Exploratory analysis using machine learning to predict for chest wall pain in patients with stage I non-small-cell lung cancer treated with stereotactic body radiation therapy.

Background and purposeChest wall toxicity is observed after stereotactic body radiation therapy (SBRT) for peripherally located lung tumors. We utilize machine learning algorithms to identify toxicity predictors to develop dose-volume constraints.Materials and methodsTwenty-five patient, tumor, and dosimetric features were recorded for 197 consecutive patients with Stage I NSCLC treated with SBRT, 11 of whom (5.6%) developed CTCAEv4 grade ≥2 chest wall pain. Decision tree modeling was used to determine chest wall syndrome (CWS) thresholds for individual features. Significant features were determined using independent multivariate methods. These methods incorporate out-of-bag estimation using Random forests (RF) and bootstrapping (100 iterations) using decision trees.ResultsUnivariate analysis identified rib dose to 1 cc < 4000 cGy (P = 0.01), chest wall dose to 30 cc < 1900 cGy (P = 0.035), rib Dmax < 5100 cGy (P = 0.05) and lung dose to 1000 cc < 70 cGy (P = 0.039) to be statistically significant thresholds for avoiding CWS. Subsequent multivariate analysis confirmed the importance of rib dose to 1 cc, chest wall dose to 30 cc, and rib Dmax. Using learning-curve experiments, the dataset proved to be self-consistent and provides a realistic model for CWS analysis.ConclusionsUsing machine learning algorithms in this first of its kind study, we identify robust features and cutoffs predictive for the rare clinical event of CWS. Additional data in planned subsequent multicenter studies will help increase the accuracy of multivariate analysis

Bringing the Kok effect to light: A review on the integration of daytime respiration and net ecosystem exchange

Net ecosystem exchange (NEE) represents the difference between carbon assimilated through photosynthesis, or gross primary productivity (GPP), and carbon released via ecosystem respiration (ER). NEE, measured via eddy covariance and chamber techniques, must be partitioned into these fluxes to accurately describe and underst and the carbon dynamics of an ecosystem. GPP and daytime ER may be significantly overestimated if the light inhibition of foliar mitochondrial respiration, or "Kok effect," is not accurately estimated and further integrated into ecosystem measurements. The light inhibition of respiration, a composite effect of multiple cellular pathways, is reported to cause between 25-100% inhibition of foliar mitochondrial respiration, and for this reason needs to be considered when estimating larger carbon fluxes. Partitioning of respiration between autotrophic and heterotrophic respiration, and applying these scaled respiratory fluxes to the ecosystem-level proves to be difficult, and the integration of light inhibition into single and continuous measures of ecosystem respiration will require new interpretations and analysis of carbon exchange in terrestrial ecosystems

Seasonal variations of leaf and canopy properties tracked by ground-based NDVI imagery in a temperate forest

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1267, doi:10.1038/s41598-017-01260-y.Changes in plant phenology affect the carbon flux of terrestrial forest ecosystems due to the link between the growing season length and vegetation productivity. Digital camera imagery, which can be acquired frequently, has been used to monitor seasonal and annual changes in forest canopy phenology and track critical phenological events. However, quantitative assessment of the structural and biochemical controls of the phenological patterns in camera images has rarely been done. In this study, we used an NDVI (Normalized Difference Vegetation Index) camera to monitor daily variations of vegetation reflectance at visible and near-infrared (NIR) bands with high spatial and temporal resolutions, and found that the infrared camera based NDVI (camera-NDVI) agreed well with the leaf expansion process that was measured by independent manual observations at Harvard Forest, Massachusetts, USA. We also measured the seasonality of canopy structural (leaf area index, LAI) and biochemical properties (leaf chlorophyll and nitrogen content). We found significant linear relationships between camera-NDVI and leaf chlorophyll concentration, and between camera-NDVI and leaf nitrogen content, though weaker relationships between camera-NDVI and LAI. Therefore, we recommend ground-based camera-NDVI as a powerful tool for long-term, near surface observations to monitor canopy development and to estimate leaf chlorophyll, nitrogen status, and LAI.This research was supported by US Department of Energy Office of Biological and Environmental Research Grant DE-SC0006951, National Science Foundation Grants DBI-959333 and AGS-1005663, and the University of Chicago and the MBL Lillie Research Innovation Award to J.T. and China Scholarship Council (CSC) to H.Y

