Digital Commons Network^™

Telomere-To-Telomere Genome Assembly And A Pangenome For The Rat., Kai Li, Julia L Ciosek, Sergey Koren, Adam M Phillippy, Yaming Zhu, William A Lauer, Shelise Y Brooks, Gerard G Bouffard, Brandon D Pickett, Beth L Dumont, Melissa L Smith, Theodore S Kalbfleisch, Peter A Doris

Faculty Research 2026

We report a complete rodent telomere-to-telomere genome assembly from the brown rat, Rattus norvegicus. Annotation was enriched with multi-tissue long-read RNA sequencing and uncovered numerous novel genes. Assembly of both sex chromosomes reveals the absence of gene coding in the presumed pseudo-autosomal regions and the presence of centromeric satellite repeats on distal chromosome Y (chrY). We provide evidence of meiotic conjunction between Xp and Yq. The genome assembly reveals several expanded autosomal regions enriched for testis-expressed genes. Finally, we have generated a pangenome from recent high-quality assemblies of 8 distinct inbred rat strain genomes. This allows the strain-specific distribution of …

Interview With Cecilia 'Sue' Sill, Cecilia 'Sue' Sill, Logan Dovalina

Rio Grande Valley Oral Histories

Cecilia 'Sue' Sill (b. 1939, Woodward, Oklahoma) recounts a life shaped by mobility, scientific curiosity, and engagement with the natural world of South Texas and Mexico. The daughter of a pipeline welder, she moved frequently as a child before settling for a time in Pharr, Texas, in 1950. She later spent roughly forty years in Corpus Christi, where she raised two sons, pursued higher education later in life, and earned a Ph.D. focused on the systematics of Tillandsia (air plants), describing several new species centered in Mexico.

After her divorce in 1990, Sill lived for eight years on a mountainside …

The Gut-Bladder Axis: How Symbiont Microbes Alter Urinary Tract Infections, Benjamin S. Olson

Arts & Sciences Graduate Student Theses and Dissertations

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. Consequently, they are one of the leading indications for antibiotic prescription. Despite the typically successful treatment of an acute UTI, recurrent infections are exceedingly common, particularly among women. Nearly a quarter of otherwise healthy women will suffer recurrent UTIs (rUTI) after a primary UTI; why these select individuals are continually afflicted is unkown. There are no successful therapeutics to treat rUTI representing a gap not just in the medical toolkit but in our understanding of why rUTI is so prevalent. There are many hypotheses for the risk factors …

Integrative Evidence For Cryptic Diversity In The Thomomys Mazama Species Complex: Phylogenetics, Cranial Morphometrics, And Ecological Niche Modeling, Jessica Kate St. Michael

Dissertations and Theses

The population genetic structure and geographic distribution of the pocket gopher genus Thomomys Wied-Neuwied, 1839, lends itself to speciation events. Conserved morphology, ecological specialization, and high rates of molecular evolution may increase the probability of allopatric speciation, thereby contributing to the presence of morphologically cryptic taxa. In light of these patterns of evolution, we assessed genetic divergence and phylogenetic relationships, cranial morphometric differentiation, and ecological divergence among taxa in the Thomomys mazama species complex to test the hypothesis that T. mazama is a single species. Species delimitation analysis using Bayesian Poisson Tree Processes (bPTP) and data from the mitochondrial cytochrome …

Sac Newsletter 2026, South Asia Center

Newsletters from the South Asia Center

No abstract provided.

