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KBase Narrative - Supplemental Data for "Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes"

Here we provide the complete set of circular elements produced by SCAPP from metagenomic data that may represent mobile genetic elements (MGEs). For the publication, these sequences were de-replicated within the high [U] and low [U] sample sets. Additionally, 98 of the circular elements were removed for downstream analysis due to high suspicion of being (1) chloroplast or mitochondrial sequences or (2) erroneously circularized long repeat regions. The complete list of circular elements used for the analysis along with metadata can be found in Tables S5 and S6.

Goff, Jennifer↗

A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2

Abstract The Mediator complex coordinates regulatory input for transcription driven by RNA polymerase II in eukaryotes. reduced epidermal fluorescence4-3 (ref4-3) is a semidominant mutation that results in a single amino acid substitution in the Mediator tail subunit Med5b. Previous characterization of ref4-3 revealed altered expression of a variety of loci in Arabidopsis, including those contributing to phenylpropanoid biosynthesis. Examination of existing RNA-seq data indicated that loci enriched for the transcriptionally repressive chromatin modification H3K27me3 are overrepresented among genes that are misregulated in ref4-3. We used ChIP-seq and RNA-seq to examine the possibility that perturbation of H3K27me3 homeostasis in ref4-3 plants contributed to altered transcript levels. We observed that ref4-3 results in a modest global reduction of H3K27me3 at enriched loci and that this reduction is not dependent on gene expression; however, altered H3K27me3 was not strongly predictive of altered expression in ref4-3 plants. Instead, our analyses revealed a substantial enrichment of targets of the MYC2 transcriptional regulator among genes that exhibit decreased expression in ref4-3. Consistent with previous characterization of ref4-3, we observed that ref4-3-dependent decreased expression of MYC2 targets can be suppressed by loss of another Mediator tail subunit, MED25. This observation is consistent with previous biochemical characterization of MYC2. Our data highlight the diverse and distinct impacts that a single amino acid change in the tail subunit of Mediator can have on transcriptional circuits and raise the prospect that Mediator directly contributes to H3K27me3 homeostasis in plants.

Long, Jiaxin (ORCID:0000000335150706)↗

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations inTP53,PLXNB3, Zinc finger genes, and fewer mutations inSDC2,CDH1,PIK3CA,SVIL, andPTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, includingKIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1, andRBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. Conclusions This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Oncology↗

Radiogenic Ingrowth of 40CA from Decay of 40K Provides a Powerful Tracer for Understanding the Origins of Felsic Magmas

Over time high K/Ca continental crust produces a unique Ca isotopic reservoir, with measurable 40Ca excesses compared to Earth's mantle (ɛCa=0). Thus, values of ɛCai > 1 indicate a significant crustal contribution to a magma. Values of ɛCai (<1) indistinguishable from mantle Ca indicate that the Ca in those magmas is either directly from the mantle, or is from partial melting of newly formed crust. So, whereas 40Ca excesses clearly define crustal contributions, mantle-like 40Ca/44Ca ratios are not as definitive. Here we present Ca isotopic measurements of intermediate to felsic igneous rocks from the western United States, and two crustal xenoliths found within the Fish Canyon Tuff (FCT). The two crustal xenoliths found within the 28.2 Ma FCT of the southern Rocky Mountain volcanic field (SRMVF) yield ɛCa values of ~4 and ~7.5, respectively. The 40Ca excesses of these possible source rocks are due to long-term in situ 40K decay and suggest that they are Precambrian in age. However, the FCT (ɛCai ~0.3) is within uncertainty of the mantle 40Ca/44Ca. Together, these data indicate that little Precambrian crust was involved in the petrogenesis of the FCT. Nd isotopic analyses of the FCT imply that it was generated from 10- 75% of an enriched component, and the Ca isotopic data appear to restrict that component to newly formed lower crust, or enriched mantle. However, the Ca isotopic data do permit assimilation of some crust with low Ca/Nd; decreasing the 143Nd/144Nd without adding much excess 40Ca to the FCT. Several other large tuffs from the SRMVF and from Yellowstone have ɛCai indistinguishable from the mantle. However, a few large tuffs from the SRMVF show significant 40Ca excesses. These tuffs (Wall Mountain, Blue Mesa, and Grizzly Peak) are likely sourced from near, or within the Colorado Mineral Belt. New isotopic measurements of Mesozoic and Tertiary granites from across the northern Great Basin show a range of ɛCai from 0 to ~3. In these samples ɛCai is generally correlated with ɛSri and is broadly negatively correlated with ɛNdi. However, for granites with similar ɛNdi at a given general location ɛCai can vary significantly (1 to 2 epsilon units). In rocks where low ɛNdi could also be due to melting from enriched reservoirs in the mantle lithosphere, the combination of high ɛCai with low ɛNdi clearly identifies crustal melts.

