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From Burden to Breakthrough: Rapid and Collaborative Open Textbook Creation
No full textThis interactive session will invite audiences to critically think about their use and perception of course materials as presenters explore open educational resources (OER), writing sprints, and collaborative authorship through the experiences of the 2025-26 VIVA Rapid Publishing Program. This approach incorporates institutional support-including week-long in-person facilitation, instructional design, copyright and publishing expertise, and hospitality-in an effort to leverage the benefits of collaboration and reduce faculty burdens for authoring OER. Through the guidance of panelists, attendees will begin to explore what course materials actually benefit them and their students and potential avenues of support to reach those ideals.
Open Educational Resources (OER)(1), including open textbooks, are used by 33% of higher education faculty. They are increasingly selected because of their equal or better student learning outcomes (in contrast to commercial course materials), zero-cost access, unrestricted redistribution and opportunities to customize for individual classes and implement innovative pedagogies (Elder, 2019; Cozart et. al., 2021; Seaman & Seaman, 2025).
Although using OER saves faculty significant effort, gaps in available disciplinary resources generate an additional burden to create new materials. And while OER are often lauded as “free,” this minimizes the extensive efforts required to create them. While some faculty author OER independently (Burnett, 2025; Guzman & Woolley, 2021; Marsh et al., 2022), an increasing number of OER programs provide authorship compensation; some also provide support structures similar to traditional book publishers (Walz et. al, 2016; Santiago & Rey, 2020).
To help overcome the OER authorship burden at its 70 institutions, VIVA, Virginia’s Academic Library Consortium, established the Rapid Publishing Program (VIVA, n.d.). This program builds on prior collaborative writing sprint models (Book Sprints Limited, n.d.; Baker et al., 2014; Jhanghiani et al., 2016). After identifying a gap in OER in an area of high need for Virginia higher education, VIVA forms a multi-institutional team of faculty instructor/subject-matter experts to author the text and librarians and instructional designers to instruct, provide framing, and support authorship. VIVA provides funding, infrastructure, and program coordination for authorship, review, production, and outreach. Authorship is viewed from a connectivist lens, leveraging multiple preparatory online sessions to plan features and content of the resource (Maawali, 2022; Tham et al., 2021). During a week-long, in-person structured writing sprint, authors establish and refine shared understanding of the task (Vygotsky, 1978), write in teams, offer constructive feedback, and create a first draft of the text.
This interactive session will invite audiences to critically think about their use and perception of course materials as presenters explore OER, writing sprints, and collaborative authorship through the experiences of the 2025-26 VIVA Rapid Publishing Program. This program gathered 7 faculty and 3 librarians to author an introductory leadership studies textbook during Summer 2025. Project librarians will share the program’s planning and organizational framework and lessons learned. The participating faculty will describe their experience and accomplishments, as well as reflect on benefits and challenges. Faculty will discuss how programs such as the Rapid Publishing Program 1) provide value through structured writing, review, and management of ongoing editorial and production services, 2) enable instructors to reach their goal of drafting an open textbook in five days, and 3) expand instructors’ thinking about teaching, design of teaching resources, and consideration for use of OER. Audience engagement will be included throughout the session and ample time will be reserved for audience Q&A.
