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DOE OSTI2024

Microbial abundances and carbon use under ambient temperature or experimental warming in a southern boreal peatland

Abstract Organic peat soils occupy relatively little of the global land surface area but store vast amounts of soil carbon in northern latitudes where climate is warming at a rapid pace. Warming may result in strong positive feedbacks of carbon loss and global climate change driven by microbial processes if warming alters the balance between primary productivity and decomposition. To elucidate effects of warming on the microbial communities mediating peat carbon dynamics, we explored the abundance of broad microbial groups and their source of carbon (i.e. old carbon versus more recently fixed photosynthate) using microbial lipid analysis (δ 13 C PLFA) of peat samples under ambient temperatures and before/after initiation of experimental peat warming (+ 2.25, + 4.5, + 6.75, and + 9 °C). This analysis occurred over a profile to 2 m depth in an undrained, ombrotrophic peat bog in northern Minnesota. We found that the total microbial biomass and individual indicator lipid abundances were stratified by depth and strongly correlated to temperature under ambient conditions. However, under experimental warming, statistically significant effects of temperature on the microbial community were sporadic and inconsistent. For example, 3 months after experimental warming the relative abundance of Gram-negative bacterial indicators across depth combined and > 50 cm depth and Gram-positive bacterial indicators at 20–50 cm depth showed significant positive relationships to temperature. At that same timepoint, however, the relative abundance of Actinobacterial indicators across depth showed a significant negative relationship to temperature. After 10 months of experimental warming, the relative abundance of fungal biomarkers was positively related to temperature in all depths combined, and the absolute abundance of anaerobic bacteria declined with increasing temperature in the 20–50 cm depth interval. The lack of observed response in the broader microbial community may suggest that at least initially, microbial community structure with peat depth in these peatlands is driven more by bulk density and soil water content than temperature. Alternatively, the lack of broad microbial community response may simply represent a lag period, with more change to come in the future. The long-term trajectory of microbial response to warming in this ecosystem then could either be direct, after this initial lag time, or indirect through other physical or biogeochemical changes in the peat profile. These initial results provide an important baseline against which to measure long-term microbial community and carbon-cycling responses to warming and elevated CO 2 .

Felice, Mark↗

DOE OSTI2026

Benchmarking Cylindrical Blast Wave Theory Against the OSIRIS-REx Sample Return Capsule Reentry

Weak shock theory based on cylindrical blast waves has been used to interpret meteor infrasound, but it has not been systematically benchmarked against a non-ablating hypersonic source with independently known parameters. The objective of this study is not to propose a new theoretical framework, but to evaluate the operational validity of the existing suite of blast radius formulations against a high-fidelity ground truth dataset. The OSIRIS-REx Sample Return Capsule reentry on 24 September 2023 provides such a benchmark because the capsule geometry, trajectory, and infrasound emission points are constrained from mission data and ray tracing, reducing source-side uncertainty associated with ablation. Using observations from 39 infrasound stations, this benchmarking study evaluates six published blast radius (${R}_{0}$ ) formulations and three weak-shock transition coefficients ( C ) within a stratified atmospheric propagation model to predict signal period and peak overpressure. The benchmarking identifies the Sakurai formulation as the best-performing formulation for non-ablating bodies, with the Jones/Plooster formulation performing comparably when a physically appropriate C is adopted. Sakurai and Jones/Plooster yield linear-period median absolute percentage residuals of 9% and 11%, respectively. The period predictions show only weak sensitivity to C at these propagation distances. The Mach-diameter approximation commonly used in meteor studies overestimates ${R}_{0}$ by more than a factor of 3 in the absence of ablation. Finally, these results establish a performance baseline for applying cylindrical blast wave theory to effectively non-ablating hypersonic bodies and demonstrate that the signal period is a robust observable for constraining ${R}_{0}$.

atmospheric entry↗

DOE OSTI2025

Effect of seasonal anoxia on geochemical cycling in a stratified pond: Comparison to cooler pond conditions 40 years ago

