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Phylogenomics And Biogeography Of Zinniinae (Asteraceae: Heliantheae) Using Plastome And Nuclear Datasets, Samuel Victor Skibicki

Graduate Theses, Dissertations, and Problem Reports (ETD)

Zinniinae is a subtribe of plants in the daisy family (Asteraceae) and the sunflower tribe (Heliantheae). Traditionally, seven genera were included in the subtribe: Echinacea, Heliopsis, Philactis, Sanvitalia, Tehuana, Trichocoryne, and Zinnia. The subtribe is poorly understood from a phylogenetic and taxonomic standpoint, and I undertook a phylogenetic investigation of Zinniinae, using both the plastid genome (plastomes) and the nuclear genome, to learn more about the evolutionary history of this clade. Plastomes were assembled to build a phylogenetic tree, targeted sequence capture was used to compile the nuclear datasets, and a chronogram was created to estimate date ranges for …

Comparison Of Compositional Characteristics Of Protein Extracted From Spent Hemp Seed Cakes By One-Step Defatting With Organic Solvents Followed By Isoelectric Solubilization Precipitation Using Strong And Weak Acids, Miah Nicole Gathman

Graduate Theses, Dissertations, and Problem Reports (ETD)

Hemp seed cakes (HSC) are the byproduct of pressing hemp seeds for oil and are a significant agricultural waste product, with hundreds of tons produced annually. These nutrient-rich cakes have potential for sustainable applications in animal feed and food products. However, they could offer even greater value to the food industry through further extraction of the lipids and separation of the proteins they contain. Protein is a key nutritional component and companies are seeking cost-effective, time-efficient processes to concentrate protein from underutilized resources like HSC. Hexane (HEX) is a common solvent used in one-step defatting processes but may cause issue …

Evaluating The Adaptation Of Taro (Colocasia Esculenta) To West Virginia Climatic Conditions, Kayode Joseph Ajayi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Climate change impacts agriculture and food security across the globe, therefore higher temperatures could increase in the length of the growing period and new crops would take advantages of. Research was conducted in Morgantown, WV in 2022 and 2023 to understand the growth pattern of Taro in West Virginia, and to analyzing the chemical composition of the Taro plant. The experiment was a completely randomized design in direct planting-low tunnel technology (2 replications, and 10- plants/plot), and two fertilization treatments (fertilized and non-fertilized). Spacing was 1 m within and between rows. Data were subjected to ANOVA using SAS. Dependent variables …

The Characterization Of Il-27 Production And Its Impact On T Cell Antigen-Specificity And Diversity In A Neonatal Bcg Vaccination Model, Ashley M. Divens

Graduate Theses, Dissertations, and Problem Reports (ETD)

Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), and it has plagued humans for most of recorded history. Despite strong efforts to prevent and treat TB, it remains the leading cause of death due to a pathogen and is most prevalent in certain regions of Asia and Africa. Currently, the only approved vaccine to prevent TB is the live-attenuated Bacillus Calmette-Guérin (BCG) vaccine. Most countries have a universal BCG vaccination policy, but the vaccine ultimately fails to be protective. The BCG vaccine is most effective in children and protects against disseminated TB, but protection wanes 10-15 years after vaccination causing …

Biomechanics Of Teeth Alignment Using Clear Aligners With Various Attachment Shapes And Orientations, Egon Mamboleo

Graduate Theses, Dissertations, and Problem Reports (ETD)

Clear aligners have emerged as the most popular and preferred method of treatment for patients with orthodontic malocclusions. This is greatly due to the comfort and aesthetically appealing factors when compared to fixed appliances . Clear aligners are either thermoformed or 3D direct-printed plastics that apply biomechanical forces to the surface of teeth to trigger tooth movement and bone remodeling process. Common Class I malocclusions with mild or moderate crowding can be treated with clear aligners alone. However, treatment of Class II and Class III malocclusions that require extraction of permanent teeth or correction of severe rotations, and teeth extrusions …

