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At least 199 records · Page 11

Genome-scale analysis of interactions between genetic perturbations and natural variation

Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.

59 BASIC BIOLOGICAL SCIENCES↗

Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability: Supporting Data and Code

This repository contains R code and associated datasets for reproducing the analysis described in the manuscript titled “Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability” (DOI: 10.1029/2024JG008604). The provided scripts facilitate a comprehensive analysis of snow depth variability influenced by microtopography and vegetation distribution in a subarctic watershed. Included datasets are high-resolution spatial maps of snow depth, terrain elevation, vegetation height, and distance from shrubs taller than 1 meter, all formatted as text files (.txt). These data are fully describe in doi:10.15485/2316038. Users can adapt the provided R scripts to accommodate different data formats or larger spatial domains, noting that some output files may require modification due to their size.The code includes implementations for boosted regression tree analysis adapted from methods outlined in Elith et al. (2008). Users interested in understanding or modeling landscape-scale snow distribution patterns, particularly in Arctic or subarctic ecosystems, will find this package useful. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Plant Growth Study: Growth of Three Plant Species in 100-OL-1 Operable Unit Soils

Soil contamination from historical application of lead arsenate pesticides persists in the 100-OL-1 Operable Unit (OU) of the U.S. Department of Energy’s Hanford Site in Benton County, Washington. A remedial investigation used a portable X-ray fluorescence analyzer to estimate and map the concentrations of metals in surface soil in the 133 decision units comprising the OU. There is variability in lead and arsenic concentrations among the non-contiguous decision units, and an incomplete understanding of the ecological and human risks from soil contamination. While general screening criteria for lead are reported in literature, limited information is available on the impacts of heavy metals on site-specific plant and animal life. To address this information gap, a study on plant growth in Hanford soils was conducted using native bluegrass (Poa secunda), invasive cheatgrass (Bromus tectorum), and buttercrunch lettuce (Lactuca sativa). The latter is included because it is a common species used in plant growth studies. Soil samples were collected from a single general location within the 100-OL-1 OU, prepared, and categorized as having low, medium, or high concentrations of lead and arsenic, with the high concentration soil having concentrations of up to 3,400 and 790 mg/kg lead and arsenic, respectively. Additionally, a synthetic soil was prepared and used as a control, in accordance with standard plant growth protocols. Fifty-four seeds of each plant species were planted in each of the four soil types following the procedure outlined by the Washington State Department of Ecology. Germination rates and biomass measurements were recorded for 20 days. Both bluegrass and lettuce germination rates appeared to be reduced at the highest lead and arsenic concentrations (Pb: 3400 mg/kg, As: 790 mg/kg), while cheatgrass germination rates were unaffected. Total biomass for all species appeared to be related to the relative concentrations of lead and arsenic in the soil. Results of this growth study agree reasonably well with previous Hanford Site plant growth studies and provide additional data for assessing ecological risk at the Hanford Site.

54 ENVIRONMENTAL SCIENCES↗

Flood Susceptibility Mapping Using Machine Learning and Geospatial-Sentinel-1 SAR Integration for Enhanced Early Warning Systems

This study presents a comprehensive framework for flood susceptibility mapping by integrating geospatial factors with both statistical and machine learning models. Thirteen Flood-related factors, including DEM, slope, TWI, NDVI, etc., are extracted as features of models, and historical flood data derived from Sentinel-1 SAR from 2018 to 2023 are used as the target variables of the models. These datasets are analyzed using a frequency-based statistical model and three machine learning models, including Random Forest, XGBoost, and CNN, to generate flood susceptibility maps. The performance of each model is evaluated through AUC; and SHAP scores are separately generated for Machine learning (ML) models to explain each feature contribution in the ML model. The generated susceptibility maps are validated by high-flood-risk locations monitored by flood sensors, BLE inundation models, and flood-prone areas suggested by the Local Community Task Force. The results indicate that the XGBoost model outperforms all other models, with an AUC of 0.92 and demonstrates the highest alignment with recommended high-flood-risk locations, while the frequency-based statistical model showed the weakest performance with an AUC of 0.65. SHAP value graphs highlight the elevation, slope, and TWI as the most influential features across all models. The susceptibility maps generated by the machine learning model show strong agreement with the BLE map and high-flood-risk areas identified by the local Community Task Force.

