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At least 469 records · Page 26

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DOE OSTI2020

The state of algal genome quality and diversity

The genomic era of biology has created unprecedented opportunity to study how life works, including understanding evolutionary principles, bioprospecting for novel antibiotics, and genetic manipulation of bioeconomically-relevant species. While genome sequencing and genomic analysis was previously restricted to large-scale projects and consortia, sequencing has become democratized. However, as genomics has become commonplace, the cataloging of sequenced organisms has become challenging, and standardized practices for sequencing, assembly, and annotation have not been adopted. This is equally true in research fields such as algal biology, despite the growing importance of algae in a bio-based economy. Here, in this study, we provide a comprehensive review of the state of eukaryotic algal genomics, explore the quality of algal genome assemblies, and identify the biases and gaps in the current species distribution to inform the development of future genome projects. Overall, we find a trend of declining quality of genomic resources, including a reduction in assembly quality, gene annotation quality, and genome completeness. Potential solutions to improve genome quality include widespread utilization of long read and scaffolding technologies, implementation of standards for assembly quality, evidence-based gene annotation and requisite publication, and support of continued development of gene prediction and genome assessment software.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Grazer-induced changes in molecular signatures of cyanobacteria

Algal biomass production is an emerging renewable source of fuels, nutrients, manufacturing materials, and pharmaceuticals. Industrial-scale production is predominantly performed in open raceway ponds that are inexpensive to build, operate, and maintain compared to closed bioreactors. However, these open pond systems suffer from increased opportunities for biological contamination from predators, pathogens, and competitors, which result in reduced biomass quality and yields and often the complete destruction of the crop over a short period of time. Early detection of contaminants is a necessary step of integrated pest management for triggering and informing interventions to prevent crop losses. To develop a sensitive method of detection utilizing mass spectrometry (MS), we used three methods – imaging mass spectrometry (imaging MS), liquid chromatography MS/MS (LC-MS/MS) combined with molecular networking, and gas chromatography MS/MS (GC–MS/MS) – to observe and identify molecular signatures from a model predator-prey system of the heterolobosean amoeba HGG1 preying on the filamentous cyanobacterium Anabaena sp. PCC 7120. Imaging MS enabled the association of molecules with the crop, the predator, or the activity of protozoan grazing, while LC-MS/MS-based molecular networking identified a subset of the grazing-specific signals as the chlorophyll breakdown products pyropheophytin, pheophorbide A, and pyropheophorbide. Application of MS techniques to other amoebacyanobacterial predator-prey pairs allowed categorization of grazing signatures as universal or specific to the species of prey, predator, or the prey-predator pairing, indicating that MS-based techniques can distinguish crops from competitors and potentially identify predators. Finally, GCMS/MS was shown to be capable of monitoring novel volatile organic compounds (VOCs), including those predicted to be released through chlorophyll breakdown, in the headspace over algal cultures under predation. Furthermore, these results demonstrate that the combination of multiple MS technologies creates a predictive framework to identify and catalog relevant molecular signatures for informing crop protection strategies.

09 BIOMASS FUELS↗

DOE OSTI2026

Cellulose-MOFs hybrid materials: Chemistry and mechanism of applications in biomedical - A review

Rising costs and performance limits of modern biomedical materials motivate the search for advanced, biocompatible alternatives. Cellulose-based metal-organic frameworks (cellulose-MOFs) emerge as distinctive hybrids combining renewable polymer chemistry with tunable porous architectures, enabling uncommon structure–function relationships. Their large surface area, controllable pore size, adaptable functional groups, and efficient host–guest interactions underpin diverse biomedical functions. Till now, no comprehensive, application-focused review has systematically summarized cellulose-MOFs synthesis for biomedical applications. This review critically analyzes cellulose-MOFs, emphasizing mechanistic links between chemistry, synthesis routes, interfacial interactions, and biomedical performance, rather than cataloging applications alone. Antibacterial action, targeted drug delivery, and sensing/biosensing are discussed through comparative insights. The article identifies unresolved challenges and proposes future research pathways to rationally design next-generation cellulose-MOFs systems, guiding researchers and clinicians alike.

Biomedical↗

DOE OSTI2026

Discovery and engineering of enzymes for new-to-nature photobiocatalysis

Photobiocatalysis integrates enzymatic catalysis with photochemistry, enabling challenging radical transformations with high selectivity under mild conditions. Early developments in this field were largely driven by the discovery that enzyme-bound cofactors can form photoactive charge–transfer complexes with substrates, thereby initiating radical chemistry upon light irradiation. Recent advances, however, have substantially expanded the mechanistic landscape of photobiocatalysis through diverse mechanisms. This review summarizes major developments in photobiocatalysis reported since 2024. Rather than cataloging individual reactions, we focus on the fundamental mechanisms of radical generation and interception within enzyme active sites, and discuss how these mechanistic principles guide the discovery, engineering, and design of enzymes for new-to-nature photobiocatalysis.

