EU Council failed to use readily available laws to provide a temporary protection program for Syrians displaced …

Justifying Aggression: Russia's 2020 Constitutional Amendments And The Invasion Of Ukraine, Robert C. Blitt

Vanderbilt Journal of Transnational Law

Beyond the alluring promise of an enhanced social safety net for Russian citizens, President Vladimir Putin's constitutional amendments of 2020 betrayed a distinct preoccupation with fortifying Russia's international standing and crafting a new national identity. By Putin's own account, these amendments were necessary to steel the country against the malevolent action of international conspirators committed to Russia's downfall. As this Article posits, these specific constitutional changes systematically entrenched an exceptionalist vision of Russian sovereignty and a civilizational identity that left the country constitutionally untethered from international norms and institutions, saturated in religious fervor and visions of imperial glory, and poised …

Book Review: From Thought To Action: Developing A Social Justice Orientation, Joy L. Daggs

Iowa Journal of Communication

In the second edition of From Thought to Action: Developing a Social Justice Orientation, Sanford helps to provide a framework for students’ first exposure to allyship and activism. In the preface of the book, Sanford (2024) articulates the three major purposes of the book, which include helping new allies, “a) focus on common humanity, b) feel less isolated on their social justice journey, c) figure out how to move from thought to action, either individually or collectively.” (p. xiv) The book could be used to supplement a course on Intercultural Communication, encouraging students to take their knowledge to collaborate with …

Synthesis And Characterization Of Thieno[3,4-B]Pyrazine-Based Near-Infrared Material, Spencer Gilman

Chemistry and Biochemistry

Since their first report in the 1800s, conjugated polymers have gained significant attention for their ability to exhibit the optical and electronic properties of inorganic semiconductors and the physical traits of organic plastics. This has led to the development of organic electronics with notable commercial applications, such as organic photovoltaics and organic light-emitting diodes. The tunability of these materials has also allowed for the production of materials that absorb and emit near-infrared (NIR) light, making them useful for NIR photodetection and bioimaging. NIR photodetection is important for several applications, including optical communication, artificial vision, and health monitoring. Commercially available NIR …

Organizational Identity Management Policies, Alexander Rieger, Tamara Roth, Johannes Sedlmeir, Gilbert Fridgen, Amber Young

Information Systems Faculty Publications and Presentations

Effective identity management is essential for secure organizational processes, but organizations often do not approach it strategically. To break this trajectory, organizational policymakers need to define a clear and sustainable identity management strategy. This paper presents an overview and guidelines to help shape such strategy. It analyzes the key characteristics and trade-offs of today’s identity management models. Moreover, it offers practical recommendations for organizational policymakers when choosing among these models.

Immigration Detention Abolition And The Violence Of Digital Cages, Sarah R. Sherman-Stokes

Faculty Scholarship

The United States has a long history of devastating immigration enforcement and surveillance. Today, in addition to more than 34,000 people held in immigration detention, Immigration and Customs Enforcement (“ICE”) surveils an astounding 296,000 people under its “Alternatives to Detention” program. The number of people subjected to this surveillance has grown dramatically in the last two decades, from just 1,339 in 2005. ICE’s rapidly expanding Alternatives to Detention program is marked by “digital cages,” consisting of GPS-outfitted ankle shackles and invasive phone and location tracking. Government officials and some immigrant advocates have categorized these digital cages as a humane “reform”; …

Counseling Oppression, Angelo Petrigh

Faculty Scholarship

Critical scholars and public defenders alike have grappled with the contradictions at the heart of counseling clients in a carceral system. Systems of oppression operate within the public defender - client relationship because the defender’s role in translating the law also enforces its inequities. Counseling can obscure the workings of the system, providing an illusion of choice despite privileging certain forms of knowledge and tactics.

But the counseling site is also where defenders become exposed to client’s lived experiences, encounter collectivist tactics, and critically examine the tension of their role in the system. Likewise, through counseling defenders can pull back …

Human Rights In Hospitals: An End To Routine Shackling, Neil Singh Bedi, Nisha Mathur, Judy D. Wang, Avital Rech, Nancy Gaden, George J. Annas, Sondra S. Crosby

Faculty Scholarship

Medical students (NSB, NM, JDW) spearheaded revision of the policy and clinical practice for shackling incarcerated patients at Boston Medical Center (BMC), the largest safety net hospital in New England. In American hospitals, routine shackling of incarcerated patients with metal restraints is widespread—except for perinatal patients—regardless of consciousness, mobility, illness severity, or age. The modified policy includes individualized assessments and allows incarcerated patients to be unshackled if they meet defined criteria. The students also formed the Stop Shackling Patients Coalition (SSP Coalition) of clinicians, public health practitioners, human rights advocates, and community members determined to humanize the inpatient treatment of …