Google Engine↗

Mapping tree height in complex terrain of northern China using ultra-high-resolution images

Tree height is a key parameter for estimating forest biomass and carbon sequestration. In recent years, notable progress has been made in mapping tree height using satellite imagery. However, existing tree height products show low accuracy in mountainous and complex terrains, and few studies typically addressed tree height estimations in mountain areas. This study examines the Mentougou district of Beijing, China, characterized by complex terrain and mountainous landscapes. We analyzed two methods for estimating tree height: one using only spectral features and another combining spectral features with topographic factors (elevation, slope, aspect). We used 3-m resolution PlanetScope 8-band multispectral imagery, with 710 field-measured individual tree heights averaged to obtain 471 pixel-level tree height values as ground-truth, to develop tree height prediction models using eXtreme Gradient Boosting (XGBoost), Random Forest (RF), and Gradient Boosting Machine (GBM) models. The results show that the XGBoost model consistently presented the highest accuracy for both methods evaluated. Specifically, the XGBoost model that combined spectral data with elevation and slope variables with an R² of 0.75 and an RMSE of 2.69 m. Using the XGBoost model, we generated the tree height map for the Mentougou area at 3 m resolution, showing tree heights ranging from 0.5 to 30.4 m, and the model’s prediction error standard deviations ranged from 2.50 to 4.71 m, indicating reliable performance across varied terrain. Additionally, we compared and evaluated the global tree height products, identifying limitations in the accuracy within complex terrains. This study demonstrates the potential for accurately predicting tree heights by combining high-resolution multispectral satellites with a terrain factor modeling approach.

Complex terrain↗

Evaluation of global teleconnections in CMIP6 climate projections using complex networks

In climatological research, the evaluation of climate models is one of the central research subjects. As an expression of large-scale dynamical processes, global teleconnections play a major role in interannual to decadal climate variability. Their realistic representation is an indispensable requirement for the simulation of climate change, both natural and anthropogenic. Therefore, the evaluation of global teleconnections is of utmost importance when assessing the physical plausibility of climate projections. We present an application of the graph-theoretical analysis tool δ-MAPS, which constructs complex networks on the basis of spatio-temporal gridded data sets, here sea surface temperature and geopotential height at 500 hPa. Complex networks complement more traditional methods in the analysis of climate variability, like the classification of circulation regimes or empirical orthogonal functions, assuming a new non-linear perspective. While doing so, a number of technical tools and metrics, borrowed from different fields of data science, are implemented into the δ-MAPS framework in order to overcome specific challenges posed by our target problem. Those are trend empirical orthogonal functions (EOFs), distance correlation and distance multicorrelation, and the structural similarity index. δ-MAPS is a two-stage algorithm. In the first place, it assembles grid cells with highly coherent temporal evolution into so-called domains. In a second step, the teleconnections between the domains are inferred by means of the non-linear distance correlation. We construct 2 unipartite and 1 bipartite network for 22 historical CMIP6 climate projections and 2 century-long coupled reanalyses (CERA-20C and 20CRv3). Potential non-stationarity is taken into account by the use of moving time windows. The networks derived from projection data are compared to those from reanalyses. Our results indicate that no single climate projection outperforms all others in every aspect of the evaluation. But there are indeed models which tend to perform better/worse in many aspects. Differences in model performance are generally low within the geopotential height unipartite networks but higher in sea surface temperature and most pronounced in the bipartite network representing the interaction between ocean and atmosphere.

