Science Research Weekly Mark R Williamson

Get ready for supermassive black hole mergers, ultrarare disease diagnoses, dark oceanic oxygen, super-sized T. rex, aliases for R expressions, and a grant for educational materials on scientific rigor. Science On.



References:


The Cambrian Odaraia alata and the colonization of nektonic suspension-feeding niches by early mandibulates
Self-Interacting Dark Matter Solves the Final Parsec Problem of Supermassive Black Hole Mergers
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
Evidence of dark oxygen production at the abyssal seafloor
Estimation of maximum body size in fossil species: A case study using Tyrannosaurus rex⁠
JuliCon 2024 Recap
plotting individual values within multiple groups together with their means
Text Styling With ggplot2
NINDS: Materials to Enhance Training in Experimental Rigor



R Packages:


aka: Define Aliases for R Expressions

Get ready for virus-enhanced cancer, mammalian functional diversity across the ages, characteristics of the Last Universal Common Ancestor, autocorrelation in R, and research awards from Sony. Science On.



References:


Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer
Unique functional diversity during early Cenozoic mammal radiation of North America
Saturation genome editing of BAP1 functionally classifies somatic and germline variants
The nature of the last universal common ancestor and its impact on the early Earth system
Python Software Foundation - July 2024 Newsletter
How to Extract Substring Starting from the End of a String in R
Calculating Autocorrelation in R
NIH: Building Sustainable Software Tools for Open Science
NSF: Engineering Research Initiation
Sony Research Award Program



R Packages:


rplanes: Plausibility Analysis of Epidemiological Signals
SCIntRuler: Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets
WES: Tools for Analyzing Wastewater and Environmental Sampling Data

Get ready for alarm-ringing bacteria, dark comets, weaponized introns for inter-viral competition, random walks in R, and taxonomic names in R markdown. Science On.



References:


Pneumococcal competence is a populational health sensor driving multilevel heterogeneity in response to antibiotics
The dynamical origins of the dark comets and a proposed evolutionary track
An intron endonuclease facilitates interference competition between coinfecting viruses
JuliaHub Newsletter July 2024
Exploring Random Walks with TidyDensity in R



R Packages:


glam: Generalized Additive and Linear Models (GLAM)
taxnames: Formatting Taxonomic Names in Markdown

Get ready for missing ocean nitrification, DNA transformation with IMPRINT, a Loki-inspired dinosaur discovery, Psychology in the Big Book of R, A timeline of R's first 30 years, and a grant on the gut microbiome for human health. Science On.



References:


Rhizobia–diatom symbiosis fixes missing nitrogen in the ocean
A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria
Lokiceratops rangiformis gen. et sp. nov. (Ceratopsidae: Centrosaurinae) from the Campanian Judith River Formation of Montana reveals rapid regional radiations and extreme endemism within centrosaurine dinosaurs
The extremotolerant desert moss Syntrichia caninervis is a promising pioneer plant for colonizing extraterrestrial environments
Juliacon 2024 Presentations Featuring Juliahub speakers
seven steps for data cleaning
Big Update to Big Book of R (new look, new chapter, new books)
A timeline of R's first 30 years
Something a little different: Hexbin maps
DoD: Kidney Cancer, Postdoctoral and Clinical Fellowship Award
DoD: Toxic Exposures Translational Research Award
Biocodex Microbiota Foundation American grant



R Packages:


icpack: Survival Analysis of Interval-Censored Data
simdata: Generate Simulated Datasets
gggenomes: A Grammar of Graphics for Comparative Genomics
Imneuron: AI Powered Neural Network Solutions for Regression Tasks
rush: Rapid Parallel and Distributed Computing
semlrtp: Likelihood Ratio Test P-Values for Structural Equation Models
tinyplot: Lightweight Extension of the Base R Graphics System

Get ready for waves on Titan, glassy gels, tardigrade CRISPR gene-editing, a waking black hole, Race for Your Life in R, the Genie App Competition 2024, and a grant on precision probiotic therapies.



References:


Signatures of wave erosion in Titan’s coasts
Glassy gels toughened by solvent
Plasma proteomics identify biomarkers predicting Parkinson’s disease up to 7 years before symptom onset
Aging atlas reveals cell-type-specific effects of pro-longevity strategies
Single-step generation of homozygous knockout/knock-in individuals in an extremotolerant parthenogenetic tardigrade using DIPA-CRISPR
Astronomers see a massive black hole awaken in real time
R 4.4.1 is released
The Python Language Summit 2024
Genie App Competition 2024 for Prizes
R Gganimate: How To Make Stunning Chart Animations With Ggplot2
Mind the Gap: Using R/exams to Ease the Transition into STEM Studies
The 6 Most Fundamental Functions for Data Cleaning with R
NIH: Enhancing Mechanistic Research on Precision Probiotic Therapies



R Packages:


easyORtables: Easy Odds Ratio Tables
gmfamm: Generalized Multivariate Functional Additive Models
plotor: Produces an Odds Ratio Plot from a Logistic Regression Model
rioplot: Turn a Regression Model Inside Out

Get ready for astronomy fixes for microscopy misses, 3D-printed soft robot actuator hands, cosmic kidney disease, The Hitchhiker’s Guide to Linear Models, and a grant to understand oral phage biology. Science On.



References:


Phase-diversity-based wavefront sensing for fluorescence microscopy
Fully 3D-Printed Miniature Soft Hydraulic Actuators with Shape Memory Effect for Morphing and Manipulation (paper)
Fully 3D-Printed Miniature Soft Hydraulic Actuators with Shape Memory Effect for Morphing and Manipulation (video)
Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction
A possible direct exposure of the Earth to the cold dense interstellar medium 2–3 Myr ago
The distribution of the R-square statistic
Free Report: DataCamp’s The State of Data & AI Literacy Report 2024
The Hitchhiker’s Guide to Linear Models
NIDCR: Support for Research on Understanding Phage Biology in the Oral Cavity
DoD: Breast Cancer Breakthrough Award Levels 1 and 2



R Packages:


futureverse: Easily Install and Load the 'Futureverse'
BioPred: An R Package for Biomarkers Analysis in Precision Medicine
rsurv: Random Generation of Survival Data