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Remote Sensing

MDPI AG

Preprints posted in the last 30 days, ranked by how well they match Remote Sensing's content profile, based on 10 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

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The Dark Ecology Dataset: Measurements of Aerial Biomass in US Weather Radar from 1995 to 2025

Sheldon, D.; Winner, K.; Deznabi, I.; Bernstein, G.; Bhambhani, P.; Lin, T.-Y.; Desmet, P.; Dokter, A. M.; Horton, K. G.; Nilsson, C.; Van Doren, B. M.; Farnsworth, A.; La Sorte, F. A.; Maji, S.

2026-06-23 ecology 10.64898/2026.06.20.733536 medRxiv
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The US NEXRAD radar network has monitored the aerosphere over the US and its territories continuously since the 1990s and archived nearly 300 million radar volume scans. These data contain a wealth of information about the movements of birds, bats, and insects. Historically, this biological information was difficult to access due to the amount of data and challenges in analyzing it. In the last 15 years, fueled by computational and methodological advances, large-scale aeroecology research has blossomed. However, comprehensive analyses of the NEXRAD archive remain very costly. We collected measurements of biological activity from every volume scan in the NEXRAD archive--nearly 300 million data files total--to assemble a dataset of aerial biomass over the US from 1995 to 2025. The core data are vertical profiles, which summarize biological activity at different heights above the radar station for each volume scan. We also provide time series data products that aggregate vertical profiles to point measurements at radar stations across time. These data products can support a range of aeroecology analyses at significantly reduced effort.

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Optimizing Signal Acquisition and Chemometric Pipelines for Micro NIR Plant Identification: Evaluating Spectral Backgrounds and Data Processing in Herbarium Specimens

Alves, T. C.; de Gasper, A. L.

2026-07-07 ecology 10.64898/2026.07.07.736730 medRxiv
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Premise: Rapid and accurate plant species identification is a critical challenge exacerbated by the taxonomic impediment. Although portable near-infrared (Micro NIR) spectroscopy represents a promising solution, the current absence of standardized protocols and a fundamental understanding of how critical acquisition and analysis parameters influence accuracy remain significant barriers. This study focused on the systematic optimization and validation of a comprehensive workflow designed to maximize the reliability of plant identification using this technology. To ensure methodological robustness across diverse foliar matrices, four vascular plant species were strategically selected as a representative test set to encompass morphological extremes, including significant variations in leaf thickness, pubescence, and surface texture. Methods: Using a portable spectrometer on herbarium specimens (exsiccate) of four vascular plant species, we systematically tested five spectral backgrounds, seven pre-processing methods, and four classification models. Subsequently, we optimized the number of spectral readings and evaluated the influence of the leaf scanning surface (adaxial vs. abaxial) on model accuracy. Results: The highest-performing combination was a Shiny Aluminum background, Second Derivative pre-processing, and a Random Forest model, which achieved a mean cross-validated accuracy of 99%. An average of just three spectral readings from the adaxial (upper) leaf face was sufficient to saturate model performance, proving statistically superior to other approaches (p < 0.001). Discussion: This study establishes a validated, high-accuracy protocol for plant species identification from herbarium specimens using portable NIR, offering a powerful tool for biodiversity studies. Direct applicability to fresh plants in the field requires future validation to account for the spectral influence of moisture variability.

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Leaf movements as a quantitative metric for early stress detection

Herrero, E.; Wijeweera, S.; Gill, A. R.; Bampton, C.; Sullivan, W.; Stamford, J. D.; Bromley, J.; Antoniades, A. Z.; Mortimer, J. C.; Webb, A. A. R.; Gilliham, M.; Millar, A. H.

2026-07-08 plant biology 10.64898/2026.06.16.732190 medRxiv
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Early, precise, and non-destructive stress detection is essential for maintaining crop productivity, particularly in high-density plant growth systems like controlled environment agriculture (CEA), where manual monitoring is often impractical. Using plant motion as a proxy for growth and plant health, we demonstrate a method for early, non-invasive stress detection through quantitative leaf-movement analysis in lettuce and five other CEA relevant crops. Leaf-movement dynamics under stress were imaged with a low-cost, scalable Raspberry Pi imaging setup and quantified using a repurposed open-source motion estimation algorithm; Tracking Rhythms in Plants (TRiP). Our system detected stress-induced changes in leaf-movement within 1 hour of stress, with the timing dependent on the nature of the stress. Sustained reductions in leaf-movement coincide with decreased biomass accumulation. This approach offers a non-invasive, rapid, scalable, and cost-effective solution for continuous crop monitoring, with potential for application in both terrestrial and space farming CEA systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/732190v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@19ee20eorg.highwire.dtl.DTLVardef@b0804org.highwire.dtl.DTLVardef@3b3fa8org.highwire.dtl.DTLVardef@1d04026_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Quantification of leaf-movement dynamics as a high-throughput proxy for plant physiological status, enabling early stress detection and timely intervention to mitigate yield penalties in CEA settings (image made with biorender.org). C_FIG

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Linking automated image analysis to ecological inference: high-throughput monitoring of soil fauna

Hendrikx, H.; Belaud, E.; Postic, F.; Scalabrino, M.; Lebeau, M.; Le Maire, G.; Jourdan, C.; Gallet, P.; Hedde, M.

