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  1. Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length ( GS3 ) and width ( qSW5/GW5 ) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops. 
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  2. Edge bundling is a promising graph visualization approach to simplifying the visual result of a graph drawing. Plenty of edge bundling methods have been developed to generate diverse graph layouts. However, it is difficult to defend an edge bundling method with its resulting layout against other edge bundling methods as a clear theoretic evaluation framework is absent in the literature. In this paper, we propose an information-theoretic framework to evaluate the visual results of edge bundling techniques. We first illustrate the advantage of edge bundling visualizations for large graphs, and pinpoint the ambiguity resulting from drawing results. Second, we define and quantify the amount of information delivered by edge bundling visualization from the underlying network using information theory. Third, we propose a new algorithm to evaluate the resulting layouts of edge bundling using the amount of the mutual information between a raw network dataset and its edge bundling visualization. Comparison examples based on the proposed framework between different edge bundling techniques are presented. 
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  3. Edge bundling methods can effectively alleviate visual clutter and reveal high-level graph structures in large graph visualization. Researchers have devoted significant efforts to improve edge bundling according to different metrics. As the edge bundling family evolve rapidly, the quality of edge bundles receives increasing attention in the literature accordingly. In this paper, we present MLSEB, a novel method to generate edge bundles based on moving least squares (MLS) approximation. In comparison with previous edge bundling methods, we argue that our MLSEB approach can generate better results based on a quantitative metric of quality, and also ensure scalability and the efficiency for visualizing large graphs. 
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  4. Summary

    A higher minimum (night‐time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored.

    We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome‐wide association analysis identified several HNT‐specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions.

    A novel locus contributing to grain width under HNT conditions colocalized withFie1, a component of the FIS‐PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript‐level response ofFie1in grains developing under HNT stress.

    We present evidence to support the role ofFie1in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.

     
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