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At least 163 records · Page 9

Adaptive Sampling for In Situ Cloud Probe (Final Report)

Clouds play a leading role in the Earth's global energy and solar radiation balance and hydrological cycle. Improving cloud models requires detailed information on the cloud microphysical properties, such as droplet size distribution and number density, liquid water content and cloud composition (droplets, ice particles), which can only be provided by aerial in situ measurements. However, for many atmospheric measurement instruments, the lack of flexibility in selecting the operational mode during operation can lead to uncertainties in sampling and measurement characteristics under continuously varying atmospheric conditions. This SBIR project is developing an advanced, compact optical imaging technology for in situ characterization of cloud hydrometeors. The development involves a deep modification of the existing Mesa Photonics’ Cloud Droplet Measurement System (CDMS) in order to implement real-time automatic adaptive sampling based on the acquired in situ data and environmental parameters. The new system, CDMS-2, implements two measurement modes: side-scatter imaging for smaller hydrometeors and direct bright-field-illumination imaging for larger hydrometeors in a significantly larger sample volume. The system measures the droplet size distribution (DSD) and number density with an added capability of discriminating between liquid water and ice hydrometeors (based on polarization-resolved side-scatter imaging). The instrument will implement automatic switching or alternating between the regular side-scatter imaging mode and sparse/large hydrometeor mode (based on the acquired data). Other adaptive sampling capabilities include variable sample volume and dynamic range (based on the measured DSD). The preferred deployment platforms are uncrewed aircraft systems (UAS) and tethered balloon/kite systems (TBS). The Phase I project achieved (or exceeded) the goals listed in the Work Plan. A CDMS-2 laboratory prototype implementing the polarization-resolved side-scatter imaging mode and direct bright-field-illumination imaging mode was designed and built. Additional capabilities included the variable illumination pulse energy and sample volume. The smallest detectable droplet diameter was improved to 3–4 μm (from the nominal 10 μm value specified for the original CDMS). Discrimination between water droplets and ice particles was experimentally demonstrated. The Phase I prototype was extensively tested and calibrated in the laboratory and also tested in the Pi Cloud Chamber at Michigan Technological University (MTU). The two intensive experimental campaigns at MTU provided unique opportunities of testing the CDMS-2 laboratory prototype under realistic warm and mixed-phase cloud conditions (stable for long periods of time), testing different sampling modes and intercomparing the CDMS-2 prototype to other co-located cloud characterization instruments. The Phase I project successfully demonstrated the feasibility of the proposed technology and identified the engineering challenges of designing a field deployable prototype instrument in Phase II. The Phase I study provides a solid basis for development, characterization and field-testing of the proposed advanced cloud probe with adaptive sampling in Phase II followed by commercialization of the technology in Phase III.

47 OTHER INSTRUMENTATION↗

An Analysis of Shallow Orographic Cumulus Clouds Observed During the CACTI Field Campaign: A SULI Internship Final Report

In 2018, the Atmospheric Radiation Measurement Aerial Facility (AAF) deployed its G-1 research aircraft to the Sierras de Córdoba mountain range in north-central Argentina to support the research of environmental factors on deep convective cycles as part of the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign. The aircraft was fitted with a suite of instruments to holistically measure in situ the current state of the atmosphere. In this study, we organize the campaign’s 22 flights by environmental conditions. Data from each flight was transected by the aircraft’s position relative to cloud, allowing for in depth analysis of cloud processing on aerosol populations. My project was a case study of selected flights where warm, shallow orographic cumulus clouds were observed.

54 ENVIRONMENTAL SCIENCES↗

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework

Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.

