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1. Correcting tree-ring δ13C time series for tree-size effects in eight temperate tree species

   https://doi.org/10.1093/treephys/tpz138  

   Vadeboncoeur, Matthew A; Jennings, Katie A; Ouimette, Andrew P; Asbjornsen, Heidi (January 2020, Tree Physiology)

   Cernusak, Lucas (Ed.)

   Abstract Stable carbon isotope ratios (δ13C) in tree rings have been widely used to study changes in intrinsic water-use efficiency (iWUE), sometimes with limited consideration of how C-isotope discrimination is affected by tree height and canopy position. Our goals were to quantify the relationships between tree size or tree microenvironment and wood δ13C for eight functionally diverse temperate tree species in northern New England and to better understand the physical and physiological mechanisms underlying these differences. We collected short increment cores in closed-canopy stands and analyzed δ13C in the most recent 5 years of growth. We also sampled saplings in both shaded and sun-exposed environments. In closed-canopy stands, we found strong tree-size effects on δ13C, with 3.7–7.2‰ of difference explained by linear regression vs height (0.11–0.28‰ m−1), which in some cases is substantially stronger than the effect reported in previous studies. However, open-grown saplings were often isotopically more similar to large codominant trees than to shade-grown saplings, indicating that light exposure contributes more to the physiological and isotopic differences between small and large trees than does height. We found that in closed-canopy forests, δ13C correlations with diameter at breast height were nonlinear but also strong, allowing a straightforward procedure to correct tree- or stand-scale δ13C-based iWUE chronologies for changing tree size. We demonstrate how to use such data to correct and interpret multi-decadal composite isotope chronologies in both shade-regenerated and open-grown tree cohorts, and we highlight the importance of understanding site history when interpreting δ13C time series. 

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2. Revealed strength of preference: Inference from response times

   Konovalov, Arkady; Krajbich, Ian. (July 2019, Judgment and decision making)

   null (Ed.)

   Revealed preference is the dominant approach for inferring preferences, but it is limited in that it relies solely on discrete choice data. When a person chooses one alternative over another, we cannot infer the strength of their preference or predict how likely they will be to make the same choice again. However, the choice process also produces response times (RTs), which are continuous and easily observable. It has been shown that RTs often decrease with strength-of-preference. This is a basic property of sequential sampling models such as the drift diffusion model. What remains unclear is whether this relationship is sufficiently strong, relative to the other factors that affect RTs, to allow us to reliably infer strength-of-preference across individuals. Using several experiments, we show that even when every subject chooses the same alternative, we can still rank them based on their RTs and predict their behavior on other choice problems. We can also use RTs to predict whether a subject will repeat or reverse their decision when presented with the same choice problem a second time. Finally, as a proof-of-concept, we demonstrate that it is also possible to recover individual preference parameters from RTs alone. These results demonstrate that it is indeed possible to use RTs to infer preferences. 

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3. Differences in soil organic matter between EcM ‐ and AM ‐dominated forests depend on tree and fungal identity

   https://doi.org/10.1002/ecy.3929  

   Hicks Pries, Caitlin E.; Lankau, Richard; Ingham, Grace Anne; Legge, Eva; Krol, Owen; Forrester, Jodi; Fitch, Amelia; Wurzburger, Nina (November 2022, Ecology)

   Yavitt, Joseph B. (Ed.)

