The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the
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Huang, Ji↗
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Results for “CLARIFY”
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Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication
The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.
definitions↗
BUTTER-Clarifier [SWR-23-61]
This repository contains a python package of neural network interpretability techniques (interpretability) and a keras callback to easily compute and capture data related to these techniques (values metrics) during training. It was developed to be used with NREL's BUTTER Deep Learning Experimental Framework, but does not depend on this framework and may be useful to projects outside of this framework. The vision for this codebase is to collect algorithms for explainable artificial intelligence (XAI) in a single framework that is easy to use, easy to read, and can be expand upon. Here, we package XAI algorithms into a module called "metrics", which are implemented as python functions. The return type of a metric is typically a dictionary holding data of multiple data types, such as real values and numpy matrices. Callbacks and any other connector code is provided as necessary in a separate module to make these metrics more easily usable. This project depends on Tensorflow's Keras API, although it would be nice to try and support multiple backends one day. Related to: https://github.com/NREL/BUTTER-Empirical-Deep-Learning-Experimental-Framework
Perr-Sauer, Jordan↗
Clarifying remotely-retrieved precipitation of shallow marine clouds from the NSF/NCAR Gulfstream V
Precipitation is a key process within the shallow cloud lifecycle. The Cloud System Evolution in the Trades (CSET) campaign included the first deployment of a 94 GHz Doppler radar and 532 nm lidar. Despite a larger sampling volume, initial mean radar/lidar retrieved rain rates (Schwartz et al. 2019) based on the upward-pointing remote sensor datasets are systematically less than those measured by in-situ precipitation probes in the cumulus regime. Subsequent retrieval improvements produce rainrates that compare better to in-situ values, but still underestimate. Retrieved shallow cumulus drop sizes can remain too small and too few, with an overestimated shape parameter narrowing the raindrop size distribution too much. Three potential causes for the discrepancy are explored: the gamma functional fit to the dropsize distribution, attenuation by rain and cloud water, and an underaccounting of Mie dampening of the reflectivity. A truncated exponential fit may represent the dropsizes below a showering cumulus cloud more realistically, although further work would be needed to fully evaluate the impact of a different dropsize representation upon the retrieval. The rain attenuation is within the measurement uncertainty of the radar. Mie dampening of the reflectivity is shown to be significant, in contrast to previous stratocumulus campaigns with lighter rain rates, and may be difficult to constrain well with the remote measurements. An alternative approach combines an a priori determination of the dropsize distribution width based on the in-situ data with the mean radar Doppler velocity and reflectivity. This can produce realistic retrievals, although a more comprehensive assessment is needed to better characterize the retrieval errors.
54 ENVIRONMENTAL SCIENCES↗
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly
Abstract Background Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. Results Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. Conclusion We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.
Krinos, Arianna I. (ORCID:0000000197678392)↗
AI-Assisted Parameter Tuning Will Speed Development and Clarify Uncertainty in E3SM
Focal Area: This idea is best aligned with predictive modeling. It targets Earth System Model improvement and uncertainty quantification
54 ENVIRONMENTAL SCIENCES↗
Time resolved in-situ small angle X-ray scattering clarifies the competition between continuous and discontinuous precipitation in U-6wt%Nb
In-situ high energy x-ray scattering experiments enable high temporal resolution investigations of precipitation kinetics; Continuous and discontinuous precipitation are competitive near the TTT nose (~525°C); The incubation time for discontinuous precipitation increases significantly at temperatures below the TTT nose; Additional evidence for the divergent interlamellar spacing was observed at 434°C and 466°C
36 MATERIALS SCIENCE↗
Initial User Study Insights Clarified Community Requirements & Early Feedback on Conceptual Design
The HPDF User Experience (UX) team conducted eight semi-structured interviews with twelve individuals leading data and computing infrastructure work at DOE Office of Science (SC) user facilities or projects. This report presents key takeaways synthesizing community perspectives and needs, along with recommendations for the project. These insights should be considered as conceptual design work continues, early partnerships begin, workflow readiness activities evaluate and enhance key scientific tools, and early access systems are made available to the Office of Science (SC) community. Vigilance in meeting community requirements and ensuring workflow readiness will be needed to ensure HPDF’s success.
