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At least 217 records · Page 12

Conditional Filamentation of Paraburkholderia elongata 5N - Data Container

Overview of Dataset This narrative contains assemblies for all Paraburkholderia discussed in Karasz et al. 2022, where their phosphate-solubilizing activity was measured. Assemblies were downloaded from NCBI and annotated with Prokka. These genomes were created in many Narratives and collected here to be more accessible Note: The following naming of assemblies does not correspond with current taxonomic names for the following: Paraburkholderia 5N = Paraburkholderia elongata 5NT Paraburkholderia 1N = Paraburkholderia solitsuga 1NT Paraburkholderia vancouverensis = Paraburkholderia madseniana RL16

59 BASIC BIOLOGICAL SCIENCES↗

Nuclear Data Libraries Sensitivity Studies for ORSA Using SCALE

Subcritical assemblies offer valuable training capabilities in nuclear criticality safety (NCS) for individuals handling fissile material. At Oak Ridge National Laboratory(ORNL), the Oak Ridge Subcritical Assembly (ORSA), a new experimental facility, is being established to provide hands-on training for the Nuclear Criticality Safety Program (NCSP).It is essential to accurately determine the neutron multiplication factor (keff) to ensure that ORSA remains subcritical and safe during operations. This study investigated the sensitivity of keff to variations across Evaluated Nuclear Data File (ENDF/B) libraries, consisting of ENDF/B-VII.1, ENDF/B-VIII.0, and ENDF/B-VIII.1. The analysis was conducted using the CSAS6 sequence in the SCALE-6.3 code system. Individual isotopes in the ORSA model were replaced one at a time with ENDF/B-VII.1 as the base library and changing to ENDF/B-VIII.0or ENDF/B-VIII.1. The results demonstrated that the changes in keffof the nuclides associated with the ORSA model were mostly within the uncertainty of the base model (~24 pcm), except for primary nuclides like Uranium-235and H-poly with few other nuclides. The relative delta keff values of Uranium-235 and H-poly, expressed in pcm, were +280 and -212 in ENDF/B-VIII.0 and +332 and -275 in ENDF/B-VIII.1, respectively, which were notable changes in reactivity. These results demonstrated that ORSA was largely insensitive to variations across these nuclear data libraries.

Hong, Evan [North Carolina State University]↗

Examination of Digital-Delay Rossi-$\alpha$ for 252 Cf-Driven Highly Enriched Uranium Using Organic Scintillators

Neutron noise techniques constitute several analysis methods applicable to non-destructive assay. One technique is the Rossi-α method to calculate the prompt neutron decay constant (α) or its inverse, the prompt neutron period (1/α), for assemblies of fissionable material. This work evaluates a high-data-throughput measurement at the National Criticality Experiments Research Center (NCERC) with organic scintillators measuring a subcritical assembly of highly enriched uranium (HEU) metal (93% 235 U). The assembly comprises hemi shells stacked together to form fully closed shells and is driven by a Cf source at the center. The assembly is a total of 59.85 kg HEU and a k eff of 0.99, according to MCNP6.2 KCODE simulations. Measurements were acquired with a three-by-four array of 5.08-cm-diameter by 5.08-cm-length trans-stilbene crystals 166 cm from the assembly center. Two types of coincident binning methods are used to build the Rossi-α distribution of coincident neutron detections: A) type 1 binning, also known as any-and-all forward time differences, and B) type 1 binning with a digital-delay technique that is analogous to Orndoff’s use of delay cabling in early Rossi-alpha measurements. Method B) disregards same-detector coincidences and once all nearest time coincidences are collected between all detectors after a trigger, a time delay of 0.75 µs is implemented. The measured prompt neutron decay constants for both techniques are calculated from single exponential fits and the two methods are compared. Method A) shows an apparent timing discontinuity near 500 ns time differences. This timing discontinuity interferes with the fitting method used to calculate the prompt neutron decay constant. Method B) mitigates the artificial timing discontinuity and removes the disagreement of the fit. Future work will model the time-dependent detector response to discern why this timing discontinuity occurs, discern how Method B) reduces the amplitude of this timing discontinuity, and apply this method to critical assembly measurements to ultimately confirm the recommendation to use Method B) for high-data-throughput measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota

