Science Research Weekly

Get ready for Parkinson’s disease sniffing dogs; the bladed microtube scheme for massive magnetic fields; a giant, spinning black hole merger; ghost galaxies; lasagna plots in SAS; and an NSF grant on Programmable Cloud Laboratories. Science On.

References:

• Trained dogs can detect the odor of Parkinson's disease
• Gigagauss magnetic field generation by bladed microtube implosion
• Dynamic Organization of Cells in Colonic Epithelium is Encoded by Five Biological Rules
• GW231123: a Binary Black Hole Merger with Total Mass 190-265
• Encoding hierarchical 3D architecture through inverse design of programmable bonds
• 100 ghost galaxies may be orbiting the Milky Way—and we’re just now uncovering them
• Journal of Statistical Software Volume 113
• Use a lasagna plot to visualize US gas prices
• Exploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025
• How to choose an IDE
• Standard Deviation vs. Standard Error: Meaning, Misuse, and the Math Behind the Confusion
• NSF Test Bed: Toward a Network of Programmable Cloud Laboratories
• NASA ROSES 2025: F.9 Citizen Science Seed Funding Program

R Packages:

• rfriend: Provides Batch Functions and Visualisation for Basic Statistical Procedures
• clusterWebApp: Universal Clustering Analysis Platform
• fusedTree: Fused Partitioned Regression for Clinical and Omics Data
• ironseed: Improved Random Number Generator Seeding
• junco: Create Common Tables and Listings Used in Clinical Trials
• ggtranslate: A 'ggplot2' Extension for Translating Plot Text

Get ready for Big Five Workouts, CryoRhodopsins, double detonation supernovae, moon-rice, the 4 layers of testing for R packages, and a three-track grant from the NSF on Translation to Practice. Science On.

References:

• Personality traits can predict which exercise intensities we enjoy most, and the magnitude of stress reduction experienced following a training program
• CryoRhodopsins: A comprehensive characterization of a group of microbial rhodopsins from cold environments
• The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagma
• Regulating Multifunctional Oxygen Vacancies for Plasma-Driven Air-to-Ammonia Conversion
• Calcium in a supernova remnant as a fingerprint of a sub-Chandrasekhar-mass explosion
• Restoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s disease–linked LRRK2-mutant mice
• Moon-Rice: Developing the perfect crop for space-bases
• The 4 Layers of Testing Every R Package Needs
• Elevate Your Skills and Boost Your Career with Jumping Rivers Free Monthly Webinars
• NSF: National Science Foundation Translation to Practice

R Packages:

• BMIselect: Bayesian MI-LASSO for Variable Selection on Multiply-Imputed Datasets
• gggda: A 'ggplot2' Extension for Geometric Data Analysis
• reptiledbr: Interface to the Reptile Database for Querying and Retrieving Taxonomic Data
• semEffect: Structural Equation Model Effect Analysis and Visualization

Get ready for cancer cell states, ADHD diagnosis difficulties, body profiles from Ediacaran trace fossils, LMMS for work you can do yourself, May 2025 Top 40 New CRAN Packages, and a Google Research grant for Quantum Neuroscience. This episode covers materials from June 27th to July 3rd. Science On.

References:

• AAnet resolves a continuum of spatially-localized cell states to unveil intratumoral heterogeneity
• Diagnosing ADHD in adults in randomized controlled studies: a scoping review
• Quantitative decoding of Ediacaran locomotory trace fossil morphologies: Evidence for the emergence of slender anterior-posterior body profiles
• Size-Insensitive Vapor Diffusion Enabled by Additive Freeze-Printed Aerogels for Scalable Desalination
• You can outsource the grunt work to an LLM, not expertise
• May 2025 Top 40 New CRAN Packages
• Beyond the Basics: Books to Supercharge Your R Skills
• DOD: Air Force Fiscal Year 2026 Young Investigator Program (YIP)
• NASA: Innovative Advanced Concepts (NIAC) Phase I
• Google Research: Quantum Neuroscience

R Packages:

• autograph: Automatic Plotting of Many Graphs
• gemR: General Effect Modelling

Get ready for UV-resistant lichen, microbes for bioprinting Martian regolith, a new mammalian organelle called the hemifusome, and ways to make candlestick and segmented total bar charts in R. Science On.