Path Nets: Concurrence And Recurrence In The Dynamics Of Organizing, Brian T. Pentland, Waldemar Kremser, Kenneth T. Goh

Research Collection Lee Kong Chian School Of Business

This article proposes a link between temporal structuring and the dynamics of organizing that is manifest in a fabric of concurrent paths that we call a path net. Path nets are shaped by mechanisms of temporal structuring, such as entrainment, planning, agency, and chance. Path nets materialize the effects of temporal structuring “here” and “now” in the comings and goings of actors and resources, thereby setting the stage for doings and sayings of situated practice and shaping the dynamics of organizing. Path nets offer a parsimonious system of picturing the complexity of organizing that is built on a processual ontology …

Volumetric Comparison Of Overall Brain And Neuropil Size Between Social And Non-Social Spiders: Exploring The Social Brain Hypothesis, Vanessa Penna-Gonçalves, Donald James Mclean, Nikolas J. Willmott, Michael B.J. Kelly, Jay R. Black, Elizabeth C. Lowe, Marie E. Herberstein

Research outputs 2022 to 2026

The social brain hypothesis predicts that the relative size of specific brain regions is driven by the cognitive capacity required to manage complex (social) situations. Spiders are intriguing models to test this hypothesis, as sociality is rare in this usually solitary and aggressive group. Here, we used microCT to compare the central nervous system and brain volumes between social and solitary females of the species in two taxonomic groups, huntsman and crab spiders. Overall, we found no difference in relative CNS and brain volume between social and solitary species. However, social huntsman spiders Delena cancerides had larger arcuate and mushroom …

Inferred Developmental Origins Of Brain Tumors From Single-Cell Rna-Sequencing Data, Su Wang, Rachel Naomi Curry, Malcolm F Mcdonald, Hyun Yong Koh, Anders W Erickson, Claudia L Kleinman, Michael D Taylor, Ganesh Rao, Benjamin Deneen, Arif O Harmanci, Akdes Serin Harmanci

Faculty, Staff and Students Publications

Background: The reactivation of neurodevelopmental programs in cancer highlights parallel biological processes that occur in both normal development and brain tumors. Achieving a deeper understanding of how dysregulated developmental factors play a role in the progression of brain tumors is therefore crucial for identifying potential targets for therapeutic interventions. Single-cell RNA-sequencing (scRNA-Seq) provides an opportunity to understand how developmental programs are dysregulated and reinitiated in brain tumors at single-cell resolution. The aim of this study is to identify the developmental origins of brain tumors using scRNA-Seq data.

Methods: Here, we introduce COORS (Cell Of ORigin like CellS), a computational tool …

Molecular Diagnostic Patenting After Mayo V. Prometheus: An Empirical Analysis, Colleen V. Chien, Jenna Clark, Arti K. Rai

Faculty Scholarship

Since the United States Supreme Court's 2012 decision in Mayo v. Prometheus announced a new legal test for patent-eligible subject matter, policymakers, and scholars have vigorously debated the decision's impact on molecular diagnostics innovation. Molecular diagnostics serve as the cornerstone of personalized medicine and its promise of treatments with fewer side effects and better outcomes for patients. This article contributes to the presently thin evidence base on the impact of Mayo by using data on patent applications, examinations, and grants from 2010 to 2019 to comprehensively trace the effects of the test and subsequent related developments. Using descriptive data as …

The Future Of Ai Regulation In Drug Development: A Comparative Analysis, Gabriela Lenarczyk, Timo Minssen, Nicholson Price, Arti Rai

Faculty Scholarship

As artificial intelligence (AI) transforms drug development, regulatory frameworks are evolving to oversee its implementation, particularly at the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA). This paper makes three contributions to understanding emerging regulatory approaches. First, we offer a comparative analysis of how these agencies have responded to AI-driven advances, incorporating new US executive orders and the European Union (EU)’s AI Act. Second, we propose a novel analytical framework to understand regulatory divergence: the FDA’s flexible, dialog-driven model contrasts with the EMA’s structured, risk-tiered approach, reflecting broader institutional and political-economic differences. While the former encourages …