Bai, Zibo [University of Illinois Urbana-Champaign↗

DOE OSTI2021

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Saddle point sampling using scaled normal coordinates

The sampling of saddle points (SPs) on a potential energy surface (PES) is critical for describing the dynamics and transport properties of materials. In this paper we propose a saddle point search (SPS) method that enables efficient sampling of practically meaningful SPs around a local minimum by converting the PES to the scaled normal coordinates (SNCs), together with the dimer method. We find that the pathway leading to a SP using SNCs is highly efficient and is independent of the system size. This results in the significantly increased SPS efficiency and the enhanced possibility of a complete catalog of the SPs. In addition, we perform SPSs using the SNCs for the diffusion of a vacancy and a dumbbell in body-centered cubic Fe and demonstrate (1) the required number of system force evaluations for a SPS decreases by at least an order of magnitude, (2) the effects of the system size on the number of force evaluations are greatly decreased, and (3) the effects of the number of atoms involved in the SPS on the probability of finding practically meaningful SPs is mostly eliminated. We also discuss the computational cost of introducing the SNCs. It should be highlighted that the SNCs could also be applied to other minimum-mode following methods, demonstrating the general versatility of the proposed method.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Challenges for the statistical gravitational-wave method to measure the Hubble constant

Gravitational waves (GW) can be employed as standard sirens that will soon measure the Hubble constant with sufficient precision to weigh in on the ~5σ Hubble tension. Most GW sources will have no identified electromagnetic counterpart, leading to uncertainty in the redshift of the source, and in turn a degeneracy between host galaxy distance, redshift, and H 0 . In the case where no electromagnetic counterparts are identified, it has been proposed that a statistical canvassing of candidate GW hosts, found in a large galaxy survey for example, can be used to accurately constrain the Hubble constant. We study and simulate this "galaxy voting" method to compute H 0 . Here, we find that the Hubble constant posterior is in general biased relative to the true value even when making optimistic assumptions about the statistical properties of the sample. Using the MICECAT light-cone catalog, we find that the bias in the H0 posteriors depends on the realization of the underlying galaxy sample and the precision of the GW source distance measurement.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A research agenda for the science of actionable knowledge: Drawing from a review of the most misguided to the most enlightened claims in the science-policy interface literature

Linking science with action affords a prime opportunity to leverage greater societal impact from research and increase the use of evidence in decision-making. Success in these areas depends critically upon processes of producing and mobilizing knowledge, as well as supporting and making decisions. For decades, scholars have idealized and described these social processes in different ways, resulting in numerous assumptions that now variously guide engagements at the interface of science and society. We systematically catalog these assumptions based on prior research on the science-policy interface, and further distill them into a set of 26 claims. We then elicit expert perspectives (n = 16) about these claims to assess the extent to which they are accurate or merit further examination. Out of this process, we construct a research agenda to motivate future scientific research on actionable knowledge, prioritizing areas that experts identified as critical gaps in understanding of the science-society interface. The resulting agenda focuses on how to define success, support intermediaries, build trust, and evaluate the importance of consensus and its alternatives – all in the diverse contexts of science-society-decision-making interactions. We further raise questions about the centrality of knowledge in these interactions, discussing how a governance lens might be generative of efforts to support more equitable processes and outcomes. We offer these suggestions with hopes of furthering the science of actionable knowledge as a transdisciplinary area of inquiry.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