2026-06-16 ecology 10.64898/2026.06.16.732537 medRxiv
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1 - Automated in situ sensors - e.g., buried scanners - are transforming biodiversity monitoring by generating data at spatio-temporal resolutions unattainable through traditional sampling, including in cryptic environments such as soil that have remained largely inaccessible to existing methods. However, extracting ecologically meaningful information from these data streams requires substantial image processing effort that currently constitutes a critical bottleneck, particularly when the signal-to-noise ratio is low and annotated training data are scarce. 2 - Standard end-to-end deep learning detection pipelines offer unsatisfactory results due to the lack of training data and heterogeneity of the taxa of interest. We explore the potential of combining traditional computer vision algorithms with state-of-the-art deep learning models to build an efficient raw data processing pipelines from limited annotation effort. Specifically, based on the observation that the background barely changes, we focus on the differences between two consecutive images to turn the initial detection problem (with very low signal) into a simpler classification problem, which we solve by fine-tuning foundation models on limited annotated data. 3 - Our approach significantly reduces the annotation effort, allowing us to release an open dataset with about 600 soil scans and more than 8 000 labeled invertebrate occurrences across nine taxa. Using this dataset to train our models, we obtained population count estimates with relative errors ranging from 10% to 61% across taxa over a three-month period. Ecological validation through a land-use stability analysis showed full directional congruence between automated and expert-annotated classifications across all nine taxa examined, with effect-size discrepancies proportional to per-taxon classification accuracy. 4 - These results demonstrate that combining domain-specific heuristics with fine-tuned foundation models provides an effective and data-efficient strategy for automating ecological image processing workflows in low-signal, data-scarce contexts. The validated pipeline removes the manual annotation bottleneck that has historically limited scanner-based soil monitoring to short observational windows and restricted taxonomic scope, opening the way for continuous, large-scale tracking of soil invertebrate community dynamics at resolutions previously unachievable.

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Application of Machine Learning Tools for Waterbird Colony Monitoring Provides Gains in Precision and Temporal Efficiency

Vallery, A. C.; Kabra, K.; Gibbons, R.; Arnold, H.; Minnich, N.; Barman, A.

2026-07-02 ecology 10.64898/2026.07.01.735369 medRxiv
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Waterbirds serve as important indicators of both aquatic and terrestrial ecosystem health, making effective monitoring essential for tracking population health and identifying potential causes of decline. Drones have provided opportunities to overcome historic waterbird monitoring challenges, but the expertise and time required for manual image analysis creates a major bottleneck. Recent advances in deep learning-based object detection have enabled rapid, automatic detection of features in complex ecological imagery, though applications have largely been limited to single-species colonies, and practitioners lack quantitative comparisons of annotation time and accuracy across different levels of automation. We systematically compared four waterbird monitoring approaches using identical survey areas from Chester Island, a mixed-species colony in Matagorda Bay, Texas, in 2025: (1) traditional ground-based counts, (2) manual drone imagery-based counts, (3) computer-assisted counts using pre-annotations from an object detector with manual human verification (Human+ML), and (4) fully automated counts using object detector annotations (ML-only). We trained a YOLOv10 object detection model on manually annotated imagery of Chester Island in 2021 and applied it to the 2025 imagery. Manual drone annotation detected 6,530 birds in 40.5 hr and served as the primary reference standard. Human+ML detected 5,826 birds (89% of manual) in 7.7 hr, an 81% reduction in annotation time. ML-only detected 5,679 birds (87% of manual) in approximately 46 min, a 98% reduction. Ground counts recorded 5,868 birds (90% of manual). Detection generalized well across species while classification depended heavily on training data and morphological distinctiveness. The Human+ML workflow emerged as a practical middle ground, providing practitioners with empirical data to evaluate partial versus full automation strategies based on monitoring objectives.

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Standardizing image-derived fish length-frequency distributions to reference measurements using bin-specific error matrices

Shibata, Y.; Iwahara, Y.; Hino, H.; Tsukada, A.; Kisara, Y.; Nishino, T.; Endo, H.