Footnotes
(1) "[OER are] learning, teaching and research materials in any format and medium that reside in the public domain or are under copyright that have been released under an open license, that permit no-cost access, re-use, re-purpose, adaptation and redistribution by others” (UNESCO, 2019)
Reference List
Baker, R., Berry, D., Brokering, M., Dieter, M., French, A., & Ruhling, B. (2014). On Book Sprints v1.1. http://data.booksprints.net/books/On_Book_Sprints_v1_1.pdf
Book Sprints Limited. (n.d.). Booksprints. OER World Map. https://oerworldmap.org/resource/urn%3Auuid%3A0dc55f0f-5467-466c-9047-8c07b129346d
Burnett, M. (2025). Publishing OER on a shoestring: Manifold to the rescue. Iowa OER listserv. (February 4, 2025) https://web.archive.org/web/20250902193257/https://groups.google.com/g/iowa-oer/c/GOvBLBs3T5Q
Elder, A. (2019). OER starter kit. Iowa State University Digital Press. https://iastate.pressbooks.pub/oerstarterkit/
Cozart, D. L., Horan, E. M., & Frome, G. (2021). Rethinking the traditional textbook: A case for open educational resources (OER) and no-cost learning materials. Teaching & Learning Inquiry, 9(2). https://doi.org/10.20343/teachlearninqu.9.2.13
Guzman, I., & Woolley, S. (2021). A shoestring grassroots approach to publishing an open educational resource engineering textbook. 2021 Fall ASEE Middle Atlantic Section Meeting Proceedings. https://peer.asee.org/a-shoestring-grassroots-approach-to-publishing-an-open-educational-resource-engineering-textbook
Jhangiani, R., Green, A. G., & Belshaw, J. (2016). Three approaches to open textbook development. In P. Blessinger & T. J. Bliss (Eds.), Open education: International perspectives in higher education (pp. 178-198). Open Book Publishers. https://doi.org/10.11647/OBP.0103
Maawali, W. (2022). Experiential writing through connectivism learning theory: A case study of English language students in Oman higher education. Reflective Practice, 23(3), 305-318. https://doi.org/10.1080/14623943.2021.2021167
Marsh, C., Marsh, J., & Chesnutt, K. (2022). Exploring OER as a mediator for equity gaps in student course success rates for introductory biology courses in the NCCCS. North Carolina Community College Journal of Teaching Innovation, 6-12. https://www.ncccfa.org/_files/ugd/40c3b6_3309827827f24f9a9d14574282b848aa.pdf
Santiago, A., & Ray, L. (2020). Navigating support models for OER publishing: Case studies from the University of Houston and the University of Washington. Reference Services Review, 48(3), 397-413. https://doi.org/10.1108/RSR-03-2020-0019
Seaman, J. E., & Seaman, J. (2025). Deeply digital: Educational resources in higher education. Bayview Analytics. https://www.bayviewanalytics.com/reports/deeplydigital2025.pdf
Tham, J., Duin, A., Veeramoothoo, S., & Fuglsby, B. (2021). Connectivism for writing pedagogy: Strategic networked approaches to promote international collaborations and intercultural learning. Computers and Composition, 60, 102643. https://doi.org/10.1016/j.compcom.2021.102643
UNESCO. (2019). Open educational resources. https://www.unesco.org/en/open-educational-resources
VIVA. (n.d.). VIVA rapid publishing program. VIVA Publishing. https://vivalib.org/va/open/publishing
Vygotsky, L. S. (1978). Mind in society: The development of higher psychological processes. Harvard University Press.
Walz, A., Jensen, K., & Salem, J. A., Jr. (2016). SPEC Kit 315: Affordable course content and open educational resources. Association of Research Libraries. https://publications.arl.org/Affordable-Course-Content-Open-Educational-Resources-SPEC-Kit-35
Exploring Science Teacher's Concerns and Self-Efficacy Toward Implementing Engineering Practices in Science Education
No full textExploring Science Teacher's Concerns and Self-Efficacy Toward Implementing Engineering Practices in Science Education Angela Sanders Morris Scholarly Abstract The purpose of this study was to examine the levels of concern and self-efficacy held by Virginia secondary science teachers regarding the implementation of engineering practices as an instructional strategy to teach science. With the 2018 Virginia Science Standards of Learning requiring engineering integration, understanding teacher readiness for this shift is essential.
Participants were high school science teachers from counties across Virginia's eight regions. Of the 1,536 teachers invited, 75 completed the STR4UEP survey. Using the Stages of Concern Questionnaire (SoCQ) and the Teaching Engineering Self-Efficacy Scale (TESS), this study measured teachers' concerns, confidence, and perceived readiness. Findings revealed high internal concerns across all demographic groups, particularly regarding awareness, information needs, personal ability, and classroom management related to engineering implementation. TESS results showed low-to-moderate confidence, with consistently modest scores for Engineering Pedagogical Content Knowledge (KS) and Outcome Expectancy (OE). An inverse relationship emerged between concerns and self-efficacy: teachers with higher concerns reported lower confidence in their ability to implement engineering practices effectively. Overall, the results indicate that Virginia secondary science teachers possess a relatively low level of readiness to integrate engineering practices into science instruction, underscoring the need for targeted professional development and sustained instructional support.Doctor of EducationExploring Science Teacher's Concerns and Self-Efficacy Toward Implementing Engineering Practices in Science Education Angela Sanders Morris General Audience Abstract This study explored how prepared Virginia high school science teachers feel to use engineering activities as part of their science instruction. In 2018, Virginia updated its Science Standards of Learning to require the integration of engineering practices, making it important to understand whether teachers feel confident and supported in making this change.
