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Terrestrial Life in the Paleozoic: An Integrated Analysis of Body Fossils, Trace Fossils, and Biomarkers
No full textPaleontology is a largely umbrella term for the study of ancient life. In practice, paleontologists specialize into various subdisciplines: i.e. vertebrate or invertebrate, paleobotany, micropaleontology, ichnology, etc. This dissertation blurs these distinctions and examines the evolution and ecology of terrestrial organisms of the Carboniferous through multiple lines of evidence and across subdisciplines. By integrating the study of trace fossils, body fossils, and molecular signatures, a more holistic view of behavior, community structure, and organismal interactions in early terrestrial ecosystems is achieved.
In Chapter 1, a new fossil Lagerstätte, or site of exceptional preservation, is described from the Early Pennsylvanian of Massachusetts. This site illuminates the complexity of late Paleozoic terrestrial ecosystems within the context of a rarely preserved proximal clastic environment. Exceptionally well-preserved trace fossils of vertebrates (synapsids, diadectomorphs, amniotes, temnospondyl amphibians, fish) as well as trace and body fossils of invertebrates (adult and nymphal pterygote and apterygote insects, myriapods, xiphosurans, thelyphonids, ricinuleids), along with 131 plant fossil-taxa, that includes 83 distinct foliage morphotypes, support this conclusion. Plant-insect interactions (3 functional feeding groups) preserved in the Wamsutta include the earliest currently known evidence of insect oviposition and some of the oldest documented occurrences of gall damage in the fossil record.
In Chapter 2, a new species of fossil whip scorpion, (Arachnida: Uropygi: Thelyphonida) as well as the first ichnospecies (full-body impression) assignable to this group, is described from the Carboniferous Narragansett Basin of Massachusetts, USA. The body fossil from the Rhode Island Formation (Moscovian) is referred to as Parilisthelyphonus bryantae gen. nov., sp. nov.. At more than 34 mm long it represents both the largest known Paleozoic whip scorpion and the first fossil arachnid found in the Rhode Island Formation in nearly 130 years of scrutiny. The whip scorpion trace fossil, comprising a full-body impression and associated tracks, is described from the subjacent Wamsutta Formation (Late Bashkirian) of Massachusetts, USA as Inmontibusichnus charleshenryturneri igen. nov., isp. nov. With an estimated body length of less than 10 mm, the producer would be the smallest known Paleozoic thelyphonid. These discoveries within the Narragansett Basin represent only the second site in the western hemisphere, in what was western Laurasia, to yield Paleozoic whip scorpions.
In Chapter 3, a trace fossil on seed-fern foliage is described from the Middle Pennsylvanian (c. 312 Ma) of the Rhode Island Formation of Massachusetts, USA, representing the earliest indication of endophytic feeding. Although lacking the full features of extant leaf mines, this specimen provides evidence of how endophytic mining behavior may have originated. Likely made by a holometabolous insect larva, this fossil is coeval to the earliest evidence of metamorphism in the fossil record.
Chapter 4 redescribes Palaeocampa anthrax from the Carboniferous Mazon Creek (USA) and Montceau-les-Mines (France) Lagerstätten as a lobopodian. First published in 1865, nearly fifty years before the discovery of the Burgess Shale, Palaeocampa is historically the first discovered lobopod and its presence at the slightly younger Montceau-les-Mines (Gzhelian), makes this the youngest known fossil ‘xenusiid’ lobopodian species. The case is presented that Palaeocampa most likely inhabited a freshwater environment, contesting the view that Paleozoic lobopodians were exclusively marine. Palaeocampa bears biomineralized dorso-lateral and lateral sclerite sets (n= ~ 1,000) with a unique architecture unseen in other lobopodian sclerites. Fourier transform infrared spectroscopy (FTIR) analysis suggests Palaeocampa’s sclerites may have been capable of secreting defensive chemicals at their tips. Palaeocampa anthrax represents a major evolutionary step in lobopodians, both in environmental adaptations and in defensive abilities.Biology, Organismic and Evolutionar
Bridging Data Gaps and International Governance Challenges for Sharks and Rays in the Pacific Ocean
Full text linkImpacts from industrialized fisheries in areas beyond national jurisdiction have led to population declines among several shark and ray species. Sustainable fisheries management and the reduction of significant adverse impacts from those fisheries are principles firmly anchored in the United Nations Fish Stocks Agreement and the United Nations Convention on the Law of the Sea, leading to the creation of several regional fisheries management organizations (RFMOs) and other ocean governance instruments. Several species of sharks and rays traverse the Pacific Ocean, crossing several RFMOs in these shared waters. While many governance instruments exist to reduce impacts from high seas fisheries and regulate the trade of elasmobranchs, these efforts are often not coordinated and leave a patchwork of varying policies that hinder effective conservation and management.