Chlorophyll fluorescence tracks seasonal variations of photosynthesis from leaf to canopy in a temperate forest

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Global Change Biology 23 (2017): 2874-2886, doi: 10.1111/gcb.13590.Accurate estimation of terrestrial gross primary productivity (GPP) remains a challenge despite its importance in the global carbon cycle. Chlorophyll fluorescence (ChlF) has been recently adopted to understand photosynthesis and its response to the environment, particularly with remote sensing data. However, it remains unclear how ChlF and photosynthesis are linked at different spatial scales across the growing season. We examined seasonal relationships between ChlF and photosynthesis at the leaf, canopy, and ecosystem scales, and explored how leaf-level ChlF was linked with canopy-scale solar induced chlorophyll fluorescence (SIF) in a temperate deciduous forest at Harvard Forest, Massachusetts, USA. Our results show that ChlF captured the seasonal variations of photosynthesis with significant linear relationships between ChlF and photosynthesis across the growing season over different spatial scales (R2=0.73, 0.77 and 0.86 at leaf, canopy and satellite scales, respectively; p<0.0001). We developed a model to estimate GPP from the tower-based measurement of SIF and leaf-level ChlF parameters. The estimation of GPP from this model agreed well with flux tower observations of GPP (R2=0.68; p<0.0001), demonstrating the potential of SIF for modeling GPP. At the leaf scale, we found that leaf Fq’/Fm’, the fraction of absorbed photons that are used for photochemistry for a light adapted measurement from a pulse amplitude modulation fluorometer, was the best leaf fluorescence parameter to correlate with canopy-SIF yield (SIF/APAR, R2=0.79; p<0.0001). We also found that canopy-SIF and SIF-derived GPP (GPPSIF) were strongly correlated to leaf-level biochemistry and canopy structure, including chlorophyll content (R2=0.65 for canopy-GPPSIF and chlorophyll content; p<0.0001), leaf area index (LAI) (R2=0.35 for canopy-GPPSIF and LAI; p<0.0001), and normalized difference vegetation index (NDVI) (R2=0.36 for canopy-GPPSIF and NDVI; p<0.0001). Our results suggest that ChlF can be a powerful tool to track photosynthetic rates at leaf, canopy, and ecosystem scales.This research was supported by U.S. Department of Energy Office of Biological and Environmental Research Grant DE-SC0006951, National Science Foundation Grants DBI-959333 and AGS-1005663, and the University of Chicago and the MBL Lillie Research Innovation Award to J. Tang, National Science Foundation of China Grants (41671421) to Y. Zhang, and China Scholarship Council (CSC) to H. Yang.2017-12-1

Macromolecular Rate Theory (MMRT) Provides a Thermodynamics Rationale to Underpin the Convergent Temperature Response in Plant Leaf Respiration