High school science teachers from across Virginia were invited to participate, with 75 teachers completing a survey about their concerns, confidence, and readiness to teach using engineering approaches. The results showed that many teachers have significant concerns about implementing engineering in their classrooms. These concerns included needing more information, feeling unsure about their own skills, and managing engineering activities during class time.
Teachers also reported only low to moderate confidence in their ability to teach engineering concepts effectively and to help students succeed through these practices. Overall, teachers who expressed higher levels of concern tended to feel less confident about using engineering in their instruction.
These findings suggest that many Virginia high school science teachers do not yet feel fully prepared to integrate engineering practices into their teaching. The study highlights the need for focused professional development and ongoing support to help teachers feel more confident and successful as they bring engineering into science classrooms
International Journal of Pavement Engineering
No full textThe Balanced Mix Design (BMD) has emerged as a promising approach for mitigating cracking in high reclaimed asphalt pavement (HRAP) mixtures. This study evaluated the cracking performance of a control asphalt mixture and five BMD-optimized asphalt surface mixtures. The mixtures featured various RAP contents, two binder performance grades, a recycling agent, and a warm mix asphalt additive. The analysis integrated continuous longitudinal strain monitoring from Accelerated Pavement Testing (APT), cracking surveys, and laboratory tests. To quantify APT-measured cracking performance, three primary response phases were identified from the continuous strain monitoring. Residual strain was used to determine the initiation of cracking, and deformation uniformity was employed as a data quality indicator. The findings from strain analysis matched APT cracking surveys. Laboratory tests on field cores confirmed no structural damage for the evaluated mixtures, except for a 60% RAP section. All other BMD mixtures demonstrated better cracking resistance over the control mixture, with HRAP BMD mixtures (>30% RAP) outperforming conventional RAP mixtures (≤30% RAP). Correlation analysis between APT and BMD tests examined and supported the corresponding laboratory test thresholds. This study enhanced insights into pavement performance monitoring and highlighted the efficacy of the BMD concept in optimizing the design of HRAP mixtures.Accepted versio
Compost effects on plectosporium blight
No full textPlectosporium blight, also known as Plecto, is an emerging pumpkin, zucchini, and squash disease persistent in the eastern United States since the late 1980s. Its pathogen, Plectosporium tabacinum, is a fungal saprophyte capable of surviving in the soil for several years with limited research available on its life cycle. Compost is widely used as a tool to improve soil health with the assumption of preventing or mitigating disease effects, but this is not always the case. Compost is most often characterized as having a suppressive effect; however, in rare instances, it has been found to increase disease. To better understand the mechanisms driving compost effects, this study examines the role of compost source versus microbial activity in P. tabacinum growth in vitro and in vivo.
In a laboratory setting, five replicates of plant, animal, vermicompost, and mixed source compost treatments, with and without microbial sterilization, were added to 150 mm x 15 mm petri dishes centrally inoculated with P. tabacinum. After 7 days of incubation, the pathogen growth was measured radially using a spatial divider. Analysis revealed a significant interaction effect between the compost source and microbial activity (P = 0.01). The sterilized animal compost (4.6 ± 0.6, mean ± SE) and unsterilized mixed compost (5.0 ± 0.6, mean ± SE) resulted in significantly decreased growth of P. tabacinum (cm of radial growth) compared to the non-amended control (5.8 ± 0.2, mean ± SE). In contrast, the sterilized mixed compost (6.6 ± 0.6, mean ± SE) significantly increased its growth compared to the control. Each treatment underwent a nutrient and enzyme analysis to provide insight to their varied outcomes. There was a significant relationship between P. tabacinum growth and the enzymatic activity of β-glucosidase (BG) (P < 0.05). These findings suggest that the source material and microbial communities associated with composts both have varying effects of compost on P. tabacinum growth in vitro. Additionally, the enzymatic activity related to the breakdown of cellulose may play a role in the effects of compost on P. tabacinum growth.