Seasonal stratification in temperate lakes deeper than a few meters creates favorable conditions for pronounced vertical redox zones, often resulting in anaerobic hypolimnions and significant geochemical changes. Here, this study examined thermocline formation and trace element behavior in a seasonally stratified pond amid rising air temperatures. Over two years, data were collected from Pond B at the US Department of Energy Savannah River Site in Aiken, South Carolina. Pond B, a man-made monomictic reservoir, received cooling water from a nuclear reactor from 1961 to 1964. Strong thermal stratification forms a distinct thermocline in May and progresses downward until November. Compared to the 1980s, this study shows a delayed onset and extended duration of stratification. The prolonged summer stratification reduces deep water oxygen replenishment, extending hypoxic conditions. Trace and major elements sampled in the water column revealed strong correlations between As, Fe, and Mn profiles, with concentrations increasing by 1–2 orders of magnitude in the anaerobic hypolimnion. This period captured the seasonal transition from winter mixing to summer stratification to fall overturn. Under anoxic conditions, Fe(III) reduces to Fe(II) in the sediment, releasing dissolved iron into the water column. The extended anoxic periods likely promoted arsenic release from sediments. Prolonged anoxia may enhance arsenic mobilization and solubility in the lake. This study illustrates how climate-induced changes in seasonal stratification of contaminated waters can convert contaminant sinks into sources, offering insights into the cycling of arsenic and other dissolved ions in stratified lakes and their implications for water quality management.

Anoxic conditions↗

DOE OSTI2025

The impact of kidney function on Alzheimer’s disease blood biomarkers: implications for predicting amyloid-β positivity

Impaired kidney function has a potential confounding effect on blood biomarker levels, including biomarkers for Alzheimer’s disease (AD). Given the imminent use of certain blood biomarkers in the routine diagnostic work-up of patients with suspected AD, knowledge on the potential impact of comorbidities on the utility of blood biomarkers is important. We aimed to evaluate the association between kidney function, assessed through estimated glomerular filtration rate (eGFR) calculated from plasma creatinine and AD blood biomarkers, as well as their influence over predicting Aβ-positivity. We included 242 participants from the Translational Biomarkers in Aging and Dementia (TRIAD) cohort, comprising cognitively unimpaired individuals (CU; n = 124), mild cognitive impairment (MCI; n = 58), AD dementia (n = 34), and non-AD dementia (n = 26) patients all characterized by [ 18 F] AZD-4694. Plasma samples were analyzed for Aβ42, Aβ40, glial fibrillary acidic protein (GFAP), neurofilament light chain (NfL), tau phosphorylated at threonine 181 (p-tau181), 217 (p-tau217), 231 (p-tau231) and N-terminal containing tau fragments (NTA-tau) using Simoa technology. Kidney function was assessed by eGFR in mL/min/1.73 m 2 , based on plasma creatinine levels, age, and sex. Participants were also stratified according to their eGFR-indexed stages of chronic kidney disease (CKD). We evaluated the association between eGFR and blood biomarker levels with linear models and assessed whether eGFR provided added predictive value to determine Aβ-positivity with logistic regression models. Biomarker concentrations were highest in individuals with CKD stage 3, followed by stages 2 and 1, but differences were only significant for NfL, Aβ42, and Aβ40 (not Aβ42/Aβ40). All investigated biomarkers showed significant associations with eGFR except plasma NTA-tau, with stronger relationships observed for Aβ40 and NfL. However, after adjusting for either age, sex or Aβ-PET SUVr, the association with eGFR was no longer significant for all biomarkers except Aβ40, Aβ42, NfL, and GFAP. When evaluating whether accounting for kidney function could lead to improved prediction of Aβ-positivity, we observed no improvements in model fit (Akaike Information Criterion, AIC) or in discriminative performance (AUC) by adding eGFR to a base model including each plasma biomarker, age, and sex. While covariates like age and sex improved model fit, eGFR contributed minimally, and there were no significant differences in clinical discrimination based on AUC values. We found that kidney function seems to be associated with AD blood biomarker concentrations. However, these associations did not remain significant after adjusting for age and sex, except for Aβ40, Aβ42, NfL, and GFAP. While covariates such as age and sex improved prediction of Aβ-positivity, including eGFR in the models did not lead to improved prediction for any biomarker. Our findings indicate that renal function, within the normal to mild impairment range, does not seem to have a clinically relevant impact when using highly accurate blood biomarkers, such as p-tau217, in a biomarker-supported diagnosis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression

Although ~40% of screen-detected prostate cancers (PCa) are indolent, advanced-stage PCa is a lethal disease with 5-year survival rates around 29%. Identification of biomarkers for early detection of aggressive disease is a key challenge. Starting with 52 candidate biomarkers, selected from existing PCa genomics datasets and known PCa driver genes, we used targeted mass spectrometry to quantify proteins that significantly differed in primary tumors from PCa patients treated with radical prostatectomy (RP) across three study outcomes: (i) metastasis ≥1-year post-RP, (ii) biochemical recurrence ≥1-year post-RP, and (iii) no progression after ≥10 years post-RP. Sixteen proteins that differed significantly in an initial set of 105 samples were evaluated in the entire cohort (n = 338). A five-protein classifier which combined FOLH1, KLK3, TGFB1, SPARC, and CAMKK2 with existing clinical and pathological standard of care variables demonstrated significant improvement in predicting distant metastasis, achieving an area under the receiver-operating characteristic curve of 0.92 (0.86, 0.99, p = 0.001) and a negative predictive value of 92% in the training/testing analysis. This classifier has the potential to stratify patients based on risk of aggressive, metastatic PCa that will require early intervention compared to low risk patients who could be managed through active surveillance.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia

Acute myeloid leukemia is a poor prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and don’t always predict therapeutic response. Here we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measured the proteome and phosphoproteome of 210 patients and combined them with genomics and transcriptomic measurements to identify four proteogenomic subtypes that complemented existing genetic subtypes. We then built a predictor to classify samples into subtypes based on 147 molecular features and mapped them to a ‘landscape’. Each region of this landscape corresponded to specific drug response patterns. We then built a drug response prediction model to identify drugs that target distinct subtypes. We can ultimately use these models to predict drug treatment response and prioritize treatments. Finally, we extended our models and mapped a series of cell lines representing various stages of quizartinib resistance into our subtype landscape, predicting and experimentally validating a switch in sensitivity to venetoclax to panobinostat, two drugs with very different mechanisms than quizartinib. Our results show how multi-omics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Quantifying wind plant blockage under stable atmospheric conditions

Wind plant blockage reduces the wind velocity upstream undermining turbine performance for the first row of the plant. We assess how atmospheric stability modifies the induction zone of a wind plant in flat terrain. We also explore different approaches to quantifying the magnitude and extent of the induction zone from field-like observations. To investigate the influence from atmospheric stability, we compare simulations of two stable boundary layers using the Weather Research and Forecasting model in large-eddy simulation mode, representing wind turbines using the generalized actuator disk approach. We find a faster cooling rate at the surface, which produces a stronger stably stratified boundary layer, amplifies the induction zone of both an isolated turbine and of a large wind plant. A statistical analysis on the hub-height wind speed field shows wind slowdowns only extend far upstream (up to 15D) of a wind plant in strong stable boundary layers. To evaluate different ways of measuring wind plant blockage from field-like observations, we consider various ways of estimating the freestream velocity upstream of the plant. Sampling a large area upstream is the most accurate approach to estimating the freestream conditions, and thus of measuring the blockage effect. Also, the choice of sampling method may induce errors of the same order as the velocity deficit in the induction zone.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Organochlorine pesticides and risk of papillary thyroid cancer in U.S. military personnel: a nested case-control study

Background: The effects of organochlorine pesticide (OCP) exposure on the development of human papillary thyroid cancer (PTC) are not well understood. A nested case-control study was conducted with data from the U.S. Department of Defense Serum Repository (DoDSR) cohort between 2000 and 2013 to assess associations of individual OCPs serum concentrations with PTC risk. Methods: This study included 742 histologically confirmed PTC cases (341 females, 401 males) and 742 individually-matched controls with pre-diagnostic serum samples selected from the DoDSR. Associations between categories of lipid-corrected serum concentrations of seven OCPs and PTC risk were evaluated for classical PTC and follicular PTC using conditional logistic regression, adjusted for body mass index category and military branch to compute odds ratios (OR) and 95% confidence intervals (CIs). Effect modification by sex, birth cohort, and race was examined. Results: There was no evidence of associations between most of the OCPs and PTC, overall or stratified by histological subtype. Overall, there was no evidence of an association between hexachlorobenzene (HCB) and PTC, but stratified by histological subtype HCB was associated with significantly increased risk of classical PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 1.61, 95% CI, 1.09, 2.38; p for trend = 0.05) and significantly decreased risk of follicular variant PTC (third tertile above the limit of detection (LOD) vs. <LOD, OR = 0.38, 95% CI, 0.16, 0.91; p for trend = 0.04). Further stratified by sex, risk of classical PTC was higher for females (third tertile above LOD vs. <LOD, OR = 2.23, 95% CI: 1.23, 4.06; p-trend = 0.02) than for males (OR = 1.22, 95%CI: 0.72–2.08; p-trend = 0.56), though the test for interaction by sex was not statistically significant (p-interaction = 0.30). Similarly, β-hexachlorocyclohexane (β-HCCH) was associated with a higher risk for classical PTC for women with concentrations ≥LOD versus <LOD (OR = 1.76, 95% CI: 1.07, 2.89), while the effects were null for men. There were no consistent trends when stratified by race or birth year. Conclusions: The U.S. Environmental Protection Agency has classified HCB and other OCPs we studied here as probable human carcinogens. Our findings of increased risks for classical PTC associated with increased concentrations of HCB and β-HCCH, which were stronger among females, should be replicated in future studies of other populations.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