Mills, Ryan D.↗

Integral Experiment Request 523 CED-2 Report

This report documents the final design phase of the Critical Experiment Design (CED-2) conducted as part of integral experiment request (IER) 523. The purpose of IER 523 is to determine critical configurations of 35 weight percent (wt%) enriched uranium dioxide beryllium oxide (UO 2 -BeO) material driven by an annular ring of Seven Percent Critical Experiment (7uPCX) fuel rods at Sandia National Laboratories (Sandia). The experiments will provide benchmark data on water moderated, intermediately enriched UO2 systems as well as Be nuclear data. The experiment will also provide partial validation for the beryllium oxide (BeO) thermal neutron scattering law (TSL) in the thermal energy range. Experiment design concepts, neutronic analysis results, and proposed paths for continuing the CED process are presented. This report builds on the feasibility and justification of experimental need report (CED-0) and preliminary experiment design report (CED-1) completed in December 2021 and September 2023, respectively [1, 2].

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nuclear Data–Induced Uncertainties in Criticality Safety Analyses for High-Burnup and Extended Enrichment Fuels

Criticality safety analyses are conducted to show compliance with regulatory standards and to demonstrate safe operational conditions during the storage and transportation of spent nuclear fuel. Given the increased interest in the industry in low-enriched uranium plus (LEU+) and higher-burnup fuel, it is important to study the impact of such fuels’ use on criticality safety analyses and the resulting nuclear data–induced uncertainties. Here, in this work, nominal pressurized water reactor assemblies with LEU+ fuel enrichments up to 8 wt% 235 U and high burnups up to 80 GWd/tonne U were studied. The assemblies were placed in a generic burnup credit cask GBC-32. As a result of the different covariance libraries, using the ENDF/B-VII.1 nuclear data library consistently resulted in lower nuclear data uncertainties than did the use of the ENDF/B-VIII.0 data library. The highest contribution in the nuclear data–induced uncertainties resulted from the major actinides, and their contribution increased with increasing burnup and enrichment.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Mining Twitter Data to Augment NASA GPM Validation

The Twitter data stream is an important new source of real-time and historical global information for potentially augmenting the validation program of NASA's Global Precipitation Measurement (GPM) mission. There have been other similar uses of Twitter, though mostly related to natural hazards monitoring and management. The validation of satellite precipitation estimates is challenging, because many regions lack data or access to data, especially outside of the U.S. and in remote and developing areas. The time-varying set of "precipitation" tweets can be thought of as an organic network of rain gauges, potentially providing a widespread view of precipitation occurrence. Twitter provides a large source of crowd for crowdsourcing. During a 24-hour period in the middle of the snow storm this past March in the U.S. Northeast, we collected more than 13,000 relevant precipitation tweets with exact geolocation. The overall objective of our project is to determine the extent to which processed tweets can provide additional information that improves the validation of GPM data. Though our current effort focuses on tweets and precipitation, our approach is general and applicable to other social media and other geophysical measurements. Specifically, we have developed an operational infrastructure for processing tweets, in a format suitable for analysis with GPM data; engaged with potential participants, both passive and active, to "enrich" the Twitter stream; and inter-compared "precipitation" tweet data, ground station data, and GPM retrievals. In this presentation, we detail the technical capabilities of our tweet processing infrastructure, including data abstraction, feature extraction, search engine, context-awareness, real-time processing, and high volume (big) data processing; various means for "enriching" the Twitter stream; and results of inter-comparisons. Our project should bring a new kind of visibility to Twitter and engender a new kind of appreciation of the value of Twitter by the science research communities.

validatio↗

Deciphering the Distribution and Crystal-Chemical Environment of Arsenic, Lead, Silica, Phosphorus, Tin, and Zinc in a Porous Ferrihydrite Grain Using Transmission Electron Microscopy and Atom Probe Tomography

