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Missing microbial eukaryotes and misleading meta-omic conclusions

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

59 BASIC BIOLOGICAL SCIENCES↗

Optimal Transport as a Tool for Scientific Discovery in Radiation Biology

This report summarizes findings from research conducted for the “Exploration of the Poten tial for Artificial Intelligence and Machine Learning to Advance Low-Dose Radiation Biology Re search” (RadBio-AI) program, supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, under Awards KP1601011/FWP CC121 and KP1601017/FWP CC121. The research reported here was undertaken in an effort to assess the potential of optimal measure transport methods as components within the larger scope of a com putational framework envisioned to support research in the radiation biology domain. Within this effort, our interest centered on enabling a unified generic framework where probabilistic modeling, inference, and statistical learning can be carried out for a wide range of data distributions. As described next in Section 1 (and in more detail in our original publication), optimal measure transport offers the possibility of such unified approach.

97 MATHEMATICS AND COMPUTING↗

Building Environmental Justice and Equity into the Development of Critical Mineral Industries

The global transition toward low-carbon energy not only means an increase in demand for clean electricity and renewable resources, but also an increase in demand for the critical minerals (CMs) and rare earth elements (REEs) that these technologies rely upon. Indeed, low-carbon energy technologies, such as those used for wind turbines and electric vehicle motors, require significantly more lithium, nickel, cobalt, manganese, graphite, and other CMs than fossil-based energy technologies. The growing demand for new forms of low- carbon energy will necessitate a proportional scale-up of CM and REE extraction and processing. Presently, the majority of extraction and processing activities for CMs and REEs are concentrated in very few countries, primarily in China and the Global South. CM and REE supply chain activities conducted in or controlled by these countries are commonly associated with widespread and well- documented human rights abuses and environmental degradation. As a result of concerns related to supply chain security, worker welfare, and the overall need for additional sources of CMs and REEs, governments worldwide have begun to explore policy pathways for the development of new supply chains. The development of new supply chains for CMs and REEs re s a multifold opportunity to accelerate the global deployment of low-carbon energy fleets, reduce global carbon emissions, build political resilience—and also to enhance policy objectives of environmental justice and equity in the clean energy transition. Fulfilling these policy objectives requires energy producers to navigate a maze of global supply chain policies designed to shape and accelerate the growth of new markets. In the United States, for instance, President Biden recently implemented fiscal and trade policies that incentivize both domestic and global reliance on U.S.-produced CMs and REEs, leveraging key relationships in Asia and Europe to ensure the accelerated buildout of the U.S. supply chain. The Biden Administration’s framework also emphasizes that new supply chains for CMs, REEs, and other low-carbon energy pathways must generate benefits for marginalized and disadvantaged communities, build energy equity, and contribute to the Biden Administration’s vision of environmental justice. present CM and REE supply chains include several stages, including mining, processing, transport, utilization, and disposal, each of which involves different environmental justice considerations and potential injustices. This study explores how technical innovation, paired with responsible community engagement and empowerment, can help inform the development of energy equity and environmental justice at all stages of new supply chains. The study highlights these opportunities on a broad scale. We also lend a specific focus to research at the University of Wyoming School of Energy Resources that aims to guide the development of CM and REE industries in communities with high economic dependence on coal and other fossil fuel industries, identifying pathways to grow a U.S. domestic supply chain by producing CMs from coal, coal by-products, and coal waste streams. These production pathways represent a potential new supply for CMs across the U.S. and elsewhere, thereby enhancing national security and accelerating the widespread deployment of low-carbon energy technologies, while also generating alternative applications for remaining coal reserves and aiding in a just transition for rural energy-producing communities.

Gerace, Selena↗

Using a Genetic Algorithm to Optimize Configurations in a Data-Driven Application

Users of highly-configurable software systems often want to optimize a particular objective such as improving a functional outcome or increasing system performance. One approach is to use an evolutionary algorithm. However, many applications today are data-driven, meaning they depend on inputs or data which can be complex and varied. Hence, a search needs to be run (and re-run) for all inputs, making optimization a heavy-weight and potentially impractical process. In this paper, we explore this issue on a data-driven highly-configurable scientific application. We build an exhaustive database containing 3,000 configurations and 10,000 inputs, leading to almost 100 million records as our oracle, and then run a genetic algorithm individually on each of the 10,000 inputs. We ask if (1) a genetic algorithm can find configurations to improve functional objectives; (2) whether patterns of best configurations over all input data emerge; and (3) if we can we use sampling to approximate the results. We find that the original (default) configuration is best only 34% of the time, while clear patterns emerge of other best configurations. Out of 3,000 possible configurations, only 112 distinct configurations achieve the optimal result at least once across all 10,000 inputs, suggesting the potential for lighter weight optimization approaches. We show that sampling of the input data finds similar patterns at a lower cost.