58 GEOSCIENCES↗

Simulated Feasibility of 3-D Lightning Mapping From Space

In addition to the awe it inspires, lightning can illuminate the microphysical processes hidden away within deep convection. The current generation of space-based lightning mapping uses mostly 2-D optical imaging to connect overall flash characteristics to their parent storm dynamics, but are missing a dimension’s worth of information. With lightning now classified as an essential climate variable, future spaceborne mappers will need improved capabilities to take advantage of the 3-D structure of lightning flashes to support meteorological and climate modeling. We report here on a study of the feasibility of high-resolution 3-D lightning mapping using a radio frequency (RF)-based network of satellites from low-Earth orbit (LEO). Lightning sources are simulated using existing lightning mapping array (LMA) tools, modified for orbital detection, and spatially reconstructed using a Levenberg–Marquardt geolocation algorithm to assess sources of uncertainty in these solutions. We analyze the benefits and limitations of this approach compared to existing orbital and ground-based methods. Results of this study show that lightning can be mapped in 3-D with a vertical location accuracy better than 2 km using as few as five satellites in LEO capable of measuring the time-of-arrival of impulsive RF signals in the very high-frequency (VHF) band. The consequence of this study is that high-resolution, spaceborne 3-D mapping of lightning is achievable across most of the globe, having crucial implications for our understanding of not only lightning, but also severe weather development, climate science, and more.

47 OTHER INSTRUMENTATION↗

Citizen and machine learning-aided high-resolution mapping of urban heat exposure and stress

Abstract Through conversion of land cover to more built-up, impervious surfaces, cities create hotter environments than their surroundings for urban residents, with large differences expected between different parts of the city. Existing measurements of ambient air temperature and heat stress, however, are often insufficient to capture the intra-urban variability in heat exposure. This study provides a replicable method for modeling air temperature, humidity, and moist heat stress over the urban area of Chapel Hill while engaging citizens to collect high-temporal and spatially-resolved air temperature and humidity measurements. We use low-cost, consumer-grade sensors combined with satellite remote sensing data and machine learning to map urban air temperature and relative humidity over various land-cover classes to understand intra-urban spatial variability of ambient heat exposure at a relatively high resolution (10 m). Our findings show that individuals may be exposed to higher levels of air temperature and moist heat stress than weather station data suggest, and that the ambient heat exposure varies according to land cover type, with tree-covered land the coolest and built-up areas the warmest, and time of day, with higher air temperatures observed during the early afternoon. Combining our resulting dataset with sociodemographic data, policymakers and urban planners in Chapel Hill can use data output from this method to identify areas exposed to high temperature and moist heat stress as a first step to design effective mitigation measures.

54 ENVIRONMENTAL SCIENCES↗

Field Validation of Air-Source Heat Pumps for Cold Climates

Heating energy is the largest end-use for U.S. residential buildings accounting for approximately one-third of residential building energy consumption (EIA 2021). Historically, air-source heat pumps have been limited to temperate climates because of subpar performance at extremely cold outdoor air temperatures. However, recent advances to cold-climate air-source heat pump technology, which typically rely on inverter-driven, variable-speed compressors and variable-speed fans, have significantly improved low-temperature heat pump performance enabling the technology to save energy for many homes in cold climates. The primary objective of this project was to measure in-field performance of centrally ducted, variable-capacity air-source heat pumps in cold climates to validate performance and develop field-based performance maps. The project focused on quantifying heat pump performance at cold temperatures. The sites identified for the study were primarily located in the Northwest United States since homes in the region tend to have all-electric space heating systems and high-efficiency heat pumps have been incentivized in the region for several years. NREL partnered with Ecotope, Inc., a small energy consulting firm located in Seattle, WA, for site recruitment, monitoring equipment installation, data quality management. All the sites included in the study had previously installed a high-efficiency, central heat pump system. One site was in a Denver, CO suburb, which was the only dual fuel heat pump in the study. We used airside and power measurements, collected at 5-second intervals, to quantify heat pump capacity, coefficient of performance (COP), and auxiliary heater energy consumption. We developed algorithms to automatically determine the heat pump operating mode including defrost and auxiliary heating operation. A whole-house thermal and duct audit was completed during the initial site visit to estimate winter heating loads and assess heat pump sizing. Whole-home heating design loads were calculated at ASHRAE 99% design temperatures and compared to manufacturer-reported maximum capacities to assess the heat pump sizing at each site.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A Comparison of Properties of Quasars with and without Rapid Broad Absorption Line Variability