2026-07-06 ecology 10.64898/2026.07.06.736664 medRxiv
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Artificial intelligence (AI)-based image analysis can efficiently estimate fish length, but differences in devices, imaging conditions, operators, and AI models limit comparability among surveys. We propose a standardization framework that estimates a bin-specific error matrix from paired reference measurements and AI-derived lengths and applies it to standardize (correct) AI-derived length-frequency distributions. The Richardson-Lucy expectation-maximization algorithm was used, with the number of iterations selected via cross-validation. Simulations based on empirical length-frequency data from 110 species showed that standardization reduced relative bias and distributional discrepancy; median relative-bias and root mean square error ratios were below 1, and the performance was more affected by the amount of paired data than by the number of cross-validation folds. In real data from 957 Japanese jack mackerel, standardized AI-derived distributions approached human-observer histograms, although discrepancies remained in the range of 160-230 mm. The proposed framework provides a practical approach for improving the comparability of image-derived length-frequency data using paired calibration data, without retraining the underlying AI model.

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Laser scanning identifies large trees as a major source of uncertainty in mangrove carbon accounting

Jackson, T. D.; Feyen, J.; Lozano-Arias, L.; Caicedo-Garcia, J.-P.; Sierra-Correa, P. C.; Montes-Chaura, C. C.; Sanjur, A. A.; Hoyos-Santillan, J.; Castillo, D.; Castillo, Y.; Wortel, V.; Ouboter, M. P.; Tjong-A-Hung, N. S.; Amiemba, D. L.; Rambharos, C. S.; Paloeng, C. P.; Moe Soe Let, V. A.; Hardin, R.; Porter, F. R.; Kerr, O. O.; Rodriguez Hernandez, D. I.; Digby, M. A.; Jucker, T.; Fischer, F. J.; Calders, K.; Price, C. A.; Mathura, F.; Asmath, H.

2026-06-16 ecology 10.64898/2026.06.12.731900 medRxiv
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BackgroundMangrove forests are crucial ecosystems which support biodiversity, protect coastlines and store vast amounts of carbon. Mangrove conservation and protection rely on accurate carbon accounting to unlock investment. However, the allometric equations underpinning these carbon estimates remain poorly constrained, particularly for the large trees. MethodsWe used terrestrial laser scanning (TLS) to estimate the biomass of 187 mangrove stems across Suriname, Panama, Colombia and Jamaica, including 84 stems >20 cm DBH. TLS-derived biomass estimates were used to evaluate local, regional and pantropical allometric equations. ResultsMost diameter-based allometric equations underestimated biomass by 8-65%. Equations additionally incorporating tree height performed better, but still underestimated biomass by 12-16% on average. Applying alternative allometries to a representative mangrove inventory from Panama produced biomass estimates ranging from 80 to 200 Mg ha-{superscript 1}, demonstrating that allometric uncertainty alone can generate more than a two-fold difference in estimated carbon stocks. ConclusionsCurrent allometric equations systematically underestimate the biomass of large mangrove trees and are therefore likely to underestimate mangrove carbon stocks. TLS provides a practical, non-destructive approach for expanding biomass datasets and improving allometric equations. Reducing allometric uncertainty should be a priority for strengthening blue carbon accounting and mangrove conservation.

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Rootquant: Automated Root Trait Quantification Fromminirhizotron Images Using Deep Learning

Parth, K.; Varela, S.; Liu, Z.; Martini, K. M.; Rajurkar, A.; Allan, D.; McCoy, S.; Ruhter, J.; Walker, S.; Goldenfeld, N.; Leakey, A.

2026-07-08 plant biology 10.64898/2026.07.07.737053 medRxiv
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Quantifying root traits such as root length (RL) and root surface area (RSA) from minirhizotron imagery is a valuable approach for overcoming the phenotyping bottleneck that limits understanding and improvement of crop productivity, resource use efficiency and resilience in field experiments. However, current approaches remain labor-intensive, and deep learning (DL) methods suffer from limited generalization ability. We present RootQuant, an end-to-end DL model that simultaneously predicts RL and RSA directly from minirhizotron images using only whole-image trait values as supervision, thereby eliminating the need for pixel-level annotations. The models generalization ability was evaluated across species and fine-tuning configurations. The practical applicability of the model was further assessed under field conditions by converting image-derived RL estimates into volumetric root length density (vRLD). Using 118,191 maize and soybean images collected between 2009 and 2020, RootQuant trained on both species achieved an R2 of 0.90 and an RMSE of 2.9 mm for RL, and an R2 of 0.88 and an RMSE of 4.2 mm2 for RSA. The same mixed-species model generalized strongly across species, yielding an 8% relative improvement in R2 and a 30% lower RMSE on maize compared with the same architecture trained on a single species and applied zero-shot. Image-derived RL predictions converted to vRLD showed the expected depth-dependent decline in vRLD, as was also found by coincident destructive quantification of roots washed out of soil cores. By providing a generalist backbone model trained on a large dataset from two major crop species, RootQuant enables high-throughput simultaneous estimation of two relevant root traits directly from raw imagery without task-specific fine-tuning, thereby accelerating in situ root system analysis and phenotyping applications.