Temperature is a crucial factor in determining the rates of ecosystem processes, for example, leaf respiration (R) – the flux of plant respired CO₂ from leaves to the atmosphere. Generally, R increases exponentially with temperature and formulations such as the Arrhenius equation are widely used in earth system models. However, experimental observations have shown a consequential and consistent departure from an exponential increase in R. What are the principles that underlie these observed patterns? Here, we demonstrate that macromolecular rate theory (MMRT), based on transition state theory (TST) for enzyme-catalyzed kinetics, provides a thermodynamic explanation for the observed departure and the convergent temperature response of R using a global database. Three meaningful parameters emerge from MMRT analysis: the temperature at which the rate of respiration would theoretically reach a maximum (the optimum temperature, Tₒₚₜ), the temperature at which the respiration rate is most sensitive to changes in temperature (the inflection temperature, Tᵢₙf) and the overall curvature of the log(rate) versus temperature plot (the change in heat capacity for the system, ΔCǂₚ). On average, the highest potential enzyme-catalyzed rates of respiratory enzymes for R are predicted to occur at 67.0 ± 1.2°C and the maximum temperature sensitivity at 41.4 ± 0.7°C from MMRT. The average curvature (average negative ΔCǂₚ) was −1.2 ± 0.1 kJ mol⁻¹ K⁻¹. Interestingly, Topt, Tᵢₙf and ΔCǂₚ appear insignificantly different across biomes and plant functional types, suggesting that thermal response of respiratory enzymes in leaves could be conserved. The derived parameters from MMRT can serve as thermal traits for plant leaves that represent the collective temperature response of metabolic respiratory enzymes and could be useful to understand regulations of R under a warmer climate. MMRT extends the classic TST to enzyme-catalyzed reactions and provides an accurate and mechanistic model for the short-term temperature response of R around the globe

Differential physiological responses to environmental change promote woody shrub expansion

Direct and indirect effects of warming are increasingly modifying the carbon-rich vegetation and soils of the Arctic tundra, with important implications for the terrestrial carbon cycle. Understanding the biological and environmental influences on the pr

Differential physiological responses to environmental change promote woody shrub expansion

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 3 (2013): 1149–1162, doi:10.1002/ece3.525.Direct and indirect effects of warming are increasingly modifying the carbon-rich vegetation and soils of the Arctic tundra, with important implications for the terrestrial carbon cycle. Understanding the biological and environmental influences on the processes that regulate foliar carbon cycling in tundra species is essential for predicting the future terrestrial carbon balance in this region. To determine the effect of climate change impacts on gas exchange in tundra, we quantified foliar photosynthesis (Anet), respiration in the dark and light (RD and RL, determined using the Kok method), photorespiration (PR), carbon gain efficiency (CGE, the ratio of photosynthetic CO2 uptake to total CO2 exchange of photosynthesis, PR, and respiration), and leaf traits of three dominant species – Betula nana, a woody shrub; Eriophorum vaginatum, a graminoid; and Rubus chamaemorus, a forb – grown under long-term warming and fertilization treatments since 1989 at Toolik Lake, Alaska. Under warming, B. nana exhibited the highest rates of Anet and strongest light inhibition of respiration, increasing CGE nearly 50% compared with leaves grown in ambient conditions, which corresponded to a 52% increase in relative abundance. Gas exchange did not shift under fertilization in B. nana despite increases in leaf N and P and near-complete dominance at the community scale, suggesting a morphological rather than physiological response. Rubus chamaemorus, exhibited minimal shifts in foliar gas exchange, and responded similarly to B. nana under treatment conditions. By contrast, E. vaginatum, did not significantly alter its gas exchange physiology under treatments and exhibited dramatic decreases in relative cover (warming: −19.7%; fertilization: −79.7%; warming with fertilization: −91.1%). Our findings suggest a foliar physiological advantage in the woody shrub B. nana that is further mediated by warming and increased soil nutrient availability, which may facilitate shrub expansion and in turn alter the terrestrial carbon cycle in future tundra environments.This study was supported by the National Science Foundation #0732664; Australian Research Council DP0986823; and Marsden Fund of the Royal Society of New Zealand

Foliar phosphorus fractions reveal how tropical plants maintain photosynthetic rates despite low soil phosphorus availability