A statistical approach to screening isotopic signatures in monitoring for underground nuclear explosions

The ability to differentiate between atmospheric radionuclide signatures from underground nuclear explosions (UNEs) and signals from other sources, such as medical isotope-production facilities and nuclear reactors, can be critical to the detection and monitoring of unannounced, low-yield nuclear events. Signatures having anomalously high amplitudes, compared to background levels, remain the best indicator in screening for a UNE. However, isotopic composition can further validate a suspected UNE signature, but separation from any atmospheric background composition is first necessary. To date, evaluating the challenges of performing this separation has typically involved comparing an observed background with a highly idealized deterministic model of radioxenon signature production by a UNE that does not consider the influence of post-detonation chemical/physical processes in the detonation cavity or the subsequent gas transport mechanisms that can also affect the isotopic composition of the detected gas signature. In addition, purely deterministic models, as previously employed, overlook the uncertainty inherent in estimating critical parameters characterizing the UNE and its detonation environment. In this paper, we create detailed, multi-parameter models of radionuclide evolution using the widely accepted England and Rider post-detonation radionuclide decay-chain network coupled to detailed models simulating physical production and transport processes affecting the gas signature. Because these models are governed by uncertain parameters including barometric fluctuations, realistic ranges of variation for each of the parameters influencing isotopic composition are then defined. A Latin-Hypercube sampling approach is used to obtain a random distribution of isotopic production and gas transport results associated with a given value of each parameter. We apply these results to background histories of two stations, one providing 4-isotope background measurements and the other providing two-isotope measurements associated with the 2013 DPRK announced UNE.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2022

Probing eddy size and its effective mixing length in stably stratified roughness sublayer flows

Stably stratified roughness sublayer flows are ubiquitous yet remain difficult to represent in models and to interpret using field experiments. Here, continuous high-frequency potential temperature profiles from the forest floor up to 6.5 times the canopy height observed with distributed temperature sensing (DTS) are used to link eddy topology to roughness sublayer stability correction functions and coupling between air layers within and above the canopy. The experiments are conducted at two forest stands classified as hydrodynamically sparse and dense. Near-continuous profiles of eddy sizes (length scales) and effective mixing lengths for heat are derived from the observed profiles using a novel conditional sampling approach. The approach utilizes potential temperature isoline fluctuations from a statically stable background state. The transport of potential temperature by an observed eddy is assumed to be conserved (adiabatic movement) and we assume that irreversible heat exchange between the eddy and the surrounding background occurs along the (vertical) periphery of the eddy. This assumption is analogous to Prandtl's mixing-length concept, where momentum is transported rapidly vertically and then equilibrated with the local mean velocity gradient. A distinct dependence of the derived length scales on background stratification, height above ground, and canopy characteristics emerges from the observed profiles. Implications of these findings for (1) the failure of Monin–Obukhov similarity in the roughness sublayer and (2) above-canopy flow coupling to the forest floor are examined. The findings have practical applications in terms of analysing similar DTS data sets with the proposed approach, modelling roughness sublayer flows, and interpreting nocturnal eddy covariance measurements above tall forested canopies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Three-Dimensional Pore Networks in Miocene Stevens Sandstone of California: Implications for CO 2 Geologic Storage

