Science Research Weekly

Get ready for a review of acetaminophen and neurodevelopmental disorders, dehydration and stress response, Hycean world woes, hints at the compositional protein code, fraudulent publishing in mathematics, R Journal Volume 17/1, and a grant on microbial dust control for mining operations. Science On.

References:

• Evaluation of the evidence on acetaminophen use and neurodevelopmental disorders using the Navigation Guide methodology
• Habitual fluid intake and hydration status influence cortisol reactivity to acute psychosocial stress
• Sub-Neptunes Are Drier than They Seem: Rethinking the Origins of Water-rich Worlds
• A domed pachycephalosaur from the early Cretaceous of Mongolia
• Tracing the Origin of the Genetic Code and Thermostability to Dipeptide Sequences in Proteomes
• Tiny protein pairs may hold the secret to life’s origin
• How to Fight Fraudulent Publishing in the Mathematical Sciences: Joint Recommendations of the IMU and the ICIAM

• Fraudulent Publishing in the Mathematical Sciences
• The R Journal Volume 17/1
• Birthdays and the coupon collector's problem
• NIH: Pilot Projects to Enhance the Human Virome Program
• NIH: Clinical Trial Readiness for Rare Diseases, Disorders, and Syndromes
• NSF/CASIS Transport Phenomena Research at the International Space Station to Benefit Life on Earth
• Microbial dust control and surface stabilization

R Packages:

• bnpMTP: Bayesian Nonparametric Sensitivity Analysis of Multiple Testing Procedures for p Values
• MicrobTiSDA: Microbiome Time-Series Data Analysis
• plumber2: Easy and Powerful Web Servers
• ggDNAvis: 'ggplot2'-Based Tools for Visualising DNA Sequences and Modifications

Get ready for maize shoot stem cells, a five image Einstein cross, identity of some Little Red Dots, ATREIDES for exo-Neptunes, Volume 114 of the Journal of Statistical Software, ggplot2 geoms and stats, and Classic Scientific Paper Review. Science On.

References:

• Journal of Statistical Software Volume 114
• Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation
• HerS-3: An Exceptional Einstein Cross Reveals a Massive Dark Matter Halo
• A remarkable ruby: Absorption in dense gas, rather than evolved stars, drives the extreme Balmer break of a little red dot at z = 3.5
• Journal of Statistical Software Volume 114
• All the Ways to Programmatically Edit or Parse R Markdown / Quarto Documents
• Learning About Assemblying DNA, BLAST, and Multiple Loci Sequence Testing (MLST) – A Note To Myself
• Exploring {ggplot2}’s Geoms and Stats
• Classic Scientific Paper Review

R Packages:

• henna: A Versatile Visualization Suite
• ccar3: Canonical Correlation Analysis via Reduced Rank Regression
• SurvGME: Analysis of Survival Data under Graphical and Measurement Error Models
• workspace: Manage Collections of Datasets and Objects

Get ready for Martian mudstone biosignatures, a wide-ranging dwarf planet candidate, mapping mammoth microbes, ice gliding diatoms, extrachromosomal Inocles of the oral microbiome, DNA sequence alignment from scratch in R, and an invitation to check out Science Spotlight. Science On.

References:

• Redox-driven mineral and organic associations in Jezero Crater, Mars
• Discovery of a dwarf planet candidate in an extremely wide orbit: 2017 OF201
• Ancient host-associated microbes obtained from mammoth remains
• Ice gliding diatoms establish record-low temperature limits for motility in a eukaryotic cell
• Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome
• Creating and managing Canvas quizzes with R/exams and vvcanvas
• Building DNA Sequence Alignment With Needleman-Wunsch Algorithm From Scratch - A Note To My Self
• Science Spotlight

R Packages:

• factorH: Multifactor Nonparametric Rank-Based ANOVA with Post Hoc Tests
• ivolcano: Interactive Volcano Plot
• REXoplanets: Creates Interface with NASA 'Exoplanets Archive API'
• pmsesampling: Sample Size Determination for Accurate Predictive Linear Regression
• minipdf: PDF Document Creator
• power4mome: Power Analysis for Moderation and Mediation

Get ready for the failure of beta-blockers, cathartocytosis, flagging suspicious journals with AS, extreme ankylosaur armor, the basics of phylogenetic analysis in R, and a tiny space grant from DevelopSpace. Science On.

