Computationally Optimized New World Arenavirus Glycoprotein Epigraphs are Displayed and Functional in VSVdG Vectors
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Johnson, Dylan Mac Gregor [Sandia National Laborat↗
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Some techniques for stable hypersonic cfd simulations
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Maeng, Jungyeoul Brad [Sandia National Laboratorie↗
Grid Topology Discovery Algorithm Evaluation of Suitability for Utility Deployment (CRADA 606 Final Report)
This work presents the results of a field-informed demonstration aimed at evaluating the practical suitability of a topology discovery algorithm for utility environments. We demonstrated an algorithm that uses a graph-theory-informed state estimation approach for model selection. In collaboration with Survalent and Peninsula Light Co., the algorithm was applied to real feeder models and field measurements from supervisory control and data acquisition (SCADA) and advanced metering infrastructure (AMI) systems to identify the operational topology of a power distribution system. The demonstration assessed the algorithm’s performance under realistic data conditions, including sparse and noisy measurements, and examined its ability to identify the most likely network configurations. The results confirmed that the approach can effectively narrow down feasible topologies, providing operators with improved situational awareness of network status. Key lessons learned emphasize the need for systematic data validation and strategic sensor placement to enhance observability. These insights inform future deployment strategies and guide refinements for broader adoption in utility operations.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization
Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.
Biochemistry & Molecular Biology↗
KBase Narrative - MRA Genome Announcement Bradyrhizobium NP1
We report the complete genome sequence of Bradyrhizobium strain NP1, which was isolated from forest soil that had been subject to chronic warming. The diverse genus Bradyrhizobium is predicted to contain approximately 800 species (1) and includes non-symbiotic species that dominate forest soil (2). Bradyrhizobium NP1 was isolated from a Long-Term Ecological Research site in the Harvard Forest (HRF), in Petersham, MA (42.54, -72.18).
Morrow, Maureen↗
Impacts of Water-Related Building Moratoria on California’s Housing Crisis
California is facing a housing affordability crisis, which has been partially blamed on building moratoria enacted to address the state’s severe water shortages. This study uses data on the enactment of moratoria in California from 2010 to 2018 to examine their impact on new housing supply and prices. We find that the short-term impact of the moratoria on housing supply is small, but the effect grows over time and becomes more significant in later years, especially for locally mandated moratoria. We do not, however, find that these supply shocks have had an impact on housing prices.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
How Well Do U.S. Western Water Markets Convey Economic Information?
An efficient market implies that potential gains from trade are fully captured. Achieving this requires a well-functioning market where prices reflect all available information. In the case of water rights markets, this implies that the permanent water rights transfer price reflects the sum of discounted returns to this asset (i.e., the lease price), the market interest rate, and a risk premium that reflects potential future water scarcity. Here, the purpose of this study is to assess the efficiency of western U.S. water markets by using the asset pricing model to measure how well prices reflect long-run returns to permanent water rights.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
A perfused multi-well bioreactor platform to assess tumor organoid response to a chemotherapeutic gradient
There is an urgent need to develop new therapies for colorectal cancer that has metastasized to the liver and, more fundamentally, to develop improved preclinical platforms of colorectal cancer liver metastases (CRCLM) to screen therapies for efficacy. To this end, we developed a multi-well perfusable bioreactor capable of monitoring CRCLM patient-derived organoid response to a chemotherapeutic gradient. CRCLM patient-derived organoids were cultured in the multi-well bioreactor for 7 days and the subsequently established gradient in 5-fluorouracil (5-FU) concentration resulted in a lower IC 50 in the region near the perfusion channel versus the region far from the channel. We compared behaviour of organoids in this platform to two commonly used PDO culture models: organoids in media and organoids in a static (no perfusion) hydrogel. The bioreactor IC 50 values were significantly higher than IC 50 values for organoids cultured in media whereas only the IC 50 for organoids far from the channel were significantly different than organoids cultured in the static hydrogel condition. Using finite element simulations, we showed that the total dose delivered, calculated using area under the curve (AUC) was similar between platforms, however normalized viability was lower for the organoid in media condition than in the static gel and bioreactor. Our results highlight the utility of our multi-well bioreactor for studying organoid response to chemical gradients and demonstrate that comparing drug response across these different platforms is nontrivial.