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Acoustic detection of a rarely vocalising invasive mammal from sparse data

Gibbons, A.; Parnell, A.; Donohue, I.; Ogasawara, M.; Ross, S. R. P.-J.

2026-06-23 ecology 10.64898/2026.06.19.733324 medRxiv
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O_LIMonitoring and limiting the spread of invasive species on islands requires efficient detection and population estimation methods. However, elusive species can be difficult to monitor using traditional methods, making autonomous approaches such as camera trapping and acoustic monitoring increasingly valuable. C_LIO_LIOn the island of Okinawa, Japan, the small Indian mongoose ( Urva auropunctata) threatens many native species since its introduction in 1910. Listed among the worlds worst invasive species, effective monitoring of U. auropunctata in Okinawa is critical. The Okinawa Environmental Observation Network (OKEON) uses camera traps to detect U. auropunctata, but success depends on precise placement. Though OKEON also includes a high-resolution acoustic monitoring programme, no audio classification model currently exists for U. auropunctata. Developing such a model could improve substantially our capacity to detect and manage the species. C_LIO_LIUsing sparse U. auropunctata vocalisations collected from camera trap videos, we built a lightweight Convolutional Neural Network distilled from a more complex model for classifying contact calls and alarm calls of U. auropunctata. Our distilled model performed similarly to the full model at detecting vocalisations from training data, but was considerably faster. C_LIO_LIWe applied the distilled classifier to [~]486 hrs of audio collected over eight years from southern Okinawa, where we successfully detected U. auropunctata a handful of times in each year of recording. In spite of strong model performance on test data, our model did not transfer well to unseen data, perhaps owing to the rarity of U. auropunctata calls and consequent small training dataset size, limiting its utility for ecological monitoring. C_LIO_LIPractical implication. The use of sparse audio data from camera trap videos to train an acoustic classifier had limited utility to detect the rarely vocalising U. auropunctata from passive acoustic monitoring data. We provide several recommendations for enhancing classifier performance to provide robust actionable insights into the distribution and spread of U. auropunctata, and aid targeted conservation efforts for Okinawas threatened biodiversity. C_LI

10
Internal decay in living trees: a quantitative tomography framework and its application in a temperate forest

Thompson, G.; Lutz, M. P.; Lucey, T. K.; Duncan, B.; Yang, M.; Jurado, S.; Matthes, J. H.; Marra, R. E.; Gewirtzman, J.

2026-06-14 ecology 10.64898/2026.06.10.730433 medRxiv
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Internal decay in living trees is an important component of carbon and nutrient cycling as well as species and structural diversity maintenance in forest ecosystems. We used sonic and electrical resistance tomography to evaluate and compare the prevalence and severity of stem decay in 57 living trees among four common species (Acer rubrum L., Nyssa sylvatica Marsh., Quercus rubra L., and Tsuga canadensis (L.) Carriere)) with overlapping and non-overlapping distributions across wetland and upland habitat types at the Harvard Forest in Petersham, MA, USA. Independent of tree size, site identity best explained variation in the prevalence of decay across trees sampled, whereas species identity best explained the severity of decay. We categorized trees as having no decay, incipient decay, active decay, or cavities based on combined sonic and electrical resistance metrics, the latter generated by a custom image analysis application. About 31% of wetland trees exhibited incipient decay (compared to 11% in the upland), whereas about 32% of upland trees exhibited active decay (compared to 10% in the wetland). Our study highlights a new quantitative framework for decay categorization through normalized principal component analysis (PCA) and decay analysis software that complements dual tomographic methodology for future investigations of ecological drivers of decay presence and susceptibility.

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Bathymetric Resolution-Dependent Biases in Antarctic Benthic Biodiversity Models: Hotspots Hold, Counts Shift

Potter, S.; Jansen, J.; Hill, N.; Lucieer, V.