Geothermal Play Fairway Analysis, Part 2: GIS methodology

Play Fairway Analysis (PFA) in geothermal exploration originates from a systematic methodology developed within the petroleum industry and is based on a geologic, geophysical, and hydrologic framework of identified geothermal systems. We tailored this methodology to study the geothermal resource potential of the Snake River Plain and surrounding region, but it can be adapted to other geothermal resource settings. We adapted the PFA approach to geothermal resource exploration by cataloging the critical elements controlling exploitable hydrothermal systems, establishing risk matrices that evaluate these elements in terms of both probability of success and level of knowledge, and building a code-based ‘processing model’ to process results. A geographic information system was used to compile a range of different data types, which we refer to as elements (e.g., faults, vents, heat flow, etc.), with distinct characteristics and measures of confidence. Discontinuous discrete data (points, lines, or polygons) for each element were transformed into continuous interpretive 2D grid surfaces called evidence layers. Because different data types have varying uncertainties, most evidence layers have an accompanying confidence layer which reflects spatial variations in these uncertainties. Risk layers, as defined here, are the product of evidence and confidence layers, and are the building blocks used to construct Common Risk Segment (CRS) maps for heat, permeability, and seal, using a weighted sum for permeability and heat, but a different approach with seal. CRS maps quantify the variable risk associated with each of these critical components. In a final step, the three CRS maps were combined into a Composite Common Risk Segment (CCRS) map, using a modified weighted sum, for results that reveal favorable areas for geothermal exploration. Additional maps are also presented that do not mix contributions from evidence and confidence (to allow an isolated view of evidence and confidence), as well as maps that calculate favorability using the product of components instead of a weighted sum (to highlight where all components are present). Our approach helped to identify areas of high geothermal favorability in the western and central Snake River Plain during the first phase of study and helped identify more precise local drilling targets during the second phase of work. By identifying favorable areas, this methodology can help to reduce uncertainty in geothermal energy exploration and development.

15 GEOTHERMAL ENERGY↗

DOE OSTI2024

Seismic monitoring of EGS fracture stimulations at Utah FORGE (Part 1): Time-lapse variations of b-values and Shear-wave Splitting Rates of induced microearthquakes

Characterizing geologic formations near geothermal wells is crucial for efficient extraction of subsurface geothermal energy resources. To monitor effective fracture stimulation of enhanced geothermal systems (EGS), we analyze a catalog of induced microearthquakes to characterize seismicity induced by Phase 2C fracture stimulations of the Utah FORGE project and derive the b-values for 424 induced microearthquakes in three stages of fracture stimulation. Here, we find the time-lapse variations of these b-values. We apply eigenvector rotation and waveform correlation to 3C geophone data to separate fast S 1 and slow S 2 waves, determine their directions, measure their lag time, and calculate the S-wave splitting rate (SSR) for six induced microearthquakes in Stage 1 and 21 in Stage 3. Both SSR values and b-values increase with time. The increase in these values may be related to heavily fractured zones created by fracture stimulations during Stage 2 injections. Large and highly variable SSR values in Stage 3 may reflect heterogeneities in the fracture zones. Time-lapse variations of SSR values and b-values may be one of the most useful approaches to monitoring and characterizing the effectiveness and efficiency of various types of fracture stimulations.

58 GEOSCIENCES↗

DOE OSTI2022

SNAD transient miner: Finding missed transient events in ZTF DR4 using k-D trees

Here we report the automatic detection of 11 transients (7 possible supernovae and 4 active galactic nuclei candidates) within the Zwicky Transient Facility fourth data release (ZTF DR4), all of them observed in 2018 and absent from public catalogs. Among these, three were not part of the ZTF alert stream. Our transient mining strategy employs 41 physically motivated features extracted from both real light curves and four simulated light curve models (SN Ia, SN II, TDE, SLSN-I). These features are input to a k-D tree algorithm, from which we calculate the 15 nearest neighbors. After pre-processing and selection cuts, our dataset contained approximately a million objects among which we visually inspected the 105 closest neighbors from seven of our brightest, most well-sampled simulations, comprising 89 unique ZTF DR4 sources. Our result illustrates the potential of coherently incorporating domain knowledge and automatic learning algorithms, which is one of the guiding principles directing the SNAD team. It also demonstrates that the ZTF DR is a suitable testing ground for data mining algorithms aiming to prepare for the next generation of astronomical data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Distinct Assembly Processes and Microbial Communities Constrain Soil Organic Carbon Formation

Soil stores more carbon (C) than all vegetation and the atmosphere combined. Soil C stocks are broadly shaped by temperature, moisture, soil physical characteristics, vegetation, and microbial-mediated metabolic processes. The efficiency with which microorganisms use soil C regulates the balance between C storage in soil and the atmosphere. In this review, we discuss how microbial physiology and community assembly processes determine microbial growth rate and efficiency and, in turn, soil organic C cycling through the lens of community ecology. We introduce a conceptual framework cataloging life history (i.e., growth rate, resource acquisition, and stress tolerance) and assembly traits (i.e., competition, facilitation, and dispersal) that correspond with different growth efficiencies. We also compare how dominant mycorrhizal fungal type affects growth efficiency. We propose that further development and inclusion of specific community parameters in microbial-explicit Earth system models are needed for accurately predicting soil organic C responses to global change.