97 MATHEMATICS AND COMPUTING↗
Process Intensification and Scale-Up of a Continuous Enzymatic Hydrolysis and Separation Process
Combining separate unit operations into one where the best of each part can be maximized is one of the benefits of process intensification. An example is the combination of lignocellulosic biomass enzymatic hydrolysis with the downstream solid-liquid separation step to produce clarified sugars ready for fermentation or catalytic upgrading. The productivity and endpoint yield of enzymatic hydrolysis both enjoy the benefits of reduced feedback inhibition through the continuous removal of sugars by incorporating separations into the reactor. Likewise, the efficiency of recovering clarified sugars from the enzymatic hydrolysis slurry can be enhanced by operating separations equipment at steady-state conditions simultaneously with the continuously fed hydrolysis process. A key parameter that enables greater processing capacity while also raising the risks of failure is the solids loading or concentration. Higher solids loading allows for smaller reactor vessels and results in clarified sugars of higher concentration; however, required pumping power increases, reactor agitation may become ineffective, and membrane flux suffers. Feedstock material attributes influenced by upstream pretreatment must also be scrutinized more carefully: dilute-acid pretreated and deacetylated-and-disc-refined feedstocks exhibit different characteristics that affect agitation and pumping. The authors invite you to further explore the process science enabling the scale-up of this technology from conceptual work at the bench to pilot-scale industrially-relevant equipment where the challenges and solutions of integration and process optimization are expounded upon.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Assessing the link between aerosol mixing state, structure and composition and their optical properties: Ascension Island as a testbed for the South‐East Atlantic aerosol regimes
Forest and savanna fires are a major source of pollution over the globe. Such fire events emit to the atmosphere a considerable amount of “fluffy” fractal black looking particles that are often referred to as black carbon (BC) or soot aerosols. In fact, BC particles (aerosols) emitted from savanna and agricultural fires over the African continent play an important role in the region’s and the global climate. These fires occur each year between July and October, which is referred to as the biomass burning (BB) season and are considered among the globe's largest man-made emission sources of BC particles. However, during these fire events, not only BC particles are emitted, but also other types of particles and gases that can interact with each other to create new particles, generating a slew of particles often generally referred to as BB aerosols. Although the majority of the fire emissions occur inland in the sub-Saharan part of Africa, their effect reaches far beyond the continent due to the prevailing easterly winds, which transport those aerosols over the South-East Atlantic (SEA) ocean, off the west-coast of Africa. The reason why these particles are so important to the regional and global climate is that they absorb sunlight radiation, which overall warms the climate. However, the magnitude of this warming effect is highly uncertain and depends upon a multitude of aspects. Our overarching goal for this project was to better understand the changes in the aerosol properties as they transport from fire sources downstream toward the ocean and how this can eventually affect the earth's radiative budget in terms of warming or cooling. Following the above, our work here was focused on the investigation of the African BB aerosol plumes mixing state (mixing of BB aerosols and other aerosol types), composition and size distribution as they transport from the African continent towards the SEA ocean, and their link with some of the commonly measurable bulk optical properties such as mass absorption coefficient (MAC) and single scattering albedo (SSA). We utilized three field missions that were conducted over the SEA ocean between 2016 and 2018. Specifically, we used (1) ground-based measurements from the DOE ARM Mobile Facility (AMF1), which was deployed at Ascension Island (ASI) for the LASIC (Layered Atlantic Smoke Interactions with Clouds) campaign between June 2016 and October 2017, (2) airborne measurements from the UK CLARIFY (Clouds and Aerosol Radiative impacts and Forcing) campaign during Aug-Sep-2017, and (3) airborne measurements from the ORACLES (Observations of Aerosols above Clouds and their interactions) campaign during Aug-2017, and Sep-Oct-2018. The three campaigns cover a relatively large region, from the western African coast on the east towards Ascension Island in the middle of the SEA to the west. We used the data gathered by these campaigns to find how BB properties and composition change from near emission sources (the ORACLES campaign flights) downstream (the CLARIFY flights and the ground based LASIC measurements). We used particle trajectory following methodologies to connect the measurements from the different campaigns, which allowed us to follow a certain aerosol plume (airmass) from near-source towards Ascension Island. We found out that atmospheric aging processes governed by the UV light from the sun (photochemistry) and cloud processes (aqueous chemistry) govern the changes seen in the particle composition during the transport were more dominant in dictating aerosol composition than specific emission composition or source types. We assessed how aerosol optical properties change during the BB season and what are the main drivers of this change. We found that the enhanced ratio of BC to CO is well correlated with single scattering albedo (SSA) and mass absorption coefficient (MACBC), providing a simple way to estimate the aerosol optical characteristics in the south-eastern Atlantic Ocean. From the analysis of the location of BB, the primary source fuel, the water content in the fuel, combined with the mean cloud cover and precipitation in the transport areas of the BB plume, we conclude that the increase in BC/CO from June to August is likely to be caused by burning becoming more flaming (hot fires), and the decrease in BC/CO in September and October may be caused by smoldering (colder) fires. We found that aerosol hygroscopicity increases with decreasing altitude below 2km, and that enhanced BB hygroscopicity at lower altitudes is mainly due to a lower organic aerosol (OA) fraction, increased sulfate fraction, and greater hygroscopicity parameter of OA at lower altitudes.