To better understand management loopholes, I examined elasmobranch regulations, monitoring programs, and cooperative efforts across the six RFMOs in the Pacific Ocean. This was done by comparatively analyzing RFMOs through their Conventional mandates, conservation and management measures (CMMs), observer program requirements, performance reviews, and cooperative agreements with other intergovernmental bodies.
In this thesis, I argue that localized elasmobranch conservation efforts would greatly benefit from improved coordination and alignment of regulations between these RFMOs. Protecting and managing elasmobranchs is a large and complex problem.
However, RFMOs must scale their current conservation efforts and bolster their cooperation with other regulatory bodies to prevent overfishing and rebuild much needed elasmobranch populations.Extension Studie
Correlated interlayer excitons in van der Waals semiconductor heterostructures
Full text linkInterlayer excitons (IXs) are bound pairs of spatially-separated electrons and holes that occur in in type-II van der Waals heterostructures. They exhibit long lifetimes and mutual dipolar repulsion, in addition to strong interactions with unpaired electrons and holes that lead to the formation of charged IXs. To study the effect of correlations and manipulate the IXs, we design highly tunable nanodevices based on atomically thin semiconductors. Our efforts enable the study of a wealth of correlated excitonic states. In two-dimensional light-emitting diodes, we reveal the effects of defect-mediated electron localization on IXs and diode operation. We unveil the novel phenomenon of steady state cooperative electroluminescence from incoherently injected, electrically generated IXs. Lastly, we employ gate-mediated electrostatic confinement to controllably trap IXs and study their behavior at high densities, discovering novel features about the IX ionization phase diagram. These results expand our understanding of non-equilibrium phases of matter, and hold promise for creating optoelectronic devices for both future classical and quantum technologies.Engineering and Applied Sciences - Applied Physic
The Endurance of Fiqh in an Age of Sharīʿa: Islamic Law in Late Colonial Sudan
No full textThis dissertation explores Islamic law and reform in colonial Sudan. It relocates study of the period from state judiciaries and reformist polemics, both well attested to in the literature, to the learning circles of Sudan’s Mālikī school of law (madhhab). It focuses on three scholars active in that country’s mid-twentieth century: ʿUthmān b. Ḥasanayn Barrī al-Jaʿalī (d. 1960), Muḥammad al-Amīn al-Shinqīṭī (d. 1974), and Abū Ṭāhir Ḥasan Fāy al-Bijāwī (d. 1984). Through a close reading of their work, oral accounts of their lives, and unstudied biographical notes, this dissertation examines the ways that each attempted to resuscitate a Mālikī tradition beset by colonial reforms from above and revisionist critiques from below. The following chapters contend that their doing so problematizes a number of assumptions common to the study of Islamic law and Africa. Rather than a Sudan indifferent to the legal debates more often associated with Islamic scholarship elsewhere, al-Jaʿalī, al-Shinqīṭī, and al-Bijāwī were deeply invested in contests over law and authority circulating throughout the Islamic World. Their preoccupation with law and particularly legal methodology was not unique. It built on a tradition of Mālikī teaching, scholarship, and jurisprudence (fiqh) in Sudan that stretched back some four centuries. Their scholarship also calls for revisiting Islamic law today. Al-Jaʿalī’s revision of imitation (taqlīd) and al-Shinqīṭī and al-Bijāwī’s use of proof texts (dalīl) present a vision of traditionalism and reform in which neither was exclusive of the other. Their efforts to transform Islamic law from within the madhhab rather than from outside it suggest that the postformative legal tradition was perhaps more resilient – and elastic – than is often supposed. Together they present the case of a madhhab in modernity deeply involved in its own tradition of reform.Near Eastern Languages and Civilization
China’s Command Revolution: Reforms, Adaptation, and Emerging Innovations in Chinese Military Command Capabilities