Pre-Implementation Factors For Active Music Engagement (Ame): Barriers And Facilitators To Integrating An Evidence-Based Dyadic Intervention Into Pediatric Oncology Care., Kristin M. Story, Elizabeth Harman, Kristin Stegenga, Jelena Golubovic, Sheri L. Robb

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Pediatric cancer treatment is a difficult and distressing experience that often results in sustained, interrelated distress in young children and parents, and traumatic stress symptoms for some parents. Few evidence-based interventions address this dyadic distress. Active Music Engagement (AME) is a manualized, evidence-based music play intervention that significantly reduces distress in child/parent dyads and mitigates traumatic stress and improves well-being among highly distressed parents and those experiencing sociodemographic risk. Successfully integrating AME into standard care requires a systematic understanding of implementation factors. This study aimed to identify site-specific barriers and facilitators that influenced successful AME delivery during a recently …

Role Of Central And Peripheral Nlrp3 In Parkinson's Disease Models, Elisa Carloni

Dartmouth College Ph.D Dissertations

Neuroinflammation, particularly NLRP3 inflammasome activation, has been implicated in Parkinson's disease (PD) neurodegeneration, but the cell-type-specific contributions of NLRP3 activity remain poorly understood. This dissertation tested whether NLRP3 activation in microglia versus peripherally derived myeloid cells differentially drives Parkinsonian pathology. Microglial NLRP3 gain-of-function was achieved using Nlrp3^L351P crossed with Tmem119-CreER, both on an Nlrp3^⁻/⁻background. For peripheral myeloid cells, an analogous Ms4a3-Cre-driven strategy resulted in perinatal lethality of animals with Nlrp3^L351P restricted to granulocyte-monocyte progenitors (GMPs). Instead, we used Ms4a3-Cre tdTomato reporter mice generated on wild-type and Nlrp3^⁻/⁻backgrounds to fate-map GMP-derived …

Philosophical Education As A Vision For Lasting Peace: Keynote Address At The Phase 1 Workshop Of “Ethics, Society, And Education: Empowering Early Career Philosophers In The Philippines”, Armin A. Luistro Fsc

SDRC Media Releases

Background

This keynote address was delivered by Br. Armin A. Luistro, FSC, during the Phase 1 Workshop of Ethics, Society, and Education: Empowering Early Career Philosophers in the Philippines on 12 August 2026 at De La Salle University.

The project aims to strengthen the research, writing, and professional capacities of early career philosophers in the Philippines. It is supported by the British Academy International Writing Workshops 2025 Programme under the United Kingdom Government’s International Science Partnerships Fund. The initiative is led by Dr. Hazel T. Biana of the De La Salle University Department of Philosophy, in partnership with Durham University …

"Tithing Is An Insurance Premium": A Framing Analysis Of Speaker Innovation And Diachronic Trends In Latter-Day Saint Religious Discourse, Reid Empey

Theses and Dissertations

Religious language relies on shared metaphor and frames that contextualize religious experience and practice. Current approaches to frame semantics (Fillmore 1982) and cognitive metaphor (Lakoff & Johnson 1980) lend important insight into religious language, particularly in describing the role that figurative language serves in a religious speech community. However, a vital component of many religious speech communities is the presence of and engagement with a scriptural canon, which often contains metaphorical and framing language that religious speakers can directly reference. Yet, past conceptualizations of speech communities have not accounted for this engagement with a shared canon. To illustrate the role …

Explicit Writing Instruction Across Content Areas: A Professional Development, Bethany B. Richardson

Masters Projects

Research shows that writing instruction has diminished in the elementary classroom due to high stakes testing in reading and math.  Writing is a driving force for literacy achievement and should be prioritized.  In order to improve writing instruction, teachers need professional development in explicit instructional strategies for writing in other content areas.  According to cognitive processing theory, students are using multiple cognitive and metacognitive processes to complete a singular writing task.  Using scaffolds like write alouds, mentor texts, and graphic organizers can help teachers support students in their writing. Scaffolding theory suggests that students need high levels of support in …

Telomere-To-Telomere Genome Assembly And A Pangenome For The Rat, Kai Li, Julia L Ciosek, Sergey Koren, Adam M Phillippy, Yaming Zhu, William A Lauer, Shelise Y Brooks, Gerard G Bouffard, Brandon D Pickett, Beth L Dumont, Melissa L Smith, Theodore S Kalbfleisch, Peter A Doris