The International Risk Governance Council: Reflections On A 20-Year Experiment In Support Of Improved Risk Governance, M. Granger Morgan, Marie-Valentine Florin, Igor Linkov, Kenneth A. Oye, Arthur C. Petersen, Ortwin Renn, Jonathan B. Wiener, Lan Xue

Faculty Scholarship

The International Risk Governance Council (IRGC) was a nonprofit foundation, based first as an independent, freestanding Swiss foundation in Geneva from 2003 to 2012, and then affiliated with École Polytechnique Fédérale de Lausanne in Lausanne from 2012 to 2023. IRGC's mission was to identify and improve the governance of emerging and systemic risks that have, or could have, impacts on human and environmental health, the economy and society, and overall sustainability. In this paper, we recount IRGC's history, describe its many reports, workshops, and conference activities (including tables referencing the many published products), and provide six brief case histories of …

Theories Of Child Development & Theories Of Religious And Spiritual Development (Rsd) In Children, Marjorie Lindner Gunnoe

University Faculty Publications and Creative Works

This essay introduces readers to the foundational theories of child development and the ways in which these theories have been applied or extended to children’s religious and spiritual development (RSD). By “foundational theories,” I mean the theories introduced in the opening chapters of developmental textbooks. This essay is not a theological critique of psychological theories (for this, see Gunnoe, 2022), nor a “state of the field” review of RSD (for this, see Boyatzis, 2023). Rather, it is a primer on the broad theoretical approaches that scaffold contemporary research on RSD.

Notice Pleading’S Quiet Return, Alexander A. Reinert

Articles

Fifteen years ago, the Supreme Court announced two significant civil procedure decisions – Bell Atlantic Corp. v. Twombly, 550 U.S. 544 (2007), and Ashcroft v. Iqbal, 556 U.S. 662 (2009). Together, Iqbal and Twombly marked a new approach to pleading in federal courts. No longer would courts apply the forgiving notice pleading standard, in force since the 1938 adoption of the Federal Rules of Civil Procedure. In its place, the Court introduced plausibility pleading, inviting district courts to apply their “judicial experience and common sense” to decide whether a claim was “plausible.” Commentators expressed alarm, predicting that the new standard …

Shifting Attention: Assessing Antennular ‘Gaze’ In The Hermit Crab Pagurus Bernhardus, Ari Drummond, John Spicer, Lucy Turner, Alexander Wilson, Mark Briffa

School of Biological and Marine Sciences

Attention (focused information gathering) is crucial for many cognitive processes. Traditionally dichotomised as reflexive or voluntary, behavioural research often relies on vision for assessments of attention. However, invertebrate information acquisition often utilises chemosensation or mechanosensation, potentially limiting the efficacy of a vision-based approach. We examined attention in Pagurus bernhardus hermit crabs, using antennules (the crustacean first antennae) as indicators of attentional shifts. Considering a change in flicking direction as analogous to a shift in gaze, we examined if hermit crabs show evidence of reflexive or voluntary attention. We exposed crabs to a chemosensory stimulus while manipulating factors influencing vulnerability (i.e., …

From Attention To Action: Advancing Inclusivity In The Landscape Of Anatomy Education, Siobhan M. Moyes, Lily Evans, Katie Snow, Aiden Jayanth

Peninsula Medical School

Conversations about inclusivity in anatomy education are at a critical juncture. While the need for a more equitable discipline is widely recognised, significant challenges remain. As this project aimed to reimagine what a truly inclusive learning experience could like and how it might be best achieved, an inclusive approach to research methodology was essential to ensure robust and representative results. Due to the paucity in anatomical literature on this topic, the authors applied concepts from sociological research methodology and innovative methods of demographic data collection to their own discipline.