In an outdoor pot experiment, a compact variety of 'Black Beauty' zucchini (Cucurbita pepo) was transplanted into 24.3-liter pots that were amended with six replicates of sterilized and unsterilized treatments of plant, animal, and worm source composts. After establishing in the treated pots for two weeks, the plants were inoculated with P. tabacinum using a drench method applied to the stems and leaves. Plants were checked weekly for the following five weeks to record crop growth stage, disease severity, fruit production, and week of death. Plectosporium blight disease severity was only significantly affected by compost source in Week 5 (P < 0.001). The animal source compost presented significantly lower disease severity than the plant and worm composts during Week 5 with 30% less symptomatic area; this was most similar to the disease severity of the control. However, all plants regardless of treatment reached total plant death by Week 8. Plectosporium blight limited overall fruit production but did not significantly differ across treatment types. This in vivo study indicates that compost of varying sources and microbial activity had little to no overall effect on the disease plectosporium blight in zucchini.Master of Science in Life SciencesThis thesis investigates compost effects on plectosporium blight in a laboratory setting and an outdoor pot experiment. The fungal plant pathogen, Plectosporium tabacinum, causes the disease plectosporium blight which considerably reduces pumpkin, squash, and zucchini yields across the eastern United States. Compost is widely used as a tool to prevent or improve disease outcomes, though it has mixed effects. Compost may increase or decrease the pathogen depending on a variety of factors from its beneficial microorganisms to its nutrient content. To better understand what drives compost effects, this study examines the role of compost source versus microbial activity in compost effects on plectosporium blight.
In a laboratory setting, composts made from plant, animal, worm, and mixed sources, with and without the presence of microorganisms, were placed in a petri dish with P. tabacinum. After incubating together for one week, the growth of the pathogen was measured by dividing the plate into sections to see how far the plectosporium spread from its starting point. Our results found that the source and presence of microorganisms associated with composts both had varying effects of compost on P. tabacinum growth. Each compost underwent a nutrient and enzyme analysis to provide insight to their varied outcomes. This analysis suggested that the enzymatic activity related to the breakdown of cellulose may play a role in the effects of compost on P. tabacinum growth.
In an outdoor pot experiment, zucchini was grown in large pots containing treatments of composts made from plant, animal, and worm sources, with and without the presence of microorganisms. The pathogen P. tabacinum was then introduced to the plants through application to the stems and leaves. Plants were checked each week for stem, leaf, and fruit growth, and disease severity until total plant death. Plectosporium blight disease severity was found to be significantly affected by compost source in terms of week. The no compost added control and animal source compost presented lower disease severity than the plant and worm composts during several of the weeks; however, all plants regardless of treatment reached total plant death by Week 8. This study indicates that compost of varying sources and microorganism activity had little to no overall effect on the disease plectosporium blight in zucchini
Developmental origins of cortical circuit dysfunction in a 22q11 deletion mouse model
No full textCortical circuit development is tightly regulated by programs of progenitor proliferation, neurogenesis, and neuronal maturation. Disruptions in these processes contribute to the cortical circuit pathology observed in neurodevelopmental disorders such as schizophrenia and autism, intellectual disability. The 22q11.2 deletion syndrome (22q11DS) is a major genetic risk factor for psychiatric illness and provides an optimal genetic model disease to explore how gene dosage imbalance impacts cortical circuit development. Study 1 examined the developmental origin of upper layer 2/3 projection neuron (PNs) deficits in the LgDel mouse model of 22q11DS. Bulk and single cell RNA sequencing revealed transient, cell state dependent changes in intermediate basal progenitors at the peak of upper layer neurogenesis. These changes are characterized by reduced proliferation, increased neurogenic gene expression and altered DNA methylation. The divergent progenitor progression resulted in a selective decline and shift in identity of L2/3 PNs generated during this critical developmental window, while earlier and later population of progenitors as well progeny remained unaffected. Study 2 investigated how 22q11 deletion alters L2/3 PN growth and development. LgDel neurons displayed oxidative stress, mitochondrial dysfunction, and reduced neurite growth. Treatment with the antioxidant N-acetylcysteine (NAC) improved axonal and dendritic growth but did not restore expression of deleted or differentially expressed genes in LgDel PNs. Instead, NAC induced a distinct antioxidant response via Nrf2 signaling pathway. Together, these studies link early transcriptional dysregulation in cortical progenitors to later metabolic and functional deficits in projection neurons, highlighting oxidative stress as a modifiable driver of cortical circuit dysfunction in 22q11DS.Doctor of PhilosophyThe human brain relies on precisely organized networks of neurons to support learning, memory, and social behavior. These networks are built during development as neural stem cells divide and form specialized neurons that connect different regions of the cortex. When this process is broken, it can lead to conditions such as autism, intellectual disability, or schizophrenia. One genetic cause of such disruption is the 22q11.2 deletion syndrome (22q11DS), in which a small part of chromosome 22 is missing. This dissertation investigates how the 22q11 deletion alters brain development using a mouse model (LgDel). The first study