The Miocene Stevens Sandstone in the San Joaquin Basin of California is increasingly recognized as a promising candidate for CO 2 geological storage due to the enormous storage capacity, proven sealing, and existing infrastructure. In this study, computed microtomography imaging and pore network modeling were employed to investigate the influence of pore geometry and wettability on the CO 2 injectivity and residual trapping. Image analysis revealed that a significant fraction of the cement and matrix consists of microporous regions. The microporosity can substantially increase the overall pore space, yet its contribution to permeability remains modest, particularly in samples with low permeability. The intrinsic heterogeneity of turbidite reservoirs further complicates the reservoir properties among different layers. Two-phase flow simulations under varying wettability conditions (water-wet, weak water-wet, and neutral-wet) demonstrated that the CO 2 injection is predominantly controlled by macropores. CO 2 invades microporous regions only after these larger pores are filled. The presence of microporosity leads to a decrease in both initial and residual CO 2 saturations, with the magnitude of the reduction being influenced by wettability. Neutral-wet scenarios exhibit higher CO 2 mobility and thus lower residual trapping than water-wet scenarios. The results imply that heterogeneity in pore geometry and cement distribution across different layers can result in stratified CO 2 flow pathways, complicating efforts to predict injection performance. Overall, the Stevens Sandstone shows considerable promise for CO 2 geologic storage, but effective implementation will require detailed characterization of the pore structure as well as the integration of reactive fluid flow to account for potential mineral dissolution and fines migration.

fluids↗

DOE OSTI2023

Verifying Ray Tracing Amplitude Methods for Global Magnetospheric Modeling

Abstract Ray tracing is a commonly used method for modeling the propagation of electromagnetic waves in Earth's magnetosphere. To apply ray tracing results to global models of wave‐particle interaction such as energetic electron scattering, it is useful to map the discrete rays to a volume filling mesh. However, some methods have inherent losses of energy from the wave source, or do not account for the full range of wave properties within a sample volume. We have developed and tested a 3D magnetospheric ray tracing code “MESHRAY” which resolves these issues. MESHRAY uses the conservation of Poynting flux through ray triplets with finite volume to determine the local field amplitudes. Electromagnetic wave energy density from all ray data points is mapped to a mesh and verified against the wave source power for energy conservation varying time step length, number of rays, and total time steps. We find that the method is self‐consistent and numerically robust. We further investigate whether the neglect of phase information and superposition has a significant impact on the accuracy of mapping wave intensity to a mesh. We find excellent agreement between the analytic solution for waves emitted by a line source in a plane‐stratified medium and an equivalent ray tracing solution. When phase information is excluded, ray tracing reproduces an average amplitude spread over regions of coherent constructive and destructive interference. This may be an important consideration for interpolating ray tracing results of longer wavelength waves such as magnetosonic, electromagnetic ion cyclotron, or ULF waves.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

In situ aerobic methane oxidation rates in a stratified lake

Abstract Microbial aerobic methane oxidation is an important sink for aquatic methane worldwide. Despite its importance to global methane fluxes, few aerobic methane oxidation rates have been obtained in freshwater or marine environments without imposing changes to the microbial community through use of ex situ methods. A novel in situ incubation method for continuous time‐series measurements was used in Jordan Lake, North Carolina, during 2020–2021, to determine reaction kinetics for aerobic methane oxidation rates across a wide range of naturally varying methane (55–1833 nM) and dissolved oxygen (DO; 28–366 μM) concentrations and temperatures (17–30°C). Methane oxidation began immediately at the start of each of 21 incubations and methane oxidation rates were 1 st order with respect to methane. The data density allowed for accurate calculation of 1 st ‐order rate constants,k, that ranged from 0.018 to 0.462 h −1 (R 2 > 0.967). Addition of ammonium (20–45 μM) to natural concentrations ranging from 0.057 to 2.4 μM did not change aerobic methane oxidation rate kinetics, suggesting that the natural population of aerobic methane oxidizers in this eutrophic lake was not nitrogen limited. Values ofkinversely correlated most strongly with initial DO concentrations (R 2 = 0.82) rather than temperature. Values forkincreased with Julian day throughout our sampling period, suggesting seasonal influences on methane oxidation via responses to geochemical changes or shifts in microbial community abundance and composition. These experiments demonstrate a high variability in the enzymatic capacity for 1 st ‐order methane oxidation rates in this eutrophic lake that is tightly and inversely coupled to oxygen concentrations. Measurements of in situ aerobic methane oxidation rate constants allow for the direct quantification and modeling of the microbial community's capacity for methane oxidation over a wide range of natural methane concentrations.