We investigate the correlation between rest-frame UV flux variability of broad absorption line (BAL) quasars and their variability in BAL equivalent widths (EWs) in a various timescale from <10 days to a few years in the quasar rest frame. We use the data sets of BAL EWs taken by the Sloan Digital Sky Survey Reverberation Mapping project and photometric data taken by the intermediate Palomar Transient Factory in the g and R bands and the Panoramic Survey Telescope and Rapid Response System in grizy bands. Our results are summarized as follows: (1) the distributions of flux variability versus BAL variability show weak, moderate, or a strong positive correlation; (2) there is no significant difference in flux variability amplitudes between BAL quasars with significant short timescale EW variability (called class S1) and without (class S2); (3) in all timescales considered in this paper, the class S1 quasars show systematically larger BAL variability amplitudes than those of the class S2 quasars; and (4) there are possible correlations between BAL variability and physical parameters of the quasars such as black hole masses (moderate positive), Eddington ratios, and accretion disk temperature (strong negative) in the class S2 quasars. These results indicate that the BAL variability requires changing in the ionizing continuum and an ancillary mechanism such as variability in X-ray shielding gas located at the innermost region of an accretion disk.

79 ASTRONOMY AND ASTROPHYSICS↗

Spatial variability in Arctic–boreal fire regimes influenced by environmental and human factors

Abstract Wildfire activity in Arctic and boreal regions is rapidly increasing, with severe consequences for climate and human health. Regional long-term variations in fire frequency and intensity characterize fire regimes. The spatial variability in Arctic–boreal fire regimes and their environmental and anthropogenic drivers, however, remain poorly understood. Here we present a fire tracking system to map the sub-daily evolution of all circumpolar Arctic–boreal fires between 2012 and 2023 using 375 m Visible Infrared Imaging Radiometer Suite active fire detections and the resulting dataset of the ignition time, location, size, duration, spread and intensity of individual fires. We use this dataset to classify the Arctic–boreal biomes into seven distinct ‘pyroregions’ with unique climatic and geographic environments. We find that these pyroregions exhibit varying responses to environmental drivers, with boreal North America, eastern Siberia and northern tundra regions showing the highest sensitivity to climate and lightning density. In addition, anthropogenic factors play an important role in influencing fire number and size, interacting with other factors. Understanding the spatial variability of fire regimes and its interconnected drivers in the Arctic–boreal domain is important for improving future predictions of fire activity and identifying areas at risk for extreme events.

Geology↗

Review of Technical Photovoltaic Key Performance Indicators and the Importance of Data Quality Routines

Technical key performance indicators (KPIs) are important metrics used to assess and quantitatively summarize various aspects of photovoltaic (PV) systems, including long-term performance, economic viability, and carbon footprint. Herein, a group of experts of the International Energy Agency's Photovoltaic Power Systems Programme Task 13 collect and describ the most important technical KPIs used in the industry. Thereby, a set of best practices for reliably handling PV system data is presented and the impact of data quality and climatic variability on KPI calculation is investigated. Further, the effective use of technical KPIs allows triggering data-driven and informed decisions to optimize PV systems and providing a comprehensive overview of how PV systems operate across different conditions and climates. With the worldwide growth of the PV industry, more companies operate/own PV systems in different regions, where the climatic and seasonal profiles differ. This requires context-aware evaluation of KPIs, or the judicious application of multiple KPIs, to ensure that each asset is evaluated correctly. Beyond that, there is untapped potential in the utilization of KPIs through geospatial mapping and extrapolation of fleet KPIs. This study demonstrates that the uncertainty in KPI estimation is not well understood and depends on data quality, climatic variability, and system configuration.