examines early brain development and found that the deletion affects a group of rapidly dividing neural stem cells that give rise to neurons that reside in upper layer cortex. These changes reduce the number and alter the identity of upper layer neurons that play a significant role in connecting different areas of the cortex which enable complex processes like cognition and behavior. The second study is focused on how these upper layer neurons grow and function after birth. These neurons from deletion mice have reduced growth and signs of oxidative stress, which is a type of injury to a cell due to energy imbalance. We showed that treating these neurons with the antioxidant N-acetylcysteine (NAC) improved their growth. Although, it did not correct the underlying genetic changes due to the deletion. Together, these studies show that the 22q11 deletion affects both the formation and later function of cortical neurons, and that reducing oxidative stress may help restore healthier brain development in 22q11DS
From Community Service to Critical Inquiry: Redesigning Service-Learning at The STEAD School
No full textService-learning projects in School-Based Agricultural Education (SBAE) often emphasize task completion over the critical examination of systemic inequities. This project examined the current state of service-learning at The STEAD School, a project-based agricultural high school in Colorado, to identify the conditions necessary for implementing a critical service-learning model aligned with the school’s mission of developing “lifelong learners, thinkers, creators, and activists.” A multi-method needs assessment was conducted through semi-structured interviews with four guides and four students, along with a survey of 68 stakeholders. Interview data were analyzed using Braun and Clarke’s (2006) thematic analysis
framework, while survey data were analyzed using descriptive statistics. The conceptual framework drew on Paulo Freire’s principles of critical pedagogy to propose a Freirean-adapted version of the National FFA Service Planning Guide.
Five themes emerged: (1) Current Practices Lack Depth and Structure, (2) Purposeful Integration is Inconsistent but Desired, (3) Systemic Challenges Impede Impact, (4) Student Agency is Central to Engagement, and (5) Transformative Potential Exists When Framed Intentionally. Survey results indicated that while 85% of respondents had participated in service learning, only 19% rated it “very effective.” The analysis identified five conditions necessary for effective service-learning: a shared schoolwide framework, purposeful curricular integration, student voice and co-creation, structured reflection, and reciprocal community partnerships. This project proposes a Freirean-adapted framework as one approach for establishing these conditions through four stages: Investigate, Plan, Serve, and Evaluate. While requiring future implementation and evaluation, this project contributes to a practical example of how critical pedagogy can inform service-learning within agricultural education.MAL
Applying Art-based Embodied Knowledge to Further Artistic Objectives with Technology and Support Creative Thinking in Computing
No full textAs computers have advanced, their use cases have expanded to support many human-centric activities. Computing's place in the creation and consumption of art has been called into question in recent years with the emergence of generative artificial intelligence (GenAI), which can produce creative works such as paintings, music, and creative writings almost instantly. However, before the introduction of GenAI, software had been used for decades across all vantages of influence to expedite human expression. Society is grappling with the question of how to approach technology's influence on all forms of art: how to effectively apply computing's capabilities without impeding the agency of the artist. Furthermore, there is a lack of influence from the world of art on directing the immense force of technology on the modern world. This dissertation sought to build a tighter bidirectional relationship between art and technology by understanding how technology can further the objectives of the artist through studies 1 and 2 and investigating how embodied logic in art can be used to support the algorithmic thinking required in computing in Study 3.
Study 1 focused on capturing embodied knowledge in the procedures of an art form through motion sensors to communicate physical routines through sound. This work was completed by building a prototype sonification system which dynamically classified segments of a stitch in crochet, and then conducting co-design sessions with stakeholders. Results demonstrated that using novel sensory-perceptual modalities such as audition to express abstract concepts can be used as a novel UX design tool. In study 2 I sought to understand the potential for human biases against technology's use in art. I built two different technologically-augmented dance performances, one with artificial intelligence (AI) and one without, and withheld information on how the performances were built in order to capture audience responses on the creative merits of the technological components of the two works. Results highlighted significantly higher ratings on questions of artistic merit for the AI performance version when implementation information was withheld compared to when this information was divulged, suggesting a potential for bias. This offered insight into the deployment of AI art in the future. Study 3 focused on teaching and using embodied logic in art to assess analytical thinking skills in computing. The study surrounded teaching individuals how to interpret and write crochet patterns using two different methods: with or without the accompanying physical procedures. After the lessons, written tests on patterns in crochet and computer programming were administered. Results showed a positive correlation between programming and crochet test scores of individuals for the majority of participants across all condition groups. Interview transcriptions pointed to similarities in approaching questions on the two tests and a desire for visual aids from participants who didn't learn the physical procedures.