2026-06-24 ecology 10.64898/2026.06.23.734136 medRxiv
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Antarctic benthic organisms are highly diverse and play a critical role in the Southern Ocean ecosystem. Despite decades of sampling, vast areas of the Antarctic continental shelf remain biologically unsurveyed due to logistical and financial constraints, limiting baseline knowledge essential for effective conservation planning. Species distribution models (SDMs) allow biodiversity to be inferred in the absence of biological data by linking benthic community patterns to environmental predictors. However, the resolution of the environmental predictors, particularly bathymetry, varies significantly between regions, casting doubt about how reliably SDMs can be used to predict into regions where only coarse-resolution data are available. Here, we show that SDMs trained on high-resolution data underestimate Antarctic benthic morphospecies richness by up to 18% when applied to aggregated coarse-resolution environmental data (and up to 50% when using satellite-derived ETOPO bathymetry). Using six systematically degraded versions of high-resolution multibeam bathymetry and annotated seafloor imagery across three Antarctic regions, we evaluate SDM performance both with and without additional environmental variables. High-resolution bathymetry captures terrain complexity most effectively, but we find that the spatial distribution of richness hotspots and the median richness per cell remain consistent, provided models are applied at the same resolution at which they were trained. Our results suggest that while high-resolution bathymetry may enhance local predictions, coarse-resolution data may be more robust for regional-scale predictions, such as those used for Antarctic shelf-wide spatial planning.

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DeepPheno: A Deep Learning Framework for Linking Hyperspectral Imaging and SNP Genotypes in Lettuce

Okyere, F. G. G.; Mehrem, S. L.; Snoek, B. L.; Van den Ackerveken, G.; Abeln, S.

2026-07-10 plant biology 10.64898/2026.07.09.737449 medRxiv
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While whole genome sequencing captures millions of single nucleotide polymorphisms (SNPs) and hyperspectral imaging (HSI) enables non destructive plant phenotyping, integrating these modalities to link genotype to phenotype remains challenging due to their high dimensionality and non linearity. This study presents DeepPheno a deep learning framework that predicts SNP genotypes from HSI data, using model predictability as a proxy for genotype phenotype association. HSI data were acquired from 194 lettuce genotypes under field conditions. HSI data patches (20 x 20 pixels x 224 spectral bands) were used to train a hybrid CNN to predict the variant of a specific SNP. The framework was validated on SNPs with known phenotypic effects (anthocyanin, leaf serration, pale pigmentation), achieving high predictive performance (AUC ranging from 0.806 to 0.935), whereas models trained on randomly shuffled labels performed at chance (mean AUC {approx} 0.51). Extending the workflow to 50 randomly selected putatively neutral SNPs, most yielded low predictability, but two showed high performance (AUC > 0.76), suggesting uncharacterized genotype phenotype links. Explainable AI, including SHAP and Grad CAM, identified relevant spectral and spatial features driving these predictions, particularly the green and red edge wavelengths associated with pigment dynamics and leaf structure. These results establish a framework for understanding complex genotype phenotype interactions in plants and extracting these links from HSI data without predefining the exact trait values. It provides an avenue for high throughput trait discovery and description and extends the integration of image based phenomics with plant genetics.

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Guiding the development of climate counterfactuals for health impact attribution studies

Charnley, G. E. C.; Kotz, M.; Kawiecki Peralta, A.; Grayson, K. M.

2026-06-18 epidemiology 10.64898/2026.06.16.26355779 medRxiv
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Climate change detection and attribution (D&A) methods have become vital for quantifying the influence of anthropogenic forcing on the Earth's systems, including human health. Health impact attribution (HIA) studies seek to disentangle climate-driven health effects from natural variability yet are often constrained by the availability of accessible counterfactual climate scenarios. This tutorial paper presents a flexible, reproducible framework for developing counterfactual climates without reliance on computationally intensive global circulation models. We provide practical, R-based methodologies for constructing both trend-based (temperature and non-temperature) and event-based counterfactual, using a variety of techniques including model residual detrending, data-driven decomposition (e.g., Singular Spectrum Analysis and Empirical Mode Decomposition) and stochastic weather generators. The tutorial also explores the incorporation of greenhouse gas concentrations as forcing variables, rather than global mean temperature anomalies. By operationalising these methods through worked examples and an open code repository, this paper aims to build capacity within the HIA community, enhance methodological transparency, and foster interdisciplinary collaboration between climate and health researchers.

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Research protocol for a multidimensional environmental and health impact study of petrochemical plant emissions in Calvert city, Kentucky

Huntington-Moskos, L.; Cave, M.; Reynolds, L.; Anderson, L.; Housman, B.; Abolins-Abols, M.; Fratzke, R.; Holm, R.; Smith, T. R.