14 SOLAR ENERGY↗

Time-series machine-learning error models for approximate solutions to parameterized dynamical systems

This work proposes a machine-learning framework for modeling the error incurred by approximate solutions to parameterized dynamical systems. In particular, we extend the machine-learning error models (MLEM) framework proposed in Ref. Freno and Carlberg (2019) to dynamical systems. The proposed Time-Series Machine-Learning Error Modeling (T-MLEM) method constructs a regression model that maps features – which comprise error indicators that are derived from standard a posteriori error-quantification techniques – to a random variable for the approximate-solution error at each time instance. The proposed framework considers a wide range of candidate features, regression methods, and additive noise models. We consider primarily recursive regression techniques developed for time-series modeling, including both classical time-series models (e.g., autoregressive models) and recurrent neural networks (RNNs), but also analyze standard non-recursive regression techniques (e.g., feed-forward neural networks) for comparative purposes. Finally, numerical experiments conducted on multiple benchmark problems illustrate that the long short-term memory (LSTM) neural network, which is a type of RNN, outperforms other methods and yields substantial improvements in error predictions over traditional approaches.

42 ENGINEERING↗

Polarization-resolved core exciton dynamics in LiF using attosecond transient absorption spectroscopy

The ability to control absorption by modifying the polarization of light presents an exciting opportunity to experimentally determine the orbital alignment of absorption features. Here, attosecond extreme ultraviolet (XUV) transient absorption spectroscopy is used to investigate the polarization dependence of core exciton dynamics in LiF thin films at the Li + K edge. XUV pulses excite electrons from the Li 1s core level into the conduction band, allowing for the formation of a p-orbital-like core exciton, aligned along the XUV light polarization axis. A sub-5 fs near-infrared (NIR) probe pulse then arrives at variable time delays, perturbing the XUV-excited states and allowing the coherence decay of the core exciton to be mapped. The coherence lifetimes are found to be ≈ 2.4 ± 0.4 fs, which is attributed to a phonon-mediated dephasing mechanism as in previous core exciton studies. The differential absorption features are also shown to be sensitive to the relative polarization of the XUV and NIR fields. The parallel NIR probe induces couplings between the initial XUV-excited p-like bright exciton and s-like dark excitons. When crossed pump and probe polarizations are used, the coupling between the bright and dark states is no longer dipole-allowed, and the transient absorption signal associated with the coupling is suppressed by approximately 90%. This interpretation is supported by simulations of a few-level model system, as well as analysis of the calculated band structure. Here, the results indicate that laser polarization can serve as a powerful experimental tool for exploring the orbital alignment of core excitonic states in solid-state materials.

Attosecond laser spectroscopy↗

New insights into the natural history of bronchopulmonary dysplasia from proteomics and multiplexed immunohistochemistry

Bronchopulmonary dysplasia (BPD) is a disease of prematurity related to the arrest of normal lung development. The objective of this study was to better understand how proteome modulation and cell-type shifts are noted in BPD pathology. Pediatric human donors aged 1–3 yr were classified based on history of prematurity and histopathology consistent with “healed” BPD (hBPD, n = 3) and “established” BPD (eBPD, n = 3) compared with respective full-term born (n = 6) age-matched term controls. Proteins were quantified by tandem mass spectroscopy with selected Western blot validations. Multiplexed immunofluorescence (MxIF) microscopy was performed on lung sections to enumerate cell types. Protein abundances and MxIF cell frequencies were compared among groups using ANOVA. Cell type and ontology enrichment were performed using an in-house tool and/or EnrichR. Proteomics detected 5,746 unique proteins, 186 upregulated and 534 downregulated, in eBPD versus control with fewer proteins differentially abundant in hBPD as compared with age-matched term controls. Cell-type enrichment suggested a loss of alveolar type I, alveolar type II, endothelial/capillary, and lymphatics, and an increase in smooth muscle and fibroblasts consistent with MxIF. Histochemistry and Western analysis also supported predictions of upregulated ferroptosis in eBPD versus control. Finally, several extracellular matrix components mapping to angiogenesis signaling pathways were altered in eBPD. Despite clear parsing by protein abundance, comparative MxIF analysis confirms phenotypic variability in BPD. This work provides the first demonstration of tandem mass spectrometry and multiplexed molecular analysis of human lung tissue for critical elucidation of BPD trajectory-defining factors into early childhood.

