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At least 37 records · Page 2

Persistent urinary metabolic signatures in children with type 1 diabetes

There are an estimated 3.7 million people with undiagnosed type 1 diabetes (T1D), living primarily in poor areas of the globe. Therefore, there is a need for non-invasive, affordable tests to provide accurate diagnosis despite the time post-disease onset and fasting state. Here, we studied persistent urinary T1D biomarkers that can be used to develop such tests. Here, we analyzed the urine metabolomes of three independent cohorts of samples collected within 48 h (from Indiana University), and 1 year (from University of Colorado) and 1–10 years (6 years in average) (from Children’s National Medical Center) post-diagnosis. Samples were submitted to gas chromatography-mass spectrometry and machine learning an0alyses to determine diagnostic metabolite panels. The data were also mapped into a metabolic pathway to understand persistently regulated processes in T1D. Seven metabolites showed consistent increases in all three cohorts: d-glucose, d-mannose, myo-inositol, 3-hydroxyisobutyric acid, gluconolactone, d-gluconic acid, and d-glucuronic acid. A combination of machine learning analysis and metabolite ratios as biomarker candidates diagnosed T1D with high sensitivity and specificity across different cohorts and times. Mapping the regulated metabolites into a pathway showed impairment in glycolysis and overflow of glucose towards other pathways in subjects with T1D that was persistent over time. We identified and cross-validated highly specific and sensitive urinary biomarkers. This opens opportunities to develop affordable, robust, and non-invasive tests. The results also show that most of the biomarkers were signatures of dysregulated glucose metabolism.

Type 1 diabetes

Contextualizing Non-Powered Dam Site Selection for Archimedes Screw Turbines: A Methodology for Responsible Archimedes Screw Turbine Conversion at Existing Dams

Non-powered dams represent 97% of dams in the United States and their energy generation potential has not been fully realized. The use of an Archimedes screw turbine to generate power at non-powered dams offers a dual benefit; producing electricity, and acting as downstream fish passage, helping to reconnect previously separated ecosystems. In this study, we assess the technical, environmental, social, and economic feasibility of generating power at non-powered U.S. dam sites using Archimedes screw turbines by integrating mechanical constraints, social impact metrics, proximity to infrastructure, and environmental sensitivity data. Results account for future precipitation predictions and show, between 2024 and 2050, the number of sites where Archimedes screw turbines are viable decreases by one site, but overall generation capacity increases due to increased flow rates across persisting locations. Our analysis identified 82 non-powered dam sites with a mean generation capacity of 49 kW that meet the mechanical requirements for Archimedes screw turbine technology in 2024. Our analysis presents a framework for considering social, environmental, and economic impacts of specific turbine technologies to convert non-powered dams to generate power.

Archimedes screw turbine

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.

Interpretation of high-harmonic fast-wave propagation in the scrape-off layer of NSTX-U as a geometrically bounded-waveguide mode

This paper revisits the onset of high-harmonic fast-wave (HHFW) propagation in the scrape-off layer (SOL) plasma of the NSTX/NSTX-U spherical tokamak, motivated by past HHFW heating and current drive experiments and modelling. Previously, the fast-wave propagation in the SOL was correlated with the opening (suppression) of the fast-wave right-hand cutoff layer in front of the antenna. In this work, the SOL propagation is interpreted as a geometric waveguide mode guided by the SOL geometry, whose radial width can be comparable to the wave’s perpendicular wavelength in the HHFW regime. A two-dimensional circular model is first employed using full-wave solvers to characterise the poloidal eigenmode structures and to clarify their relationship to annulus resonance. By progressively adding a tokamak-like magnetic-field configuration, starting from a uniform axial field, the effects of magnetic-field gradients and pitch on the SOL waveguide mode are characterised. The poloidal mode numbers supported by the SOL plasma agree well with analytic estimates, indicating that an anisotropic plasma in a bounded geometry selectively supports and amplifies the resonant poloidal mode number. Additionally, two-dimensional axisymmetric NSTX-U simulations demonstrate that the SOL eigenmode features identified in the circular model persist in the experimentally relevant configurations. A control approach based on lengthening the wave perpendicular wavelength relative to the SOL width, including a higher magnetic (B)-field operation, is discussed. The analysis here shows the key role of a bounded geometry in interpreting HHFW eigenmode coupling and propagation in the NSTX-U SOL plasma.

plasma heating

Persistence and potential of soil organic carbon in nature‐based climate solutions: A review of managed disturbances