Marine & Freshwater Biology↗

DOE OSTI2025

Updating Critical Temperature Calculations for Several Secondary High Explosives

In designing experiments where high explosives (HEs) are heated, it is important to have an understanding of where thermal runaway may occur. This determination is often done by using the Frank-Kamenetskii (FK) equation. For several highly-studied HEs, the parameters necessary for FK calculations are typically referenced from decades-old literature, and more recent experimental data have shown that these values require adjustment. For example, some of the legacy parameters dangerously overpredict the critical temperature by tens of degrees relative to more recent observed values. Herein, we first summarize historical results and highlight the importance of insulation effects when estimating critical temperatures for small samples, which is especially relevant to small-scale aging, compatibility, and characterization experiments. Here, we then present updated FK parameters for several common secondary CHNO HEs like RDX, HMX, PETN, and TATB, as well as the first reported values for 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105). Our updated parameters produce critical-temperature curves that are consistent with both mm-scale differentical scanning calorimetry (DSC) measurements and cm-scale data from the Lawrence Livermore National Laboratory one-dimensional time-to-explosion (ODTX) experiment. In analyzing the critical temperature versus sample size curves derived from the transcendental FK equation, we discovered that these curves are remarkably well described by a simple power-law function with a universal power of 0.142 and a HE-specific scaling factor.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2024

Longitudinal analysis of host protein serum signatures of treatment and recovery in pulmonary tuberculosis

A better understanding of treatment progression and recovery in pulmonary tuberculosis (TB) infectious disease is crucial. This study analyzed longitudinal serum samples from pulmonary TB patients undergoing interventional treatment to identify surrogate markers for TB-related outcomes. Serum that was collected at baseline and 8, 17, 26, and 52 weeks from 30 TB patients experiencing durable cure were evaluated and compared using a sensitive LC-MS/MS proteomic platform for the detection and quantification of differential host protein signatures relative to timepoint. The global proteome signature was analyzed for statistical differences across the time course and between disease severity and treatment groups. A total of 676 proteins showed differential expression in the serum over these timepoints relative to baseline. Comparisons to understand serum protein dynamics at 8 weeks, treatment endpoints at 17 and 26 weeks, and post-treatment at 52 weeks were performed. The largest protein abundance changes were observed at 8 weeks as the initial effects of antibiotic treatment strongly impacted inflammatory and immune modulated responses. However, the largest number of proteome changes was observed at the end of treatment time points 17 and 26 weeks respectively. Post-treatment 52-week results showed an abatement of differential proteome signatures from end of treatment, though interestingly those proteins uniquely significant at post-treatment were almost exclusively downregulated. Patients were additionally stratified based upon disease severity and compared across all timepoints, identifying 461 discriminating proteome signatures. These proteome signatures collapsed into discrete expression profiles with distinct pathways across immune activation and signaling, hemostasis, and metabolism annotations. Insulin-like growth factor (IGF) and Integrin signaling maintained a severity signature through 52 weeks, implying an intrinsic disease severity signature well into the post-treatment timeframe. Previous proteome studies have primarily focused on the 8-week timepoint in relation to culture conversion status. While this study confirms previous observations, it also highlights some differences. The inclusion of additional end of treatment and post-treatment time points offers a more comprehensive assessment of treatment progression within the serum proteome. Examining the expression dynamics at these later time periods will help in the investigation of relapse patients and has provided indicative markers of response and recovery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Mapping brucellosis risk in Kenya and its implications for control strategies in sub-Saharan Africa