Nitrogen (N) and phosphorus (P) are essential nutrients for plant metabolism, and their availability often limits primary productivity. Whereas the effects of N availability on photosynthetic capacity are well established, we still know relatively little about the effects of P availability at a foliar level, especially in P‐limited tropical forests. We examined photosynthetic capacity, leaf mass per area (LMA) and foliar P fractions in five woody plant species after 6 years of N and P fertilization in a lowland tropical forest. Foliar N:P ratios indicated P limitation of the unfertilized plants; accordingly, photosynthetic P‐use efficiency (PPUE) and LMA decreased with P addition, and foliar N and P concentrations increased, whereas N addition had little effect on measured foliar traits. However, P addition enhanced photosynthetic capacity only in one species and not in other four species. We then assessed plant acclimation to low P availability by quantifying four fractions of foliar P representing different functional pools: structural P, metabolic P (including inorganic P), nucleic acid P, and residual P. We found that P addition enhanced the concentrations of metabolic, structural, and nucleic acid P fractions in all species, but the magnitude of the effect was species‐specific. Our findings indicate that tropical species acclimate to low P availability by altering allocation of foliar P to meet the demand of P for photosynthesis. Importantly, species typical of lowland tropical forests in East Asia maintained their photosynthetic rate under low P availability. We conclude that P limitation of leaf photosynthetic capacity may not be as common as previously assumed due to plant acclimation mechanisms in low‐P tropical forests. Species‐specific strategies to allocate P to different foliar fractions represent a potentially important adaptive mechanism for plants in P‐limited systems

A gradient of nutrient enrichment reveals nonlinear impacts of fertilization on Arctic plant diversity and ecosystem function

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 7 (2017): 2449–2460, doi:10.1002/ece3.2863.Rapid environmental change at high latitudes is predicted to greatly alter the diversity, structure, and function of plant communities, resulting in changes in the pools and fluxes of nutrients. In Arctic tundra, increased nitrogen (N) and phosphorus (P) availability accompanying warming is known to impact plant diversity and ecosystem function; however, to date, most studies examining Arctic nutrient enrichment focus on the impact of relatively large (>25x estimated naturally occurring N enrichment) doses of nutrients on plant community composition and net primary productivity. To understand the impacts of Arctic nutrient enrichment, we examined plant community composition and the capacity for ecosystem function (net ecosystem exchange, ecosystem respiration, and gross primary production) across a gradient of experimental N and P addition expected to more closely approximate warming-induced fertilization. In addition, we compared our measured ecosystem CO2 flux data to a widely used Arctic ecosystem exchange model to investigate the ability to predict the capacity for CO2 exchange with nutrient addition. We observed declines in abundance-weighted plant diversity at low levels of nutrient enrichment, but species richness and the capacity for ecosystem carbon uptake did not change until the highest level of fertilization. When we compared our measured data to the model, we found that the model explained roughly 30%–50% of the variance in the observed data, depending on the flux variable, and the relationship weakened at high levels of enrichment. Our results suggest that while a relatively small amount of nutrient enrichment impacts plant diversity, only relatively large levels of fertilization—over an order of magnitude or more than warming-induced rates—significantly alter the capacity for tundra CO2 exchange. Overall, our findings highlight the value of measuring and modeling the impacts of a nutrient enrichment gradient, as warming-related nutrient availability may impact ecosystems differently than single-level fertilization experiments.NASA Terrestrial Ecology Grant Number: NNX12AK83G; National Science Foundation Division of Graduate Education Grant Number: DGE-11-4415

Plant respiration : Controlled by photosynthesis or biomass?

Abstract Two simplifying hypotheses have been proposed for whole-plant respiration. One links respiration to photosynthesis; the other to biomass. Using a first-principles carbon balance model with a prescribed live woody biomass turnover, applied at a forest research site where multidecadal measurements are available for comparison, we show that if turnover is fast the accumulation of respiring biomass is low and respiration depends primarily on photosynthesis; while if turnover is slow the accumulation of respiring biomass is high and respiration depends primarily on biomass. But the first scenario is inconsistent with evidence for substantial carryover of fixed carbon between years, while the second implies far too great an increase in respiration during stand development ? leading to depleted carbohydrate reserves and an unrealistically high mortality risk. These two mutually incompatible hypotheses are thus both incorrect. Respiration is not linearly related either to photosynthesis or to biomass, but it is more strongly controlled by recent photosynthates (and reserve availability) than by total biomass.Peer reviewe