2026-07-09 occupational and environmental health 10.64898/2026.07.07.26356427 medRxiv
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While exposure to volatile organic compounds such as ethylene dichloride and vinyl chloride monomer is a well-established cause of liver disease, particularly hepatic hemangiosarcoma, characterizing real-world exposure profiles in communities surrounding industrial centers remains challenging. Calvert City, Kentucky (population ~2,500), provides a unique setting characterized by both active industrial emissions and legacy sources of air toxics. To address these complexities, this method paper describes the framework for the Biomonitoring and Environmental Assessment for Community Outreach and Neighborhood Safety (BEACON) study. By utilizing a novel, multi-dimensional exposure assessment strategy, BEACON aims to characterize air toxic exposures and provide actionable data for community health and safety. For the BEACON study, we will leverage Kentucky Department of Air Quality measures of air toxics, analyze urine samples in a small cohort of community volunteers, analyze community urine via wastewater in an adjacent community, geocode citizen odor reporting, assess blood markers in wildlife, survey small and large animal veterinarians in the area for anomalies in morbidity and mortality, and work with the regional health system to enhance vigilance for health issues associated with toxicants present in the area. In addition, blood samples will be collected at three time points and biobanked for future analyses. Efforts will be made to link this study to additional large-scale long-term cohorts where possible. Throughout the project, community engagement will play a critical role by raising awareness, fostering collaboration, and ensuring that the voices of affected residents are heard.

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Automated Parameter Estimation for Camera Trap Density Models Using Computer Vision-Enhanced Distance Sampling

McMurry, S.; Alyetama, M.; Goldstein, B.; Kays, R.

2026-06-16 ecology 10.64898/2026.06.14.732225 medRxiv
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Models for estimating animal density from camera traps require four parameters informing detection: movement speed, daily activity level, staying time (duration animals remain within the detection zone), and effective detection distance. These parameters traditionally come from labor-intensive manual measurements and auxiliary telemetry. Recent advances in computer vision can provide the positions of animals in camera trap images, which have been used for distance sampling. We extend this approach to extract all four parameters from imagery, providing the first AI-derived estimates of movement speed and staying time from automated coordinate tracking. We also introduce a new joint multi-species hierarchical distance function that estimates deployment-specific effective detection distances while borrowing strength across species through partial pooling. Our pipeline integrates MegaDetector for animal detection, the Segment Anything Model for segmentation, and Dense Prediction Transformers for monocular depth estimation. From frame-level coordinates, we reconstruct movement trajectories across burst sequences to estimate speed with size-biased distribution corrections, calculate staying time through bounding box interpolation, and estimate activity levels from detection timestamps. The joint hierarchical distance function decomposes the detection scale parameter into a shared deployment-level effect and species-specific offsets, so species effects represent deviations from the multi-species average, allowing data-rich species to inform detection conditions where rare species have few observations. AI-derived scene depth enters the model as a covariate on detection range, providing a vegetation openness metric from the same pipeline. To address position errors from depth estimation, we apply data quality filters. We processed 122,574 frames from 181 deployments across montane forests in Washington and Montana, generating parameter estimates for 12 species without manual annotation. Automated speed estimates produced day ranges 2.7 to 4.3 times GPS telemetry-derived daily distances, reflecting differences between encounter velocity within detection zones and landscape-scale displacement. Deployment-level variation in detectability exceeded species-level differences 3:1, with scene depth strongly predicting detection range; mean effective detection distances ranged from 4.1 to 7.6 m. Applied to a Random Encounter Model, these parameters yielded a white-tailed deer density estimate of 21.4 animals/km{superscript 2} and the Random Encounter Staying Time model yielded 11.6animals/km{superscript 2} in Montana. This pipeline enables scalable density estimation across large camera trap networks.

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Mixed-Frequency Regression Model for Short-Term Environmental Exposure-Response Modelling: A Simulation Study

Shukla, N.; Tahir, H.; Smart, S.; Bartington, S. E.; Hansell, A. L.; Lucas, T. C.

2026-06-29 epidemiology 10.64898/2026.06.24.26356336 medRxiv
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Background: Extreme environmental events, such as extreme temperatures and air pollution, have become a global concern due to their detrimental effects on human health. Short-term peak exposure episodes, despite lasting only a few hours, are crucial for exposure-response modelling. The use of time-aggregated exposure data often overlooks the impact of peak exposures on human health. However, studies employing high-temporal resolution exposure data are rare due to the limited availability of high-temporal resolution health outcomes across various scenarios. Therefore, to address the limitations associated with exposure-response modelling using aggregated exposure data, we have developed a model referred to as the mixed-frequency distributed lag non-linear model (mf-DLNM). Methods: In this work, a simulation study was conducted to further validate the mf-DLNM for hourly-daily mixed-frequency data, using data on hourly temperature and daily respiratory mortality for the West Midlands, UK. Given that the focus was on extreme exposures, Relative Risks (RR) at the 5th and 95th temperature quantiles were considered as the estimands of interest. Model performance was evaluated based on the bias, empirical standard error (EmpSE), and coverage of these estimands. Additionally, the model was assessed across various scenarios, considering data size (1, 3, 5, and 11 years with a 24-hour lag), lag length (12 and 24 hours with 11 years), seasonal variation (summer months with 11 years and 24-hour lag) and distribution (Poisson and negative binomial). Results: The mf-DLNM effectively captured the true parameters of the model. The model, fitted to 11 years of simulated data, a 24-hour lag and a Poisson distribution, observed a bias of 0.011 (0.0009) and 0.011 (0.001) for the RR at the 5th and 95th temperature quantiles, respectively, with Monte Carlo SEs (MCSEs) in parentheses. Furthermore, the model exhibited coverage of 0.94 and 0.93 for RR at the 5th and 95th temperature quantiles, respectively. In addition, the mf-DLNM with hourly and daily data demonstrated satisfactory performance across all scenarios except for the RR at 95th temperature quantiles in the seasonal analysis. Conclusions: Researchers are encouraged to adopt mf-DLNM in instances where high-temporal resolution exposure data are available alongside low-resolution health data. It serves as an alternative to traditional approaches that aggregate high-frequency exposure data. By preserving the temporal information of environmental exposures, mf-DLNM enables a more precise assessment of exposure-response relationships, thereby improving the accuracy and reliability of health risk estimates. This approach offers a promising opportunity for informed decision-making and the development of effective interventions for vulnerable populations and healthcare facilities to address short-term environmental episodes.

