Josh Sumner
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View article: The Root-Associated Microbiome and Metabolome Spatially Vary Across the Root System of a Mature Maize Plant and Are Inconsistently Altered by Microbial Treatment
The Root-Associated Microbiome and Metabolome Spatially Vary Across the Root System of a Mature Maize Plant and Are Inconsistently Altered by Microbial Treatment Open
Many microbes provide benefits to their plant hosts. Over 100 microbial-based products are available to farmers, but their performance is highly variable. Little is known about the factors that influence the colonization and persistence of…
View article: Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in <i>Brassica napus</i>
Homoeolog expression divergence contributes to time of day changes in transcriptomic and glucosinolate responses to prolonged water limitation in <i>Brassica napus</i> Open
SUMMARY Water availability is a major determinant of crop production, and rising temperatures from climate change are leading to more extreme droughts. To combat the effects of climate change on crop yields, we need to develop varieties th…
View article: Modification of Non-photochemical Quenching Pathways in the C<sub>4</sub>Model Plant <i>Setaria viridis</i> Revealed Shared and Unique Photoprotection Mechanisms as Compared to C<sub>3</sub>Plants
Modification of Non-photochemical Quenching Pathways in the C<sub>4</sub>Model Plant <i>Setaria viridis</i> Revealed Shared and Unique Photoprotection Mechanisms as Compared to C<sub>3</sub>Plants Open
Summary Light is essential for photosynthesis; however, excess light can increase the accumulation of photoinhibitory reactive oxygen species that reduce photosynthetic efficiency. Plants have evolved photoprotective non-photochemical quen…
View article: Three <i>Xanthomonas</i> Cell Wall Degrading Enzymes and Sorghum <i>Brown midrib12</i> Contribute to Virulence and Resistance in the Bacterial Leaf Streak Pathosystem
Three <i>Xanthomonas</i> Cell Wall Degrading Enzymes and Sorghum <i>Brown midrib12</i> Contribute to Virulence and Resistance in the Bacterial Leaf Streak Pathosystem Open
With an increasing demand for renewable fuels, bioenergy crops are being developed with high sugar content and altered cell walls to improve processing efficiency. These traits may have unintended consequences for plant disease resistance.…
View article: pcvr: An R package and tutorials for guided statistical analysis of plant phenotyping data
pcvr: An R package and tutorials for guided statistical analysis of plant phenotyping data Open
PlantCV is a Python-based image analysis tool that lowers the barrier to entry for complex image analysis workflows in plant phenotyping. To provide support for subsequent analysis steps of measured trait data we have developed pcvr, an R …
View article: Exploring Maize Stress Response Phenotypes via High-Throughput Imaging
Exploring Maize Stress Response Phenotypes via High-Throughput Imaging Open
This study aimed to investigate the physiological and morphological responses of maize seedlings to environmental stressors. High-throughput imaging analysis was used to characterize the stress response phenotypes of 47 distinct maize geno…
View article: Natural variation in <i>Brachypodium distachyon</i> responses to combined abiotic stresses
Natural variation in <i>Brachypodium distachyon</i> responses to combined abiotic stresses Open
SUMMARY The demand for agricultural production is becoming more challenging as climate change increases global temperature and the frequency of extreme weather events. This study examines the phenotypic variation of 149 accessions of Brach…
View article: RipetaScore: Measuring the Quality, Transparency, and Trustworthiness of a Scientific Work
RipetaScore: Measuring the Quality, Transparency, and Trustworthiness of a Scientific Work Open
A wide array of existing metrics quantifies a scientific paper's prominence or the author's prestige. Many who use these metrics make assumptions that higher citation counts or more public attention must indicate more reliable, better qual…
View article: Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping
Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping Open
Earth and Space Science Open Archive This is a preprint and has not been peer reviewed. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are…
View article: Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping
Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping Open
Earth and Space Science Open Archive This is a preprint and has not been peer reviewed. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are…
View article: Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping
Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping Open
Earth and Space Science Open Archive This is a preprint and has not been peer reviewed. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are…
View article: Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping
Bayesian hierarchical approach to longitudinal high-throughput plant phenotyping Open
Earth and Space Science Open Archive This is a preprint and has not been peer reviewed. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are…
View article: A Curious Case within Preprints: Is the Author Real?
A Curious Case within Preprints: Is the Author Real? Open
An assumption at the heart of the scientific publication process is that the author of a manuscript is a scientist. But how can we tell when that is not the case? This supplements an article in The Scholarly Kitchen highlighting one case o…
View article: Dataset for Manuscript: An analysis of form and function of a research article between and within publishers and journals
Dataset for Manuscript: An analysis of form and function of a research article between and within publishers and journals Open
Dataset resulting from an article heading form and function analysis across 12 publishers including both research articles and non research articles. Our aim was to: (1) Identify each of the labelled sections used by research articles, def…
View article: An analysis of form and function of a research article between and within publishers and journals
An analysis of form and function of a research article between and within publishers and journals Open
The identification and subsequent analysis of research articles for machine learning and natural language processing is a complicated task given the lack of consistent article organization principles and heading naming conventions across p…
View article: Reproducibility and reporting practices in COVID-19 preprint manuscripts
Reproducibility and reporting practices in COVID-19 preprint manuscripts Open
The novel coronavirus, COVID-19, has sparked an outflow of scientific research seeking to understand the virus, its spread, and best practices in prevention and treatment. If this international research effort is going to be as swift and e…
View article: Making Science Better: Reproducibility, Falsifiability and the Scientific Method
Making Science Better: Reproducibility, Falsifiability and the Scientific Method Open
Making Science Better: Reproducibility, Falsifiability and the Scientific Method looks at the current state of reproducibility in 2019, as well as the importance of falsifiability in the research process.The analysis comes from the Digital…
View article: Investigating the Perceived Effectiveness of Digital Technology for Elite Athlete Support in Golf
Investigating the Perceived Effectiveness of Digital Technology for Elite Athlete Support in Golf Open
Digital technologies have enabled vast and varied amounts of data to be captured on elite athletes. The data is intended for use by athletes, coaches and support team e.g. physiotherapists, sports scientists for many purposes including p…