Long-term hindcasts of wheat yield in fields using remotely sensed phenology, climate data and machine learning

Satellite remote sensing offers a cost-effective means of generating long-term hindcasts of yield that can be used to understand how yield varies in time and space. This study investigated the use of remotely sensed phenology, climate data and machine learning for estimating yield at a resolution suitable for optimising crop management in fields. We used spatially weighted growth curve estimation to identify the timing of phenological events from sequences of Landsat NDVI and derive phenological and seasonal climate metrics. Using data from a 17,000 ha study area, we investigated the relationships between the metrics and yield over 17 years from 2003 to 2019. We compared six statistical and machine learning models for estimating yield: multiple linear regression, mixed effects models, generalised additive models, random forests, support vector regression using radial basis functions and deep learning neural networks. We used a 50-50 train-test split on paddock-years where 50% of paddock-year combinations were randomly selected and used to train each model and the remaining 50% of paddock-years were used to assess the model accuracy. Using only phenological metrics, accuracy was highest using a linear mixed model with a random effect that allowed the relationship between integrated NDVI and yield to vary by year (R2 = 0.67, MAE = 0.25 t ha−1, RMSE = 0.33 t ha−1, NRMSE = 0.25). We quantified the improvements in accuracy when seasonal climate metrics were also used as predictors. We identified two optimal models using the combined phenological and seasonal climate metrics: support vector regression and deep learning models (R2 = 0.68, MAE = 0.25 t ha−1, RMSE = 0.32 t ha−1, NRMSE = 0.25). While the linear mixed model using only phenological metrics performed similarly to the nonlinear models that are also seasonal climate metrics, the nonlinear models can be more easily generalised to estimate yield in years for which training data are unavailable. We conclude that long-term hindcasts of wheat yield in fields, at 30 m spatial resolution, can be produced using remotely sensed phenology from Landsat NDVI, climate data and machine learning

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

<p>Abstract</p> <p>Background</p> <p>Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as <it>Arabidopsis thaliana </it>do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied.</p> <p>Results</p> <p>Several molecular biology tools were used to isolate flower-specific gene promoters from <it>Oncidium </it>'Gower Ramsey' (<it>Onc</it>. GR). A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in <it>Onc</it>. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (<it>TI</it>) genes (<it>OnTI1</it>, <it>OnTI2 </it>and <it>OnTI3</it>), which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable <it>A. thaliana </it>transformation analyses.</p> <p>Conclusions</p> <p>By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.</p

Dynamic Evolution of a Quasi-Spherical General Polytropic Magnetofluid with Self-Gravity

In various astrophysical contexts, we analyze self-similar behaviours of magnetohydrodynamic (MHD) evolution of a quasi-spherical polytropic magnetized gas under self-gravity with the specific entropy conserved along streamlines. In particular, this MHD model analysis frees the scaling parameter $n$ in the conventional polytropic self-similar transformation from the constraint of $n+\gamma=2$ with $\gamma$ being the polytropic index and therefore substantially generalizes earlier analysis results on polytropic gas dynamics that has a constant specific entropy everywhere in space at all time. On the basis of the self-similar nonlinear MHD ordinary differential equations, we examine behaviours of the magnetosonic critical curves, the MHD shock conditions, and various asymptotic solutions. We then construct global semi-complete self-similar MHD solutions using a combination of analytical and numerical means and indicate plausible astrophysical applications of these magnetized flow solutions with or without MHD shocks.Comment: 21 pages, 7 figures, accepted for publication in APS

Knockout of p75 neurotrophin receptor attenuates the hyperphosphorylation of Tau in pR5 mouse model

p75 neurotrophin receptor (p75NTR) has been implicated in Alzheimer's disease (AD). However, whether p75NTR is involved in Tau hyperphosphorylation, one of the pathologies observed in AD, remains unclear. In our previous study, the extracellular domain of p75NTR blocked amyloid beta (Aβ) toxicity and attenuated Aβ-induced Tau hyperphosphorylation. Here we show that, in the absence of Aβ, p75NTR regulates Tau phosphorylation in the transgenic mice with the P301L human Tau mutation (pR5). The knockout of p75NTR in pR5 mice attenuated the phosphorylation of human Tau. In addition, the elevated activity of kinases responsible for Tau phosphorylation including glycogen synthase kinase 3 beta; cyclin-dependent-kinase 5; and Rho-associated protein kinase was also inhibited when p75NTR is knocked out in pR5 mice at 9 months of age. The increased caspase-3 activity observed in pR5 mice was also abolished in the absence of p75NTR. Our study also showed that p75NTR is required for Aβ- and pro-brain derived neurotrophin factor (proBDNF)-induced Tau phosphorylation, in vitro. Overall, our data indicate that p75NTR is required for Tau phosphorylation, a key event in the formation of neurofibrillary tangles, another hallmark of AD. Thus, targeting p75NTR could reduce or prevent the pathologic hyperphosphorylation of Tau.Noralyn B. Mañucat-Tan, Lin-Lin Shen, Larisa Bobrovskaya, Mohammed Al-hawwas, Fiona H. Zhou, Yan-Jiang Wang, Xin-Fu Zho