59 BASIC BIOLOGICAL SCIENCES↗
Tradeoffs and Synergies in Tropical Forest Root Traits and Dynamics for Nutrient and Water Acquisition: Field and Modeling Advances
Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.
54 ENVIRONMENTAL SCIENCES↗
Acidification in the U.S. Southeast: Causes, Potential Consequences and the Role of the Southeast Ocean and Coastal Acidification Network
Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments in the region. Here we review acidification issues in the U.S. Southeast, including the regional mechanisms of acidification and their potential impacts on biological resources and coastal communities. We recommend research and monitoring priorities and discuss the role SOCAN has in advancing acidification research and mitigation of and adaptation to these changes.
54 ENVIRONMENTAL SCIENCES↗
Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using an expanded high-density resequencing microarray platform
Introduction: Nucleic acid tests for blood donor screening have improved the safety of the blood supply; however, increasing numbers of emerging pathogen tests are burdensome. Multiplex testing platforms are a potential solution. Methods: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) can perform multiplex detection and identification of 80 viruses, bacteria and parasites. This study evaluated pathogen detection in human blood or plasma. Samples spiked with selected pathogens, each with one of 6 viruses, 2 bacteria and 5 protozoans were tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of primers, and hybridized to a microarray. The reported sequences were aligned to a database to identify the pathogen. To directly compare the microarray to an emerging molecular approach, the amplified nucleic acids were also submitted to nanopore next generation sequencing (NGS). Results: The BBP-RMAv.2 detected viral pathogens at a concentration as low as 100 copies/ml and a range of concentrations from 1,000 to 100,000 copies/ml for all the spiked pathogens. Coded specimens were identified correctly demonstrating the effectiveness of the platform. The nanopore sequencing correctly identified most samples and the results of the two platforms were compared. Discussion: These results indicated that the BBP-RMAv.2 could be employed for multiplex detection with potential for use in blood safety or disease diagnosis. The NGS was nearly as effective at identifying pathogens in blood and performed better than BBP-RMAv.2 at identifying pathogen-negative samples.
59 BASIC BIOLOGICAL SCIENCES↗
Estimation of extreme temperatures in direct solar methane pyrolysis within a porous medium
Porous media have wide application in renewable energy conversion processes, such as solar-thermal fuels production and decarbonization. Heat transport mechanisms within porous media can be highly complex, particularly under extreme conditions encountered in concentrated solar thermal reactors in which direct measurement of temperature is challenging. Here, we implement and report an inverse heat conduction model to estimate the temperature distribution throughout a porous substrate domain in a direct solar methane pyrolysis process. By solving a two-dimensional heat transfer problem and applying an inverse optimization algorithm, we estimate the quasi-steady state spatial temperature distribution in a fibrous porous carbon substrate. The results are validated indirectly by experimentally measured graphite deposition and a simplified reaction kinetic model.
finite difference method↗
Differential transcriptomic alterations in nasal versus lung tissue of acrolein-exposed rats
Introduction: Acrolein is a significant component of anthropogenic and wildfire emissions, as well as cigarette smoke. Although acrolein primarily deposits in the upper respiratory tract upon inhalation, patterns of site-specific injury in nasal versus pulmonary tissues are not well characterized. This assessment is critical in the design of in vitro and in vivo studies performed for assessing health risk of irritant air pollutants. Methods: In this study, male and female Wistar-Kyoto rats were exposed nose-only to air or acrolein. Rats in the acrolein exposure group were exposed to incremental concentrations of acrolein (0, 0.1, 0.316, 1 ppm) for the first 30 min, followed by a 3.5 h exposure at 3.16 ppm. In the first cohort of male and female rats, nasal and bronchoalveolar lavage fluids were analyzed for markers of inflammation, and in a second cohort of males, nasal airway and left lung tissues were used for mRNA sequencing. Results: Protein leakage in nasal airways of acrolein-exposed rats was similar in both sexes; however, inflammatory cells and cytokine increases were more pronounced in males when compared to females. No consistent changes were noted in bronchoalveolar lavage fluid of males or females except for increases in total cells and IL-6. Acrolein-exposed male rats had 452 differentially expressed genes (DEGs) in nasal tissue versus only 95 in the lung. Pathway analysis of DEGs in the nose indicated acute phase response signaling, Nrf2-mediated oxidative stress, unfolded protein response, and other inflammatory pathways, whereas in the lung, xenobiotic metabolism pathways were changed. Genes associated with glucocorticoid and GPCR signaling were also changed in the nose but not in the lung. Discussion: These data provide insights into inhaled acrolein-mediated sex-specific injury/inflammation in the nasal and pulmonary airways. The transcriptional response in the nose reflects acrolein-induced acute oxidative and cytokine signaling changes, which might have implications for upper airway inflammatory disease susceptibility.
