Nitrogen Fertilizer and Irrigation Effects on Seed Yield and Oil in Camelina

Interest is growing in camelina (Camelina sativa L. Crantz) as a biofuel feedstock. However, there has been little camelina research in irrigated arid systems. A 2-yr field study in Maricopa, AZ, under an overhead sprinkler irrigation system determined the effects of 10 water levels (irrigation fraction 0.5–1.1) and five N fertilizer rates (38–150 kg N ha–1) on seed yield, seed oil content, and N use efficiency. Cultivar Robinson was planted in December 2012 and 2013. Nitrogen fertilizer (urea ammonium nitrate) was applied in three split applications. Irrigation amounts were from 125 to 380 mm, and in-season rain was 70 and 50 mm, in 2013 and 2014, respectively. Camelina seed yields were maximum at water level 7 (irrigation fraction 0.93) in 2013 at 1800 kg ha–1. Maximum seed yields were 1600 kg ha–1 at water level 6 (irrigation fraction 0.83) in 2014. These highest seed yields were achieved with 150 kg N ha–1 in both years. Oil content (maximum 41%) decreased with N rate but increased with water level. Seed N increased with N rate but decreased with irrigation level. Recovery efficiency of N fertilizer by camelina ranged from 12 to 72%. The results indicate that good high-oil camelina yields can be produced in the southwestern United States with 320 to 380 mm irrigation plus rain and N fertilizer rates of 150 kg N ha–1

A proximal sensing cart and custom cooling box for improved hyperspectral sensing in a desert environment

BackgroundAdvancements in field spectrometry have the potential to increase understanding of crop growth and development in response to hot and dry environments. However, as with any instrument used for scientific advancement, it is important to continue developing and optimizing data collection protocols to promote efficiency, safety, and data quality. The goal of this study was to develop a novel data collection method, involving a proximal sensing cart with onboard cooling equipment, to improve deployments of a field spectroradiometer in a hot and dry environment. Advantages and disadvantages of the new method were compared with the traditional backpack approach and other approaches reported in literature.ResultsThe novel method prevented the spectroradiometer from overheating and nearly eliminated the need to halt data collection for battery changes. It also enabled data collection from a significantly larger field area and from more field plots as compared to the traditional backpack method. Use of a custom cooling box to stabilize operating temperatures for the field spectroradiometer also improved stability of white panel data both within and among collections despite outside air temperatures in excess of 30°C.ConclusionsAs compared to traditional data collection approaches for measuring spectral reflectance of field crops in a hot and dry environment, use of a proximal sensing cart with a customized equipment cooling box improved spectroradiometer performance, increased practicality of equipment transport, and reduced operator safety concerns

Adaptive Management Framework for Evaluating and Adjusting Microclimate Parameters in Tropical Greenhouse Crop Production Systems

High operational costs of greenhouse production in hot and humid climate condition due to the initial investments on structure, equipment, and energy necessitate practicing advanced techniques for more efficient use of available resources. This chapter describes design and concepts of an adaptive management framework for evaluating and adjusting optimality degrees and comfort ratios of microclimate parameters, as well as predicting the expected yield in greenhouse cultivation of tomato. A systematic approach is presented for automatic data collection and processing with the objective to produce knowledge‐based information in achieving optimum microclimate for high‐quality and high‐yield tomato. Applications of relevant computer models are demonstrated through case‐study examples for use in an iterative way to simulate and compare different scenarios. The presented framework can contribute to future studies for providing best management decisions such as site selection, optimum growing season, scheduling efficiencies, energy management with different climate control systems, and risk assessments associated with each task

Assimilating Remote Sensing Observations of Leaf Area Index and Soil Moisture for Wheat Yield Estimates: An Observing System Simulation Experiment

Observing system simulation experiments were used to investigate ensemble Bayesian state updating data assimilation of observations of leaf area index (LAI) and soil moisture (theta) for the purpose of improving single-season wheat yield estimates with the Decision Support System for Agrotechnology Transfer (DSSAT) CropSim-Ceres model. Assimilation was conducted in an energy-limited environment and a water-limited environment. Modeling uncertainty was prescribed to weather inputs, soil parameters and initial conditions, and cultivar parameters and through perturbations to model state transition equations. The ensemble Kalman filter and the sequential importance resampling filter were tested for the ability to attenuate effects of these types of uncertainty on yield estimates. LAI and theta observations were synthesized according to characteristics of existing remote sensing data, and effects of observation error were tested. Results indicate that the potential for assimilation to improve end-of-season yield estimates is low. Limitations are due to a lack of root zone soil moisture information, error in LAI observations, and a lack of correlation between leaf and grain growth

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN