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Creators/Authors contains: "Kelly, M."

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  1. Free, publicly-accessible full text available September 11, 2025
  2. Evaluating two‐terminal network reliability is a classical problem with numerous applications. Because this problem is #P‐Complete, practical studies involving large systems commonly resort to approximating or estimating system reliability rather than evaluating it exactly. Researchers have characterized signatures, such as the destruction spectrum and survival signature, which summarize the system's structure and give rise to procedures for evaluating or approximating network reliability. These procedures are advantageous if the signature can be computed efficiently; however, computing the signature is challenging for complex systems. With this motivation, we consider the use of Monte Carlo (MC) simulation to estimate the survival signature of a two‐terminal network in which there are two classes of i.i.d. components. In this setting, we prove that each MC replication to estimate the signature of a multi‐class system entails solving a multi‐objective maximum capacity path problem. For the case of two classes of components, we adapt a Dijkstra's‐like bi‐objective shortest path algorithm from the literature for the purpose of solving the resulting bi‐objective maximum capacity path problem. We perform computational experiments to compare our method's efficiency against intuitive benchmark approaches. Our computational results demonstrate that the bi‐objective optimization approach consistently outperforms the benchmark approaches, thereby enabling a larger number of MC replications and improved accuracy of the reliability estimation. Furthermore, the efficiency gains versus benchmark approaches appear to become more significant as the network increases in size. 
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    Free, publicly-accessible full text available July 28, 2025
  3. Abstract This field study examined how sediment macroinfauna change patterns of sediment oxygen demand (SOD) throughout a diel oxygen cycle. Sediments with a greater faunal presence would be expected to have greater overall SOD, and at night may alter their behavior and influence SOD depending on their response to low-oxygen stress. Dynamic faunal bioturbation or bioirrigation behavior would also result in corresponding variation in SOD values on short time scales. In situ flow-through benthic metabolism chambers were used to measure SOD at a high temporal resolution in discrete sediment patches. Sediments with more macroinfauna had greater average SOD over the diel cycle, consistent with previous studies. Where more macroinfauna were present, they drove greater SOD during nightly low oxygen, presumably by enhancing their burrowing and irrigation activities. SOD was also more variable on a sub-diel timescale in sediments with more macroinfauna. Sediment oxygen demand is dynamic and highly sensitive both temporally, on very short timescales, and spatially, in terms of resident fauna, and their interaction produces heretofore unaccounted complexity in patterns of SOD particularly in shallow coastal systems. Extrapolations of temporally and spatially limited SOD measurements to a system-wide scale that do not account for the short-term and spatially variable effects of fauna may produce imprecise and misleading estimates of this critical ecosystem function. 
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    Free, publicly-accessible full text available July 23, 2025
  4. Abstract Muddy marine sediments are elastic materials in which bubbles grow and worms extend their burrows by fracture. Bubble growth and burrowing behavior are dependent on the stiffness and fracture toughness (KIc) of these muds. This article describes a custom laboratory apparatus to measure the fracture toughness of muddy, cohesive sediments using a bubble injection method. The system induces fracture in sediment samples by incrementally injecting air through a needle inserted into the sediment. The increasing pneumatic pressure is monitored until it drops abruptly, indicating bubble formation. Fracture toughness is then calculated from the peak pressure at which fracture occurred, following cavitation rheology methods developed for soft gels. The system has produced measurements that compare well to previous data but with better spatial resolution, allowing for characterization of spatial heterogeneity on small scales. 
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    Free, publicly-accessible full text available August 1, 2025
  5. Data-driven many-body simulations provide the first realistic view of water harvesting in metal–organic frameworks as a function of relative humidity. 
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    Free, publicly-accessible full text available April 3, 2025
  6. Mooney, Scott David (Ed.)
    Fire is a key disturbance process that shapes the structure and function of montane temperate rainforest in the Pacific Northwest (PNW). Recent research is revealing more frequent historical fire activity in the western central Cascades than expected by conventional theory. Indigenous peoples have lived in the PNW for millennia. However, Indigenous people's roles in shaping vegetation mosaics in montane temperate forests of the PNW has been overlooked, despite archaeological evidence of long-term, continuous human use of these landscapes. In this paper, we present a generalizable research framework for overcoming biases often inherent in historical fire research. The framework centers Indigenous perspectives and ethnohistory, leveraging theory in human ecology and archaeology to interpret fire histories. We apply this framework to place-based, empirical evidence of Indigenous land use and dendroecological fire history. Our framework leads us to conclude that the most parsimonious explanation for the occurrence of historical high fire frequency in the western Cascades is Indigenous fire stewardship. Further, our case study makes apparent that scholars can no longer ignore the role of Indigenous people in driving montane forest dynamics in the PNW. 
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    Free, publicly-accessible full text available June 26, 2025
  7. The recent rise of ‘omics and other molecular research technologies alongside improved techniques for tissue preservation have broadened the scope of marine mammal research. Collecting biological samples from wild marine mammals is both logistically challenging and expensive. To enhance the power of marine mammal research, great effort has been made in both the field and the laboratory to ensure the scientific integrity of samples from collection through processing, supporting the long‐term use of precious samples across a broad range of studies. However, identifying the best methods of sample preservation can be challenging, especially as this technological toolkit continues to evolve and expand. Standardizing best practices could maximize the scientific value of biological samples, foster multi‐institutional collaborative efforts across fields, and improve the quality of individual studies by removing potential sources of error from the collection, handling, and preservation processes. With these aims in mind, we summarize relevant literature, share current expert knowledge, and suggest best practices for sample collection and preservation. This manuscript is intended as a reference resource for scientists interested in exploring collaborative studies and preserving samples in a suitable manner for a broad spectrum of analyses, emphasizing support for ‘omics technologies. 
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    Free, publicly-accessible full text available October 1, 2025