carbon sequestration↗

DOE OSTI2025

An end-to-end deep learning solution for automated LiDAR tree detection in the urban environment

Cataloging and classifying trees in the urban environment is a crucial step in urban and environmental planning; however, manual collection and maintenance of this data is expensive and time-consuming. Although algorithmic approaches that rely on remote sensing data have been developed for tree detection in forests, they generally struggle in the more varied urban environment. This work proposes a novel end-to-end deep learning method for the detection of trees in the urban environment from remote sensing data. Specifically, we develop and train a novel PointNet-based neural network architecture to predict tree locations directly from LiDAR data augmented with multi-spectral imagery. We compare this model to a number of high-performing baselines on a large and varied dataset in the Southern California region, and find that our method outperforms all baselines in terms of tree detection ability (75.5% F-score) and positional accuracy (2.28 meter root mean squared error), while being highly efficient. We then analyze and compare the sources of errors, and how these reveal the strengths and weaknesses of each approach. Our results highlight the importance of fusing spectral and structural information for remote sensing tasks in complex urban environments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Standardized nomenclature for photovoltaic connectors

Photovoltaic (PV) systems rely on discrete connectors for the efficient and safe flow of power from module to module and from strings to combiner boxes and inverters. Despite their functional importance, no common nomenclature for PV connectors currently exists, resulting in confusion and miscommunication. Misunderstood terms like "MC4 compatible", "cross-mating", "intermating", "female", and "male" can lead to installation and maintenance errors and compromise system reliability. We believe a standardized terminology will reduce confusion, help support installation best practices, aid in maintenance and repair, inform next-generation designs, and provide a technical basis for improved codes and standards. To that end, we are proposing a standardized glossary for 4 mm PV connectors (the most common type of connector used in PV applications) based on, and validated by, a Sandia National Laboratories' investigation that included the following sources: 1) a comprehensive review of official documents from 20 connector manufacturers, including schematics, datasheets, installation manuals, and catalogs, as well as relevant patents; 2) two rounds of surveys distributed to stakeholders, including connector manufacturers, engineers, asset owners, test labs, and researchers; and 3) visual examination of 25 different models of 4 mm single-pole DC PV connectors to document variations in design and functionality. This work provides a foundation for establishing a clear and consistent terminology for PV connectors that will in turn enable progress toward greater reliability and collaboration across the industry.

14 SOLAR ENERGY↗

DOE OSTI2026

Evaluating the role of green infrastructure features in post-disaster recovery – Case Study of Beaumont, Texas after tropical storm imelda

While green infrastructure (GI) can provide multiple environmental benefits, its role in post-disaster economic and social recovery remains relatively underexplored. This article investigates whether different characteristics of GI, such as size, shape, connectivity, and amenities, affect the resilience of local businesses following Tropical Storm Imelda in Beaumont, Texas. The study utilizes SafeGraph mobility data to analyze foot traffic patterns to local businesses before, during, and after the disaster. FRAGSTATS indices measure GI characteristics (e.g., area, shape index, fractal dimension, proximity) while park features such as sports facilities, playgrounds, water features, and accessibility are cataloged through manual observation. Ordinary Least Squares regression models assess the relationship between park characteristics and post-recovery business performance, controlling for demographic variables including income, race, and poverty levels. Results indicate that certain GI attributes significantly enhance business recovery. Points of interest within walking distance (0.5 miles) of parks demonstrated better post-recovery status compared to those beyond this range. Specifically, parks with larger areas (p < 0.01) and more complex shapes measured by fractal dimension index (p < 0.01) had the strongest positive impact on surrounding businesses' recovery. Interestingly, playgrounds showed a negative correlation with recovery (p < 0.05), likely due to flood damage rendering them unusable during the immediate recovery period. Social vulnerability factors, including higher poverty rates and minority populations, negatively affected recovery outcomes despite park proximity.