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A multiregional image-text dataset and benchmark for vision-language modeling of plant diseases

Nguyen, T. V.; Quoc, K. N.; Harwath, D.; Quach, L.-D.; Dao, P. D.

2026-07-09 plant biology 10.64898/2026.07.01.735881 medRxiv
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Plant diseases remain a major challenge to global food production, and timely, accurate, and scalable detection of plant stress is critical to reducing these losses. Recent advances in digital imaging and artificial intelligence offer unprecedented opportunities for precision crop disease detection and management. Yet, existing plant disease datasets remain often fragmented across crop and disease systems, and are largely dominated by controlled-environment imagery. The lack of standardized, interoperable, and representative datasets limits reproducibility, transferability, and scalability of AI systems, thereby constraining their deployment in operational agricultural applications. Here we present LeafMD, an integrated multimodal plant disease dataset and benchmark resource that includes LeafNet 2.0, a large-scale multimodal digital image dataset comprising 255,855 image-text pairs across 37 crop species, 197 crop-disease classes, and 9 geographic regions spanning tropical, subtropical, and temperate agricultural systems. Unlike conventional datasets, LeafNet 2.0 integrates biologically grounded symptom descriptions with image-level annotations of early and late disease stages, enabling symptom-aware analysis of disease progression under realistic field conditions. We further introduce LeafBench 2.0 as part of LeafMD, a visual-question answering benchmark covering nine fine-grained plant pathology tasks, including pathogen classification, lesion characterization, symptom interpretation, and disease severity assessment. Evaluation across 16 vision-language models revealed substantial performance gaps between coarse disease recognition and fine-grained pathological reasoning, while agriculture-adapted models consistently outperformed several larger general-domain architectures on symptom-oriented tasks. Together, LeafNet 2.0 and LeafBench 2.0 establish LeafMD as a multimodal resource for developing disease-aware agricultural foundation models and studying fine-grained pathological reasoning in real-world environments.

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Accounting for Human Movement to Improve Exposure-Health Models

Tahir, H.; Smart, S.; Cai, S.; Ng, A.; Vande Hey, J.; Lucas, T. C.

2026-06-17 epidemiology 10.64898/2026.06.15.26355663 medRxiv
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Background. Current exposure-health models rely on averaged, residential-based environmental exposures, failing to account for human movement. This aggregation can lead to exposure misclassification and biased exposure-response estimates, potentially distorting our understanding of the true health effects of environmental conditions. We developed exposure disaggregation regression models that explicitly account for human movement when linking environmental exposures to health outcomes. Methods. By weighting pixel-level exposures according to distance from home as a simple proxy for human movement, our model linked disaggregated environmental exposures to individual-level health outcomes. Weights were either fixed a priori or derived from a latent distance-decay power parameter learned from the data. We additionally evaluated model performance under a nonlinear exposure-response relationship. Model performance was assessed across multiple sample sizes (N = 1,114; 50,000; and 100,000). A simulation study examined parameter recovery using bias, empirical standard error (EmpSE), and credible interval coverage. As a case study, Demographic and Health Surveys (DHS) data from Albania were used to link acute respiratory infection (ARI) outcomes among children under five to pixel-level NDVI within a 3 km buffer around DHS cluster centroids, and the proposed models were applied to these data. Results. Across all models (fixed-weight, learned-weight, and restricted cubic spline models), parameter recovery improved with increasing sample size. At N = 1,114, estimates were biased and imprecise, with incorrect effect direction for exposure-response parameters (e.g., learned-weight {beta}1 bias = - 0.79; EmpSE = 2.61; coverage = 0.88). In contrast, the models accurately recovered parameters at larger sample sizes, including the latent distance-decay parameter (bias = - 0.02; EmpSE = 0.15; coverage = 0.95 at N = 100,000), demonstrating their ability to reliably learn movement-based exposure weights when sufficient data were available. Conclusion. Instead of relying on arbitrarily-sized buffers, this statistical framework provides a novel method for studying environmental exposure-health relationships whilst accounting for human movement. With sufficiently large sample sizes, it can accurately estimate the influence of disaggregated environmental exposures on individual-level health and help address exposure misclassification arising from residential-only metrics. This methodological framework remains scalable, interpretable, and adaptable to other exposures and outcomes, offering a foundation for future work that integrates richer mobility-informed exposure-health research.