No full textHow and why has the Chinese People’s Liberation Army’s (PLA) approach to military command evolved across its modern history against the backdrop of technological advancements? The PLA’s continued development of command capabilities, consisting of functional components of theories, structures, and systems that enable command, along with political work and human factors, will be consequential in shaping its future battlefield decision-making and performance. The prevalent perspectives articulated within salient academic literatures and among U.S. military observers have anticipated that the PLA, as a force subject to political control of the Chinese Communist Party (CCP), could struggle to innovate and would likely maintain a highly centralized, relatively inflexible approach to command, which could be disadvantageous in conflict. However, this dissertation contends such expectations about China’s command capabilities and its limited potential to achieve innovative developments should be reevaluated, in historical perspective and considering significant transformations ongoing in the PLA today. The reality is far more nuanced and reflects a system that, within certain limits, can be centrally controlled but also capable of facilitating greater initiative and decentralized warfighting. Indeed, the PLA’s approach to command has evolved dynamically in reaction to technological transformations that are expected to reshape future warfare. For the full extent of changes observed to occur without learning from and imminent pressures of conflict and despite expected bureaucratic impediments, is puzzling relative to prevailing expectations. The adaptations and innovations that have emerged across multiple aspects of Chinese military command are tantamount to a revolution in command with significant implications for Chinese military power. The existing literature provides several alternative explanations, to include the influence of strategic culture, dynamics of civil-military relations, organizational explanations, and military learning through emulation. However, I contend the impacts of ideation about technology in future warfare, as constructed through expert networks reacting to leadership guidance, can provide a more compelling explanation for the full extent of changes in Chinese military command and constitutes a dynamic that can be generalizable to other major domains of Chinese innovation. In the process, Chinese leaders have tended to adjust styles of command across domains and levels of warfare in a manner that balances between political control and autonomy based on a calculus of risks and benefits.
This dissertation introduces a theory of command innovation based on ideation that accounts for major changes in China’s approach to military command. Chapter 1 and 2 introduce that theory and its primary mechanism, examining the process through which ideation about technology in future warfare takes shape through a dynamic involving not only high-level direction on priorities from senior leadership but also construction and socialization of new concepts among key strategic, military, and scientific experts. In the process, I argue the PLA tends to be informed by not only its study of global trends in technology and assessments of foreign military approaches but also its uniquely scientific outlook on warfare, as reflected in its evolving approach within the discipline of military command science. Chapters 3-7 center on a series of case studies examining each major functional component of Chinese command capabilities, based on an approach of process tracing that considers changes in Chinese command concepts, structures, political work, systems, and approach to human factors (i.e., training and education of commanders) respectively. To that end, I leverage a range of primary source materials, including close reading of Chinese military textbooks, journals, and media products, as well as vignettes from Chinese military history and contemporary operations. Chapter 8 continues by examining current debates and the ideation process ongoing today within the Chinese military and scientific spheres focused on implications of artificial intelligence (AI) for future warfare. The final chapter concludes by considering how this theory of command innovation contributes to literatures on military and defense innovation, while evaluating theoretical generalizability and implications.