Alewel, Devin I.↗
A Vibrational Energy Harvesting Sensor Based on Linear and Rotational Electromechanical Effects
In this investigation, a magnetically coupled double-spring design is presented for harvesting low-level non-stationary random vibrational energy. The sensor relies on multimodal coupling between the translation and rotation of a two-spring magnet and coil system to widen the harvesting bandwidth. Energy methods are used to develop a model to characterize the electromechanical response of the system, the solution of which is obtained using stochastic techniques based on a particle swarm algorithm. This approach provides an efficient method to estimate system parameters that otherwise are difficult or impossible to determine with independent measurements. The experimental results demonstrate agreement with the theoretical predictions over a limited bandwidth. The sensor can effectively harvest non-stationary vibration energy down to 10 -4 g within a limited bandwidth of 130–150 Hz. The sensor prototype has an operational volume of 2.6 cm 3 with a calculated power density of 0.2 W/cm 3 . The sensor’s small size results in a coupling efficiency of approximately 6% across the tested bandwidth.
42 ENGINEERING↗
Epidemic Intelligence Service Alumni in Public Health Leadership Roles
Since 1951, the Epidemic Intelligence Service (EIS) of the U.S. Centers for Disease Control and Prevention (CDC) has trained physicians, nurses, scientists, veterinarians, and other allied health professionals in applied epidemiology. To understand the program’s effect on graduates’ leadership outcomes, we examined the EIS alumni representation in five select leadership positions. These positions were staffed by 353 individuals, of which 185 (52%) were EIS alumni. Among 12 CDC directors, four (33%) were EIS alumni. EIS alumni accounted for 29 (58%) of the 50 CDC center directors, 61 (35%) of the 175 state epidemiologists, 27 (56%) of the 48 Field Epidemiology Training Program resident advisors, and 70 (90%) of the 78 Career Epidemiology Field Officers. Of the 185 EIS alumni in leadership positions, 136 (74%) were physicians, 22 (12%) were scientists, 21 (11%) were veterinarians, 6 (3%) were nurses, and 94 (51%) were assigned to a state or local health department. Among the 61 EIS alumni who served as state epidemiologists, 40 (66%) of them were assigned to a state or local health department during EIS. Our evaluation suggests that epidemiology training programs can serve as a vital resource for the public health workforce, particularly given the capacity strains brought to light by the COVID-19 pandemic.
60 APPLIED LIFE SCIENCES↗
Low Molecular Weight Volatile Organic Compounds Indicate Grazing by the Marine Rotifer Brachionus plicatilis on the Microalgae Microchloropsis salina
Microalgae produce specific chemicals indicative of stress and/or death. The aim of this study was to perform non-destructive monitoring of algal culture systems, in the presence and absence of grazers, to identify potential biomarkers of incipient pond crashes. Here, we report ten volatile organic compounds (VOCs) that are robustly generated by the marine alga, Microchloropsis salina, in the presence and/or absence of the marine grazer, Brachionus plicatilis. We cultured M. salina with and without B. plicatilis and collected in situ volatile headspace samples using thermal desorption tubes over the course of several days. Data from four experiments were aggregated, deconvoluted, and chromatographically aligned to determine VOCs with tentative identifications made via mass spectral library matching. VOCs generated by algae in the presence of actively grazing rotifers were confirmed via pure analytical standards to be pentane, 3-pentanone, 3-methylhexane, and 2-methylfuran. Six other VOCs were less specifically associated with grazing but were still commonly observed between the four replicate experiments. Through this work, we identified four biomarkers of rotifer grazing that indicate algal stress/death. This will aid machine learning algorithms to chemically define and diagnose algal mass production cultures and save algae cultures from imminent crash to make biofuel an alternative energy possibility.
headspace sampling↗