Societal Impact Statement Implementing nature-based climate solutions is important for mitigating climate change, which is a global issue, but requires local adjustments in management practices. Using the association between soil carbon and minerals as a proxy for carbon persistence, we evaluated the effect of different management regimes on soil carbon sequestration and loss. We identified areas where management practices that increase carbon inputs should be prioritized and areas where management should focus on avoiding severe disturbances. Using this storage-potential-and-persistence framework to identify how to increase or maintain soil organic carbon storage locally will increase the effectiveness of nature-based climate solutions globally. Summary Increasing soil organic carbon storage could reduce the pace of climate change, but the longevity of this nature-based climate solution depends on the persistence of carbon in soils, not just the input rates into soils. We apply a framework for considering how soil carbon persistence—namely, via the association with minerals—sheds light on soil carbon sequestration. We review how management of disturbances, such as prescribed burning, forestry, and grazing, can change soil carbon storage, persistence, and potential. Past work demonstrated that management of disturbances can sequester soil carbon, but it remains unclear how the potential stabilization of that accrual and vulnerability to loss varies across disturbance types and geographies. We found that there is substantial geographical heterogeneity in the overlap among estimates of carbon accrual, disturbance occurrence, and potential stabilization: Fire-prone grasslands and intensively grazed rangelands occur in areas estimated to have high potential to store mineral-associated organic carbon, and studies also find that adjusted fire and grazing can promote mineral-associated organic carbon. Plantation forestry and burned area span large regions where particulate organic matter is the dominant form, and studies find that particulate organic carbon is disproportionately lost following intense wildfires and forest harvests. Thus, areas with high mineral-associated organic carbon deficits should be prioritized for practices that increase carbon inputs; whereas areas with high proportions of particulate organic carbon should be prioritized for practices that help to avoid severe disturbances. Taken together, the distribution of and changes in persistence mechanisms shed light on the durability of nature-based climate solutions.

fire

Flame Chemistry Workshop: a perspective on challenges and strategic actions in combustion experiments and chemical kinetics modeling

Continued progress in the development of predictive models for combustion chemistry—including ignition and flame behavior, species evolution, and combustion system performance—relies on overcoming enduring and emerging challenges in experimental measurements, theoretical formulations, and chemical kinetics mechanism construction. As combustion science continues to coincide with advances in sustainable fuels development, plasma technologies, and automated modeling capabilities, the need for coordinated, community-driven strategies is essential. The Flame Chemistry Workshop (FCWS), held biennially before the International Symposium on Combustion, serves as a dedicated platform to identify, consolidate, and address these challenges in a structured and collaborative manner. This perspective arises from discussions at the 7th FCWS in Milan, Italy (2024), and presents a collective view of the critical barriers currently limiting progress. Across the five technical domains discussed during the 7th FCWS – sustainable fuels combustion, advanced diagnostics for combustion measurements, experiments and modeling in plasma combustion, artificial intelligence and automated methods for theory and mechanisms generation, and chemical kinetic models—a series of persistent and emerging scientific challenges were identified, highlighting the need for deeper integration between three areas: theory, experiments, and modeling. In conclusion, the present article concisely describes present challenges that were identified in each of the technical domains in an effort to streamline and coordinate solutions to accelerate progress in combustion science.

Chemical kinetics

Residual symmetries and scalar multiplet vacuum alignment in non-Abelian flavour models

We demonstrate that, upon minimizing a renormalizable, single-scalar potential invariant under a non-Abelian symmetry, special orientations in the associated vacuum alignment of the scalar multiplet correspond to the preservation of a discrete residual flavour symmetry in the broken phase of the theory. Conversely, we show that these special scalar alignments are perturbed when additional Lagrangian operators (e.g. renormalizable, multi-flavon operators and/or effective, higher-dimensional operators) are present that break said residual symmetry, leading to a vacuum reorientation and phenomenological consequences. We therefore construct a one-to-one correspondence principle between broken residual symmetries and vacuum alignment corrections, providing a mechanism to identify (and correct) a subtle but persistent form of phenomenologically relevant fine-tuning embedded in — but often ignored by — most successful non-Abelian flavour models. We first establish this correspondence in a set of toy models based on the S4 permutation symmetry, and then apply the lessons learned to the more realistic A4 Altarelli-Feruglio and ∆(27) Universal Texture Zero models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Comparing multi-source urban flood indicators: satellite, simulation, and citizen-reported data