This dissertation also seeks to contribute to understanding the implications of these trends for the future of command and evolving military balance. Across recent decades, the PLA has pursued informatization (信息化), an agenda centered on leveraging information technology as a core enabler of military power, which has reshaped dynamics of command. Presently, the PLA is pursuing an agenda of military intelligentization (智能化) to capitalize upon advances in artificial intelligence (AI) and related technologies. These trends have generated debates within the PLA on the complex interplay of human factors and technology, which PLA scientists and strategists believe necessitates renewed emphasis on human-machine integration, especially in command. Among impactful applications are support to military decision-making, including through automated processing and integration of intelligence information. Looking forward, Chinese leaders regard emerging capabilities as critical to contesting advantage in future conflict scenarios, yet the ultimate impacts on the military balance remain uncertain. Such uncertainty about impacts of disruptive technologies and their applications could increase the risks of misperception, especially as international competition intensifies, and could exacerbate security dilemmas. PLA efforts to operationalize new complex systems might increase frictions that could undercut intended advantages for decision-making, while potentially increasing the possibility of accidents, crisis instability, or misperceptions. In this regard, the PLA’s evolving approach to command decision-making also has significant implications for future strategic stability and deterrence.Governmen
Decision-Focused Learning for the Masses With Applications to Public Health
Full text linkIn this thesis, I aim to better understand how to best train Machine Learning models for decision-making under uncertainty. Specifically, I focus on the ``Predict-then-Optimize'' framework, in which uncertain quantities are predicted using ML models, and decisions are made by solving optimization problems parameterized by these predictions. While past Decision-Focused Learning (DFL) methods show that optimizing directly for decision quality leads to improved outcomes, existing approaches typically require extensive manual effort—such as designing differentiable surrogate optimization tasks—limiting their applicability to arbitrary problems. Moreover, evaluating the real-world impact of these models in resource-constrained settings poses additional challenges.
This thesis, therefore, addresses the central question: Can we create generalizable methods to train and evaluate decision-focused learning models on arbitrary decision-making tasks so that DFL can be more practically useful? In response, I introduce methods that distill task-specific decision-making structures into a learned, differentiable ``decision loss,'' eliminating the need for handcrafted surrogates. I first propose Locally Optimized Decision Losses (LODLs), demonstrating their improved performance across multiple domains. I then extend this approach via Efficient Global Losses (EGLs), significantly enhancing generalization, efficiency, and theoretical robustness.
Additionally, I develop rigorous statistical estimators for accurately evaluating DFL models in resource allocation scenarios. Applying these estimators to real-world randomized control trials reveals insights previously hidden by existing methods. Collectively, these contributions establish a broadly applicable, reliable framework for decision-focused learning, making DFL more practically viable across diverse decision-making contexts.Engineering and Applied Sciences - Computer Scienc
The search for a Potential Novel Receptor for Human Transferrin on APCs
Full text linkIt is canonically known that Dendritic Cells (DCs) can activate T cells through its peptide-MHC binding to the T cell receptor (signal 1), in addition to its CD80/86 binding to CD28 on the T cell (signal 2). To facilitate this process, antigens undergo processing and presentation in DCs which then present linear peptides from the original protein antigen on MHC molecules. On the other hand, the ability of DCs to activate B cells has been studied less extensively. B cells, unlike T cells, are activated through direct recognition of specific epitopes on the antigen by the BCR. Based on prior data obtained in the laboratory, murine DCs appear to have a specific receptor for the display of HSA (human serum albumin); this receptor does not bind efficiently to bovine serum albumin (BSA). For the purposes of my thesis, I will be investigating the possible existence of a novel receptor that can present human transferrin to B cells. I show through flow cytometry that there is variation in the display of human transferrin on the surface of different immune cell subsets in the mouse spleen. I also show a high level of capture and display of human transferrin on the human B cell line BJAB, RAMOS and on a macrophage cell line. Preliminary data suggests that the distribution of CD71 and the receptor for display of human transferrin broadly but not completely overlap. Additionally, blocking experiments of CD71 were conducted and they showed that the blocking antibody is working properly and the data implies that a novel receptor exists. However, further data is needed before confirming these statements about the presence of a novel receptor.Graduate Educatio