59 BASIC BIOLOGICAL SCIENCES↗

Delegated Regressor, A Robust Approach for Automated Anomaly Detection in the Soil Radon Time Series Data

We propose a new method based on the idea of delegating regressors for predicting the soil radon gas concentration (SRGC) and anomalies in radon or any other time series data. The proposed method is compared to different traditional boosting e.g., Extreme Gradient Boosting (EGB) and simple regression methods e.g., support vector regressors with linear kernel and radial kernel in terms of accurate predictions. R language has been used for the statistical analysis of radon time series (RTS) data. The results obtained show that the proposed methodology predicts SRGC more accurately when compared to different traditional boosting and regression methods. The best correlation is found between the actual and predicted radon concentration for window size of 2 i.e., two days before and after the start of seismic activities. RTS data was collected from 05 February 2017 to 16 February 2018, including 7 seismic events recorded during the study period. Findings of study show that the proposed methodology predicts the SRGC with more precision, for all the window sizes, by overlapping predicted with the actual radon time series concentrations.

54 ENVIRONMENTAL SCIENCES↗

Toward equitable environmental exposure modeling through convergence of data, open, and citizen sciences: an example of air pollution exposure modeling amidst increasing wildfire smoke

Exposure modeling is critical in environmental epidemiology and human health but may face challenges (e.g., skewed data, unequal error, context-insensitive validation, and computational demands). Modeling decisions reflect the intended use of the models and the values that modelers prioritize. We aimed to provide a conceptual framework and machine learning (ML) modeling protocols that address these issues. With 500m-gridded hourly PM 2.5 and O 3 levels in Illinois before, during, and after the 2023 Canadian wildfire season as a motivating example, we conducted modeling experiments to evaluate modeling methods, guided by three domains we propose based on theories of science: 1) Data Diversity, leveraging open and citizen science data to enhance inclusivity, parsimony, and representativeness; 2) Equitable Accuracy, ensuring fairly distributed uncertainties across subpopulations; and 3) Sustainable Modeling, balancing accuracy with reducing computational demands to promote accessibility for under-resourced researchers. Here, we found that ML with publicly available data can achieve high accuracy. Depending on methods, performance may vary substantially, even with identical input data. Large but skewed data may reduce performance. Misuse of cross-validation protocols can underestimate prediction error; although we observed R 2 s of ∼98 %, the modeled estimates varied significantly, indicating the need for careful model validation. By using new modeling protocols including representativeness-considered training and validation data and a new loss function, we achieved high agreement between estimates and ground-based measurements (e.g., R 2 = ∼90 % for PM 2.5 ; ∼80 % for O 3 ), equally distributed errors across sociodemographic strata and urban–rural divides, and reduction in computation time—from several weeks or months to a few days.

Exposure assessment↗

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

MBARI WEC 2021 deployment

This dataset includes data from the Monterey Bay Aquarium Research Institute (MBARI) wave energy converter (WEC) and a nearby located Sofar Spotter buoy. The Monterey Bay Aquarium Research Institute has developed and deployed a small two-body point absorber wave energy device suitable to autonomous underwater vehicle, sensor system, and even aquaculture farm needs. For more information on the MBARI WEC see the research journal attached in the submission.

16 TIDAL AND WAVE POWER↗

Exascale Computing and Data Handling: Challenges and Opportunities for Weather and Climate Prediction

The emergence of exascale computing and artificial intelligence offer tremendous potential to significantly advance Earth system prediction capabilities. However, enormous challenges must be overcome to adapt models and prediction systems to use these new technologies effectively. A 2022 WMO report on exascale computing recommends “urgency in dedicating efforts and attention to disruptions associated with evolving computing technologies that will be increasingly difficult to overcome, threatening continued advancements in weather and climate prediction capabilities.” Further, the explosive growth in data from observations, model and ensemble output, and postprocessing threatens to overwhelm the ability to deliver timely, accurate, and precise information needed for decision-making. Artificial intelligence (AI) offers untapped opportunities to alter how models are developed, observations are processed, and predictions are analyzed and extracted for decision-making. Given the extraordinarily high cost of computing, growing complexity of prediction systems, and increasingly unmanageable amount of data being produced and consumed, these challenges are rapidly becoming too large for any single institution or country to handle. This paper describes key technical and budgetary challenges, identifies gaps and ways to address them, and makes a number of recommendations.