Urban flooding arises from complex mechanisms, making it challenging to capture accurately with a single detection method. This study evaluates three complementary approaches to detect flooding across three Chicago neighborhoods: (i) Sentinel-1 synthetic aperture radar (SAR), offering weather-independent, high-resolution (10 m) imagery of surface inundation; (ii) the storm water management model (SWMM), simulating combined sewer overflow and drainage performance; and (iii) citizen-generated 311 service requests, capturing observed flooding impacts. By analyzing six storms ranging from severe to mild, we examine how each source uniquely contributes to identifying urban flood events. SAR imagery effectively identifies standing water but can miss brief flooding due to satellite revisit constraints. SWMM provides detailed insights into system-wide drainage behavior yet may underestimate localized street-level flooding. Meanwhile, 311 calls reflect real-world flooding impacts but are vulnerable to underreporting. Statistical overlap analysis highlights chronic flood hotspots repeatedly identified across multiple detection methods, indicating persistent infrastructure and topographic vulnerabilities. Temporal analysis further reveals that while SWMM flooding aligns closely with rainfall peaks, 311 calls typically precede or persist beyond these peaks. Our findings emphasize the value of using satellite observations, hydrological modeling, and resident-reported data in a complementary manner to better interpret patterns in flood timing, severity, and spatial distribution—providing insights that can inform targeted infrastructure improvements and contribute to urban flood resilience planning.

311

Half-ice, half-fire-driven ultranarrow phase crossover in one-dimensional decorated 𝑞-state Potts ferrimagnets: An AI-co-led exploration

OpenAI’s reasoning model o3-mini-high was used to carry out an exact analytic study of one-dimensional ferrimagnetic site- and bond-decorated 𝑞-state Potts models. We demonstrate that the finite-temperature ultranarrow phase crossover (UNPC), driven by a hidden “half-ice, half-fire” state recently discovered in the 𝑞=2 case (Ising model), persists for 𝑞>2. Moreover, we identify unique features for 𝑞>2, including the dome structure in the field-temperature phase diagram, and for large 𝑞 a secondary high-temperature UNPC to the fully disordered paramagnetic state. As the UNPC quickly approaches a genuine transition by enhancing 𝐽, the interaction between the backbone spins, two distinct behaviors emerge: In the site-decorated Potts model, 𝑇 0 is independent of 𝐽 and thus remains unchanged (Type-I UNPC), and in the bond-decorated Potts model with 𝑞>2, 𝑇 0 depends on 𝐽 and quickly shifts toward a finite temperature as 𝐽 increases (Type-II UNPC). These results establish a versatile framework for engineering controlled fast state-flipping switches in low-dimensional systems. Our nine-dan artificial intelligence (AI)-contribution framework assigns AI the meritorious status of AI-co-led discovery in this work.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Aromatic amino acid metabolism and active transport regulation are implicated in microbial persistence in fractured shale reservoirs

Abstract Hydraulic fracturing has unlocked vast amounts of hydrocarbons trapped within unconventional shale formations. This large-scale engineering approach inadvertently introduces microorganisms into the hydrocarbon reservoir, allowing them to inhabit a new physical space and thrive in the unique biogeochemical resources present in the environment. Advancing our fundamental understanding of microbial growth and physiology in this extreme subsurface environment is critical to improving biofouling control efficacy and maximizing opportunities for beneficial natural resource exploitation. Here, we used metaproteomics and exometabolomics to investigate the biochemical mechanisms underpinning the adaptation of model bacterium Halanaerobium congolense WG10 and mixed microbial consortia enriched from shale-produced fluids to hypersalinity and very low reservoir flow rates (metabolic stress). We also queried the metabolic foundation for biofilm formation in this system, a major impediment to subsurface energy exploration. For the first time, we report that H. congolense WG10 accumulates tyrosine for osmoprotection, an indication of the flexible robustness of stress tolerance that enables its long-term persistence in fractured shale environments. We also identified aromatic amino acid synthesis and cell wall maintenance as critical to biofilm formation. Finally, regulation of transmembrane transport is key to metabolic stress adaptation in shale bacteria under very low well flow rates. These results provide unique insights that enable better management of hydraulically fractured shale systems, for more efficient and sustainable energy extraction.