Genomic Surveillance and Deployable Molecular Diagnostics for Emerging Infectious Diseases
No full textEmergence of novel pathogens and outbreaks of existing biothreats have significant social and economic impacts. Detecting emerging infectious disease (EID) threats early and accurately is critical for timely public health intervention and development of vaccines and therapeutics. In this work, we applied unbiased metagenomic sequencing to detect and characterize both viral and bacterial pathogens in plasma samples from a cohort of febrile patients and healthy controls in Thiès, Senegal. We identified relapsing fever Borrelia, an underrecognized tick-borne bacterial pathogen, as the most common cause of non-malarial febrile illness. Second, we took a genomics-informed approach to designing a deployable reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for Lassa virus (LASV), a seasonal hemorrhagic fever virus endemic to West Africa. We developed a high-throughput system for testing RT-LAMP primer set activity across diverse in vitro transcribed RNA targets. This massive-scale primer set screening generated important insights on the factors affecting RT-LAMP amplification speed and guided our design of candidate RT-LAMP assays for the two most prevalent lineages of LASV, Lineage II (LII) and Lineage IV (LIV). We evaluated the performance of candidate assays on clinical samples and showed they could detect LASV RNA (sensitivity compared to gold-standard qRT-PCR: Broad LII v1.1 45%, Broad LII v2 50%, Broad LIV-Liberia 33%), especially in samples with a high viral RNA load (sensitivity in samples with qRT-PCR Ct 35: Broad LII v1.1 87%, Broad LII v2 77%). Finally, we used our empirical dataset of over 3,800 unique Lassa virus RT-LAMP primer set (LPS)-target pairs to predict amplification in silico with high precision and recall (SS: Precision = 0.887, Recall = 0.873; WS: Precision = 0.952, Recal = 0.714) and explored the potential for expanding our empirical dataset and applying a biological sequence optimized machine learning architecture to create a tool for rapid RT-LAMP assay design for emerging viral threats.Biological and Biomedical Science
The Get List
No full textTV Producer Brooke Quinn escapes to a remote Alaskan fish camp. There, free from the professional pressure to stay unpregnant, she can pursue her next story. Or so she hopes. In a trade of stories with a fishwife, Brooke learns to salt salmon and what it takes to make it as an Outsider in the Alaskan Bush. A tenuous friendship builds as Brooke learns firsthand about the Alaska Native women gone missing in her fishing village, their names listed in an oilman’s yacht logbook and disguised as deckhands. The dark discovery convinces Brooke to extend her stay, immersing herself in a new language and people. Brooke wagers it all—her reputation, her marriage, her chance to start a family—to get the story that could make or break her career. But landing the logbook traced to the revered CEO of Arc’d, a major oil company celebrated for its green practices, could land her name on his “get list,” the women invited to his yacht who never return.
This creative work anchors me both in the culminating mission of my master’s–-publishing a novel—and my craft study: create intimacy with my audience through interiority. By focusing on the “inside voice” of the protagonist, Brooke Quinn, the craft challenge becomes constructing her interior world. The interiority must draw readers into a psychological escape so intoxicating that the emotional weight exchanged between the character and the reader genuinely resonates. To do this, I draw on plot-rich scenes from my professional experience: from covering an oil spill in the Gulf and dark money ties in Arctic Alaska to interviewing the CEO of the much-revered company Rivian ahead of its $5-billion electric car company being built in rural Georgia. As my muse Charlotte Brontë might say, Reader, I’m ready to write!Extension Studie
Reconnection-Driven Flares in Magnetized Astrophysical Plasmas: From the Solar Atmosphere to Sagittarius A*
Full text linkEnergetic flares are observed across magnetized astrophysical systems, from stellar coronae to the inner regions of black hole accretion flows. Interpreting their emission remains a challenge, as the underlying physics spans a vast range of spatial and temporal scales—from kinetic-scale particle acceleration to large-scale magnetic structures that govern global energy release.
On the observational side, I present the development and first flight of a high-cadence soft X-ray imaging system flown in the 2024 NASA Solar Flare Sounding Rocket Campaign. The instrument leverages delta-doped, back-illuminated CMOS sensors to achieve sub-second imaging in the 0.5–10 keV band, enabling improved temporal resolution of flare dynamics in the solar corona.
On the theoretical side, I present fully three-dimensional general relativistic particle-in-cell (GRPIC) simulations of magnetic reconnection in relativistic, high–guide field plasmas, motivated by flares from the supermassive black hole at the center of our galaxy. Through analysis of particle acceleration and synchrotron emission, we offer a physical explanation for the observed diversity in infrared and X-ray flares from Sagittarius A*.
Taken together, these efforts demonstrate how new observational tools and high-fidelity simulations can jointly advance our understanding of reconnection-driven energy release across astrophysical environments.Astronom