The study utilised questionnaires and focus groups to collect diverse data …

Practical Application Of Artificial Intelligence For Ecological Image Analysis: Trialling Different Levels Of Taxonomic Classification To Promote Convolutional Neural Network Performance, Amelia E.H. Bridges, Eleanor Cross, Kyran P. Graves, Nils Piechaud, Antony Raymont, Kerry L. Howell

School of Biological and Marine Sciences

The integration of artificial intelligence (AI), particularly convolutional neural networks (CNNs), into ecological research presents new opportunities for the automated analysis of image-based data. This study explores the practical application of CNNs for ecological image analysis by trialling annotation to different levels of taxonomic classification to determine their impact on model performance. We systematically compare various annotation strategies, evaluating their effects on the accuracy of CNNs in ecological contexts; as well as considering the feasibility of manually annotating training data to different levels. We demonstrate that variation in annotations groupings (animal, phylum or morphology) has little impact on model performance, …

Bibliography Of Scholarship From 2025, University Of San Diego

Annual Bibliography of USD Scholarship

No abstract provided.

Restoration Of River Connectivity Enables Long-Distance Spawning Migrations In A Potamodromous Fish, Dagmara Błońska, Ali Serhan Tarkan, Demetra Andreou, Jonathan D. Bolland, Peter Davies, Jamie R. Dodd, Phillipa Gillingham, Catherine Gutmann Roberts, Fatima Amat-Trigo, Sadi Aksu, Andrew Hindes, O. Jonas Palder, Mark Yeldham, J. Robert Britton

School of Biological and Marine Sciences

Rivers across the world are increasingly fragmented due to anthropogenic barriers, with the restoration of connectivity often using fish passes. Fish passes are, however, usually designed for anadromous species, despite ecologically important non-anadromous species being present in the communities impacted by fragmentation. To assess the outcomes for non-anadromous fishes of the installation of multiple fish passes and weir modifications, the movements of the potamodromous European barbel Barbus barbus were evaluated in the lower River Severn basin, western Britain, which was fragmented by six weirs (two on a tributary, four on the Severn mainstem). Movements of individual fish were measured using …

Is Sparse Local Ecological Knowledge Accurate Enough For Policy? A Seagrass Mapping Case Study From Five Greek Islands In The Eastern Aegean Sea, Konstantis Alexopoulos, Tim J. Grandjean, Anastasia Miliou, Theodoros Tsimpidis, Abigail Mcquatters-Gollop

School of Biological and Marine Sciences

The low cost, high applicability and community-based nature of Local Ecological Knowledge (LEK) data for mapping marine benthic habitats has become increasingly popular in recent years. Nonetheless, due to persisting technocratic distrust of LEK often stemming from the unquantifiable nature of bias, the embedding of empirical data at policy levels often lags. Currently, protocols rely on high participation from stakeholders, however, such quotas are often unfeasible, with common limiting factors being the low numbers of knowledgeable individuals in remote parts of the world, and the lack of community trust in the conservation mechanism. In this study, we test whether data …

A Unified, Data-Informed Model For Shoreline Evolution Due To Longshore And Cross-Shore Processes, Mark Davidson, Emily Hunt, Nieves Valiente

School of Biological and Marine Sciences

Due partially to a changing global climate, there is an increasing need to develop a modelling approach capable of providing warnings of coastal evolution, including erosion at storm, interannual and decadal timescales and in complex coastal settings. This research presents a reduced complexity model with a common approach to predicting shoreline change due to cross-shore and longshore processes. The model architecture is designed to be flexible and data-informed, incorporating an Extended Kalman (eKF) for the assimilation of field measurements of shoreline change. Depending on the values of the optimised model free parameters resulting from the eKF assimilation, the longshore and …

Surf Stewardship And Coastal Change: A Combined Report For The North Devon Unesco Biosphere Reserve And The North Devon World Surfing Reserve, Kizzy Beaumont

School of Biological and Marine Sciences

Executive summaryNorth Devon’s coastline sits within a layered governance setting, including statutory marine plans, inshore fisheries management, coastal and shoreline planning, protected areas, and seasonal bathing water monitoring, led by national regulators and local authorities. Within this wider context, this study focuses on how two non-statutory designations, the North Devon UNESCO Biosphere Reserve and the North Devon World Surfing Reserve (WSR), canwork together. The work forms part of a PhD on Transformative Ocean Governance and was motivated by the North Devon WSR’s designation and the opportunity to understand how the two designations might complement each other in practice. We convened …