   As global change shifts the species composition of forests, we need to understand which species characteristics affect soil organic matter cycling to predict future soil carbon (C) storage. Recently, whether a tree species forms a symbiosis with arbuscular (AM) versus ectomycorrhizal (EcM) fungi has been suggested as a strong predictor of soil carbon storage, but there is wide variability within EcM systems. In this study, we investigated how mycorrhizal associations and the species composition of canopy trees and mycorrhizal fungi relate to the proportion of soil C and nitrogen (N) in mineral-associations and soil C:N across four sites representing distinct climates and tree communities in the Eastern U.S. broadleaf forest biome. In two of our sites, we found the expected relationship of declining mineral-associated C and N and increasing soil C:N ratios as the basal area of EcM-associating trees increased. However, across all sites these soil properties strongly correlated with canopy tree and fungal species composition. Sites where the expected pattern with EcM basal area was observed were 1) dominated by trees with lower quality litter in the Pinaceae and Fagaceae families and 2) dominated by EcM fungi with medium distance exploration type hyphae, melanized tissues, and the potential to produce peroxidases. This observational study demonstrates that differences in soil organic matter between AM andEcM systems are dependent on the taxa of trees and EcM fungi involved. Important information is lost when the rich mycorrhizal symbiosis is reduced to two categories. 

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4. Promoting Multidimensional Equity through Collaborative Routing using Incentive Mechanisms

   Wang, C; Peeta, S (January 2024, TRB)

   Penalty-based strategies, such as congestion pricing, have been employed to improve traffic network efficiency, but they face criticism for their negative impact on users and equity concerns. Collaborative routing, which allows users to negotiate route choices, offers a solution that considers individual heterogeneity. Personalized incentives can encourage such collaboration and are more politically acceptable than penalties. This study proposes a collaborative routing strategy that uses personalized incentives to guide users towards desired traffic states while promoting multidimensional equity. Three equity dimensions are considered: accessibility equity (equal access to jobs, services, and education), inclusion equity (route suggestions and incentives that do not favor specific users), and utility equity (envy-free solutions where no user feels others have more valuable incentives). The strategy prioritizes equitable access to societal services and activities, ensuring accessibility equity in routing solutions. Inclusion equity is maintained through non-negative incentives that consider user heterogeneity without excluding anyone. An envy-free compensation mechanism achieves utility equity by eliminating envy over incentive-route bundles. A constrained traffic assignment (CTA) formulation and consensus optimization variant are then devised to break down the centralized problem into smaller, manageable parts and a decentralized algorithm is developed for scalability in large transportation networks and user populations. Numerical studies investigate the model's enhancement of equity dimensions and the impact of hyperparameters on system objective tradeoffs and demonstrate the algorithm convergence. 

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5. 3D reconstruction enables high-throughput phenotyping and quantitative genetic analysis of phyllotaxy

   https://doi.org/10.1016/j.plaphe.2025.100023  

   Davis, Jensina M; Gaillard, Mathieu; Tross, Michael C; Shrestha, Nikee; Ostermann, Ian; Grove, Ryleigh J; Li, Bosheng; Benes, Bedrich; Schnable, James C (March 2025, Plant Phenomics)

   Differences in canopy architecture play a role in determining both the light and water use efficiency. Canopy architecture is determined by several component traits, including leaf length, width, number, angle, and phyllotaxy. Phyllotaxy may be among the most difficult of the leaf canopy traits to measure accurately across large numbers of individual plants. As a result, in simulations of the leaf canopies of grain crops such as maize and sorghum, this trait is frequently approximated as alternating 180 angles between sequential leaves. We explore the feasibility of extracting direct measurements of the phyllotaxy of sequential leaves from 3D reconstructions of individual sorghum plants generated from 2D calibrated images and test the assumption of consistently alternating phyllotaxy across a diverse set of sorghum genotypes. Using a voxel-carving-based approach, we generate 3D reconstructions from multiple calibrated 2D images of 366 sorghum plants representing 236 sorghum genotypes from the sorghum association panel. The correlation between automated and manual measurements of phyllotaxy is only modestly lower than the correlation between manual measurements of phyllotaxy generated by two different individuals. Automated phyllotaxy measurements exhibited a repeatability of R2 ¼ 0.41 across imaging timepoints separated by a period of two days. A resampling based genome wide association study (GWAS) identified several putative genetic associations with lower-canopy phyllotaxy in sorghum. This study demonstrates the potential of 3D reconstruction to enable both quantitative genetic investigation and breeding for phyllotaxy in sorghum and other grain crops with similar lant architectures. 

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