60 APPLIED LIFE SCIENCES↗

Subsetted model output for static variables from a LASSO-CACTI WRF simulation

Static model output from a Weather Research and Forecasting (WRF) simulation from the Large-Eddy Simulation (LES) Atmospheric Radiation Measurement (ARM) Symbiotic Simulation and Observation (LASSO) deep-convection scenario for the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign. The LASSO-CACTI simulations span grid spacings from 7.5 km to 100 m through the use of four nested domains, labeled d1 through d4. The simulations are of convection near the Sierras de Córdoba mountain range, roughly centered on the ARM Mobile Facility. More information can be found at https://www.arm.gov/capabilities/modeling/lasso. This version of the output is a collection of variables subsetted from the raw WRF output to reduce the file overhead for users not needing the full raw dataset. The subset files are in netCDF format with the height-based variables on the raw, model eta and soil levels. The variables in this file are ones that do not change during a simulation, such as the terrain height and map-scale factors.

54 ENVIRONMENTAL SCIENCES↗

Parallel projection—An improved return mapping algorithm for finite element modeling of shape memory alloys

Here, we present a novel finite element analysis of inelastic structures containing Shape Memory Alloys (SMAs). Phenomenological constitutive models for SMAs lead to material nonlinearities, that require substantial computational effort to resolve. Finite element analysis methods, which rely on Gauss quadrature integration schemes, must solve two sets of coupled differential equations: one at the global level and the other at the local, i.e. Gauss point level. In contrast to the conventional return mapping algorithm, which solves these two sets of coupled differential equations separately using a nested Newton procedure, we propose a scheme to solve the local and global differential equations simultaneously. In the process we also derive closed-form expressions used to update the internal/constitutive state variables, and unify the popular closest-point and cutting plane methods with our formulas. Numerical testing indicates that our method allows for larger thermomechanical loading steps and provides increased computational efficiency, over the standard return mapping algorithm.

42 ENGINEERING↗

An extended polynomial chaos expansion for PDF characterization and variation with aleatory and epistemic uncertainties

This paper presents an extended polynomial chaos formalism for epistemic uncertainties and a new framework for evaluating sensitivities and variations of output probability density functions (PDF) to uncertainty in probabilistic models of input variables. An ”extended” polynomial chaos expansion (PCE) approach is developed that accounts for both aleatory and epistemic uncertainties, modeled as random variables, thus allowing a unified treatment of both types of uncertainty. We explore in particular epistemic uncertainty associated with the choice of prior probabilistic models for input parameters. A PCE-based Kernel Density (KDE) construction provides a composite map from the PCE coefficients and germ to the PDF of quantities of interest (QoI). Here, the sensitivities of these PDF with respect to the input parameters are then evaluated. Input parameters of the probabilistic models are considered. By sampling over the epistemic random variable, a family of PDFs is generated and the failure probability is itself estimated as a random variable with its own PCE. Integrating epistemic uncertainties within the PCE framework results in a computationally efficient paradigm for propagation and sensitivity evaluation. Two typical illustrative examples are used to demonstrate the proposed approach.

Aleatory uncertainty↗