Science Research Weekly

Get ready for DNA mutation rates across the generations, a potential Alzheimer’s ‘vaccine’, tissue-expansion mass-spectrometry, updating old methods in SAS, planning a statistical analysis, and seven new Cancer Grand Challenges. Science On.

References:

• Human de novo mutation rates from a four-generation pedigree reference
• Targeting of phosphorylated tau at threonine 181 by a Qβ virus-like particle vaccine is safe, highly immunogenic, and reduces disease severity in mice and rhesus macaques
• TEMI: tissue-expansion mass-spectrometry imaging
• Updating old SAS programs: A case study with PROC LOESS
• Strategies for Choosing and Planning a Statistical Analysis
• USAMRAA: Alzheimer’s Research Program Transforming Research Award
• Cancer Grand Challenges

R Packages:

• circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization
• glmfitmiss: Fitting GLMs with Missing Data in Both Responses and Covariates

Get ready for a rotating universe, universal cephalopod PCR primers, moonglass solar panels, R’s How about a Twenty-Six, SAS for Dummies 3rd Edition, and a grant for life science entrepreneurs. Science On.

References:

• Can rotation solve the Hubble Puzzle?
• Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity
• Acoustic modulation of mechanosensitive genes and adipocyte differentiation
• Moon photovoltaics utilizing lunar regolith and halide perovskites
• Journal of Statistical Software Vol 112
• SAS For Dummies: New edition for the modern SAS user
• R version 4.5.0
• R Version 4.5.0 is Out!
• What’s new in R 4.5.0?
• Announcing the Jumping Rivers Dashboard Gallery
• Getting My Feet Wet With `Plumber` and JavaScript
• NSF: Incorporating Human Behavior in Epidemiological Models
• BioInnovation Institute: Bio Studio Program

R Packages:

• fastqrs: Fast Algorithms for Quantile Regression with Selection
• vayr: Extensions for 'ggplot2' to Visualize as You Randomize
• e2tree: Explainable Ensemble Trees

Get ready for majestic herds of prehistoric rhinos, open-source 3D-printed robot parts, a mitochondrial disease therapy, a global map of human subcellular architecture, potential but scanty microbial life on Titan, and oxygen adaptation in bacteria. Science On.

References:

• Enamel carbon, oxygen, and strontium isotopes reveal limited mobility in an extinct rhinoceros at Ashfall Fossil Beds, Nebraska, USA
• Development of an Open-Source 3D-Printed Material Synthesis Robot FLUID: Hardware and Software Blueprints for Accessible Automation in Materials Science
• FLUID (Flowing Liquid Utilizing Interactive Device) in operation
• Small molecules restore mutant mitochondrial DNA polymerase activity
• Multimodal cell maps as a foundation for structural and functional genomics
• The Viability of Glycine Fermentation in Titan's Subsurface Ocean
• A geological timescale for bacterial evolution and oxygen adaptation
• Overview of Clinical & Translational Research

R Packages:

• correlationr: Conduct Robust Correlations on Non-Normal Data
• seinfitR: Modeling the Relationship Between Nematode Densities and Plant Growth
• DLMRMV: Distributed Linear Regression Models with Response Missing Variables
• lme4GS: 'lme4' for Genomic Selection

Get ready for Green Saharan genomes, super-duckweed, Alzheimer’s blood tests, Volume 112 of the Journal of Statistical Software, a Litmus test for R packages, and the Top 40 New CRAN Packages for February 2025. Science On.

References:

• Ancient DNA from the Green Sahara reveals ancestral North African lineage
• Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction
• Plasma MTBR-tau243 biomarker identifies tau tangle pathology in Alzheimer’s disease
• Genome duplication in a long-term multicellularity evolution experiment
• Cooperative hydrodynamics accompany multicellular-like colonial organization in the unicellular ciliate Stentor
• Journal of Statistical Software, Volume 112
• Did George Box say, "All models are wrong, but some are useful"?
• Nested bar charts in SAS
• Bayesian proportional hazards model for a stepped-wedge design
• Should I Use Your R Package?
• February 2025 Top 40 New CRAN Packages

R Packages:

• castgen: Estimate Sample Size for Population Genomic Studies
• ClassificationEnsembles: Automatically Builds 20 Classification Models
• ForecastingEnsembles: Time Series Forecasting Using 23 Individual Models
• NumericEnsembles: Automatically Runs 23 Individual and 17 Ensembles of Models
• pcpr: Principal Component Pursuit for Environmental Epidemiology

Get ready for nuclear batteries, DIY box filters, Asgardian microtubules, water from the cosmic dawn, FitQuantiles tables in SAS, Teaching Combinatorics Using R, The 2025 Galaxy and Bioconductor Community Conference, and Python in 10 Lunch Break sessions. Science On.

References:

• A safe nuclear battery that could last a lifetime
• Do-it-yourself box filter clears the air of indoor pollutants
• Long-chain alkanes preserved in a Martian mudstone
• Microtubules in Asgard archaea
• Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida
• Autonomous shaping of the piRNA sequence repertoire by competition between adjacent ping-pong amplification sites
• Abundant water from primordial supernovae at cosmic dawn
• The quantile fit plot: Comparing empirical and predicted quantiles for a univariate model
• A Bayesian proportional hazards model for a cluster randomized trial
• How Many Ways to Color This Grid: Teaching Combinatorics Using R
• Galaxy and Bioconductor Community Conference 2025
• Python in 10 Lunch Break Session 1

R Packages:

• COAP: High-Dimensional Covariate-Augmented Overdispersed Poisson Factor Model
• gghourglass: Plot Records per Time of Day
• GoMiner: Automate the Mapping Between a List of Genes and Gene Ontology Categories

Get ready for cell cycle synced endosymbionts, cytoskeleton densities via deep learning, taking the STING out of autoimmune diseases, constraints on the internal matter of neutron stars, and a protein association grant from the American Heart Association. Science On.