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Odor Annoyance, Sensory Irritation or Relaxation: Acute Effects of Real Pinewood Emissions in Indoor Air Scenarios

Hucke, C. I.; Gallus, V.; Butter, K.; Reiser, J. E.; Ohlmeyer, M.; van Thriel, C.

2026-07-08 physiology 10.64898/2026.07.03.736270 medRxiv
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Wood is commonly used in the building sector, emitting volatile organic compounds (VOCs) contributing to indoor air quality. These VOC profiles can have a pleasant smell and positive effects e.g., induce relaxation. Contrarily, VOCs can have adverse health effects in higher concentrations. Therefore, some VOCs are regulated by guide values (GV). Potentially positive and negative effects of pinewood emissions, ranging from 0.2 mg/m3 (German GV I for bicyclic terpenes) to 2.0 mg/m3 (GV II) were investigated in an experimental 2 h exposure study using a within-subject design. Thirty-two healthy participants rated the perception, pleasantness, symptoms of irritation, and indicators of well-being. During a demanding working memory task (n-back) and a resting period, heart rate (HR) and HR variability (HRV) changes were measured. Before and after each session physiological markers of sensory irritation were assessed. Ratings indicated that the exposure to GV I and GV II were not perceived as more intense or pleasant. Mostly concentration-independent effects were revealed, indicating that inter-individual factors influenced the ratings rather than the VOCs. The pinewood odors during the n-back task did not cause distraction nor did it facilitate performance as previously suggested. HR/V changes indicated that pinewood odors during and after the n-back tasks did not induce relaxation. Only symptoms of nasal irritation showed some weak concentration-dependency, not supported by physiological markers or comparable ratings of sensory irritation. In conclusion, the fact that no distinct odor is detected suggests that interfering factors potentially prevent the regulation of odors at relevant indoor air concentrations.

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A global analysis of climate-driven reversal risks in forests

Wu, C.; Goulden, M. L.; Randerson, J. T.; Trugman, A. T.; Wang, J. A.; Yang, L.; Acil, N.; Cook-Patton, S. C.; Cullenward, D.; Davis, S. J.; Williams, C. A.; Anderegg, W. R. L.

2026-06-22 ecology 10.64898/2026.06.19.733404 medRxiv
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The integrity of forest-based climate solutions and carbon credits requires persistent carbon storage, but climate change is increasing the risk of natural disturbances that release carbon back into the atmosphere. Using global satellite data, disturbance modeling, and machine learning, we provide the first spatially explicit and scenario-based maps of long-term probability of carbon loss in global forests under different disturbance severities and climate scenarios. We find that North American conifer forests, tropical rainforests, and Asian (sub)tropical dry forests face the greatest risks, and that Eurasian temperate forests, African (sub)tropical dry forests face the lowest. Globally, the likelihood of reversals over 100 years is 31%-42% across all scenarios. Our work helps to maximize the benefits of forest-based climate solutions by informing more strategic project placement and more robust reversal-risk compensation mechanisms, such as buffer pools, and highlights critical additional science to better understand and manage risks of these essential climate solutions. Plain Language SummaryForests can help slow and lessen climate impacts. However, in places this benefit is becoming less reliable as climate change increases natural disturbances such as wildfires, drought, storms, and insect outbreaks, which can release stored carbon back into the atmosphere. In this study, we created the first scenario-based global maps of risks and found that the risk of carbon loss is widespread and highly variable across regions, with especially high vulnerability in North American conifer forests, tropical rainforests, and Asian tropical and subtropical dry forests. Our study highlights the importance of considering disturbance risks when siting forest projects for climate mitigation, and developing protocols for carbon markets, such as in voluntary programs and under the UNFCCC Paris Agreement. Key PointsO_LIA demographic model framework estimates the reversal risk from natural disturbances over 100 years in global forests C_LIO_LISpatially explicit maps under different severity scenarios show variation in the integrated 100-year risk of carbon reversal C_LIO_LISpatially explicit maps estimate the required buffer pool needed to compensate for disturbance-driven reversals in global forests C_LI