The present body of work examined how the latest technologies can be used to further the human objectives of art, and how constructs from art can be used to advance computing objectives. The present work offers theoretical insights into using multiple sensory-perceptual modalities as system design tools, as well as practical guidance for how technologies can effectively be applied in creative, art-based contexts.Doctor of PhilosophyPeople today incorporate computing in nearly all areas of their lives. However, with the rapid developments of GenAI, the adoption of computing into certain domains has been called into question. GenAI can produce creative works like paintings, music, and writing almost instantly with relatively little help from human creators. While computing has contributed greatly to creative domains, some believe that the latest technologies can potentially threaten artistic expression. This is an urgent open question that blends art and computer science (CS), and contributes to a greater discussion of how these fields influence one another. For this dissertation I investigated methods for developing a more balanced relationship between art and technology. In Studies 1 and 2 I sought to use technology to make the artmaking process more fulfilling and enjoyable for the creator, whereas in Study 3 I tried to understand how ideas in art are similar to ideas in computing.
Study 1 focused on capturing patterns in the movements made when producing art in order to make live collaborative music. This was done by building a prototype system that converted data to sound by dividing steps in making stitches in the fiber art crochet and capturing that data in real time. People with different backgrounds in art and technology were asked for their thoughts on the system to improve it in the future. Results showed that sound can be used as a tool to help designers get impressions of activities that do not make sound. Study 2 was done to understand whether people had biases against technology when it is used for art. I built two different dance performances that used technology, one with AI and one without, and withheld information on how the performances were built to capture audience survey responses on the creativity of the two works. Results showed that people thought the AI performance was more artistic when they were not told about how the performance was built until after the survey; this indicated some bias. This study's results can help people decide whether they want to use AI tools when sharing their work with public audiences. Finally, Study 3 focused on teaching a procedural artistic task using different methods in order to evaluate thinking skills used in computing. In the study individuals were taught how to understand written crochet patterns either with or without physically learning how to crochet. After the lessons, written tests were given on crochet patterns and basic programming. Results showed positive correlations between scores on tests for the majority of participants and similarities in problem solving strategies on both tests. People who did not learn how to physically crochet thought pictures would help on the test as well.
This collection of work centered on how the latest technologies can be used to keep humans the focus of art, and how art can positively impact computing. Considering both the benefits and consequences of technology, we can support human creativity as technology advances
PERM1-Mediated Metabolic Crosstalk Between the Heart and Skeletal Muscle in Pressure Overload-Induced Heart Failure
No full textHeart failure is a complex syndrome with high mortality, as nearly 50% of patients die within five years of diagnosis. Among its systemic complications, cardiac cachexia–a condition characterized by severe unintentional weight loss due to cardiac dysfunction– serves as an independent predictor of mortality. The early stage of cachexia involves a vicious cycle between the heart and skeletal muscle driven by metabolic dysregulation; however, its underlying bioenergetics remain unclear. PERM1, a striated muscle-specific regulator of mitochondrial bioenergetics, is highly expressed in the heart and skeletal muscle. We previously demonstrated that PERM1 is downregulated in failing hearts; however, whether its downregulation also occurs in skeletal muscle during the progression of heart failure is unknown. To address this, wild-type mice underwent transverse aortic constriction (TAC) for 8 weeks. Cardiac function and body composition were assessed by echocardiography and NMR, and PERM1 expression and metabolomic profiles were analyzed by Western blotting and gas chromatography-tandem mass spectrometry (GCMS).