References:

• UVC-Intense Exoplanets May Not Be Uninhabitable: Evidence from a Desert Lichen
• Bio-Manufacturing of Engineered Living Materials for Martian Construction: Design of the Synthetic Community
• Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
• Hemifusomes and interacting proteolipid nanodroplets mediate multi-vesicular body formation
• Anatomy of a Normal Probability Plot
• How to draw a candlestick chart in R? – Both ggplot2 and plotly
• Segmented Total Bar Chart in R with “`ggsegmentedtotalbar“`
• Fantastic Graph Types and How to Make Them

R Packages:

• clinpubr: Clinical Publication
• slopes: Calculate Slopes of Roads, Rivers and Trajectories
• unsum: Reconstruct Raw Data from Summary Statistics

Get ready for Pandora’s box of respiratory pathogens, mixed-up earthworm genomes, the insane energies of Extreme Nuclear Transits, a virus-like clade of Archaea, R version 4.5.1 codename “Great Square Root", the new declarative physical modeling language Dyad, Post-Bayesianism using R, and the NIH Directors Transformative Research Awards. Science On.

References:

• Antibacterial Siderophores of Pandoraea Pathogens and Their Impact on the Diseased Lung Microbiota
• Towering behavior and collective dispersal in Caenorhabditis nematodes
• An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
• The most energetic transients: Tidal disruptions of high-mass stars
• Estimates of submicron particulate matter (PM1) concentrations for 1998–2022 across the contiguous USA: leveraging measurements of PM1 with nationwide PM2·5 component data
• Landscape-explicit phylogeography illuminates the ecographic radiation of early archosauromorph reptiles
• A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome

• R 4.5.1 is released
• 2024 PSF Annual Impact Report
• Dyad: A New Language to Make Hardware Engineering as Fast as Software
• Boost ML accuracy with hyperparameter tuning (with a fun twist)
• Creating A Question Bank Using Google Sheet, Plumber, and Digital Ocean Droplet
• Post Bayesianism? Let's Try It
• DoD: Breast Cancer, Breakthrough Award L1 & 2
• NIH: Support for Research Excellence First Independent Research (SuRE-First) Award
• NIH: Directors Transformative Research Awards

R Packages:

• geess: Modified Generalized Estimating Equations for Small-Sample Data
• gseries: Improve the Coherence of Your Time Series Data
• ssutil: Sample Size Calculation Tools
• tidyspec: Spectroscopy Analysis Using the Tidy Data Philosophy

Get ready for pain killing at the nerve level, solving an Earth science seismic anomaly, ocean giant virus genomes, the SAS Hackathon, a warning against scientific vibe coding, and a pilot study testing school lunches. Science On.

References:

• The analgesic paracetamol metabolite AM404 acts peripherally to directly inhibit sodium channels
• The texture of the post-perovskite phase controls the characteristics of the D” seismic discontinuity
• Expansion of the genomic and functional diversity of global ocean giant viruses
• SAS Hackathon
• Vibe coding with AI agents is not for scientists
• Rethinking Image Formats
• HHS: A Research Study of Contaminants in School Meals

R Packages:

• ggtime: Grammar of Graphics and Plot Helpers for Time Series Visualization
• discovr: Interactive Tutorials and Data for "Discovering Statistics Using R and RStudio"
• rifttable: Results Tables to Bridge the Rift Between Epidemiologists and Their Data

Get ready for eDNA everything, Romer’s Gap tetrapods, dinosaur soft tissues for cancer research, the R Journal Volume 16/3, and a caution about correlation versus causation. Science On.