References:

• Human endogenous retrovirus K (HERV-K) envelope structures in pre- and postfusion by cryo-EM
• Beta-Blockers after Myocardial Infarction without Reduced Ejection Fraction
• Cathartocytosis: Jettisoning of cellular material during reprogramming of differentiated cells
• Estimating the predictability of questionable open-access journals
• Extreme armour in the world’s oldest ankylosaur
• Patterned invagination prevents mechanical instability during gastrulation
• Learning The Basics of Phylogenetic Analysis
• DevelopSpace grant

R Packages:

• blendR: Blended Survival Curves
• CompClassMetrics: Classification Measures when Subclasses are Involved
• TrialSimulator: Clinical Trial Simulator
• Rnaught: Estimate the Basic Reproduction Number (R0)
• metamorphr: Tidy and Streamlined Metabolomics Data Workflows
• tastyR: Recipe Data from 'Allrecipes.com'

Get ready for deep-ocean oxidation dates, no giant impact for Jupiter’s core, common meds making antibiotic resistance worse, arsenic-mineralizing marine worms, the July 2025 Top 40 new CRAN packages, a plea for PyPAN: the Python Package Archive Network, and a grant on aging mammalian tissues in vitro. Science On.

References:

• Mid-Devonian ocean oxygenation enabled the expansion of animals into deeper-water habitats
• No dilute core produced in simulations of giant impacts on to Jupiter
• The effect of commonly used non-antibiotic medications on antimicrobial resistance development in Escherichia coli
• A deep-sea hydrothermal vent worm detoxifies arsenic and sulfur by intracellular biomineralization of orpiment (As2S3)
• July 2025 Top 40 New CRAN Packages
• How many parameters does GPT-5 have?
• Python needs its CRAN
• The European Bioconductor Conference
• NIH: Aging Mammalian Tissues In Vitro
• NIH: Stephen I. Katz Early Stage Investigator Research Project Grant (non-clinical trial)
• NIH: Stephen I. Katz Early Stage Investigator Research Project Grant (human subjects)

R Packages:

• ham: Healthcare Analysis Methods
• multideploy: Deploy File Changes Across Multiple 'GitHub' Repositories
• SampleSizeCalculator: Sample Size Calculator under Complex Survey Design
• tidypopgen: Tidy Population Genetics
• mlspatial: Machine Learning and Mapping for Spatial Epidemiology
• gwas2crispr: GWAS-to-CRISPR Data Pipeline for High-Throughput SNP Target Extraction
• ggdiceplot: Dice Plot Visualization for 'ggplot2'

Get ready for a potential cancer vaccine, a carbon ring stabilized by smaller rings, Uranus’ newest tiny moon, absurd conversions in R, and funding from the American Lung Association. Science On.

References:

• Sensitization of tumours to immunotherapy by boosting early type-I interferon responses enables epitope spreading
• Solution-phase stabilization of a cyclocarbon by catenane formation
• SwRI-led Webb Telescope survey discovers new moon orbiting Uranus
• Python Developers Survey 2024 Results
• Handling Missing Data in R: A Comprehensive Guide
• Learning Antimicrobial Resistance (AMR) genes with Bioconductor
• Little useless-useful R functions – Absurd converter with Markdown report
• American Lung Association: Awards and Grants Opportunities

R Packages:

• Nematode: Ecological Indices Calculator for Nematode Communities
• confidenceCurves: Frequentist Confidence Analysis for Clinical Trials
• ggdiagram: Object-Oriented Diagram Plots with 'ggplot2'
• csdb: An Abstracted System for Easily Working with Databases with Large Datasets
• gtregression: Tools for Creating Publication-Ready Regression Tables

Get ready for Antarctic submarine canyons, a medicated gel for diabetic wound healing, rapid electronic detection of infectious and chronic diseases, SAS and R in tandem, and several grants from private foundations. Science On.