Abstract The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

The NtrYX Two-Component System Regulates the Bacterial Cell Envelope

ABSTRACT Activity of the NtrYX two-component system has been associated with important processes in diverse bacteria, ranging from symbiosis to nitrogen and energy metabolism. In the facultative alphaproteobacterium Rhodobacter sphaeroides , loss of the two-component system NtrYX results in increased lipid production and sensitivity to some known cell envelope-active compounds. In this study, we show that NtrYX directly controls multiple properties of the cell envelope. We find that the response regulator NtrX binds upstream of cell envelope genes, including those involved in peptidoglycan biosynthesis and modification and in cell division. We show that loss of NtrYX impacts the cellular levels of peptidoglycan precursors and lipopolysaccharide and alters cell envelope structure, increasing cell length and the thickness of the periplasm. Cell envelope function is also disrupted in the absence of NtrYX, resulting in increased outer membrane permeability. Based on the properties of R. sphaeroides cells lacking NtrYX and the target genes under direct control of this two-component system, we propose that NtrYX plays a previously undescribed, and potentially conserved, role in the assembly, structure, and function of the cell envelope in a variety of bacteria. IMPORTANCE The bacterial cell envelope provides many important functions. It protects cells from harsh environments, serves as a selective permeability barrier, houses bioenergetic functions, defines sensitivity to antibacterial agents, and plays a crucial role in biofilm formation, symbiosis, and virulence. Despite the important roles of this cellular compartment, we lack a detailed understanding of the biosynthesis and remodeling of the cell envelope. Here, we report that the R. sphaeroides two-component signaling system NtrYX is a previously undescribed regulator of cell envelope processes, providing evidence that it is directly involved in controlling transcription of genes involved in cell envelope assembly, structure, and function in this and possibly other bacteria. Thus, our data report on a newly discovered process used by bacteria to assemble and remodel the cell envelope.

59 BASIC BIOLOGICAL SCIENCES↗

Evidence for galaxy assembly bias in BOSS CMASS redshift-space galaxy correlation function

ABSTRACT Building accurate and flexible galaxy–halo connection models is crucial in modelling galaxy clustering on non-linear scales. Recent studies have found that halo concentration by itself cannot capture the full galaxy assembly bias effect and that the local environment of the halo can be an excellent indicator of galaxy assembly bias. In this paper, we propose an extended halo occupation distribution (HOD) model that includes both a concentration-based assembly bias term and an environment-based assembly bias term. We use this model to achieve a good fit (χ2/degrees of freedom = 1.35) on the 2D redshift-space two-point correlation function (2PCF) of the Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxy sample. We find that the inclusion of both assembly bias terms is strongly favoured by the data and the standard five-parameter HOD model is strongly rejected. More interestingly, the redshift-space 2PCF drives the assembly bias parameters in a way that preferentially assigns galaxies to lower mass haloes. This results in galaxy–galaxy lensing predictions that are within 1σ agreement with the observation, alleviating the perceived tension between galaxy clustering and lensing. We also showcase a consistent 3σ–5σ preference for a positive environment-based assembly bias that persists over variations in the fit. We speculate that the environmental dependence might be driven by underlying processes such as mergers and feedback, but might also be indicative of a larger halo boundaries such as the splashback radius. Regardless, this work highlights the importance of building flexible galaxy–halo connection models and demonstrates the extra constraining power of the redshift-space 2PCF.

79 ASTRONOMY AND ASTROPHYSICS↗

2024 Buildings Technology Baseline: Dataset Documentation

The Buildings Technology Baseline is a curated and regularly updated dataset of current and projected performance, retail, and installed price data for all major building energy technologies needed to enable cost/benefit analyses. Building technology analyses require an up-to-date understanding of installation costs and cost-effectiveness of key building energy efficiency technologies. The dataset was assembled by Guidehouse during fiscal year 2024. Data was gathered from the 2024 National Residential Efficiency Measures Database (NREMDB), the 2023 Energy Information Administration Updated Buildings Sector Appliance and Equipment Costs and Efficiencies ("EIA Building Data Report"), DOE Lighting Market Model, the 2023 RSMeans database, and the 2020 Grid-Interactive Efficient Building Technology Cost, Performance, and Lifetime Characteristics ("GEB Data Report"), Lawrence Berkeley National Laboratory, various literature, as well as new data from online retailers, stakeholder interviews, and contractor databases in 2023 and 2024. The dataset has been reviewed by subject matter experts at NREL and DOE. The 2024 dataset release is intended to be a starting point for interested users to provide feedback. This database is not intended to provide specific cost estimates for a specific project. The cost estimates do not include any rebates or tax incentives that may be available for the measures. Rather, it is meant to help determine which measures may be more cost-effective. The National Renewable Energy Laboratory (NREL) makes every effort to ensure accuracy of the data; however, NREL does not assume any legal liability or responsibility for the accuracy or completeness of the information.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Forecasting Battery Electrode Performance via Electrochemical Fluorescence Microscopy and Machine-Learning

