ggplot2: Elegant Graphics for Data Analysis (2nd ed.)

Villanueva, Randle Aaron Molina; Chen, Zhuo Job

doi:10.1080/15366367.2019.1565254

Cited by 723 publications

(535 citation statements)

References 1 publication

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“…Each subplot depicts mean rCBF values (y-axis) at each time-interval (x axis), for each method of administration in each ROI. Regression lines were fitted using a non-parametric regression method that fits multiple regressions in local neighbourhood (Locally estimated scatterplot smoothing -LOESS) to the time-course of mean rCBF in each ROI for each method of administration separately (the shadows denote the 95% confidence interval for each fitted line) 97 . To avoid the potential confounding effects of nominal changes in global CBF across time or between methods of administration, we used demeaned values of mean ROI rCBF estimates, which correspond to subtracting global CBF estimates from the raw mean rCBF in each ROI.…”

Section: Discussionmentioning

confidence: 99%

Effects of route of administration on oxytocin-induced changes in regional cerebral blood flow in humans

et al. 2020

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Could nose-to-brain pathways mediate the effects of peptides such as oxytocin (OT) on brain physiology when delivered intranasally? We address this question by contrasting two methods of intranasal administration (a standard nasal spray, and a nebulizer expected to improve OT deposition in nasal areas putatively involved in direct nose-to-brain transport) to intravenous administration in terms of effects on regional cerebral blood flow during two hours post-dosing. We demonstrate that OT-induced decreases in amygdala perfusion, a key hub of the OT central circuitry, are explained entirely by OT increases in systemic circulation following both intranasal and intravenous OT administration. Yet we also provide robust evidence confirming the validity of the intranasal route to target specific brain regions. Our work has important translational implications and demonstrates the need to carefully consider the method of administration in our efforts to engage specific central oxytocinergic targets for the treatment of neuropsychiatric disorders.

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Section: Discussionmentioning

confidence: 99%

Effects of route of administration on oxytocin-induced changes in regional cerebral blood flow in humans

et al. 2020

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“…Perplexity was set to 30 (default). t-SNE plots were generated using R package ggplot2 63 . Clustering was done first by establishing a shared nearest neighbor and then conducting Luvain-Jaccard analysis on the resulted graph using FindClusters function from Seurat with default setting.…”

Section: Methodsmentioning

confidence: 99%

Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly

Wang

Sievert

et al. 2020

Nat Commun

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Asparaginyl-tRNA synthetase1 (NARS1) is a member of the ubiquitously expressed cytoplasmic Class IIa family of tRNA synthetases required for protein translation. Here, we identify biallelic missense and frameshift mutations in NARS1 in seven patients from three unrelated families with microcephaly and neurodevelopmental delay. Patient cells show reduced NARS1 protein, impaired NARS1 activity and impaired global protein synthesis. Cortical brain organoid modeling shows reduced proliferation of radial glial cells (RGCs), leading to smaller organoids characteristic of microcephaly. Single-cell analysis reveals altered constituents of both astrocytic and RGC lineages, suggesting a requirement for NARS1 in RGC proliferation. Our findings demonstrate that NARS1 is required to meet protein synthetic needs and to support RGC proliferation in human brain development.

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“…Different trees were constructed for (I) PKs from Sbi; (II) PKs from Ssp; and (III) PKs from both Sbi and Ssp. The dendrogram visualization and plotting were generated using R statistical software (R Core Team, 2013) with the ggtree (Yu et al, 2017) and ggplot2 (Villanueva and Chen, 2019) packages.…”

Section: Methodsmentioning

confidence: 99%

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

Aono

Pimenta

Garcia

et al. 2020

Preprint

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The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs.HighlightThis study describes the catalog of kinase gene family in Saccharum spontaneum and Sorghum bicolor, providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.

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ggplot2: Elegant Graphics for Data Analysis (2nd ed.)

Cited by 723 publications

References 1 publication

Effects of route of administration on oxytocin-induced changes in regional cerebral blood flow in humans

Effects of route of administration on oxytocin-induced changes in regional cerebral blood flow in humans

Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

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