Globalism, Localism And Blue Food Systems – How Can Cross-Scale Tensions Be Reduced? A Production Perspective From Uk Seafood Stakeholders, Alex J. Caveen, Bryce D. Stewart, Cameron Moffat, Daniel Skerritt, Estelle Jones, Huw Thomas, Lara Funk, Magnus Johnson, Mike Cohen, Michael Roach, Neil A. Auchterlonie, Samuel Peacock, Sarah Hussey, Tim Gray, Tom Pickerell, Umi Muawanah, Vasiliki Kioupi, Yvonne Sadovy De Mitcheson, Neil M. Burns, Charlotte R. Hopkins

School of Biological and Marine Sciences

‘Blue foods’ are derived from aquatic species that are caught or cultivated and are amongst the most globally traded commodities. Growing emphasis is being placed on blue foods in future transitions to sustainable food systems. However, recent international events such as the Covid-19 pandemic, UK-EU ‘Brexit’, and Russia-Ukraine war have caused renewed interest in ideological debates between globalism and localism and associated cross-scale tensions. Here, we aim to provide further insight into cross-scale tensions in blue food systems through a literature review and UK-based seafood stakeholder workshop. From our literature review, the evidence for cross-scale tensions was linked to the …

Climate Adaptation For A Natural Atoll Island In The Maldives - Predicting The Long-Term Morphological Response Of Coral Islands To Sea Level Rise And The Effect Of Hazard Mitigation Strategies, F. E. Roelvink, G. Masselink, C. Stokes, R. T. Mccall

School of Biological and Marine Sciences

Coral atoll islands, common in (sub)tropical oceans, consist of low-lying accumulations of carbonate sediment produced by fringing coral reef systems and are of great socio-economic and ecological importance. Previous studies have predicted that many atoll islands will become uninhabitable before the end of this century due to sea level rise exacerbating wave-driven flooding. However, the assumption that such islands are morphologically static has been challenged by observations and modeling that show the potential for overwashing and sediment deposition to maintain island freeboard. Reliable long-term predictions of island change and future flood risk, essential for adaptation planning, are, however, lacking. Here, …

Measuring Juvenile Habitat Quality For Fishes And Invertebrates, Benjamin J. Ciotti, Elliot J. Brown, Francesco Colloca, David B. Eggleston, A. Challen Hyman, Olivier Le Pape, Romuald N. Lipcius, Margot A. M. Maathuis, Suzanne S. H. Poiesz, Kenneth A. Rose, Rochelle D. Seitz, Daniele Ventura, Karen E. Van De Wolfshaar

School of Biological and Marine Sciences

Identifying the role of marine and estuarine habitats in supporting fish and invertebrate populations during vulnerable juvenile life stages is essential to achieve effective conservation and fisheries management. There remains general agreement that: (i) the quality of juvenile habitat is best measured as the contribution of juveniles to adult populations (here “juvenile–adult contribution”) and (ii) this contribution may be measured directly or inferred from habitat-specific abundance, growth and survival. Obtaining effective estimates of juvenile habitat quality using these four metrics, however, is challenging. Through a systematic review of approaches to measure juvenile habitat quality, we critically evaluate current abilities to …

Characterisation Of Tyre Wear Particle Transport From Road Runoff To Sea In Coastal Environments, Florence N.F. Parker-Jurd, Geoffrey D. Abbott, Daniel C. Conley, Cijo M. Xavier, Florian Pohl, Richard C. Thompson

School of Biological and Marine Sciences

Data on the fate of tyre wear particles (TWPs) within aquatic environments is limited. This study quantified TWPs entering estuaries in stormwater drainage and atmospheric fallout, and once they have reached the marine environment, within surface waters and sediments. TWPs were found at concentrations of 0.4 mg/L, 2.55 mg/m2/d, 0.00063 mg/L, and 0.96 g/kg respectively. Samples were partitioned by size to examine the distribution of TWP mass. 80-90% of TWP mass entering marine systems (stormwater and atmospheric fallout) lay between 31-125 µm. Larger particles preferentially accumulated in sediments where ∼50 % of TWP mass was >250 μm, compared to surface …