References:

The geomorphometry of Antarctic submarine canyons

Engineered sEVs encapsulated in GelMA facilitated diabetic wound healing by promoting angiogenesis via targeting thrombospondin-1

Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at the Subfemtomolar Level

Building seamless data pipelines across multiple languages: A life sciences and healthcare use case leveraging R and SAS

Gateway for Cancer Research Grant Program

IAFNS Cognitive Health Committee Request for Proposals

Simons Collaborations in Ecology and Evolution

Get ready for the power of iNaturalist in biodiversity research, mechanisms behind lightning strikes, multi-region brain organoids, programmable chromosome engineering, an idealized double-slit experiment, why hardware may need a new foundation, animated maps in R, and a grant from PepsiCo on novel proteins. Science On.

• References:
• iNaturalist accelerates biodiversity research
• Photoelectric Effect in Air Explains Lightning Initiation and Terrestrial Gamma Ray Flashes
• Multi-Region Brain Organoids Integrating Cerebral, Mid-Hindbrain, and Endothelial Systems
• Iterative recombinase technologies for efficient and precise genome engineering across kilobase to megabase scales
• Inhibition of the minor spliceosome restricts the growth of a broad spectrum of cancers
• Coherent and Incoherent Light Scattering by Single-Atom Wave Packets
• Einstein was wrong: MIT just settled a 100-year quantum debate
• Surfactants Steer Supraparticle Structure
• Journal of Statistical Software Volume 113
• Why Hardware Needs a New Foundation
• 3 ways to estimate parameters when fitting a distribution to data
• Introduction to Generalised Linear Models with Prussian Horse Kicks
• Animated Maps with {ggplot2} and {gganimate}
• Novel proteins, peptides and amino acids with health benefits

Get ready for radiation-hardened data chips, a universal Deepfake detector, plant virus cancer immunotherapy, June’s top 40 new CRAN packages, and a grant from the NSF on Future Computing Research. Science On.

References:

• A Radiation-Hard 8-Channel 15-Bit 40-MSPS ADC for the ATLAS Liquid Argon Calorimeter Readout
• Towards a Universal Synthetic Video Detector: From Face or Background Manipulations to Fully AI-Generated Content
• Comparative analyses for plant virus-based cancer immunotherapy drug development
• June 2025 Top 40 New CRAN Packages
• NSF Computer and Information Science and Engineering (CISE): Future Computing Research

R Packages:

• ggdibbler: Add Uncertainty to Data Visualisations
• simIC: Simulate and Analyze Interval- and Mixed-Censored Survival Data
• suRface.analytics: Statistical Analysis and Visualization of Surface-Engineered Material Properties
• staninside: Facilitating the Use of 'Stan' Within Packages
• ggcorrheatmap: Make Flexible 'ggplot2' Correlation Heatmaps

Get ready for cancer cells going up in sugary flames, live-action planetary formation, deep sea plastic biodegradation, a 150-year-old museum fossil specimen finally gets figured out, The R Journal: Volume 16/4, dealing with non-values in R, and some Science Spotlights. Science On.

References:

• A Novel Exopolysaccharide, Highly Prevalent in Marine Spongiibacter, Triggers Pyroptosis to Exhibit Potent Anticancer Effects
• LiDO: Discovery of a 10:1 Resonator with a Novel Libration State
• Refractory solid condensation detected in an embedded protoplanetary disk
• Unveiling deep-sea biodegradation of microbially produced lactate-based polyester (LAHB) via plastisphere metagenomics and metatranscriptomics
• Palaeocampa anthrax, an armored freshwater lobopodian with chemical defenses from the Carboniferous
• The R Journal: Volume 16/4
• Let’s talk about NA-s!
• What is Biological Dark Matter?
• What Makes Functional Precision Cancer Therapy Useful?

R Packages:

• dependentsimr: Simulate Omics-Scale Data with Dependency
• ROCnGO: Fast Analysis of ROC Curves