04 OIL SHALES AND TAR SANDS

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing

Dynamical Generation of Higher-Order Spin-Orbit Coupling, Topology, and Persistent Spin Texture in Light-Irradiated Altermagnets

Altermagnets have been identified as the third category of magnetic materials, exhibiting momentum-dependent spin splitting characterized by even powers of momentum. Here, in this Letter, we show that when subjected to elliptically polarized light, these materials serve as an exemplary framework for the dynamic generation of topological bands featuring higher-order spin-orbit coupling (SOC). Notably, while the generated Zeeman field remains invariant to the particular altermagnetic ordering, the induced higher-order SOCs are related to the magnitude and symmetry of the altermagnetic order. Specifically, we show that an altermagnet exhibiting 𝐤 2⁢𝑛 -spin splitting can generate odd-in-𝐤 spin-orbit couplings up to 𝐤 2⁢𝑛−1 . In the limit of circularly polarized light, the only correction is 𝑘 2⁢𝑛−1 , with all lower-order contributions being nullified. Interestingly, light-induced SOCs significantly impact the low-energy band topology, where their Chern numbers change by Δ⁢𝐶 = ±1, 2, 3 for 𝑑, 𝑔, 𝑖-wave altermagnets. Finally, we find a critical field in which a persistent spin texture is realized, a highly desirable state with predicted infinite spin lifetime. Our Letter showcases light as a powerful, controllable tool for engineering complex and exciting phenomena in altermagnets.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

Design of Experiments for Dynamic Test Runs in Solvent-Based CO 2 Capture Pilot Plants

Test runs in the pilot plants consume significant resources, and therefore, the learning from test runs should be maximized. Test runs conducted in the pilot plants are often steady state. It takes several hours for reaching steady-state in the pilot plants, and thus, the duration of the test runs needs to be long even for collecting few steady-state data points. On the other hand, a large number of measurements can be collected through dynamic test runs in a short span of time. This paper presents a systematic design of dynamic experiments (DoDEs) for identifiability of model parameters, which is achieved by persistently exciting the inputs signals. A pseudorandom binary sequence (PRBS) is designed as the input signal for DoDE due to its efficiency in obtaining sufficient spectral content. However, due to the long sequence size of the PRBS signal, a Schroeder-phase input signal, which is a multisine signal, is also designed. Tests for both types of signals are run in the Pilot Solvent Test Unit (PSTU) at the National Carbon Capture Center in Wilsonville, Alabama. The transient data are used to solve dynamic data reconciliation and parameter estimation problem. The estimated parameters are found to be not only superior to those estimated from using data collected from hundreds of steady-state test runs in a nonreactive (air–water) system, but the parameters could be estimated by using the dynamic data collected for about 24 h from the pilot plant for the MEA-H 2 O–CO 2 system.

CO2 capture

Rolling Root Mean Square Based Multimodal Anomaly Detection for Real Time Monitoring of Smart Grid

Reliable real-time monitoring is valuable for maintaining the operational integrity of modern electrical smart grids. Deployment of heterogeneous sensing technologies in substations has enabled high-resolution, multichannel waveform monitoring, but also introduces challenges for anomaly detection due to noise, baseline drift, and modality-dependent signal characteristics. In this work, we present a computationally efficient unsupervised method for multimodal event detection based on Rolling Root Mean Square based Event Detection (RRMSED). The method is developed using in-house, field deployed sensors collecting data at a utility substation. The sensing system comprises voltage and current sensors, triaxial accelerometers, and magnetometers, collectively capturing electrical, vibrational, and magnetic waveform measurements at high temporal resolution. RRMSED operates by extracting rolling RMS energy features and their first-order temporal differences from consecutive waveform segments for each channel and then applying channel-specific statistical thresholds learned from historical data. A persistence-based exceedance logic is employed to robustly identify transient events while suppressing impulsive noise, and to provide precise temporal localization with high resolution. The framework is designed for continuous server-side operation and can be deployed in real time without requiring complex models. Experiments on simulated waveform data with known ground truth demonstrate low false positive (FP) and false negative (FN) rates. Application to real substation data shows RRMSED to identify events that are not captured by conventional monitoring indicators including fast transient detection algorithm currently deployed in the system. These results indicate that rolling RMS based features provide an effective and practical basis for real-time multimodal event detection in smart-grid substations.