Here the interaction of contaminants and nutrients with soil constituents is controlled by processes in intergranular and intragranular pore spaces of organic matter or/and common secondary minerals such as ferrihydrite, ~Fe 3+ 10 O 14 (OH) 2 . This contribution shows that distribution and clustering of the contaminants As, P, Pb, Si, Sn, and Zn in a porous ferrihydrite grain is greatly affected by the heterogeneous size distribution and chemical composition of the pores as well as the ability of their polyhedra to polymerize with the same type of polyhedron. Transmission electron microscopy (TEM) and atom probe tomography (APT) studies are conducted on focused ion beam (FIB) sections extracted from a porous ferrihydrite grain from the smelter-impacted topsoil in Sudbury, Ontario, Canada. The ferrihydrite grain has pore spaces ranging in diameter from tens to hundreds of nanometers. TEM and scanning-TEM studies indicate that the surfaces of the pore walls are enriched in Si. APT data in conjunction with First Near Neighbor (1NN) analyses indicate different degrees of clustering of Pb, As, Sn, Zn, Si, and P within the sample and selected domains. Careful evaluations of 3D atomic plots and 1NN distances indicates the occurrence of polymerized arsenite-, silica-, Sn-, and Zn-polyhedra within pore spaces of the ferrihydrite. Deciphering adsorption, polymerization, and nucleation processes in porous Fe-(hydr)oxides and other soil constituents requires multianalytical approaches and, in this regard, we discuss the advantages and disadvantages of the combination of TEM and APT for characterizing complex environmental samples at the atomic to nanometer scale.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ATIS

Any Threat Intelligence to STIX (ATIS) autogenerates and enriches STIX bundles with data from open source threat intelligence sources.

McCampbell, Taylor↗

Statistical and Machine Learning Approaches to Analyzing Pipeline Incidents in the United States (2010–2024)

This study applies machine learning methods to analyze natural gas pipeline incidents in the United States using the Pipeline and Hazardous Materials Safety Administration (PHMSA) Gas Distribution Incident Dataset (2010–2024). The dataset includes over 600 variables describing incident characteristics, infrastructure attributes, and contributing factors associated with unintentional gas releases. The objective is to assess whether these features can reliably predict the underlying cause of pipeline failures. Multinomial logistic regression and Random Forest models were developed to classify incident causes, including excavation damage, corrosion, equipment failure, and natural forces. Results show that excavation damage is both the most frequent and most predictable cause, with models achieving strong performance for this category. However, when excavation damage is excluded, model accuracy declines significantly, with some models performing near random levels. Across all approaches, severe class imbalance and limited variability in key predictors constrain predictive performance. Pipeline age and diameter emerge as the most influential variables, but they provide insufficient discriminatory power to distinguish among less frequent failure types. These findings indicate that non-excavation-related incidents are rare, heterogeneous, and weakly represented in the dataset, limiting the effectiveness of machine learning classification. Overall, this study highlights the structural limitations of the PHMSA dataset for predictive modeling and underscores the need for improved data balance and feature enrichment. The results reinforce excavation damage prevention as the most impactful strategy for reducing pipeline incidents.

03 NATURAL GAS↗

Corrosion Compatibility of Stainless Steels and Nickel in Pyrolysis Biomass-Derived Oil at Elevated Storage Temperatures

Corrosion compatibility of stainless steels and nickel (Ni200) was assessed in fast pyrolysis bio-oil produced from pyrolysis of high ash and high moisture forest residue biomass. Sample mass change, ICP-MS and post-exposure electron microscopy characterization was used to investigate the extent of corrosion. Among the tested samples, type 430F and type 316 stainless steels (SS430F and SS316) and Ni200 (~98.5% Ni) showed minimal mass changes (less than 2 mg∙cm−2) after the bio-oil exposures at 50 and 80 °C for up to 168 h. SS304 was also considered to be compatible in the bio-oil due to its relatively low mass change (1.6 mg∙cm−2 or lower). SS410 samples showed greater mass loss values even after exposures at a relatively low temperature of 35 °C. Fe/Cr values from ICP-MS data implied that Cr enrichment in stainless steels would result in a protective oxide layer associated with corrosion resistance against the bio-oil. Post exposure characterization showed continuous and uniform Cr distribution in the surface oxide layer of SS430F, which showed a minimal mass change, but no oxide layer on a SS430 sample, which exhibited a significant mass loss.