The Brown Foundation: Institute of Molecular Medicine

We report a complete rodent telomere-to-telomere genome assembly from the brown rat, Rattus norvegicus. Annotation was enriched with multi-tissue long-read RNA sequencing and uncovered numerous novel genes. Assembly of both sex chromosomes reveals the absence of gene coding in the presumed pseudo-autosomal regions and the presence of centromeric satellite repeats on distal chromosome Y (chrY). We provide evidence of meiotic conjunction between Xp and Yq. The genome assembly reveals several expanded autosomal regions enriched for testis-expressed genes. Finally, we have generated a pangenome from recent high-quality assemblies of 8 distinct inbred rat strain genomes. This allows the strain-specific distribution of …

The Byu Advocate, J. Reuben Clark Law School

The BYU Advocate (& Annual Reports)

"Experiential learning opportunities in law school have expanded dramatically, but pressure remains for students to graduate ready to practice. Artificial intelligence (AI) is transforming education and legal practice, generating questions about how and what to teach and raising uncertainties about future employment. At the same time, big firms are interviewing students in their first semester and extending offers before or shortly after first-semester grades are out."

– David H. Moore

Promoting The Bipartisan Dimension Of Political Leadership: A Study Of The Impact Of A Normative Intervention With Newly Elected Members Of Congress, Jaime M. Ruvalcaba

Dissertations

The U.S. political system is more polarized now than at any time in the past century, as evidenced by the rise of political incivility, legislative gridlock, and hyperpolarization. To date, most studies and efforts have focused on institutional strategies to explain, transform, and mitigate the challenges posed to the political environment. By contrast, little attention has been paid to the normative or values-based behaviors of leaders to either explain or influence political leadership in ways that positively impact the political environment. Fortunately, some organizational programs, like Harvard’s Bipartisan Program for Newly Elected Members of Congress, have taken a different tack, …

Bcg Overexpressing Ag85b Reprograms Host Immune Response Through Coordinated Transcriptional Networks, Vivek Chauhan, Rakesh Kumar, Raja Veerapandian, Enrique I. Ramos, Chinnaswamy Jagannath, Shrikanth Gadad, Subramanian Dhandayuthapani

School of Medicine Publications

Antigen 85B (Ag85B), an immunodominant protein secreted by Mycobacterium tuberculosis (Mtb), induces robust T-cell-mediated immunity in host cells. Previous studies have demonstrated that recombinant BCG strains overexpressing Ag85B (BCG85B) confer significant protection against tuberculosis in mouse models. This study hypothesized that enhanced protection by recombinant BCG85B results from modulation of host immune gene expression by the Ag85B antigen. To test this, RNA-seq analysis was performed on splenocytes from mice immunized with the wild-type BCG (BCG-WT) and BCG85B strains. Differentially expressed genes (DEGs) in the splenocytes of BCG85B-immunized mice indicated upregulation of immune-related KEGG pathways, including Th1/Th2 and Th17 differentiation, NF-kappa …

New Locality Records And Future Habitat Suitability Of Sassanidotus Gracilis (Birula, 1900) (Scorpiones: Buthidae) In The Iran–Afghanistan–Pakistan Arid Belt, Ersen A. Yağmur, Kerim Çiçek, Homa Barati, Mohammad Moradi

Euscorpius

This study reports new locality records from Iran and a climate-based habitat suitability assessment for Sassanidotus gracilis (Birula, 1900) (Scorpiones: Buthidae) in the Iran–Afghanistan–Pakistan arid belt. We document new specimens from Sistan and Baluchestan Province, Iran, with an updated distribution map and illustrations, and we model the species' potential distribution across south-eastern Iran and adjacent parts of Afghanistan and Pakistan.