Sinha, Urjoshi↗

Enhancing Knowledge Capture and Management within a Knowledge-Driven Workforce [Capstone Project]

This project aimed to understand how the collective knowledge of a group of engineers or ‘knowledge-based workers’ can be baselined through use of qualitative questionnaires based on input from subject matter experts. The results of the questionnaires were then used to inform management and the group where to focus efforts on terms of training and mentoring. With use of re-administering the qualitative questionnaire to gauge progress over time. Additionally, the development a knowledge-based wiki was explored to help shape group culture from one where ideas and knowledge tend to be siloed, into one where information is traded freely across the group and with external customers and collaborators.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

IRIS-GNN: Leveraging Graph Neural Networks for Scheduling on Truly Heterogeneous Runtime Systems

The diversity of accelerators in computer systems poses significant challenges for software developers, such as managing vendor-specific compiler toolchains, code fragmentation requiring different kernel implementations, and performance portability issues. To address these, the Intelligent Runtime System (IRIS) was developed. IRIS works across various systems, from smartphones to supercomputers, enabling automatic performance scaling based on available accelerators. It introduces abstract tasks for seamless execution transitions between accelerators while ensuring memory consistency and task dependencies. Although IRIS simplifies system details, optimal dynamic scheduling still requires user input to understand workload structures. To address this, we introduce a new scheduling policy for IRIS, termed IRIS-GNN, which is the first IRIS hybrid policy that operates in conjunction with the dynamic policies. This policy employs a Graph-Neural Network (GNN) to conduct Graph Classification of any task graphs submitted to IRIS. This GNN analyzes the structure and attributes of the task graph, categorizing it as either locality, concurrency, or mixed. This classification subsequently guides the selection of the dynamic policy used by IRIS. We provide a comparison of the performance of IRIS-GNN against the complete spectrum of IRIS’s dynamic policies, assess the overhead introduced by the GNN within this scheduling framework, and ultimately explore its practical application in real-world scenarios.

Johnston, Beau↗

Correlating Mechanical Sensitivity with Spin Transition in the Explosive Spin Crossover Complex [Fe(Htrz) 3 ] n [ClO 4 ] 2 n

Spin crossover complexes are known to undergo bond length, volume, and enthalpy changes during spin transition. In an explosive spin crossover complex, these changes could affect the mechanical and initiation sensitivity of the explosive and lead to the development of a new class of sensitivity switchable materials. To explore this relationship, the well-known spin crossover compound [Fe(Htrz) 3 ] n [ClO 4 ] 2n (1) was re-evaluated for its explosive properties, and its mechanical impact sensitivity was correlated to spin transition. A variable temperature impact test was developed and used to evaluate the impact sensitivity of 1 in the low spin (LS, S = 0), thermally accessed high spin (HS, S = 2), and mixed LS and HS states. For comparison, the structurally similar Ni compound, [Ni(Htrz) 3 ] n [ClO 4 ] 2n (2), which does not undergo a spin transition at accessible temperatures, was synthesized and characterized, and its explosive properties and variable temperature impact sensitivity measured. These results reveal a correlation between impact sensitivity and spin transition, where 1 exhibits lower impact sensitivity in the LS state and increases in sensitivity upon transition to the HS state. Here, density functional theory was used to predict structural changes that occur upon spin transition that correlate to the change in sensitivity. This demonstrates, for the first time, an explosive spin crossover compound (ExSCO) that exhibits switchable impact sensitivity with a fully reversible internal switching mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Challenges in Firmware Re-Hosting, Emulation, and Analysis

System emulation and firmware re-hosting have become popular techniques to answer various security and performance related questions, such as determining whether a firmware contain security vulnerabilities or meet timing requirements when run on a specific hardware platform. While this motivation for emulation and binary analysis has previously been explored and reported, starting to either work or research in the field is difficult. To this end, we provide a comprehensive guide for the practitioner or system emulation researcher. Here, we layout common challenges faced during firmware re-hosting, explaining successive steps and surveying common tools used to overcome these challenges. We provide classification techniques on five different axes, including emulator methods, system type, fidelity, emulator purpose, and control. These classifications and comparison criteria enable the practitioner to determine the appropriate tool for emulation. We use our classifications to categorize popular works in the field and present 28 common challenges faced when creating, emulating, and analyzing a system from obtaining firmwares to post emulation analysis.