TAC reduced systolic function and downregulated PERM1 to a comparable extent in both tissues. Global PERM1 knockout (KO) mice exhibited lean mass loss with an increase in adiposity and no change in body weight, indicating sarcopenic phenotype and not cachectic phenotype. Partial loss of PERM1 in heterozygous mice accelerated systolic decline and mortality and modulated metabolomic programs linked to ketone handling, branched and medium chain fatty acid oxidation, malate-aspartate shuttling, amino acid anaplerosis, nitrogen recycling, and membrane/cofactor biosynthesis. In vitro, PERM1 silencing in C2C12 myotubes induced a compensatory shift toward glycolysis. AAV-PERM1 preserved systolic function and remodeled metabolomes modestly in the heart and robustly in skeletal muscle as compared AAV-GFP controls. In summary, this study provides the first coordinated PERM1 downregulation and distinct metabolic alterations, which may contribute to systemic myopathy. These findings highlight PERM1 as a potential regulator of metabolic crosstalk between the heart and skeletal muscle during the progression of heart failure.Master of ScienceHeart failure is a common and deadly health issue with about half of patients dying within five years and it does not only damage the heart. Many patients also lose muscle mass and strength. With some developing cardiac cachexia which is a serious unintended weight loss syndrome that worsens survival. Early in this process, the heart and skeletal muscle appear to drive each other into further trouble through faulty energy use, but the details are not well understood. This study focuses on PERM1, a protein found mainly in the heart and skeletal muscle that helps mitochondria make energy. We asked two questions: how does PERM1 change during heart failure-like stress, and can boosting it protect the heart and muscles? In mice, we created heart failure-like symptoms by tightening the aorta for eight weeks through a surgery called transverse aortic constriction (TAC), then measured heart pumping efficiency by ultrasound, body composition, PERM1 levels by gene and protein level assays, and metabolomic fingerprints of fuels and by-products in the heart and skeletal muscle. We also downregulated PERM1 off in muscle cells grown in the lab and tested a gene therapy style approach that increases PERM1 expression. In mice studies, TAC weakened the heart and lowered PERM1 expression in both the heart and skeletal muscle. Mice completely lacking PERM1 had less lean mass and more body fat without losing overall weight–a pattern more consistent with sarcopenia (loss of muscle) than cachexia. Mice with only one working PERM1 copy declined with more dying more often and showed shifts in how their tissues used fuels. In cultured muscle cells, reducing PERM1 pushes cells to lean more on sugar. By contrast, boosting PERM1 in the mouse heart preserved pumping function and reshaped metabolism modestly in the heart and more strongly in skeletal muscle (toward stronger mitochondrial energy production). Together, these results suggest that PERM1 helps coordinate energy use between the heart and skeletal muscle in heart failure and highlight PERM1 as a promising target for future therapies
Hetero-functional Graph Theory for Convergent Systems of Systems: Model-Based Applications in Watershed and Economic Systems
No full textModern societal challenges defined by the Sustainable Development Goals of the United Nations are deeply interconnected. Addressing issues such as water scarcity, ecosystem degradation, or food security requires understanding the coupled systems that shape them, including hydrology, infrastructure, ecology, economics, and governance. While modelers within each discipline develop increasingly accurate representations of individual systems, real-world problems arise from the feedbacks between them. Actions intended to improve one domain can unintentionally disrupt another; for instance, reducing fertilizer to prevent eutrophication may also affect agricultural productivity.
To address such interdependencies, this dissertation develops a unified, ontology-based modeling framework that integrates Model-Based Systems Engineering (MBSE) with Hetero-functional Graph Theory (HFGT). The dissertation progresses from domain-specific modeling studies toward a general convergence paradigm, illustrating how environmental and economic systems can be represented within a consistent system of systems architecture.
The framework is first demonstrated in the context of simplified hydrological systems, where lakes, rivers, land segments, and outlet points are modeled using resistance-based transport laws and continuity equations adapted into the Hetero-functional Network Minimum Cost Flow (HFNMCF) optimization problem. This initial study establishes that environmental processes can be represented as a class of engineering systems within the HFGT meta-architecture when defined by an MBSE-based reference architecture.
The approach is then extended to larger watershed systems and instantiated for the Chesapeake Bay Watershed. The approach classifies watershed systems under the HFGT meta-architecture then develops a watershed-specific Weighted Least Squares Error HFGT State Estimator to infer nitrogen and phosphorus flows across land–river–estuary networks under data sparsity and structural uncertainty. The paper then simulates the Chesapeake Bay Watershed using spatially and temporally resolved data from the Chesapeake Assessment Scenario Tool (CAST). This chapter demonstrates the scalability of the MBSE–HFGT framework and highlights its capacity for transparent, extensible environmental modeling at regional watershed scales.
Having established the methodology through hydrologic and watershed applications, the dissertation then introduces a broader convergence paradigm. This chapter presents the meta-cognition map, which explains how scientific knowledge is generated across observation, abstraction, visualization, mathematics, and computation. The convergence paradigm draws directly on insights from the hydrology and watershed work as well as other domain applications to articulate the characteristics required for modeling complex Anthropocene systems of systems, including ontology, transparency, extensibility, and cross-domain alignment.