In Sub-Saharan Africa (SSA), effective brucellosis control is limited, in part, by the lack of long-term commitments by governments to control the disease and the absence of reliable national human and livestock population-based data to inform policies. Therefore, we conducted a study to establish the national prevalence and develop a risk map for Brucella spp. in cattle to contribute to plans to eliminate the disease in Kenya by the year 2040. We randomly generated 268 geolocations and distributed them across Kenya, proportionate to the area of each of the five agroecological zones and the associated cattle population. Cattle herds closest to each selected geolocation were identified for sampling. Up to 25 cattle were sampled per geolocation and a semi-structured questionnaire was administered to their owners. We tested 6,593 cattle samples for Brucella immunoglobulin G (IgG) antibodies using an Enzyme-linked immunosorbent assay (ELISA). We assessed potential risk factors and performed spatial analyses and prevalence mapping using approximate Bayesian inference implemented via the integrated nested Laplace approximation (INLA) method. The national Brucella spp. prevalence was 6.8% (95% CI: 6.2–7.4%). Exposure levels varied significantly between agro-ecological zones, with a high of 8.5% in the very arid zone with the lowest agricultural potential relative to a low of 0.0% in the agro-alpine zone with the highest agricultural potential. Additionally, seroprevalence increased with herd size, and the odds of seropositivity were significantly higher for females and adult animals than for males or calves. Similarly, animals with a history of abortion, or with multiple reproductive syndromes had higher seropositivity than those without. At the herd level, the risk of Brucella spp. transmission was higher in larger herds, and herds with a history of reproductive problems such as abortion, giving birth to weak calves, or having swollen testes. Geographic localities with high Brucella seroprevalence occurred in northern, eastern, and southern regions of Kenya all primarily characterized by semi-arid or arid agro-ecological zones dominated by livestock pastoralism interspersed with vast areas with mixed livestock-wildlife systems. The large spatial extent of our survey provides compelling evidence for the widespread geographical distribution of brucellosis risk across Kenya in a manner easily understandable for policymakers. Our findings can provide a basis for risk-stratified pilot studies aiming to investigate the cost-effectiveness and efficacy of singular and combined preventive intervention strategies that seek to inform Kenya’s Brucellosis Control Policy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Metatranscriptomics reveals a shift in microbial community composition and function during summer months in a coastal marine environment

Abstract Temperate coastal marine waters are often thermally stratified from spring through fall but can be dynamic and disrupted by tidal currents and wind‐driven upwelling. These mixing events introduce deeper, cooler water with a higher partial pressure of CO 2 (pCO2) and its associated microbial communities to the surface. Anecdotally, these events impact shellfish hatcheries and farms, warranting improved understanding of changes in composition and activity of marine microbial communities in relation to environmental processes. To characterize both compositional and functional changes associated with abiotic factors, here, we generate a reference metatranscriptome from the Strait of Georgia over representative seasons and analyze metatranscriptomic profiles of the microorganisms present within intake water containing different pCO 2 levels at a shellfish hatchery in British Columbia from June through October. Abiotic factors studied include pH, temperature, alkalinity, aragonite, calcite, and pCO 2 . Community composition changes were observed to occur at broad taxonomic levels and most notably to vary with temperature and pCO 2 . Functional gene expression profiles indicated a strong difference between early (June–July) and late summer (August–October) associated with viral activity. The taxonomic data suggest this could be due to the termination of cyanobacteria and phytoplankton blooms by viral lysis in the late season. Functional analysis indicated fewer differentially expressed transcripts associated with abiotic variables (e.g., pCO 2 ) than with the temporal effect. Microbial composition and activity in these waters vary with both short‐term effects observed alongside abiotic variation and long‐term effects observed across seasons. The analysis of both taxonomy and functional gene expression simultaneously in the same samples by environmental RNA (eRNA metatranscriptomics) provided a more comprehensive view for monitoring water bodies than either would in isolation.

Sutherland, Ben J. G.↗

DOE OSTI2020

Blazar variability power spectra from radio up to TeV photon energies: Mrk 421 and PKS 2155−304

ABSTRACT We present the results of the power spectral density (PSD) analysis for the blazars Mrk 421 and PKS 2155−304, using good-quality, densely sampled light curves at multiple frequencies, covering 17 decades of the electromagnetic spectrum, and variability time-scales from weeks up to a decade. The data were collected from publicly available archives of observatories at radio from Owens Valley Radio Observatory, optical and infrared (B, V, R, I, J, H, and Kbands), X-rays from the Swift and the Rossi X-ray Timing Explorer, high and very high energy (VHE) γ-rays from the Fermi and Very Energetic Radiation Imaging Telescope Array System as well as the High Energy Stereoscopic System. Our results are: (1) the power-law form of the variability power spectra at radio, infrared, and optical frequencies have slopes ∼1.8, indicative of random-walk-type noise processes; (2) the power-law form of the variability power spectra at higher frequencies, from X-rays to VHE γ-rays, however, have slopes ∼1.2, suggesting a flicker noise-type process; and (3) there is significantly more variability power at X-rays, high and VHE γ-rays on time-scales ≲ 100 d, as compared to lower energies. Our results do not easily fit into a simple model, in which a single compact emission zone is dominating the radiative output of the blazars across all the time-scales probed in our analysis. Instead, we argue that the frequency-dependent shape of the variability power spectra points out a more complex picture, with highly inhomogeneous outflow producing non-thermal emission over an extended, stratified volume.

Goyal, Arti↗