Dynamic Evolution Model of Isothermal Voids and Shocks

We explore self-similar hydrodynamic evolution of central voids embedded in an isothermal gas of spherical symmetry under the self-gravity. More specifically, we study voids expanding at constant radial speeds in an isothermal gas and construct all types of possible void solutions without or with shocks in surrounding envelopes. We examine properties of void boundaries and outer envelopes. Voids without shocks are all bounded by overdense shells and either inflows or outflows in the outer envelope may occur. These solutions, referred to as type $\mathcal{X}$ void solutions, are further divided into subtypes $\mathcal{X}_{\rm I}$ and $\mathcal{X}_{\rm II}$ according to their characteristic behaviours across the sonic critical line (SCL). Void solutions with shocks in envelopes are referred to as type $\mathcal{Z}$ voids and can have both dense and quasi-smooth edges. Asymptotically, outflows, breezes, inflows, accretions and static outer envelopes may all surround such type $\mathcal{Z}$ voids. Both cases of constant and varying temperatures across isothermal shock fronts are analyzed; they are referred to as types $\mathcal{Z}_{\rm I}$ and $\mathcal{Z}_{\rm II}$ void shock solutions. We apply the `phase net matching procedure' to construct various self-similar void solutions. We also present analysis on void generation mechanisms and describe several astrophysical applications. By including self-gravity, gas pressure and shocks, our isothermal self-similar void (ISSV) model is adaptable to various astrophysical systems such as planetary nebulae, hot bubbles and superbubbles in the interstellar medium as well as supernova remnants.Comment: 24 pages, 13 figuers, accepted by ApS

How to extract reliable core-volume fractions from core-shell polycrystalline microstructures using cross sectional TEM micrographs

A reliable method of extracting core-volume fraction from TEM micrographs of core-shell polycrystalline microstructures is presented. Three commonly used averaging methods based on a simple spherical model are shown to consistently underestimate the core-volume fraction due to the interpretation of a 3D structure from a 2D slice. The same trend is also revealed using Voronoi tessellated structures to mimic polycrystalline ceramics. In some cases the underestimate is less than half the true core-volume fraction. We show that using a new maximum core-volume fraction methodology can improve the extracted value to a consistent error of less than 5%. This approach uses a value taken from the largest core-volume fraction measured from 10 grains that exhibit a core-shell microstructure. This provides increasing accuracy and improvements in the confidence of the measurement when extracting core-volume fractions of polycrystalline ceramics from 2D TEM micrographs

Origin and Evolution of Saturn's Ring System

The origin and long-term evolution of Saturn's rings is still an unsolved problem in modern planetary science. In this chapter we review the current state of our knowledge on this long-standing question for the main rings (A, Cassini Division, B, C), the F Ring, and the diffuse rings (E and G). During the Voyager era, models of evolutionary processes affecting the rings on long time scales (erosion, viscous spreading, accretion, ballistic transport, etc.) had suggested that Saturn's rings are not older than 100 My. In addition, Saturn's large system of diffuse rings has been thought to be the result of material loss from one or more of Saturn's satellites. In the Cassini era, high spatial and spectral resolution data have allowed progress to be made on some of these questions. Discoveries such as the ''propellers'' in the A ring, the shape of ring-embedded moonlets, the clumps in the F Ring, and Enceladus' plume provide new constraints on evolutionary processes in Saturn's rings. At the same time, advances in numerical simulations over the last 20 years have opened the way to realistic models of the rings's fine scale structure, and progress in our understanding of the formation of the Solar System provides a better-defined historical context in which to understand ring formation. All these elements have important implications for the origin and long-term evolution of Saturn's rings. They strengthen the idea that Saturn's rings are very dynamical and rapidly evolving, while new arguments suggest that the rings could be older than previously believed, provided that they are regularly renewed. Key evolutionary processes, timescales and possible scenarios for the rings's origin are reviewed in the light of tComment: Chapter 17 of the book ''Saturn After Cassini-Huygens'' Saturn from Cassini-Huygens, Dougherty, M.K.; Esposito, L.W.; Krimigis, S.M. (Ed.) (2009) 537-57

Quantifying atmospheric nitrogen deposition through a nationwide monitoring network across China

A Nationwide Nitrogen Deposition Monitoring Network (NNDMN) containing 43 monitoring sites was established in China to measure gaseous NH3, NO2, and HNO3 and particulate NH4+ and NO3− in air and/or precipitation from 2010 to 2014. Wet/bulk deposition fluxes of Nr species were collected by precipitation gauge method and measured by continuous-flow analyzer; dry deposition fluxes were estimated using airborne concentration measurements and inferential models. Our observations reveal large spatial variations of atmospheric Nr concentrations and dry and wet/bulk Nr deposition. On a national basis, the annual average concentrations (1.3–47.0 μg N m−3) and dry plus wet/bulk deposition fluxes (2.9–83.3 kg N ha−1 yr−1) of inorganic Nr species are ranked by land use as urban > rural > background sites and by regions as north China > southeast China > southwest China > northeast China > northwest China > Tibetan Plateau, reflecting the impact of anthropogenic Nr emission. Average dry and wet/bulk N deposition fluxes were 20.6 ± 11.2 (mean ± standard deviation) and 19.3 ± 9.2 kg N ha−1 yr−1 across China, with reduced N deposition dominating both dry and wet/bulk deposition. Our results suggest atmospheric dry N deposition is equally important to wet/bulk N deposition at the national scale. Therefore, both deposition forms should be included when considering the impacts of N deposition on environment and ecosystem health