97 MATHEMATICS AND COMPUTING↗

Designing Porous Ion Emitters for Thermal Ionization Mass Spectrometry: Evaluating Metal-Organic Frameworks

In this work we describe the first exploration of metal-organic frameworks (MOFs) as ‘next generation’ ion emitters for thermal ionization mass spectrometry (TIMS). MOFs were identified as promising candidates for this application given the synthetic control over their desired structural properties. This tunability results in well-ordered, high surface area, high porosity frameworks with targeted sorption affinities. Here we explored an aluminum-based, bipyridine-containing MOF (MOF-253) with and without incorporating the high work function metal, rhenium (Re). After analysis of a Nd-bearing MOF, we hypothesized that the well-dispersed, sponge-like interconnected network of the degraded structure would enhance Nd ionization more than traditional TIMS loading activators (i.e., phosphoric acid). Compared to filaments loaded with phosphoric acid that require an additional benzene carburization step, the Nd ionization efficiencies (atoms detected relative to atoms loaded) for heated filaments loaded with MOF-253 were similar (~1%). Electron microscopy after TIMS analysis demonstrated that the MOF was retained on the filament and, as hypothesized, preserved sub-micron porosity post analysis. While these results are preliminary, they demonstrate that MOFs have potential to enhance ionization and exceed the performance of traditional loading techniques by forming nano-porous ion emitters (nano-PIEs). Thus, further experimentation is likely to exceed this performance through more specific selection of the base MOF structure and modifications to porosity and composition. This work represents a novel application of MOFs and a next step in the pursuit of advanced thermal ionization with potential to expand across the periodic table.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A strain-driven thermotropic phase boundary in BaTiO 3 at room temperature by cycling compression

In BaTiO 3 single crystals, we observed a strain-driven phase transition from the tetragonal phase to the tetragonal-orthorhombic phase boundary which can be introduced by slow cycling compressions (a loading of up to 0.5 GPa, strain rate of 10 -4 s -1 , and 100 cycles) at room temperature. Different from the well-known tetragonal to cubic phase transition under stress (~2 GPa), it only takes place locally around bent 90° domain walls. The inhomogeneous local stress and electrical fields as well as the mobile point defect pinning effect contribute to the phase re-entrance. Through comparison experiments by in situ synchrotron x-ray diffraction, Raman scattering, and (scanning) transmission electron microscopy, we explored the phase transition mechanism. Based on that, we developed a mechanical method to obtain well-stabilized high-density thermotropic phase boundary structures (with tetragonal, orthorhombic, and bridging monoclinic phases) in BaTiO 3 for potential applications.

36 MATERIALS SCIENCE↗

Re-entrance to a ferromagnetic insulator with oxygen-vacancy ordering in the La 0.7 Sr 0.3 MnO 3 /SrTiO 3 superlattice

The charge-density wave is correlated with the properties in transition metal oxides, and regulating this state is important to explore the potential of oxides. Defects could modulate the local environment, in which the effect is subject to the concentration and arrangement, and an artificial arrangement of defect-ordering is highly expected to design the material properties. In this work, the ordering of oxygen vacancies with a preferred location on the (001) La/SrO plane by self-structural optimization was induced in La 0.7 Sr 0.3 MnO 3 /SrTiO 3 superlattices with medium oxygen pressure during SrTiO 3 deposition, and then the ferromagnetic charge-ordering (CO)/charge-density-wave (CDW) state was formed in La 0.7 Sr 0.3 MnO 3 with susceptibility to magnetic field, temperature, and superlattice configuration. In addition, re-entrance to the ferromagnetic insulator CO/CDW could be induced by a high magnetic field. The selective occupancy of oxygen vacancies on the (001) La/SrO plane and the phase fluctuation around the CO/CDW-to-ferromagnetic metal phase transition were critical to the above properties. The interfacial diffusion with atomic-level resolution to control oxygen vacancies could be used in other magnetoelectric systems and corresponding device applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Case Studies of Residential Façade Upgrades in Four Climate Zones