Atmosphere↗

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre

Scientific exploration of phototrophic bacteria over nearly 200 years has revealed large phylogenetic gaps between known phototrophic groups that limit understanding of how phototrophy evolved and diversified. Here, through Boreal Shield lake water incubations, we cultivated an anoxygenic phototrophic bacterium from a previously unknown order within the Chloroflexota phylum that represents a highly novel transition form in the evolution of photosynthesis. Unlike all other known phototrophs, this bacterium uses a type I reaction centre (RCI) for light energy conversion yet belongs to the same bacterial phylum as organisms that use a type II reaction centre (RCII) for phototrophy. Using physiological, phylogenomic and environmental metatranscriptomic data, we demonstrate active RCI-utilizing metabolism by the strain alongside usage of chlorosomes and bacteriochlorophylls related to those of RCII-utilizing Chloroflexota members. Despite using different reaction centres, our phylogenomic data provide strong evidence that RCI-utilizing and RCII-utilizing Chloroflexia members inherited phototrophy from a most recent common phototrophic ancestor. The Chloroflexota phylum preserves an evolutionary record of the use of contrasting phototrophic modes among genetically related bacteria, giving new context for exploring the diversification of phototrophy on Earth.

59 BASIC BIOLOGICAL SCIENCES↗

Incubating advances in integrated photonics with emerging sensing and computational capabilities

As photonic technologies grow in multidimensional aspects, integrated photonics holds a unique position and continuously presents enormous possibilities for research communities. Applications include data centers, environmental monitoring, medical diagnosis, and highly compact communication components, with further possibilities continuously growing. Herein, we review state-of-the-art integrated photonic on-chip sensors that operate in the visible to mid-infrared wavelength region on various material platforms. Among the different materials, architectures, and technologies leading the way for on-chip sensors, we discuss the optical sensing principles that are commonly applied to biochemical and gas sensing. Our focus is on passive optical waveguides, including dispersion-engineered metamaterial-based structures, which are essential for enhancing the interaction between light and analytes in chip-scale sensors. We harness a diverse array of cutting-edge sensing technologies, heralding a revolutionary on-chip sensing paradigm. Our arsenal includes refractive-index-based sensing, plasmonics, and spectroscopy, which forge an unparalleled foundation for innovation and precision. Furthermore, we include a brief discussion of recent trends and computational concepts, incorporating Artificial Intelligence & Machine Learning (AI/ML) and deep learning approaches over the past few years to improve the qualitative and quantitative analysis of sensor measurements.

Jain, Sourabh (ORCID:0000000279923275)↗

Reference-free structural variant detection in microbiomes via long-read co-assembly graphs

Motivation: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining. Results: We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, particularly as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between successive time and temperature samples, suggesting host advantage. Our approach leverages previous work in assembly graph structural and coverage patterns to provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial gene flux.

59 BASIC BIOLOGICAL SCIENCES↗

Thermodynamic characterization of synthetic lead-arsenate apatites with different halogen substitutions

Abstract Thermodynamic parameters have been measured for synthetic analogs of the mimetite-group minerals Pb5(AsO4)3X (X = OH, Cl, Br, I) belonging to the apatite supergroup. Phases precipitated from aqueous solutions under ambient conditions with well characterized structures and compositions were studied. For each phase, dissolution enthalpy was experimentally determined by oxide melt drop solution calorimetry in a molten solvent of sodium molybdate (3Na2O·4MoO3) at 976 K. The enthalpy of formation from the elements ΔHf,elo was calculated using thermochemical cycles and was −3030.6 ± 11.5, −3026.6 ± 15.8, −2967.6 ± 25.0, and −2993.1 ± 12.2 kJ/mol for Pb5.00(AsO4)3.00OH0.86(CO3)0.07, Pb5.00(AsO4)3.00Cl0.80(CO3)0.10, Pb5.00(AsO4)3.00Br0.80(CO3)0.10, and Pb5.00(AsO4)3.00I0.45OH0.35(CO3)0.10, respectively. These ΔHf,elo values exhibit typical trends for apatites: they increased (were less negative) with the increasing molar mass and ionic radius of X and decreased with the electronegativity and ionization energy of X. The compilation and comparison of data for Ca-, Pb-, P-, and As-apatites revealed correlations indicating that thermodynamic enthalpic stability is largely influenced by chemical factors (e.g., differences in electronegativities of the elements, ionization energy, or ionic characteristics of the bonds) and to a lesser extent by physical and geometric parameters in the crystal structure related to the mass and size of the X anion. Using the correlations, it was possible to estimate the value of hitherto unknown ΔHf,elo for Pb5(AsO4)3F, −3144.3 ± 66.5 kJ/mol. The observed relationships apply to the entire apatite supergroup and can be used to predict the values of ΔHf,elo for phases that have not been studied experimentally. The new data on environmentally significant phases will contribute to the modeling of mineral-water interactions, particularly for potential use in the remediation of soils and wastes contaminated with Pb and As and in the immobilization of radioactive waste containing I-129.