Predicting lithium-ion battery performance is hindered by microscale electrode heterogeneities invisible to conventional diagnostics. Here, we combine electrochemical fluorescence microscopy (EFM), which maps electronic connectivity by visualizing an electrofluorophore reaction distribution, with a multitask ElasticNet regression to forecast discharge capacity from spatial heterogeneity. Analyzing 196 images from six pilot-scale LiNi 0.5 Mn 0.3 Co 0.2 O 2 cathodes with varying carbon loadings, we extract 62 descriptors that capture morphology and texture. A compact five-feature model predicts capacity across eight discharge rates, achieving a per-target R 2 of up to 0.63 and an overall R 2 of 0.92, with a mean absolute percentage error of less than 2%. This performance rivals impedance-based approaches while avoiding their reliance on postformation data and incomplete electronic network information. Our facile and rapid, image-driven method may enable electrode quality control upstream of costly cell assembly to offer a transformative tool for data-driven battery research and manufacturing.

battery electrodes↗

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗

Machine learning for the redox potential prediction of molecules in organic redox flow battery

Here, organic redox flow batteries (ORFB) are recognized as an innovative technology for the large-scale storage of renewable energy. The redox potential of organic redox-active molecules plays a vital role in their performance. Advanced screening techniques like high-throughput experiment and machine learning (ML) have significantly enhanced organic material performance and transformed the field of ORFB. However, the scarcity of experimental data poses a considerable challenge for ML model development in this domain. In our study, we developed lightweight graph-based Gaussian process regression (GPR) models with GPU-accelerated marginalized graph kernel and hybrid kernel to predict the redox potentials of organic redox-active molecules for ORFBs, specifically focusing on small datasets. To evaluate model accuracy, we created a new experimental database of organic redox-active molecules by the data from hundreds of published papers and assembled previous computational datasets. We also considered some key parameters, such as pH conditions and solvent type, to assess their impact on redox potential prediction. Our GPR model predicted redox potentials with high accuracy across all datasets using minimal training data. The study provides powerful tools for molecule screening and design and delivers valuable guidance on designing training datasets for costly experiments.

25 ENERGY STORAGE↗

Synchrotron-based diffraction-enhanced imaging and diffraction-enhanced imaging combined with CT X-ray imaging systems to image seeds at 30 keV

Utilized the upgraded Synchrotron-based non-destructive Diffraction-enhanced imaging and Diffraction-enhanced imaging coupled with CT X-ray imaging systems to image the chickpea seeds, to enhance the contrast in plant root architecture, visibility of fine structures of root architecture growth and some aspects of physiology at acceptable level. DEI-CT images were acquired with 30 keV synchrotron X-rays. A series of DEI-CT slices were assembled together, to form a 3D data set. DEI-CT images explored more structural information and morphology. Noticed detailed anatomical, physiological observations, and contrast mechanisms. Furthermore, with these systems, some of the complex plant traits, root morphology, growth of laterals and subsequent laterals can be visualized directly.

36 MATERIALS SCIENCE↗

Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater

Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus , as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood–Ljungdahl pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of novel organic polar materials: A machine learning study with importance sampling

Recent advances in the synthesis of polar molecular materials have produced practical alternatives to ferroelectric ceramics, opening up exciting new avenues for their incorporation into modern electronic devices. However, in order to realize the full potential of polar polymer and molecular crystals for modern technological applications, it is paramount to assemble and evaluate all the available data for such compounds, identifying descriptors that could be associated with an emergence of ferroelectricity. In this paper, we utilized data-driven approaches to judiciously shortlist candidate materials from a wide chemical space that could possess ferroelectric functionalities. A machine learning study with importance sampling was employed to address the challenge of having a limited amount of available data on already-known organic ferroelectrics. Sets of molecular- and crystal-level descriptors were combined with a Random Forest Regression algorithm in order to predict the spontaneous polarization of the shortlisted compounds. First-principles simulations were performed to further validate the predictions obtained from the machine learning model.