Advancing Point-Of-Care Testing With Nanomaterials-Based Screen-Printing Electrodes, S. Nazir

School of Engineering, Computing and Mathematics

Although numerous studies have been conducted on multiple screen-printing electrodes (SPEs), little emphasis has been placed on systematically assessing scholarly work on nanomaterial-equipped SPEs in bioanalytical research. The fabrication of state-of-the-art portable screen-printing measuring devices represents significant disease monitoring and diagnosis advancements. This review classifies screen-printing electrodes based on the nanomaterials used. It discusses cost, regulatory approvals for portable screen-printing electrodes in point-of-care diagnostics, sensitivity, specificity, size reductions, and proposed solutions. It looks into the significance of new nanomaterials and substrates in fabricating point-of-care diagnostic devices and miniaturisation techniques. The review primarily focuses on the recent downsizing advances that have …

‘At Least I Wasn't In An Inner-City Flat With A Partner I Hated’: An Auto/Biographical Study Of Reflections On Well-Being By 35-65 Year Olds In Cornwall Following The Covid-19 Pandemic, Cheralyn May

School of Law, Humanities and Social Sciences Theses

The effects of the Covid-19 pandemic on mental health have been considerably researched since its start in 2019, by researchers from a range of disciplines around the world. This sociological study (using insights from social and positive psychology) contributes to our knowledge of the pandemic by using qualitative methods – fourteen semi-structured interviews and researcher auto/biography to investigate the mental health experiences of middle-aged, single adults living in Cornwall in the UK during the pandemic. In the pandemic literature, this is an under-researched, and therefore potentially less understood, group and location. The data was analysed using a combination of the …

Reassembling Anti-Oppressive Teaching Practices In Professionally Qualifying Youth And Community Work Education, Christine Smith

School of Law, Humanities and Social Sciences Theses

New and continuing formations of oppression remains a contemporary 21st Century challenge compounded by a fracturing of democratic structures that give rise to intolerance of difference and threaten social bonds. The big questions about the type of society we want to live in, what it means to be human, and the role of education are questions that are increasingly alienated from everyday lived experiences and a collective commitment to shape a fairer and more socially just world. Thus, the scale of challenges underscores a need to think differently about how Anti-Oppressive Practice (AOP) in professionally qualifying youth and community education …

Palynology, Landscape And Land Use: Retrospect, Prospect And Research Agendas, Ralph Fyfe, Kevin Edwards, Laura Scoble

More Faculty of Science and Engineering Research

This paper provides a context for the use of anthropogenic palynology in the study of landscape and land use. Retrospective considerations indicate a history to current trends and inform future developments. Recent and prospective studies secure palynology as an essential element in archaeological and related environmental research. It is stressed that palynology is an inherently spatio-temporal discipline that can use concepts such as landscape or habitat heterogeneity as a future framework. This may be possible if recent advances in quantification of local vegetation cover, for example the use of model-based correction approaches within the Landscape Reconstruction Algorithm, are more widely …

Micro(Nano)Plastics In The Fish Gastrointestinal Tract: A Mini Review And Relevance To One Health Perspective, Farhan R. Khan, Nathaniel Clark, Elvis Genbo Xu

School of Biomedical Sciences

Micro(nano)plastics (MNPs) research in the piscine gastrointestinal tract has been a significant area of study. Understanding the environmental presence of microplastics, their potential for both localised and systemic effects, and their role as a gateway for MNPs and associated chemicals to enter the tissues and the food web, including the human food chain, is crucial. The fish gut, as a critical intersection between environmental, biotic, and human health, aligns with the One Health concept. We review the likely uptake mechanisms and toxicological damage caused by ingesting MNPs and their associated chemicals in fish, contextualised within the realms of digestive physiology …