09 BIOMASS FUELS↗

The deep atmosphere of Venus revealed by high-resolution nightside spectra

The first high-resolution spectroscopic observations of the night side of Venus obtained in two narrow spectral windows centered at 1.74 and 2.3 microns, where the nightside is anomalously bright, are reported. Absorption features from CO2, CO, H2O, HDO, HCl, HF, and COS are detected, and there are a number of unidentified features. A preliminary analysis indicates that the observed radiation is thermal emission from atmospheric layers in the eight-bar pressure region for the 2.3 micron window and even deeper at 1.7 micron. The derived CO and H2O abundances agree with in situ Pioneer measurements in the deep troposphere and are consistent with the high deuterium enrichment inferred from Pioneer data. The first measurements of HCl and HF below the clouds are reported along with the first firm detection of COS.

Bezard, Bruno↗

The local metallicity-surface brightness relationship in galactic disks

We present the results of a first attempt to employ multiaperture masks to obtain spectrophotometry of H II regions in nearby galaxies. A total of 97 H II regions in six southern spiral galaxies were observed using a combination of multiaperture masks and conventional long-slit spectrophotometry. The oxygen abundances derived from the multiaperture mask observations using the empirical abundance diagnostic R(sub 23) are shown to be consistent with those from long-slit spectra and generally show better reproducibility and object definition. Although the number of objects that can be observed simultaneously with this particular system is still quite limited compared with either imaging spectrophotometry or fiber-fed spectrographs, the spectral resolution offered and high throughput in the blue help make multiaperture spectrophotometry a competitive technique for increasing the sampling of H II regions in both radial distance and luminosity. There is still no clear trend of abundance gradient with either the galaxy's luminosity or its Hubble type, although the extrapolated central abundance does appear to correlate with galaxy luminosity/mass. In order to avoid difficulty in choosing an appropriate normalizing radius, we instead plot the oxygen abundance against the underlying I-band surface brightness at the radial distance of the H II region and confirm the existence of a local metallicity-surface brightness reltaionship within the disks of spiral galaxies. Although the simple closed-boc model of galaxy evolution predicts almost the right form of this relationship, a more realistic multizone model employing expnentially decreasing gas infall provides a more satisfactory fit to the observational data, provided the expected enriched gas return from dying low-mass stars shedding their envelopes at late epochs is properly taken into account. This same model, with a star formation law based upon self-regulating star formation in a three-dimensional disk (Dopita & Ryder 1994), is equally capable of accounting for the observed relationship between recent massive star formation and stellar surface brightness (Ryder & Dopita 1994).

Ryder, Stuart D.↗

Methylhopane Biomarker and Carbon Isotopic Evidence for Late Archean Aerobic Ecosystems

Molecular fossils are particularly valuable in early Earth studies because they provide information about microbial sources and ecology. Here we report on the distribution of 2- methyl and 3-methylhopanes preserved in a 2.72-2.56 billion-year-old section of shallow and deepwater sediments of the Hamersley Province [Eigenbrode et aI., submitted]. These biomarkers are mostly from cyanobacteria and oxygen-respiring methanotrophs, respectively. The relative abundance of 2-methylhopanes increases with carbonate abundance in shallow-water facies indicating cyanobacteria were key microbes in shallow ecosystems and suggesting they supplied both molecular oxygen and fixed carbon. The relative abundance of 3-methylhopane strongly correlates with kerogen-carbon isotopic values, and is more abundant in the samples with 13C-enriched signatures. Thus, molecular data provides evidence for cycling of methane in shallow settings, even though the anoxic deeper environments bear stronger 13C-depletion, which together suggests a more complex methane cycle than previously envisioned. Detailed facies analysis of the Hamersley carbon-isotope record reveals temporal changes suggesting continued oxidation of shallow settings favoring the expansion of aerobic ecosystems and respiring organisms [Eigenbrode et aI., 2006, PNAS, 103: 15759]. Similar analysis of published carbon-isotopic records suggests similar, but diachronous, expansion of oxygenated habitats in shallow then deep waters as anaerobic microbial communities gave way to respiring communities fueled by oxygenic photosynthesis before the post 2.45-Ga atmospheric oxygenation event [Eigenbrode et aI., 2006]. The robust relationships observed provide geochemical support for methanogenesis, aerobic methanotrophy, and oxygenic photosynthesis in the late Archean, as well as major ecological shifts linked to biogeochemical reorganization.