Geochemistry & Geophysics↗

Separation of Lanthanide Isotopes from Mixed Fission Product Samples

The measurement of radioactive fission products from nuclear events has important implications for nuclear data production, environmental monitoring, and nuclear forensics. In a previous paper, the authors reported the optimization of an intra-group lanthanide separation using LN extraction resin from Eichrom Technologies®, Inc. and a nitric acid gradient. In this work, the method was demonstrated for the separation and quantification of multiple short-lived fission product lanthanide isotopes from a fission product sample produced from the thermal irradiation of highly enriched uranium. The separations were performed in parallel in quadruplicate with reproducible results and high decontamination factors for 153 Sm, 156 Eu, and 161 Tb. Based on the results obtained here, the fission yields for 144 Ce, 153 Sm, 156 Eu, and 161 Tb are consistent with published fission yields. This work demonstrates the effectiveness of the separations for the intended application of short-lived lanthanide fission product analysis requiring high decontamination factors.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

A Survey of Multizone Airflow Simulation Software

H-Canyon simulates the building and process ventilation to ensure positive contamination control for any modifications as well as evaluating off-normal conditions. Simulations can also be used to identify air quality of personnel occupied areas. The models can be classified into two groups, single and multi-zone models. As the name states, a single zone model assumes that the building can be described by a single, well-mixed zone. Whereas large buildings have structures that must be described as multizone. Multizone airflow models deal with the difficulty of flows in a building by distinguishing the effects of internal flow restrictions. Several models have been developed that take internal partitions into account. CONTAM (currently used) is a multizone airflow program created by NIST to determine airflows including infiltration, exfiltration, wind pressures acting outside the building, buoyancy effects caused by the indoor and outdoor air temperature difference. COMIS is a multizone air infiltration, ventilation, and contaminant transport model that was developed at Lawrence Berkeley National Laboratory. COMIS deals with applied pressure distribution, airflow components, HVAC systems, schedules, and contaminant transport. EnergyPlus is designed by DOE. It supports flexible component level configuration of HVAC models and simulates sub-hourly time steps to control fast dynamic systems. The program features include providing accurate environmental performance data including energy consumption and carbon emissions, and reporting solar gains on surfaces. Heavent is used to model industrial ventilation systems to control airborne contaminants. It's designed based on the American Conference of Governmental Industrial Hygienists (ACGIH) Ventilation manual. DesignBuilder is the most recognized and advanced user interface to EnergyPlus. It gives access to all of the most frequently required simulation capabilities covering building fabric, thermal mass, glazing, shading renewables, and HVAC analysis. The objective of this study is to identify all relevant software available including commercially licensed, freely licensed, and open source, that can be used to simulate large, complex process facility ventilation systems. All discovered software tools are evaluated for salient features and compared to the software tool currently used to simulate the H-Canyon ventilation system. The design criteria of a ventilation system has two basic requirements: Supplying fresh air for the occupants and changing the air in the room sufficiently; therefore, the smells, fumes, and contaminants will be removed. In this study, first, whether the software simulates airflow (infiltration, natural ventilation, and interzonal) or considers them to be inputs is discussed. Second, if indoor contaminant levels are considered; and finally suggestions on how airflow analysis can be more appropriately accounted for when performing airflow simulation of a building. All of the airflow software reviewed for this study can account for constant infiltration and natural ventilation rates that are not affected by changes in indoor and outdoor conditions. Modelling infiltration in EnergyPlus or DesignBuilder are applicable for small buildings and not appropriate for larger buildings like the H-Canyon. The effect of wind on external pressures, infiltration, and natural and mechanical ventilation, can also be calculated using all of these software. These programs have control options to switch between natural to mechanical ventilation modes or both (hybrid). Interzonal airflow can be applied which means one zone can be specified to receive a fixed amount of air from another zone. The following ventilation modeling software is recommended for further testing: CONTAM, COMIS, Heavent. The next step in evaluating the software will consist of creating test facility simulations using evaluation copies of the software.

