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Original code for the paper "LAMINAR MECHANISMS OF SACCADIC SUPPRESSION IN PRIMATE VISUAL CORTEX"

Salt stress severely constrains plant performance and global agricultural productivity. 5% of arable land, 20% of irrigated areas and 98% of water reserves worldwide are saline. Improving the salt tolerance of major crop species could help attenuate yield losses and expand irrigation opportunities and provide in situ relief in areas where poverty, food and water scarcity are prevalent. Increasing the salt tolerance of crops with high commercial and nutritional value, such as tomato (Solanum lycopersicum L.), would provide particularly significant economic and health benefits. However, salt tolerance is a complex trait with a limited genetic repertoire in domesticated crop varieties, including tomato, frustrating attempts to breed and engineer tolerant crop varieties. Here, a genome-wide association study (GWAS) was undertaken, leveraging the rich genetic diversity of the wild, salt tolerant tomato Solanum pimpinellifolium and the latest phenotyping technologies to identify traits that contribute to salt tolerance and the genetic basis for variation in those traits. A panel of 220 S. pimpinellifolium accessions was phenotyped, focusing on image-based high-throughput phenotyping over time in controlled and field conditions in young and mature plants. Results reveal substantial natural variation in salt tolerance over time across many traits. In particular, the use of unmanned aerial vehicle (UAV)-based remote sensing in the field allowed high-resolution RGB, thermal and hyperspectral mapping that offers new insights into plant performance in the field, over time. To empower our GWAS and facilitate the identification of candidate genes, a new S. pimpinellifolium reference genome was generated, 811Mb in size, N50 of ~76kb, containing 25,970 annotated genes. Analysis of this reference genome highlighted potential contributors to salt tolerance, including enrichments in genes with stress response functions and a high copy number of the salt tolerance-associated gene inositol- 3-phosphate synthase (I3PS). A recently completed full genome re-sequencing of the panel, along with a newly available pseudomolecule-level assembly of the S. pimpinellifolium genome with N50 of ~11Mb, will serve to drive a GWAS to identify loci associated with traits that contribute to salt tolerance. Further research including gene validation, breeding, genetic modification and gene editing experiments will drive the development of new salt tolerant tomato cultivars.

The revised and peer-reviewed version of this paper was published Open Access in Plant Physiology on May 2019 - please cite > DOI: https://doi.org/10.1104/pp.19.00235Modern phenotyping enables the measurement of many phenotypic traits simultaneously, yielding vast amounts of quantitative data that is hard to manage and analyze. This type of data, when adequately examined, could reveal genotype-to-phenotype relationships and meaningful relationships between individual measured traits. Efficient data mining is currently challenging for experimental biologists, as many researchers are limited by their ability to curate, integrate and explore these complex outputs. Additionally, data transparency, accessibility and reproducibility have become important considerations for scientific publication. Thus, the need for a streamlined pipeline for curating phenotypic data is now more pressing than in the past. To address that need, we developed an open-source online platform for multivariate analysis, MVApp, which allows interactive data curation, in-depth data analysis and customized visualization. MVApp was developed in R using the Shiny framework, combining several functional R modules into a comprehensive toolkit that can be used without any prior knowledge of R, programming or advanced statistics. MVApp aims to enhance data transparency, standardize and facilitate phenotypic data curation and increase statistical literacy among the scientific community. Given that contributions from users in this open-source environment is encouraged, MVApp can be continuously updated and expanded to facilitate the analysis of high-throughput phenotyping outputs.

A case of primary intramandibular adenoid cystic carcinoma of the mandible is described in an African adult. Attention is drawn to the apparent rarity of the lesion and to possible difficulties in the diagnosis.

Our eyes are in constant motion, yet we perceive the visual world as stable. Predictive remapping of receptive fields is thought to be one of the critical mechanisms for enforcing perceptual stability during eye movements. While receptive field remapping has been identified in several cortical areas, the spatiotemporal dynamics of remapping, and its consequences on the tuning properties of neurons, remain poorly understood. Here, we tracked remapping receptive fields in hundreds of neurons from visual Area V2 while subjects performed a cued saccade task. We found that remapping was far more widespread in Area V2 than previously reported and can be found in neurons from all recorded cortical layers and cell types. Surprisingly, neurons undergoing remapping exhibit sensitivity to two punctate locations in visual space. Furthermore, we found that feature selectivity is not only maintained during remapping but transiently increases due to untuned suppression. Taken together, these results shed light on the spatiotemporal dynamics of remapping and its ubiquitous prevalence in the early visual cortex, and force us to revise current models of perceptual stability., Competing Interests: DECLARATION OF INTERESTS The authors declare no competing interests.

A prevailing assumption in our understanding of how neurons in the primary visual cortex (V1) integrate contextual information is that such processes are spatially uniform. Conversely, perceptual phenomena such as visual crowding, the impaired ability to accurately recognize a target stimulus among distractors, suggest that interactions among stimuli are distinctly non-uniform. Prior studies have shown flankers at specific spatial geometries exert differential effects on target perception. To resolve this discrepancy, we investigated how flanker geometry impacted the representation of a target stimulus in the laminar microcircuits of V1. Our study reveals flanker location differentially impairs stimulus representation in excitatory neurons in the superficial and input layers of V1 by tuned suppression and untuned facilitation of orientation responses. Mechanistically, this effect can be explained by asymmetrical spatial kernels in a normalization model of cortical activity. Strikingly, these non-uniform modulations of neural representation mirror perceptual anisotropies. These results establish the non-uniform spatial integration of information in the earliest stages of cortical processing as a fundamental limitation of spatial vision.