Habitat suitability was associated mainly with precipitation seasonality, precipitation of the wettest month, precipitation of the driest month, and slope. In an arid setting these rainfall variables are unlikely to indicate a need for moist habitat; they more plausibly track …

Inclusions And Illusions: Transnational Matrix Of Subordination & The (In)Visible Hierarchies Among Racialized International Students In Ontario Universities, Shamiga S. Arumuhathas

Journal of Comparative & International Higher Education

This study critically examines the (in)visible racial hierarchies experienced by racialized international students (IS) within Ontario’s (HE) education landscape amid populist, anti-immigration backlash and expanding internationalization. Guided by Critical Race Theory (CRT) and intersectionality, this research employed narrative inquiry with 14 self-identified racialized IS at 2 public universities. Core research questions include: How do racialized IS experience belonging, racism, and institutional EDID (Equity, Diversity, Inclusion, Decolonization) in present-day Ontario? How do EDID and internationalization policies obscure or reinforce racial hierarchies? Findings reveal a transnational matrix of subordination: White IS remain proxies for institutional belonging, while racialized and domestic students act …

Tardigrade Bio-Exploration Reproduction Research Payload, Natalie Brattain, Chloe Nissen, Kylie Nager, Peter Ulrich, Enoch Tonkine

Discovery Day - Daytona Beach

The Tardigrade Bio-ExplorAtion Reproduction Research Payload (tBEARR) is an external International Space Station (ISS) standardized laboratory payload module mission under development by the Embry-Riddle Orbital Research Association (ERORA), an undergraduate research organization at Embry-Riddle Aeronautical University (ERAU) in Daytona Beach, Florida. As a club-driven mission, tBEARR provides undergraduate students with hands-on experience across all phases of space research, including payload design, biological experimentation, systems integration, and mission operations. The mission is supported by a biology research team focused on stress-response biology, experimental design, and biological validation throughout ground testing, high-altitude balloon flights, and orbital operations.   The primary objective of tBEARR …

Navigating Enhanced Exploration Assistance (Nexa), Azhari Abbas, Caleb Fakunle, Ryan Powell, Donovan Livingston

Discovery Day - Daytona Beach

NEXA is an artificial intelligence software platform developed to enhance residential security and property monitoring through seamless integration with autonomous drone systems. This research application of advanced AI in surveillance aims to create a standalone solution capable of real-time threat detection and intelligent alert management. By processing visual and sensory data, NEXA facilitates autonomous drone operation with minimal human intervention. Secure communication channels ensure that instant alerts are delivered to property owners and, potentially, law enforcement, improving response times in security incidents, search-and-rescue operations, and perimeter surveillance. Additionally, NEXA is capable of interfacing with commercially available drone platforms and presents …

Effects Of Human-Animal Interaction On Positive Youth Development: A Replication Study, Allison Pachunka, Jay Jeffries, Lisa Karr, Lena Luck, Bryan A. Reiling, Douglas H. Schultz, Jeffrey R. Stevens

People and Animals: The International Journal of Research and Practice

Interacting with animals can improve health and well-being across the lifespan. Some programs such as 4-H and FFA center around youth interacting with animals, potentially enhancing youth development. Mueller (2014) investigated whether these interactions and attitudes about animals influenced measures of positive youth development. The aim of our studies was to replicate Mueller’s methods and extend her work by evaluating whether membership in animal-focused youth programs moderate associations between interactions, attitudes, and positive youth development. We did not find strong relationships among human–animal inter-action and positive youth development, which failed to replicate Mueller’s findings. However, we did find relationships between …

Generative Alteration Of Linear Media Streams Via Multimodal Context Analysis, Harsh Rajotiya, Akash Verma

Defensive Publications Series

Linear media consumption can be a passive experience, and some interactive media formats may be limited by pre-scripted decision trees. This disclosure describes systems and methods for the generative alteration of media streams. A system can analyze a playing media program's visual, auditory, and metadata streams to build a temporal, multimodal understanding of the narrative context. When a user provides an open-ended query, such as a what-if scenario, the system can use this ingested context to interpret the request and a generative rendering engine may synthesize a new, stylistically coherent audio-visual segment reflecting the proposed alteration. This approach can allow …

Caldwell Highway Fire Shield (Chfs-1), Michael Victor Caldwell Mr.

Defensive Publications Series

The CHFS-1 (Caldwell Highway Fire Shield) is a retrofitted, remote-operated fire suppression unit designed to patrol highway shoulders during wildfires. It replaces human crews walking with hoses, utilizing a surplus military truck chassis, a slip-in water skid, remote-controlled monitors, and thermal/radar sensor fusion to operate safely in zero-visibility smoke.