Mukherjee, Subrata [ORNL] (ORCID:0000000309930338)

Batch Extraction Studies to Evaluate Trace Element Behavior in PUREX Conditions

The multilab Intentional Forensics Venture is working to identify which stable elements (i.e., taggants) at trace concentrations relative to U would persist throughout the nuclear fuel cycle in a voluntary fuel tagging scheme. A taggant would provide the nuclear forensics community with a “barcode” to help identify nuclear materials found outside of regulatory control. A portion of this project was focused on reprocessing effects and determining which, if any, elements would coextract with U(VI) in standard Pu–U reduction extraction (PUREX) conditions. Elements with a propensity to coextract could, in theory, be used as taggants from a PUREX perspective. Although retention is not a performance requirement, the taggant signature would need to partition predictably from the U stream after the PUREX process to maintain forensic utility. This report documents results from several batch extraction studies with numerous trace elements from HNO 3 (1.5–5 M), with and without U(VI), into 30% tri-n-butyl phosphate (TBP) in kerosene. Extraction and back-extraction tests were used to evaluate nearly 60 elements in surrogate conditions for PUREX, and distribution coefficients (i.e., D-values) for most species were <0.1, indicating few species are likely to co-extract with U through PUREX. Additional studies are needed to optimize sample volumes and dilutions to dial in these low D-values. The D-values (D) were determined for several of the more promising elements, including Re and Se. Ultimately, we conclude that only a limited number of the ~ 60 elements investigated are extractable in the U stream of PUREX, based on measured D values, meaning most candidate elemental taggants would likely be lost at this stage of the nuclear fuel cycle, even when considering a range of acid concentrations.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers

Adsorption-Engineered Hydrocarbon Ionomers for Durable Proton-Exchange Membrane Fuel Cells

Reducing reliance on perfluoroalkyl substances (PFAS) in proton-exchange membrane fuel cells requires hydrocarbon ionomers that combine high performance with long-term durability, a persistent challenge in catalyst-layer design. Here, we identify oxidation-driven ionomer-catalyst interfacial degradation as a dominant failure pathway in hydrocarbon ionomer-bonded cathodes and introduce an adsorption-engineering strategy to overcome this limitation. The comparison of a commercial sulfonated poly(phenylene) (Pemion) with structurally engineered sulfonated poly(fluorene)s demonstrated that electrode durability is governed by the interplay between ionomer adsorption strength and resistance to oxidative degradation on carbon-supported Pt catalysts. A poly(fluorene) ionomer with mobile alkyl sulfonic acid groups forms resilient interfaces, delivering 1.28 A cm−2 at 0.65 V under fully humidified H2/air conditions (80°C and 150 kPaabs), comparable to Pemion. After 90,000 accelerated potential cycles, the poly(fluorene)-bonded cathode exhibits significantly improved durability, with only 29% performance loss compared to 58% for Pemion; further molecular refinement reduces the loss to 17%, approaching that of Nafion-bonded cathodes (14%). These findings establish adsorption-engineered ionomer design that decouples interfacial anchoring from oxidative degradation as a general strategy for achieving durable, high-performance PFAS-free PEM fuel cell electrodes.

08 HYDROGEN

Assessing shellfish water exposure to fecal bacteria pollution in Salish Sea: three-dimensional modeling and implications for monitoring

Fecal bacteria (FB) contamination poses significant risks to shellfish safety and management in coastal and estuarine waters. Despite extensive pollution identification and correction efforts, FB contamination in shellfish-growing areas persists in the Salish Sea, highlighting the need to identify overlooked sources and better understand FB transport from riverine and shoreline inputs to shellfish beds. To address this, a high-resolution three-dimensional hydrodynamic model coupled with FB kinetics was developed and applied to a case study site in Salish Sea—Portage Bay—to simulate freshwater plume circulation, flushing dynamics, and bacterial transport. Daily FB loading from the major freshwater inflow—Nooksack River was generated by both linear interpolation and integrating a machine learning approach (XGBoost), trained on historical hydrological and meteorological data. The model successfully reproduced both the magnitude and seasonal variation of FB concentrations in Portage Bay for the year of 2021, demonstrating that simplified FB kinetics with first-order decay due to mortality was effective in this dynamic coastal environment with short flushing time. Model results identified the Nooksack River as the dominant far-field FB source, while scenario simulations showed that near-field coastal stormwater outfalls elevated local FB levels following rainfall, particularly under low-flow conditions. The XGBoost prediction provided comparable or superior accuracy to linear interpolation, particularly during periods of missing observational data, by capturing short-term variability and event-driven loading more effectively. Integrating data-driven riverine FB inputs with mechanistic coastal numerical modeling provides a robust framework for operational forecasting of shellfish bed exposure risk and supports adaptive monitoring and management of shellfish growing areas in the Salish Sea and similar coastal systems.

Salish Sea