References:

• Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation
• Nano-structured antibiofilm coatings based on recombinant resilin
• New U-Pb constraints and geochemistry of the East Kirkton Quarry, Scotland: Implications for early tetrapod evolution in the Carboniferous
• Preserving Fossilized Soft Tissues: Advancing Proteomics and Unveiling the Evolutionary History of Cancer in Dinosaurs
• A transiting giant planet in orbit around a 0.2-solar-mass host star
• R Journal 16/3
• Correlation vs Causation: Understanding the Difference

R Packages:

• glmmsel: Generalised Linear Mixed Model Selection

Get ready for cardiovascular aging via gut bacteria metabolites, the darkening of the global ocean, horizontal gene transfer in eukaryotes, long-period radio transients now with X-rays, the R Journal Volume 16/2, and an Industry-University Cooperative Research Centers Program from the NSF. Science On.

References:

• Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging
• Darkening of the Global Ocean
• Impact plasma amplification of the ancient lunar dynamo
• Horizontal transmission of functionally diverse transposons is a major source of new introns
• Detection of X-ray emission from a bright long-period radio transient
• The R Journal Volume 16/2
• useR! 2025 Virtual Conference
• Custom PowerPoints Using {officer}
• April 2025 Top 40 New CRAN Packages
• NSF: Industry-University Cooperative Research Centers Program
• SPARK NS Translational Research Program

R Packages:

• RobinCID: Robust Inference in Complex Innovative Trial Design
• missr: Classify Missing Data as MCAR, MAR, or MNAR

Get ready for spatial genome regulation in non-bilaterian animals, revamping antibiotics with endolysins, removing microplastics with okra and fenugreek, snake anti0venom from a hyperimmune legend, T. rex’s Asian heritage, the 30 Day Chart Challenge 2025, and a rare cancer grant from the Department of Defense. This episode covers material from May 2nd to May 8th. Science On.

References:

• Chromatin loops are an ancestral hallmark of the animal regulatory genome
• Bacteriophage-derived endolysins restore antibiotic susceptibility in β-lactam- and macrolide-resistant Streptococcus pneumoniae infections
• Fenugreek and Okra Polymers as Treatment Agents for the Removal of Microplastics from Water Sources
• Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder
• Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
• Rise of the king: Gondwanan origins and evolution of megaraptoran dinosaurs
• Gravity from transactions: fulfilling the entropic gravity program
• Simulating A Simple Response Adaptive Randomization – I Have To See It To Believe It
• Model Diagnostics: Statistics vs Machine Learning
• 30 Day Chart Challenge 2025
• DoD Rare Cancers, Concept Award

R Packages:

• automatedtests: Automating Choosing Statistical Tests
• tidySummaries: Tidy Statistical Summaries for Exploratory Data Analysis
• VIProDesign: A Comprehensive Tool for Protein Design

Get ready for the Eos dark molecular cloud, integrating exposomics into biomedicine, Cas9 for metabarcoding, time capsules in JuliaHub, the Top 40 New CRAN Packages for March 2025, and a grand on Exponentiating Mathematics. Science On.

References:

• A nearby dark molecular cloud in the Local Bubble revealed via H2 fluorescence
• Integrating exposomics into biomedicine
• Cas9-based enrichment for targeted long-read metabarcoding
• Reproduce Scientific Research with JuliaHub’s Time Capsule
• The SMOTE method for generating synthetic data
• March 2025 Top 40 New CRAN Packages
• flags: Fun with Flags
• Explained vs. Predictive Power: R², Adjusted R², and Beyond
• Announcing… schematic
• DOD: Exponentiating Mathematics (expMath)
• International Space Science Institute Visting Scientists

R Packages:

• robcat: Robust Categorical Data Analysis
• birdnetR: Deep Learning for Automated (Bird) Sound Identification
• connector: Streamlining Data Access in Clinical Research
• IssueTrackeR: List Things to Do