Critical Advantage: High Wind Operational Capability Unlike aerial assets (helicopters and drones) which are grounded when sustained winds exceed 35–40 mph or when gusts create turbulence, the CHFS-1 remains fully operational in 60+ mph winds. Its 10,000+ lb anchored mass provides stability where aircraft cannot fly, and its low-altitude nozzle placement …

Physiologically Derived, Per-Control Input Debouncing For Tremor-Affected Touch And Key Input, Gerard Ziemski

Defensive Publications Series

This disclosure describes an accessibility technique, making no health claim: filtering the unintended repeated activations caused by hand tremor from discrete user input, deriving the rejection window from the physiology of the tremor rather than choosing it by feel or exposing it as a user setting.

A tremor at frequency f spaces its repeats approximately 1/f apart. The method sets the debounce window to one full tremor period, W = 1/f, and makes explicit the rule that follows: a window W rejects every repeat sooner than W, and so suppresses every tremor faster than 1/W. The uncovered edge is therefore …

Transfemoral Approach To Patent Ductus Arteriosus Occlusion Using Acdo In A Dog With Complex Surgical History, Nawat Sannamwong, Hataichon Owatdhumma, Kornrawee Tharavanij, Thitinan Tangarsasilp, Nardtiwa Chaivoravitsakul, Kongthit Horoongruang, Patmanachatr Bunnag, Nakkawee Saengklub, Krishaporn Kradangnga, Sirilak Disatian Surachetpong, Anusak Kijtawornrat

The Thai Journal of Veterinary Medicine

A five-year-old spayed female Welsh Corgi weighing 12.4 kg presented with exercise intolerance and was diagnosed with a patent ductus arteriosus (PDA). Due to signs of left-sided volume overload, the dog was initially managed with oral pimobendan and was subsequently referred to the Small Animal Teaching Hospital at Chulalongkorn University for further evaluation and intervention. Upon presentation, the patient was bright, alert, and responsive, with a body condition score of 6 out of 9 and normal muscle condition. The mucous membranes were pink and moist, with a capillary refill time of 1 to 2 seconds. A continuous heart murmur was …

Evaluating The Potential Of Cajanus Cajan (L.) Millsp. Root To Improve Atopic Dermatitis With Different Anti-Inflammatory Models And Active Compounds, Shu-Er Yang, Xiang-Ming Cai, Yu-Wen Chu, Jen-Chieh Tsai, Mey-Fann Lee, Tuzz-Ying Song

Journal of Food and Drug Analysis

Atopic dermatitis (AD) is a chronic inflammatory disease characterized by recurrent bacterial infections that cause pruritus, erythema, xerosis and thickening. Cajanus cajan root extract prepared with 95% ethanol (EECR95) has been shown to possess antioxidant, anti-inflammatory, and antibacterial properties in previous studies. This study aimed to evaluate EECR95’s ability to improve AD by inhibiting methicillin-resistant Staphylococcus aureus (MRSA) growth and reducing inflammation. This study found EECR95 effectively inhibits MRSA growth (IC₅₀ = 103.74 μg/mL) and reduces pro-inflammatory cytokine production in an MRSA-keratinocyte-macrophage model. LC/MS/MS analysis revealed the presence of active compounds- flavonoids, isoflavones, and flavonoid glycosides, highlighting EECR95's potential …

The Defining Role Of Ago4 And Its Catalytic Activity During De Novo Rna-Directed Dna Methylation, Tianyi Li

Arts & Sciences Graduate Student Theses and Dissertations

Plant transposable elements and transgenes are continuously targeted for transcriptional repression via the pathway of RNA-directed DNA methylation (RdDM). Although perpetual RdDM of the endogenous genomic loci has been well studied in the field, much less is known about the de novo RdDM pathway, the pioneering round of DNA methylation responsible for triggering and initiating silencing of new transgenes. Despite being two distinct pathways, both perpetual and de novo mechanisms of RdDM require the production of small interfering RNAs (siRNAs) and the key proteins of the ARGONAUTE4 (AGO4) clade. However, the order and likely mechanism of recruitment of AGO4 to …