Cuing Safety In The Law School Classroom: Using A Polyvagal Theory Framework In Support Of Trauma-Informed Teaching Practices, Gigi Walker, Brian Flaherty

Faculty Scholarship

The past few decades have seen a welcomed focus on “Trauma-informed education.” This focus is often traced back to the 1997 Adverse Childhood Experiences study, which identified many significant negative outcomes that resulted from childhood trauma.¹ While the original study focused on outcomes such as chronic health problems, incarceration, and employment challenges, later researchers focused on the negative impacts on education and learning as a result of trauma.² Educators continue to work with this research trying to figure out how to be more “trauma-informed,” and to better reach those students whose lives and learning capacity have been affected …

Against Engagement, Neil Richards, Woodrow Hartzog

Faculty Scholarship

In this Article, we focus on a key dimension of commercial surveillance by data-intensive digital platforms that is too often treated as a supporting cast member instead of a star of the show: the concept of engagement. Engagement is, simply put, a measure of time, attention, and other interactions with a service. The economic logic of engagement is simple: more engagement equals more ads watched equals more revenue. Engagement is a lucrative digital business model, but it is problematic in several ways that lurk beneath the happy sloganeering of a “free” internet

Our goal in this Article is to isolate …

Kafka In The Age Of Ai And The Futility Of Privacy As Control, Daniel Solove, Woodrow Hartzog

Faculty Scholarship

Despite writing more than a century ago, Franz Kafka captured the core problem of digital technologies—how individuals are rendered powerless and vulnerable. Over the past fifty years, and especially in the twenty-first century, privacy laws have been sprouting up around the world. These laws are often based heavily on an Individual Control Model that aims to empower individuals with rights to help them control the collection, use, and disclosure of their data.

In this Article, we argue that although Kafka starkly shows us the plight of the disempowered individual, his work also paradoxically suggests that empowering the individual isn’t the …

Moving Beyond Statements And Good Intentions In U.S. Law Schools, Angela Onwuachi-Willig

Faculty Scholarship

This Article seeks to answer these questions about how law school leaders might help to cultivate antiracist cultures within their law schools, among their students, and across the legal profession, even in the face of a growing national backlash against antiracism, diversity, equity, and inclusion.³² Part I first establishes why it is important for law schools to "provide [an] education to law students on bias, cross-cultural competency, and racism," as the American Bar Association (ABA) requires, and to train future lawyers who have the abilities to combat racism. ³³ In so doing, Part I defines key terms such as …

The War On Higher Education, Athena Mutua, Jonathan Feingold, Angela Harris, Emily Houh, Matthew Patrick Shaw, Frank Valdes

Faculty Scholarship

Academic freedom is under assault in the United States.¹ Like the authoritarian populism rising across the globe, domestic attacks on individual professors and academic institutions buttress a broader and multifaceted campaign to undermine multiracial democracy and the institutions that sustain and safeguard it.² The individuals and entities driving this antidemocratic movement have also targeted the electoral process; public education; the right to bodily autonomy; the civil rights and liberties of minoritized and marginalized communities; and freedom of speech and expression (increasingly marshaled against pro-Palestinian advocacy).³ Their openly stated goal is to delegitimize, defund, and “lay siege to” …

Confronting Structural Inequality In State Labor Law, Andrew Elmore

Faculty Scholarship

Low-wage workers face a structural problem in seeking to improve their work standards: While companies have substantial labor market power to impose work terms and conditions, workers require affirmative state support to collectively press their workplace demands. But their employers can mobilize private capital and property rights, often with judicial deference, to fend off state intrusions into the workplace. While the National Labor Relations Act aims to resolve this structural problem by protecting the rights of workers to join unions, strike, and collectively bargain, employers, backed by judicial support for managerial prerogatives and property rights, can often leverage NLRA weaknesses …

Innovative Approaches To On-Demand Continuing Legal Education Ethics Training: A Case Study, Tigran W. Eldred, Molly J. Walker Wilson

Faculty Scholarship

In the ongoing discussions about continuing legal education (CLE), concerns have been raised about the quality of programming that is created and delivered. Critics have emphasized the weaknesses in mandatory programs, arguing that requiring annual training on topics such as legal ethics tends to fall short of stated goals.¹ Too often, it is said, such programs fail to deliver content in an engaging manner that is likely to improve competence.² The picture conjured up is of the bored lawyer, sitting in the back of a room flipping through a newspaper or some other distraction, as CLE instructors passively …