Eigenbrode, Jennifer L.↗

LU-HF Age of Martian Meteorite Larkman Nunatek 06319

Lu-Hf isotopic data were collected on mineral separates and bulk rock powders of LAR 06319, yielding an age of 197+/- 29 Ma. Sm-Nd isotopic data and in-situ LA-ICP-MS data from a thin section of LAR 06319 are currently being collected and will be presented at the 2009 LPSC. These new data for LAR 06319 extend the existing data set for the enriched shergottite group. Martian meteorites represent the only opportunity for ground truth investigation of the geochemistry of Mars [1]. At present, approximately 80 meteorites have been classified as Martian based on young ages and distinctive isotopic signatures [2]. LAR 06319 is a newly discovered (as part of the 2006 ANSMET field season) martian meteorite that represents an important opportunity to further our understanding of the geochemical and petrological constraints on the origin of Martian magmas. Martian meteorites are traditionally categorized into the shergottite, nakhlite, and chassignite groups. The shergottites are further classified into three distinct isotopic groups designated depleted, intermediate, and enriched [3,4] based on the isotope systematics and compositions of their source(s).

Shafer, J. T.↗

Correlations Among Microstructure, Morphology, Chemistry, and Isotopic Systematics of Hibonite in CM Chondrites

Introduction: Hibonite is a primary refractory phase occurring in many CAIs, typically with spinel and perovskite. Our microstructural studies of CAIs from carbonaceous chondrites reveal a range of stacking defect densities and correlated non-stoichiometry in hibonite. We also conducted a series of annealing experiments, demonstrating that the Mg-Al substitution stabilized the formation of defect-structured hibonite. Here, we continue a detailed TEM analysis of hibonite-bearing inclusions from CM chondrites that have been well-characterized isotopically. We examine possible correlations of microstructure, morphology, mineralogy, and chemical and isotopic systematics of CM hibonites in order to better understand the formation history of hibonite in the early solar nebula. Methods: Fifteen hibonite-bearing inclusions from the Paris CM chondrite were analyzed using a JEOL 7600F SEM and a JEOL 8530F electron microprobe. In addition to three hibonite-bearing inclusions from the Murchison CM chondrite previously reported, we selected three inclusions from Paris, Pmt1-6, 1-9, and 1-10, representing a range of 26Al/27Al ratios and minor element concentrations for a detailed TEM study. We extracted TEM sections from hibonite grains using a FEI Quanta 3D field emission gun SEM/FIB. The sections were then examined using a JEOL 2500SE field-emission scanning TEM equipped with a Thermo-Noran thin window EDX spectrometer. Results and Discussion: A total of six hibonite-bearing inclusions, including two platy hibonite crystals (PLACs) and four spinel-hibonite inclusions (SHIBs), were studied. There are notable differences in chemical and isotopic compositions between the inclusions (Table 1), indicative of their different formation environment or timing. Our TEM observations show perfectly-ordered, stoichiometric hibonite crystals without stacking defects in two PLACs, 2-7-1 and 2-8-2, and in three SHIBs, Pmt1-6, 1-9, and 1-10. In contrast, SHIB 1-9-5 hibonite grains contain a low density of stacking defects linked to an increase in MgO contents, indicating complex, disordered intergrowths of stoichiometric and MgO-enriched hibonites. From the data collected to date, we find no clear correlation between the microstructures of hibonite and its morphological and mineralogical types that reflect distinct chemical and isotopic systematics [6-8,10]. Interestingly, the presence of no or few stacking defects in hibonite from the PLACs and SHIBs are in contrast to our experimental studies that produced very high densities of stacking defects in hibonite [3-5]. Unlike our experi-ments, electron microprobe data from the PLACs and SHIBs hibonite grains show a strong correlation between (Ti4++Si4+) and Mg2+ cations, suggesting that coupled substitutions of (Ti4++Mg2+) and (Si4++Mg2+) for 2Al3+ inhibit the formation of defect-structured hibonite. However, our experimental studies suggest that kinetics (e.g., cooling rate) or other thermal effects also exert a strong control on the microstructures and chemical compositions of hibonite. In Pmt1-6, elongated perovskite grains present at the hibonite grain boundaries display (121) twinning, indicative of a fast cooling (>50degC/min) after high-temperature events. Therefore, the nebular microstructural characteristics of hibonite, at least in this inclusion, would not have destroyed by subsequent high-temperature annealing. Conclusions: Our TEM observations thus far show no clear correlation in microstructures, morphological and mineralogical characteristics, and chemical and isotopic systematics of hibonites from CM chondrites. The observed variation in stacking defect densities in the hibonites may be controlled by thermal processes in the early solar nebula. A detailed TEM analysis of additional CM hibonite samples is underway to evaluate this hypothesis.

Han, J.↗