Interplay Between Patterning And Morphogenesis During Zebrafish Embryonic Development, Chia-Teng Chang

Arts & Sciences Graduate Student Theses and Dissertations

Patterning and morphogenesis occur concurrently during embryonic development. In many contexts, both processes are regulated by morphogen signaling: morphogens specify spatially organized cell identities while also influencing the cell behaviors that shape tissues. This creates a reciprocal problem. Morphogen signaling can affect how cells move, while cell movement can change how cells experience and interpret morphogen signals. This dissertation investigates this reciprocal problem during zebrafish gastrulation and neurulation. First, it examines how the ventral-to-dorsal bone morphogenetic protein (BMP) activity gradient regulates germ-layer morphogenesis during gastrulation. BMP signaling is known to pattern dorsal–ventral cell fate and regulate mesodermal convergence and extension …

Th17 Effector Cytokines Induce Shared And Distinct Microglial And Endothelial Cell Responses In A Mouse Model For Post-Streptococcal Encephalitis, Charlotte Wayne, Uğur Akcan, Travis Faust, Violeta Durán-Laforet, Danny Jamoul, Luca Bremner, Nicole Ampatey, Büşra Akcan, Sarah Ho, Bogoljub Ciric, Shannon Delaney, Wendy Vargas, Susan Swedo, Vilas Menon, Dorothy Schafer, Tyler Cutforth, Dritan Agalliu

Department of Neurology Faculty Papers

Group A Streptococcus (GAS) infections cause neuropsychiatric complications in children, but the mechanisms linking peripheral infection to brain dysfunction remain unclear. Using mouse genetics, single-cell RNA sequencing, and spatial transcriptomics, we show that GAS infections induce inflammatory transcriptional programs in microglia and brain endothelial cells (BECs), accompanied by loss of blood-brain barrier (BBB) gene expression in female mice. Spatial transcriptomic analyses reveal that GAS-responsive microglia localize near infiltrating CD4+ T cells. Several microglial chemokines induced in mice are elevated in sera from affected patients. Deletion of GM-CSF in CD4⁺ T cells partially reduces microglial chemokine gene expression, without restoring BBB …

Transient Activation Of Potent Progenitor Cells Is Required For Spinal Cord Regeneration, Chase Alexander Weinholtz

Arts & Sciences Graduate Student Theses and Dissertations

Mammalian spinal cord injury is an intractable biomedical problem driven by interlocking maladaptive cellular responses that prioritize acute stabilization over long-term recovery. However, this deficient regenerative capacity is not an inherent limitation. The zebrafish, for example, capably regenerates and regains motor function with 2 months of a full transection injury. This ability is thought to rely on the transient expansion of stem cell-like progenitors marked by sox2 expression. Yet our understanding of the identities and contributions of this crucial population remains limited. Here, we determine the molecular identities and cellular contributions of sox2+ progenitors during innate spinal cord repair in …

After A Fire: Considerations Of Personal Safety When Visiting Fire-Damaged Property, Andrew J. Whelton, Todd Thalhamer, Eric Bollens

Resilience to Emergencies and Disasters

No abstract provided.

Threads Of The Frightening: The Uncanny, Alienation, And Horror In Otsuichi's Fiction, Kathryn Lawhon Stephens

Arts & Sciences Graduate Student Theses and Dissertations

The “J-horror boom” of the 1990s and early 2000s saw the international success of films like Nakata Hideo’s Ring (1998), bringing considerable and laudable attention to Japanese horror in the realm of film and media studies. Yet even Ring’s Sadako, one of the most popular contemporary figures in Japanese horror, first appeared as a literary character years before her debut on screen. The average layperson’s unfamiliarity of such a famous horror icon’s literary origins illuminates the comparative lack of literature-centric scholarship on major writers and figures of Japanese horror that this dissertation seeks to rectify.

First interrogating the fluidity …