The final chapters extend the MBSE–HFGT framework beyond environmental systems as preliminary steps to advance the cross-domain convergence paradigm. An economic input–output model is likewise classified as an engineering system under the HFGT meta-architecture and simulated as an HFNMCF optimization problem. Similarly, a system dynamics representation of the Mono Lake system is then translated into the MBSE–HFGT formalism, allowing a structural comparison between traditional causal-loop modeling and the capability-based, ontology-driven approach developed in this dissertation.
Together, these studies establish a coherent, extensible methodology for representing and estimating complex systems across environmental and economic domains. By integrating system structure and function through a common ontology and demonstrating this integration across multiple domains, this dissertation provides a pathway toward convergent modeling of coupled human–natural systems in the Anthropocene.Doctor of PhilosophyThe United Nations' 17 Sustainable Development Goals identify the planet's most urgent challenges, including clean water, sustainable agriculture, and resilient ecosystems. These goals are deeply interconnected: progress toward one often depends on understanding how others behave. For example, improving water quality requires insight not only into hydrology but also land use, agriculture, economics, and the ways these systems influence one another.
Scientists and engineers build models to study these systems, but most tools focus on a single domain. Hydrologists model how rainfall and land management shape water quality, while economists model fertilizer use, production decisions, and trade. However, natural and human systems do not operate in isolation. Actions in one domain, such as changing fertilizer practices, can ripple across others, affecting rivers, farms, and regional economies. Without a way to represent these connections, important feedbacks can be overlooked.
This dissertation develops a framework for linking these separate models into a unified system of systems. The approach combines Model-Based Systems Engineering and Hetero-functional Graph Theory to represent relationships among natural, engineered, and social systems using a shared, consistent language. This allows models from different disciplines to be described, compared, and connected more easily.
The framework is first demonstrated using simplified examples of water and nutrient movement among lakes, rivers, and land segments, showing how environmental processes can be represented within a common structure. It is then applied to the Chesapeake Bay Watershed, where diverse hydrological and land-use data are used to estimate nitrogen and phosphorus flows across thousands of interconnected segments. This produces a more transparent and flexible representation of watershed behavior.
As a first step toward integrating economic and environmental decision-making, the framework is extended to represent basic economic input–output systems, showing how production technologies and resource flows can be modeled using the same structural concepts. Finally, it is applied to a system previously modeled with system dynamics--a widely used tool for environmental decision support--to compare how the two methods represent structure and system behavior including feedbacks.
By linking scientific knowledge across disciplines, this research provides a foundation for understanding the broader consequences of environmental and policy decisions.
The framework supports more transparent and extensible strategies for sustainability, helping decision-makers navigate the complexity of interconnected human–natural systems
Scholarly Information System for Long Documents and their Elements: Structured Representation and Exploration using Knowledge Graphs and LLMs
No full textDoctor of PhilosophyEvery year, thousands of students write long and detailed theses and dissertations as part of their graduate requirement. These documents contain valuable knowledge—methods, explanations, figures, and insights—but because they are so long, it is often difficult for researchers to find exactly what they are looking for. Most search tools only point researchers to the beginning of a document, leaving them to scroll through hundreds of pages on their own. Even modern artificial intelligence (AI) tools, like large language models, that can give fluent answers, don't always know where the information came from or how the different parts of a thesis fit together. This dissertation creates a new way to explore these long academic documents. Instead of treating a thesis as one giant block of text, the system breaks it into meaningful pieces like captions, figures, and key sentences, so they can be searched directly. It also builds a structured map, called a knowledge graph, that shows how these pieces relate to each other. This allows the system to understand the document more like a human would. Using this structure, the system can answer questions in a more helpful way. Rather than giving a list of documents for the user to read, it gathers relevant information and produces clear, paragraph-level answers that are grounded in specific parts of the dissertations. To see how well this works, 47 participants from different engineering fields tested three versions of the system. The version that combined the knowledge graph aided retrieval with AI-generated summaries received far better ratings for clarity, informativeness, and overall usefulness. Users said the answers were easier to read, more complete, and more helpful than those produced by traditional search or AI alone. Overall, this dissertation shows that by combining search technology, AI, and structured representations of knowledge, we can make long academic documents far more accessible. This approach helps people find what they need faster, understand it more easily, and discover information that would otherwise be buried deep within hundreds of pages. It represents a meaningful step toward smarter, more helpful tools for navigating scholarly knowledge