54 ENVIRONMENTAL SCIENCES↗
Interdisciplinary Approaches Improve Understanding of Cryptogenic Species: A Historical Case Study of Crayfish in Montana, USA
ABSTRACT Cryptogenic species are those that are not yet “demonstrably native or introduced” in a given area, such as crayfish in western Montana, USA. Delving into evidence from diverse fields can help clarify the status of cryptogenic species. Primary historical sources and indigenous knowledge have informed various ecological questions but are seldom used to clarify the status of cryptogenic species, especially aquatic taxa. We summarize types of evidence used to illuminate species status and offer a case study applying historical sources to cryptogenic crayfish in Montana. We searched for crayfish mentions in dictionaries of indigenous languages and primary historical documents (e.g., travel journals, newspaper accounts, early biological surveys). Early explorer accounts we examined did not mention crayfish in Montana, though they noted them in the nearby Snake River drainage of Idaho and Wyoming. The first mention of crayfish in Montana that we found was from an 1868 newspaper account, probably referencing the upper Missouri River. The species was not noted, but an 1887 article suggested signal crayfish Pacifastacus leniusculus introductions near Bozeman, where non‐native signal crayfish still persist. The earliest crayfish mention we found west of the Great Divide in Montana was from 1934 in Ninepipes and probably referred to non‐native virile crayfish ( Faxonius virilis ). Signal crayfish were not mentioned west of the Divide until a 1944 newspaper account noted their 1937 introduction to the Bitterroot River drainage. The case study demonstrates the value of historical sources in identifying the absence of species and documenting their presence or introduction during periods predating scientific data.
Kennedy, Hampton L. [USDA Forest Service, Southern↗
Rapid grain refinement and compositional homogenization in a cast binary Cu50Ni alloy achieved by friction stir processing
Friction stir processing (FSP) has been increasingly adopted for joining and processing materials in automotive, aerospace and industrial construction. During FSP a dynamic competition between high-speed shear deformation and deformation-induced heating brings about a complex competition between multiple dynamic microstructural evolution mechanisms making it difficult to predict the microstructural evolution pathway. Hence, improved understanding of microstructural evolution mechanisms during FSP can be beneficial for continued growth in the adoption of FSP for demanding applications of future. Towards this goal, this study uses a model binary Cu – 50 at.% Ni alloy to clarify the effect of single and double pass FSP on the microstructural evolution of a coarse grained and compositionally heterogeneous cast microstructure. High energy synchrotron X-ray diffraction, electron backscatter diffraction, and nanoindentation are used to clarify the microstructural evolution due to FSP. The process of compositional homogenization of as-cast segregations is studied by energy dispersive spectroscopy and atom probe tomography. Our results show that a single fast FSP pass at 30 mm.s -1 produces a 100 µm deep layer of submicrometric and hall-petch hardened CuNi grains. The initial cast compositional heterogeneities in a micrometric scale is rapidly transformed to nano-sized domains, mainly confined at grain boundaries. Double pass FSP increases the penetration depth of the processed layer and leads to a 2.9 times grain growth relative to single pass FSP. Grain fragmentation, discontinuous dynamic recrystallization, grain growth, and twinning mechanisms are discussed. In conclusion, these results highlight the value of FSP for ultrafast grain refinement and compositional homogenization of cast alloys.
36 MATERIALS SCIENCE↗
Comment on “Stepped pressure profile equilibria in cylindrical plasmas via partial Taylor relaxation” [J. Plasma Physics (2006), vol. 72, part 6, pp. 1167–1171]
In an early study of the properties and capabilities of the multiregion, relaxed magnetohydrodynamic model, Hole, Hudson & Dewar claim that they are able to construct a multiregion stepped pressure cylindrical equilibrium which does not require the existence of surface currents. We present a brief argument showing that this claim is incorrect, and clarify the meaning of their statement. Furthermore, even with the statement clarified, we demonstrate that it is not possible to find solutions to reproduce the equilibrium corresponding to the parameters given in the article. We invite the authors to provide a corrigendum with the correct values of the equilibrium they constructed.
