An illustration of model agnostic explainability methods applied to environmental data.

Historically, two primary criticisms statisticians have of machine learning and deep neural models is their lack of uncertainty quantification and the inability to do inference (i.e., to explain what inputs are important).

Visual Analytics for the Coronavirus COVID-19 Pandemic.

The coronavirus disease COVID-19 was first reported in Wuhan, China, on December 31, 2019. The disease has since spread throughout the world, affecting 227.2 million individuals and resulting in 4,672,629 deaths as of September 9, 2021, according to the Johns Hopkins University Center for Systems Science and Engineering.

Loci That Control Nonlinear, Interdependent Responses to Combinations of Drought and Nitrogen Limitation.

Crop improvement must accelerate to feed an increasing human population in the face of environmental changes. Including anticipated climatic changes with genetic architecture in breeding programs could better optimize improvement strategies. Combinations of drought and nitrogen limitation already occur world-wide.

Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties.

The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations.

Loci controlling nitrate reductase activity in maize: ultraviolet-B signaling in aerial tissues increases nitrate reductase activity in leaf and root when responsive alleles are present.

Environmental factors, such as ultraviolet-B (UV-B) irradiation, have the ability to affect pathways such as nitrogen metabolism. As fixed nitrogen is the keystone mineral nutrient that controls grain crop yield, any alteration in this cycle can be detrimental to plant productivity. Nitrate reductase enzyme activity is responsible for the reduction of nitrate to nitrite, and nitrate is the major form of nitrogen assimilated in plants.

Chromosomal loci important for cotyledon opening under UV-B in Arabidopsis thaliana.

Background: Understanding of the genetic architecture of plant UV-B responses allows extensive targeted testing of candidate genes or regions, along with combinations of those genes, for placement in metabolic or signal transduction pathways.

Results: Composite interval mapping and single-marker analysis methods were used to identify significant loci for cotyledon opening under UV-B in four sets of recombinant inbred lines. In addition, loci important for canalization (stability) of cotyledon opening were detected in two mapping populations.

Maize leaf epiphytic bacteria diversity patterns are genetically correlated with resistance to fungal pathogen infection.

Plant leaves host a specific set of microbial epiphytes. Plant genetic and solar UV-B radiation effects on the diversity of the phyllosphere were examined by measuring epiphytic bacterial ribosomal DNA diversity in a maize recombinant inbred (RI) mapping population. Several chromosomal quantitative trait loci (QTL) with significant effects on bacterial diversity were identified, some of which had effects only in the presence of UV-B radiation and others that had effects both with and without UV-B.

Coordinated regulation of maize genes during increasing exposure to ultraviolet radiation: identification of ultraviolet-responsive genes, functional processes and associated potential promoter motifs.

Genetic gain in the yield of modern maize reflects increased stress tolerance. The manipulation of genes for deliberate alterations in tolerance relies on an understanding of the regulation and components of stress responses. Transcriptome analysis of an ultraviolet (UV) radiation time course with paired treatment and control measurements yielded groups of coordinately regulated genes and gene ontology processes.

Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances.

This article extends the order restricted inference approach for time-course or dose-response gene expression microarray data, introduced by Peddada and colleagues (2003) for the case when gene expression is heteroscedastic over time or dose. The new methodology uses an iterative algorithm to estimate mean expression at various times/doses when mean expression is subject to pre-defined patterns or profiles, known as order-restrictions. Simulation studies reveal that the resulting bootstrap-based methodology for gene selection maintains the false positive rate at the nominal level while competing well with ORIOGEN in terms of power.