This paper reports on a project that explored the viability of insulation and window upgrades during siding retrofits in four case studies across the United States. Thousands of homes are re-sided every year, but only a fraction of consumers add insulation and upgrade the windows at the same time, even though a siding replacement is the ideal time to update the thermal performance of building enclosures. To better understand why more siding retrofits do not include insulation and window upgrades, research staff from several organizations collaborated with the U.S. Department of Energy on a multi-faceted research project that included a cost analysis, workforce analysis, market assessment, and contractor assessment. This paper will review four in-field case studies conducted with contractors actively engaged in home re-siding projects that agreed to add rigid insulation and window upgrades as part of their projects. Findings from the case studies will be presented including contractor perspectives, cost, and technical approaches on projects, located in multiple climate zones including Bellingham WA, Jackson MS, Kalamazoo MI, and Phoenix AZ. All projects involved adding continuous rigid insulation on the exterior walls and installation of new cladding. Cladding types varied from wood and metal to fiber cement, vinyl, and traditional stucco. All homes also received a window upgrade, although upgrades varied depending on the original condition of the windows and climate; upgrades included triple-pane windows, low-e storm windows, and exterior shading. Key findings including technical approaches, opportunities, barriers, and project cost will be presented.

re-siding, insulation, rigid insulation, exterior ↗

Design-Space Data: Informing Common Design Decisions with Pre-Simulated Data

Design Space Exploration (DSE) analysis techniques represent a data-centric approach to integrating performance analysis in early design phases when there is the greatest potential to cheaply improve the energy efficiency of a building. We focus on a novel extension of DSE called Universal Design Space Exploration (UDSE), which leverages massive databases of pre-simulated analysis that represent all possible outcomes of common analysis workflows. These databases, called Design Spaces, become “universal” when a single pre-simulated design space can be re-applied to future unknown projects. Unlike current simulation methods, which require a design to exist before it can be analyzed and often take minutes or hours to simulate, UDSE leverages pre-simulation to deliver rapid and relevant insight as new designs are conceptualized. The data underpinning UDSE enables advanced statistical and Artificial Intelligence methods, allowing UDSE to deliver a greater understanding of the larger problem being explored, rather than simply delivering analysis of several pre-conceived design options. We believe that UDSE can provide instantaneous, relevant analysis for all building design projects at negligible cost. This paper has two main goals, to develop a relevant Universal Design Space that showcases the potential of UDSE and to release this data freely to industry and academia; thereby lowering the barrier to entry to digital literacy in statistics, ML and AI within the architecture, engineering, construction (AEC) industry.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Biomass burning aerosol radiative effects in the Southeast Atlantic depend strongly on meteorological forcing method

Biomass burning aerosols (BBAs) from African fires may strongly impact Earth’s radiation budget in the southeast Atlantic (SEA), but the sign and magnitude of the overall radiative effect (RE) remain uncertain. Aerosol–climate models are needed to separately quantify direct, indirect, and semi-direct REs. Here, we evaluate improved simulations with the UK Met Office's Unified Model and explore REs resulting from various methods used to match observed meteorology (nudging or running forecasts reinitialized at different frequencies). REs are calculated as differences in radiative fluxes between simulations with and without smoke emissions and with and without aerosol absorption. All model setups agree on net warming for the SEA dominated by the direct effect. Simulated smoke, clouds, and the direct effect agree better with observations than previous studies using the same model, though biases in aerosol extinction and liquid water path remain. Changes in cloud droplet number concentration due to BBA self-lofting influence how cleanly we can separate cloud effects into semi-direct and indirect effects. Total RE, which remains unaffected, ranges from +3.0 to +7.9 W m −2 . The 4.9 W m −2 spread arises mainly from simulated semi-direct effects. Forecasts three days long or less probably do not allow time for plausible differences in boundary layer properties due to semi-direct effects to accumulate. Free running simulations with and without smoke accumulate differences in meteorology that are likely spurious “butterfly effects”. We recommend future research quantifying BBA REs over weeks to months to use meteorological forcing techniques that allow aerosol absorption to affect the boundary layer.

Giuffrida, Eric [Carnegie Mellon University, Pitts↗

Gut enterotype-dependent modulation of gut microbiota and their metabolism in response to xanthohumol supplementation in healthy adults

Xanthohumol (XN), a polyphenol found in the hop plant (Humulus lupulus), has antioxidant, anti-inflammatory, prebiotic, and anti-hyperlipidemic activity. Preclinical evidence suggests the gut microbiome is essential in mediating these bioactivities; however, relatively little is known about XN’s impact on human gut microbiota in vivo. We conducted a randomized, triple-blinded, placebo-controlled clinical trial (ClinicalTrials.gov NCT03735420) to determine safety and tolerability of XN in healthy adults. Thirty healthy participants were randomized to 24 mg/day XN or placebo for 8 weeks. As secondary outcomes, quantification of bacterial metabolites and 16S rRNA gene sequencing were utilized to explore the relationships between XN supplementation, gut microbiota, and biomarkers of gut health. Although XN did not significantly change gut microbiota composition, it did re-shape individual taxa in an enterotype-dependent manner. High levels of inter-individual variation in metabolic profiles and bioavailability of XN metabolites were observed. Moreover, reductions in microbiota-derived bile acid metabolism were observed, which were enterotype-dependent. These results suggest interactions between XN and gut microbiota in healthy adults are highly inter-individualized and potentially indicate that XN elicits effects on gut health in an enterotype-dependent manner.