42 ENGINEERING↗

Local Weather Station Design and Development for Cost-Effective Environmental Monitoring and Real-Time Data Sharing

Current weather monitoring systems often remain out of reach for small-scale users and local communities due to their high costs and complexity. This paper addresses this significant issue by introducing a cost-effective, easy-to-use local weather station. Utilizing low-cost sensors, this weather station is a pivotal tool in making environmental monitoring more accessible and user-friendly, particularly for those with limited resources. It offers efficient in-site measurements of various environmental parameters, such as temperature, relative humidity, atmospheric pressure, carbon dioxide concentration, and particulate matter, including PM 1, PM 2.5, and PM 10. The findings demonstrate the station’s capability to monitor these variables remotely and provide forecasts with a high degree of accuracy, displaying an error margin of just 0.67%. Furthermore, the station’s use of the Autoregressive Integrated Moving Average (ARIMA) model enables short-term, reliable forecasts crucial for applications in agriculture, transportation, and air quality monitoring. Furthermore, the weather station’s open-source nature significantly enhances environmental monitoring accessibility for smaller users and encourages broader public data sharing. With this approach, crucial in addressing climate change challenges, the station empowers communities to make informed decisions based on real-time data. In designing and developing this low-cost, efficient monitoring system, this work provides a valuable blueprint for future advancements in environmental technologies, emphasizing sustainability. The proposed automatic weather station not only offers an economical solution for environmental monitoring but also features a user-friendly interface for seamless data communication between the sensor platform and end users. This system ensures the transmission of data through various web-based platforms, catering to users with diverse technical backgrounds. Furthermore, by leveraging historical data through the ARIMA model, the station enhances its utility in providing short-term forecasts and supporting critical decision-making processes across different sectors.

54 ENVIRONMENTAL SCIENCES↗

Data for: A Synoptic System for Capturing Ecosystem Control Points Across Terrestrial-Aquatic Interfaces

The investigation of how climate change and water level fluctuations impact variable and interconnected ecosystems, like the interfaces between terrestrial and aquatic environments, requires the collection and integration of many data types. We describe an integrative and autonomous environmental monitoring approach that uses environmental sensors and data loggers to monitor surface water, groundwater, soil, and vegetation changes and generate essential data for predictive models. We established the network at seven sites along the Chesapeake Bay and Lake Erie coastlines, including a large-scale flood manipulation experiment, collectively generating over three million observations per month. Such sensor networks hold great promise for tracking and comprehending environmental changes where land and water intersect. The sensor system and overall approach to sensor management that we have designed is intended to be widely accessible for research teams spanning in size from an individual investigator to large multi-institution projects. This dataset shows example data generated by the sensor network described above. Data output for data loggers connected to groundwater water quality sondes measuring dissolved oxygen, pH, oxidative redox potential (ORP), groundwater elevation, groundwater salinity and temperature, and groundwater elevation; replicate soil moisture and conductivity probes installed at 10 and 30 cm below the ground surface; rainfall and solar radiation; and mean sap flow from 8 replicate probes. Sensors are installed at upland forest (UP), wetlands (W), and transitional locations between these ecosystems (TR). Example datasets are from Goodwin Islands in the Chesapeake Bay and Portage River along the Lake Erie coastline.

54 ENVIRONMENTAL SCIENCES↗