References:

• A nucleus-encoded dynamin-like protein controls endosymbiont division in the trypanosomatid Angomonas deanei
• Deep learning-based cytoskeleton segmentation for accurate high-throughput measurement of cytoskeleton density
• ArfGAP2 promotes STING proton channel activity, cytokine transit, and autoinflammation
• QCD Constraints on Isospin-Dense Matter and the Nuclear Equation of State
• AHA: Pilot Grants to Explore the Use of the American Heart Association Protein Binding Atlas to Discover Novel Protein Interactions

R Packages:

• globpso: Swarm Intelligence Optimization
• minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB)
• kitesquare: Visualize Contingency Tables Using Kite-Square Plots
• SnowData: Historical Data from John Snow's 1854 Cholera Outbreak Map

Get ready for the cancer and non-cancer cells of the colocatome, tiny vortexes in semimetals, slimmed down megasharks, Pi to the power of pi, and underrated R functions. Science On.

References:

• A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens
• Imaging Orbital Vortex Lines in Three-Dimensional Momentum Space
• Reassessment of the possible size, form, weight, cruising speed, and growth parameters of the extinct megatooth shark, Otodus megalodon (Lamniformes: Otodontidae), and new evolutionary insights into its gigantism, life history strategies, ecology, and extinction
• Julia Now Available on Google Colab
• Pi to the power of pi
• Underrated Gems in R: Must-Know Functions You’re Probably Missing Out On
• 9 new books added to Big Book of R
• Customize your expedition: Create a unique documentation for your R Package

R Packages:

• datapackage: Creating and Reading Data Packages
• lavaan.mi: Fit Structural Equation Models to Multiply Imputed Data
• ParamANOVA: Fully Parameterizable ANOVA Tests
• xlr: Create Table Summaries and Export Neat Tables to 'Excel'

Get ready for synthetic microbe community therapy, VR taste testing, narwhal tusk behavior, detecting space debris, microbial patterns across the ISS, the Top 40 New CRAN Packages for January 2025, and Department of Defense grants for the MURI program. Science On.

References:

• A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance
• A sensor-actuator–coupled gustatory interface chemically connecting virtual and real environments for remote tasting
• Use of tusks by narwhals, Monodon monoceros, in foraging, exploratory, and play behavior
• The generation of whistler, lower hybrid, and magnetosonic waves by satellites passing through ionospheric magnetic field aligned irregularities
• The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
• R version 4.4.3 (Trophy Case) has been released
• A Bayesian proportional hazards model with a penalized spline
• Constructing the Hertzsprung-Russell Diagram
• Working with Clinical Trial Data? There’s a Pharmaverse Package for That
• January 2025 Top 40 New CRAN Packages
• Better documentation for R-universe!
• DoD: Multidisciplinary Research Program of the University Research Initiative (MURI)

R Packages:

• MetabolSSMF: Simplex-Structured Matrix Factorisation for Metabolomics Analysis
• mixtree: A Statistical Framework for Comparing Sets of Trees
• mbX: A Comprehensive Microbiome Data Processing Pipeline
• blit: Bioinformatics Library for Integrated Tools

Get ready for PAN-GO, tardigrade medication, the unsung biological driving forces of fire and ice, brewing tea for lead reduction, and the 2025 NASA ROSES omnibus. Science On.

References:

• A compendium of human gene functions derived from evolutionary modelling
• Local structural flexibility drives oligomorphism in computationally designed protein assemblies
• Radioprotection of healthy tissue via nanoparticle-delivered mRNA encoding for a damage-suppressor protein found in tardigrades
• The Neoproterozoic glacial broom
• Anomalous δ15N values in the Neoarchean associated with an abundant supply of hydrothermal ammonium
• Brewing Clean Water: The Metal-Remediating Benefits of Tea Preparation
• Use the EFFECTPLOT statement to visualize binomial regression models in SAS
• NASA ROSES 2025: A.58 INNOVATE

R Packages:

• mermboost: Gradient Boosting for Generalized Additive Mixed Models
• qountstat: Statistical Analysis of Count Data and Quantal Data
• codelist: Working with Code Lists

Get ready for exoplanet atmosphere, secret shark bases, 3D-printed thrusters, active matter, dependent variables that can’t be used for linear models, and bible translations in R. Science On.

References:

• Vertical structure of an exoplanet’s atmospheric jet stream
• Shallow seamounts are “oases” and activity hubs for pelagic predators in a large-scale marine reserve
• High-Impulse, Modular, 3D-Printed CubeSat ElectrosprayThrusters Throttleable via Pressure and Voltage Control
• Aberrant neuronal hyperactivation causes an age-dependent behavioral decline in Caenorhabditis elegans
• An aperiodic chiral tiling by topological molecular self-assembly
• Traveling Strings of Active Dipolar Colloids
• 6 Types of Dependent Variables that will Never Meet the Linear Model Normality Assumption
• What’s Artificial Intelligence all about?
• Generalized Linear Mixed Models for Everything
• The Last Statistical Model You’ll Ever Need in SAS
• Coupon: 92F7BB1DF31947F16207

R Packages:

• logos: Access to the Hebrew, Greek, and English Version of the Bible
• musicXML: Data Sonification using 'musicXML'
• indexr: A Thoughtful Saver of Results