59 BASIC BIOLOGICAL SCIENCES↗

VAIM-CFF: a variational autoencoder inverse mapper solution to Compton form factor extraction from deeply virtual exclusive reactions

We develop a new methodology for extracting Compton form factors (CFFs) from deeply virtual exclusive reactions such as the unpolarized DVCS cross section using a specialized inverse problem solver, a variational autoencoder inverse mapper (VAIM). The VAIM-CFF framework not only allows us access to a fitted solution set possibly containing multiple solutions in the extraction of all 8 CFFs from a single cross section measurement, but also accesses the lost information contained in the forward mapping from CFFs to cross section. We investigate various assumptions and their effects on the predicted CFFs such as cross section organization, number of extracted CFFs, use of uncertainty quantification technique, and inclusion of prior physics information. We then use dimensionality reduction techniques such as principal component analysis to visualize the missing physics information tracked in the latent space of the VAIM framework. Through re-framing the extraction of CFFs as an inverse problem, we gain access to fundamental properties of the problem not comprehensible in standard fitting methodologies: exploring the limits of the information encoded in deeply virtual exclusive experiments.

Accelerator Physics↗

Polymer-cement composites with adhesion and re-adhesion (healing) to casing capability for geothermal wellbore applications

Deterioration of cement/casing adhesion in wellbore scenarios can result in unwanted and potentially harmful leakage with the potential of serious repair costs. In this work, we explore the use of self-healing polymers added to conventional wellbore cements as a way to bring about self-healing and readhering (to steel casing) properties to the composite material. The polymers are pH resistant and seem to improve the cement integrity after exposure to typical chemical and thermal stresses encountered under geothermal wellbore conditions. We find that addition of about 10-15 wt% of polymer to the cement visually increases its resistance to fracturing from exposure to geothermal conditions, while the adhesive strength of cement/stainless steel increases with curing time for a period of about 10 days. Self-healing capability was demonstrated by permeability analysis showing that polymer-cement composites reduce flow by 50-70% at cement bulk and at the cement/steel interface. Use of atomistic simulations imply that these polymers have good wetting properties on the steel surfaces. Analysis of the interactions between steel/polymer and cement/polymer show that they are complementary, resulting in a wider range of bonding patterns. Cracks are likely to expose under-coordinated sites that result in more bonding interactions, which agrees well with the permeability measurements showing high degree of healed cracks and healed (cement-steel) interfacial gaps together with an overall increased in structural integrity of these advanced polymer-cement composite materials.

Rod, Kenton A.↗

Seasonality and Albedo Dependence of Cloud Radiative Forcing in the Upper Colorado River Basin

Mountains create and enhance their own clouds, which both scatter and absorb shortwave radiation from the sun and absorb and re-emit land surface and atmospheric longwave radiation. However, the impacts of clouds on the surface radiation balance in high elevation snowy mountain terrain are poorly explored. In this study, we use data collected by the SAIL field campaign and partner organizations in the upper elevations (2,880 m.a.s.l) of the Upper Colorado River Basin (UCRB) over a 21-month period from September 2021 to June 2023 to estimate Cloud Radiative Forcing (CRF) in the shortwave, longwave, and the net effect. Longwave warming effects dominate during the winter when snow albedos are high (0.8–0.9) and the background atmospheric precipitable water vapor is low (<0.5 cm), yielding a maximum monthly average net CRF of +34.7 W·m -2 , meaning that clouds increase the net radiation relative to clear skies during this time period. The sign of net CRF switches in the warm season as snow recedes, sun-angles increase, and the North American monsoon arrives, yielding a minimum monthly average net CRF of -47.6 W·m -2 with hourly minima of -600 W·m -2 . The sign of net CRF is typically positive, even at solar noon, when the surface is snow covered, except for a brief period over melting, low-albedo snow (0.5–0.6) impacted by dust impurities. Sensitivity tests elucidate the role of the surface albedo on the net CRF. The results suggest that net CRF will increase in magnitude and lead to a more persistent cooling effect on the surface net radiation budget as the snow cover declines.

54 ENVIRONMENTAL SCIENCES↗