Economic resilience↗

DOE OSTI2023

Automatic detection of cataclysmic variables from SDSS images

Abstract Investigating rare and new objects have always been an important direction in astronomy. Cataclysmic variables (CVs) are ideal and natural celestial bodies for studying the accretion process of semi-detached binaries with accretion processes. However, the sample size of CVs must increase because a lager gap exists between the observational and the theoretical expanding CVs. Astronomy has entered the big data era and can provide massive images containing CV candidates. CVs as a type of faint celestial objects, are highly challenging to be identified directly from images using automatic manners. Deep learning has rapidly developed in intelligent image processing and has been widely applied in some astronomical fields with excellent detection results. YOLOX, as the latest YOLO framework, is advantageous in detecting small and dark targets. This work proposes an improved YOLOX-based framework according to the characteristics of CVs and Sloan Digital Sky Survey (SDSS) photometric images to train and verify the model to realise CV detection. We use the Convolutional Block Attention Module to increase the number of output features with the feature extraction network and adjust the feature fusion network to obtain fused features. Accordingly, the loss function is modified. Experimental results demonstrate that the improved model produces satisfactory results, with average accuracy (mean average Precision at 0.5) of 92.0%, Precision of 92.9%, Recall of 94.3%, and $F1-score$ of 93.6% on the test set. The proposed method can efficiently achieve the identification of CVs in test samples and search for CV candidates in unlabeled images. The image data vastly outnumber the spectra in the SDSS-released data. With supplementary follow-up observations or spectra, the proposed model can help astronomers in seeking and detecting CVs in a new manner to ensure that a more extensive CV catalog can be built. The proposed model may also be applied to the detection of other kinds of celestial objects.

Astronomy & Astrophysics↗

DOE OSTI2024

Exploring the Influence of Linker Substitution and Ratios on Cooperative Framework Flexibility through the Mixed-Linker Approach

Cooperatively flexible metal–organic frameworks that exhibit step-shaped, or Type V-like, adsorption–desorption profiles can lower requisite pressure–temperature swings and thus energy input, necessary for an array of gas storage, delivery, and separations applications. However, such benefits are lost if the pressure threshold of the adsorption and desorption steps at a given temperature does not match the conditions dictated by the application, such as H 2 storage and delivery or olefin–paraffin separations. Unfortunately, the discovery of cooperatively flexible frameworks remains wholly serendipitous and de novo design remains impossible. Accordingly, there is a great need to further our understanding of flexibility such that we can intuitively derivatize known frameworks and, ultimately, design entirely new ones to meet the requisite conditions of energy-consumptive processes. In this work, we demonstrate that the mixed-linker, or multivariate, approach is a powerful tool for the derivation of a known flexible framework, with variances in linker substitution and ratio giving rise to a family wherein significant changes to the step-shaped adsorption–desorption profiles for multiple adsorbates are observed. Specifically, we report 12 isostructural mixed-linker derivatives of CdIF-13 (sod–Cd(benzimidazolate) 2 ) with six point-modified benzimidazole linkers spontaneously synthesized through prototypical solvothermal conditions. Furthermore, each is shown by PXRD to exhibit similar reversible flexibility to CdIF-13 and by TGA and DSC to be similarly thermally stable. Isothermal gas adsorption measurements with N 2 at 77 K, CO 2 at 195 K, and propane at 298 K demonstrate the wide-ranging, adsorbate-dependent effects of linker substitution and ratio, including dramatic reductions in the adsorption threshold pressure, evolution of multiple steps, and complete absence of observable adsorption. Aided by prior crystallographic characterization of CdIF-13, the observed trends were analyzed in an attempt to resolve the influence of linker substitution and ratios on structural behavior. In total, this work illustrates how the mixed-linker approach enables the synthesis and study of a large catalog of functionally modified frameworks, which can help identify the variables that influence flexibility and sorption behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Dynamic Earthquake Triggering in Southern California in High Resolution: Intensity, Time Decay, and Regional Variability

Abstract Earthquake triggering by seismic waves has been recognized as a phenomenon for nearly 30 years. However, our ability to study dynamic triggering has been limited by our ability to capture the triggering stresses accurately and record the resultant earthquakes. Here we use full waveforms from a dense seismic network and a modern, high‐resolution seismic catalog to measure triggering in Southern California from 2008 to 2017 based on interevent time ratios. We find that the fractional seismicity rate change, which we term triggering intensity or triggerability, as a function of peak strain change for the period of ∼20 s due to distant earthquakes is monotonically increasing and compatible with earlier measurements made with a disjoint data set from 1984 to 2008. A triggering strain of 1 microstrain is equivalent to the local productivity generated by an M 1.8 earthquakes. This result implies that a prediction of seismicity rate changes can be made based on recorded ground shaking using the same formalism as currently used for aftershock prediction. For a teleseismic event, this small level of triggering occurs throughout the region and thus aggregates to a regional effect. We find that the triggering rate decays after the triggerer follows an Omori‐Utsu law, but at a much slower rate than a typical aftershock sequence. The slow decay rate suggests that an ancillary process such as creep or fluid flow must be part of dynamic triggering. The prevalence of triggering in areas of creep or fluid involvement reinforces this inference. A triggering cascade of secondary earthquakes is insufficient to explain the data.

Miyazawa, Masatoshi↗