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Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

ABSTRACT: Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a method with which sources of environmental variation in field data can be identified and adjusted, improving our ability to resolve effects of interest and to quantify subtle phenotypes.

SUBMITTER: Berry JC

PROVIDER: S-EPMC9275819 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

Berry Jeffrey C JC Qi Mingsheng M Sonawane Balasaheb V BV Sheflin Amy A Cousins Asaph A Prenni Jessica J Schachtman Daniel P DP Liu Peng P Bart Rebecca S RS

eLife 20220712

Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within differ ...[more]

PMID: 35819140

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Project description:Lung tissue causes significant small-angle X-ray scattering, which can be visualized with grating-based X-ray dark-field imaging. Structural lung diseases alter alveolar microstructure, which often causes a dark-field signal decrease. The imaging method provides benefits for diagnosis of such diseases in small-animal models, and was successfully used on porcine and human lungs in a fringe-scanning setup. Micro- and macroscopic changes occur in the lung during breathing, but their individual effects on the dark-field signal are unknown. However, this information is important for quantitative medical evaluation of dark-field thorax radiographs. To estimate the effect of these changes on the dark-field signal during a clinical examination, we acquired in vivo dark-field chest radiographs of two pigs at three ventilation pressures. Pigs were used due to the high degree of similarity between porcine and human lungs. To analyze lung expansion separately, we acquired CT scans of both pigs at comparable posture and ventilation pressures. Segmentation, masking, and forward-projection of the CT datasets yielded maps of lung thickness and logarithmic lung attenuation signal in registration with the dark-field radiographs. Upon correlating this data, we discovered approximately linear relationships between the logarithmic dark-field signal and both projected quantities for all scans. Increasing ventilation pressure strongly decreased dark-field extinction coefficients, whereas the ratio of lung dark-field and attenuation signal changed only slightly. Furthermore, we investigated ratios of dark-field and attenuation noise levels at realistic signal levels via calculations and phantom measurements. Dark-field contrast-to-noise ratio (CNR) per lung height was 5 to 10% of the same quantity in attenuation. We conclude that better CNR performance in the dark-field modality is typically due to greater anatomical noise in the conventional radiograph. Given the high physiological similarity of human and porcine lungs, the presented thickness-normalized, ventilation-dependent values allow estimation of dark-field activity of human lungs of variable size and inspiration, which facilitates the design of suitable clinical imaging setups.

Dataset Information

Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

Publications

Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

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