Physics↗
Trisodium Phosphate Phases and Solubility in Alkaline Solutions Relevant to Radioactive Waste Processing
The U.S. Department of Energy’s Hanford Site faces significant challenges in managing millions of gallons of legacy radioactive waste, where phosphate precipitation can obstruct pipelines during retrieval and processing. To resolve long-standing inconsistencies in reported solubility and clarify factors governing trisodium phosphate hydrates, we examined the Na3PO4:NaOH:H2O system. Powder and single-crystal X-ray diffraction revealed that commercial precursors undergo transformations that produce multiple hydrates, including three previously unreported phases comprising an ordered polymorph of Na3(PO4)·12H2O·1/6NaOH, Na3PO4·5H2O, and Na3PO4·9H2O. Computational modeling indicated that the ordered dodecahydrate is more stable than its disordered counterpart, suggesting kinetic persistence of structural disorder. Solubility measurements were conducted with solutions prepared either from anhydrous Na3PO4 or from Na3(PO4)·12H2O·1/6NaOH and revealed that release of interstitial NaOH from the hydrate precursor elevated solution alkalinity, thereby significantly reducing phosphate solubility relative to solutions prepared with anhydrous Na3PO4 across 20–44 °C. These results begin to reconcile inconsistencies in prior solubility data and clarify how phase composition dictates phosphate precipitation under alkaline conditions.
Graham, Trenton R. (ORCID:0000000189078004)↗
Exotic Carbonate Mineralization Recovered from a Deep Basalt Carbon Storage Demonstration
Mitigating climate change require transformational advances for carbon dioxide removal, including geologic carbon sequestration in reactive subsurface environments. The Wallula Basalt Carbon Storage Pilot Project demonstrated that CO 2 injected into >800 m deep Columbia River Basalt Group flow top reservoirs mineralizes on month-year timescales. Herein, we present new optical petrography, micro-computed X-ray tomography, and electron microscopy results sidewall cores collected two years after CO 2 injection. As no other anthropogenic carbonates from geologic carbon storage field studies have been recovered, this world-unique sample suite provides unparalleled insight for subsurface carbon mineralization products and paragenesis. Chemically-zoned nodules with Ca/Mn-rich cores and Fe-dominant outer rims are prominent examples of the neoformed carbonate assemblages with ankerite-siderite compositions and exotic divalent cation correlations. Further, paragenetic insights for the timing of aragonite, silica, and fibrous zeolites are clarified based on mineral texture and spatial relationships, along with time-resolved downhole fluid sampling. Collectively, these results clarify the mineralogy, chemistry, and paragenesis of carbon mineralization, providing insight into the ultimate fate and transport of CO 2 in reactive mafic-ultramafic reservoirs
54 ENVIRONMENTAL SCIENCES↗
Exploring Ligand-to-Metal Charge-Transfer States in the Photo-Ferrioxalate System Using Excited-State Specific Optimization
The photo-ferrioxalate system (PFS), [Fe(III)(C 2 O 4 )] 3– , more than an exact chemical actinometer, has been extensively applied in wastewater and environment treatment. Despite many experimental efforts to improve clarity, important aspects of the mechanism of ferrioxalate photolysis are still under debate. In this paper, we employ the recently developed WΓ-CASSCF to investigate the ligand-to-metal charge-transfer states that are key to ferrioxalate photolysis. This investigation provides a qualitative picture of these states and key potential energy surface features related to the photolysis. Furthermore, our theoretical results are consistent with the prompt charge-transfer picture seen in recent experiments and clarify some features that are not visible in experiments. Two ligand-to-metal charge-transfer states contribute to the photolysis of ferrioxalate, and the avoided crossing barrier between them is low compared with the initial photoexcitation energy. Our data also clarify that one Fe–O bond cleaves first, followed by the C–C bond and the other Fe–O bond.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes
The light harvesting 2 (LH2) complex of purple bacteria has excellent energy conversion efficiency. Clarifying the design principle behind such efficiency at the atomistic level is crucial for understanding its structure–function relationship and can be utilized for the design of artificial light harvesting systems. To this end, we conducted comprehensive computational investigation of the dynamical and statistical nature of electronic excited states of pigment molecules in a natural LH2 complex with 9-fold symmetry and its two non-natural in silico analogues with 6- and 12-fold symmetries. To ensure reliable and efficient all-atomistic molecular dynamics simulations, we combined a well established interpolation approach for the construction of the potential energy surface with a neural network machine learning approach. Outcomes of these calculations clarify that non-natural forms of LH2-type complexes have significantly larger quasistatic disorder than those for the natural one. In addition, non-natural systems have more disruptions of the hydrogen bonding, underscoring its crucial role for reducing the disorder. On the other hand, local environmental dynamics are relatively insensitive to the structural changes although there is moderate enhancement in the anharmonic or interatomic components for the synthetic ones. These findings based on all-atomistic simulations provide direct computational evidence that the structure and sizes of natural LH2 complexes are designed to minimize the energetic disorder. We analyze quantitative implications of these for the energy transferring capability of the LH2 complex.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystallography, Morphology, Electronic Structure, and Transport in Non-Fullerene/Non-Indacenodithienothiophene Polymer:Y6 Solar Cells
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99 GENERAL AND MISCELLANEOUS↗