36 MATERIALS SCIENCE↗

Evidence of galaxy assembly bias in SDSS DR7 galaxy samples from count statistics

We present observational constraints on the galaxy–halo connection, focusing particularly on galaxy assembly bias from a novel combination of counts-in-cylinders statistics, P(N CIC ), with the standard measurements of the projected two-point correlation function w p (r p ), and number density n gal of galaxies. We measure n gal , w p (r p ), and P(N CIC ) for volume-limited, luminosity-threshold samples of galaxies selected from SDSS DR7, and use them to constrain halo occupation distribution (HOD) models, including a model in which galaxy occupation depends upon a secondary halo property, namely halo concentration. We detect significant positive central assembly bias for the M r < -20.0 and M r <-19.5 samples. Central galaxies preferentially reside within haloes of high concentration at fixed mass. Positive central assembly bias is also favoured in the M r < -20.5 and M r < -19.0 samples. We find no evidence of central assembly bias in the M r < -21.0 sample. We observe only a marginal preference for negative satellite assembly bias in the M r < -20.0 and M r < -19.0 samples, and non-zero satellite assembly bias is not indicated in other samples. Our findings underscore the necessity of accounting for galaxy assembly bias when interpreting galaxy survey data, and demonstrate the potential of count statistics in extracting information from the spatial distribution of galaxies, which could be applied to both galaxy–halo connection studies and cosmological analyses.

79 ASTRONOMY AND ASTROPHYSICS↗

The chemical characterization of halo substructure in the Milky Way based on APOGEE

Galactic haloes in a Λ-CDM universe are predicted to host today a swarm of debris resulting from cannibalized dwarf galaxies. The chemodynamical information recorded in their stellar populations helps elucidate their nature, constraining the assembly history of the Galaxy. Using data from APOGEE and Gaia , we examine the chemical properties of various halo substructures, considering elements that sample various nucleosynthetic pathways. The systems studied are Heracles, Gaia -Enceladus/Sausage (GES), the Helmi stream, Sequoia, Thamnos, Aleph, LMS-1, Arjuna, I’itoi, Nyx, Icarus, and Pontus. Abundance patterns of all substructures are cross-compared in a statistically robust fashion. Our main findings include: (i) the chemical properties of most substructures studied match qualitatively those of dwarf Milky Way satellites, such as the Sagittarius dSph. Exceptions are Nyx and Aleph, which are chemically similar to disc stars, implying that these substructures were likely formed in situ ; (ii) Heracles differs chemically from in situ populations such as Aurora and its inner halo counterparts in a statistically significant way. The differences suggest that the star formation rate was lower in Heracles than in the early Milky Way; (iii) the chemistry of Arjuna, LMS-1, and I’itoi is indistinguishable from that of GES, suggesting a possible common origin; (iv) all three Sequoia samples studied are qualitatively similar. However, only two of those samples present chemistry that is consistent with GES in a statistically significant fashion; (v) the abundance patterns of the Helmi stream and Thamnos are different from all other halo substructures.

79 ASTRONOMY AND ASTROPHYSICS↗

Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid's ability to detect novel plasmids.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetic Field Measurements of First Pre-series Full -Length 4.2 m Quadrupole MQXFA03 Using PCB Rotating Coils for the Hi Hi-Lumi LHC Project

The U.S. Hi-Lumi LHC Accelerator Upgrade Project (AUP) and CERN have joined efforts to develop high field quad-rupoles for the Hi-Lumi LHC upgrade. The US national laborato-ries in the AUP project will deliver 10 magnets and each cryostat has two 4.2 m high gradient quadrupoles in it. These magnets are made of Nb3Sn conductors, with large aperture (150 mm) and in-tegrated gradient of 556.9 T. This paper reports on magnetic measurements performed during the vertical test at Brookhaven National Laboratory (BNL) in 2019-2020. A warm measurement Z-Scan (+/- 15 A) with 42 Z-positions before cool-down was per-formed at BNL. The results were directly compared to field data measured at LBNL during magnet assembly. Measured harmonics and magnetic center offsets (ΔX and ΔY) have provided timely and informative diagnostics on the magnet structure’s shape at both warm and cold temperatures. A new centering fixture was de-signed and added to better center the warm bore tube which con-tains the rotating coil probe. After the quench training to 16.47 kA was achieved, a complete set of cold measurements (Z-Scan at 16.47 kA and I-Scan from 960 A to 16.47 kA and back to 960 A) was made. Periodic axial variation of allowed and nonallowed harmonics was observed which is related to the coil radial and/or mid-plane variations along the magnet axis. Overall, the average harmonics in the straight section are within the required field boundaries.

43 PARTICLE ACCELERATORS↗