Science Research Weekly

Science Research Weekly

By Mark R WilliamsonScience
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Science Research Weekly episodes

  • Mantis Shrimp's Punch-Out (Season 4: Episode 6)

    Get ready for a perfect Einstein ring, extracellular imaging adventures, into the candidate phyla radiation, mantis shrimp phononic shields, InsectNet, and musing on laziness and CRAN in R. Science On.


    References:

    • Euclid: A complete Einstein ring in NGC 6505
    • Live imaging of the extracellular matrix with a glycan-binding fluorophore
    • Minisyncoccus archaeiphilus gen. nov., sp. nov., a mesophilic, obligate parasitic bacterium and proposal of Minisyncoccaceae fam. nov., Minisyncoccales ord. nov., Minisyncoccia class. nov. and Minisyncoccota phyl. nov. formerly referred to as Candidatus Patescibacteria or candidate phyla radiation
    • Does the mantis shrimp pack a phononic shield?
    • Ocean stratification impedes particulate transport to the plumes of Enceladus
    • InsectNet: Real-time identification of insects using an end-to-end machine learning pipeline
    • Surface Lipids in Nematodes are Influenced by Development and Species-specific Adaptations
    • JuliaHub Newsletter February 2025
    • The Best Reasons to Run a Pilot Study
    • Two Way Repeated Measures ANOVA in R
    • Lazy introduction to laziness in R
    • Is CRAN Holding R Back?
    • Estimating a Bayesian proportional hazards model


    R Packages:

    • R.AlphA.Home: Feel at Home using R, Thanks to Shortcuts Functions Making it Simple
    • powerHE: Power and Sample Size Calculations with Hierarchical Endpoints
    • MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data
    14 min
  • Ribosomal Hip Check (Season 4: Episode 5)

    Get ready for asteroid collision simulations, zero thermal expansion material, effective ribosomal collisions, the benefits of cold immersion, and using AI to learn like an Oxford genius. Science On.


    References:

    • Climatic and ecological responses to Bennu-type asteroid collisions
    • Local chemical heterogeneity enabled superior zero thermal expansion in nonstoichiometric pyrochlore magnets
    • Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation
    • Effects of cold-water immersion on health and wellbeing: A systematic review and meta-analysis
    • Crane 1.0.0 released!
    • Oxford Researchers Discovered How to Use AI To Learn Like A Genius


    R Packages:

    • tergo: Style Your Code Fast
    • rmcmc: Robust Markov Chain Monte Carlo Methods
    • authoritative: Parse and Deduplicate Author Names
    8 min
  • Venti Vanilla Frozen Star, To Go (Season 4: Episode 4)

    Get ready for asteroid analysis, precision probiotics, nifty nanolattices, dark dimensions, frozen stars, and the return of the Top 40 new CRAN package blog series. Science On.


    References:

    • Abundant ammonia and nitrogen-rich soluble organic matter in samples from asteroid (101955) Bennu
    • Metabolic modeling for probiotic and prebiotic production to treat inflammatory disorders
    • Ultrahigh Specific Strength by Bayesian Optimization of Carbon Nanolattices
    • Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
    • PFAS biodegradation by Labrys portucalensis F11: Evidence of chain shortening and identification of metabolites of PFOS, 6:2 FTS, and 5:3 FTCA
    • Dark dimension with (little) strings attached
    • A “dark dimension” could help explain the origin of dark energy
    • Sourcing the Kerr Geometry
    • A theory of frozen stars challenges our understanding of black holes
    • Share Your Shiny Expertise at ShinyConf 2025!
    • December 2024 Top 40 New CRAN Packages

    • R Packages:

      • MEGB: Gradient Boosting for Longitudinal Data
      • smarter: A Collection of Modified R Functions to Make Basic Coding More Convenient
      • phylospatial: Spatial Phylogenetic Analysis
      • 12 min
      • Jello Microbe My Old Friend (Season 4: Episode 3)

        Get ready for futuristic chainmail, synthetic yeast, subsurface ammonia production, living bacterial Jello, exocomet belts, BioChatter, R Journal Volume 16/1, clearing up level confusion, R for cell biologists, and Innosphere's Life Sciences Incubator. Science On.


        References:

        • 3D polycatenated architected materials
        • Metabolomic profiles of infants classified as sudden infant death syndrome: a case-control analysis
        • Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome
        • Next generation bioelectronic medicine: making the case for non-invasive closed-loop autonomic neuromodulation
        • Geological ammonia: Stimulated NH3 production from rocks
        • An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
        • Morphogenesis of bacterial cables in polymeric environments
        • REsolved ALMA and SMA Observations of Nearby Stars (REASONS)
        • The Hubble Tension in Our Own Backyard: DESI and the Nearness of the Coma Cluster
        • A platform for the biomedical application of large language models
        • R Journal Volume 16/1
        • SAS tip: Use the hyphen and colon operators to specify multiple data sets on the SET statement
        • Confusing Statistical Term #3: Level
        • How Are P-values Distributed Under The Null?
        • Get Better: R for cell biologists
        • From code to conversation: Localized AI fun with LM Studio and the ellmer package
        • USDA: Agricultural Genome to Phenome Initiative
        • Innosphere's Life Sciences Incubator

        • R Packages:

          • MiscMath: Miscellaneous Mathematical Tools
          • parttree: Visualize Simple 2-D Decision Tree Partitions
          • phylosignalDB: Explore Phylogenetic Signals Using Distance-Based Methods
          • rwlifetable: Estimation of Life Tables Using Rolling Windows
          • 14 min
          • Antivenom from Scratch (Season 4: Episode 2)

            Get ready for long-lasting DNA lesions, DNA nanorafts, de novo antivenom, a second look at SAS blog posts, working with colors in R, and K-type award from the NIH. Science On.


            References:

            • Prolonged persistence of mutagenic DNA lesions in somatic cells
            • Stretching and immobilizing a single DNA molecule on a glass surface using pressure flow in a microchannel for super-resolution imaging
            • Morphology remodelling and membrane channel formation in synthetic cells via reconfigurable DNA nanorafts
            • An evolutionarily conserved metabolite inhibits biofilm formation in Escherichia coli K-12
            • De novo designed proteins neutralize lethal snake venom toxins
            • 12 blog posts from 2024 that deserve a second look
            • Working with Colors in R
            • NCI: Pathway to Independence Award
            • NIDDK: Small Grant Program for K01/K08/K23/K25 Recipients

            • R Packages:

              • parttree: Visualize Simple 2-D Decision Tree Partitions
              • rwlifetable: Estimation of Life Tables Using Rolling Windows
              • ProtE: Processing Proteomics Data, Statistical Analysis and Visualization
              • PSpower: Sample Size Calculation for Propensity Score Analysis
              • ggstackplot: Create Overlapping Stacked Plots
              • hhmR: Hierarchical Heatmaps
              • bnns: Bayesian Neural Network with 'Stan'
              • 10 min
              • Year of the Mollusk (Season 4: Episode 1)

                Get ready for RNA lanterns, fungal batteries, punk rock mollusks, supercharged hornworts, the top 10 DO LOOP posts of 2024, vanishing sentences in R, and a Trailblazer award from the NIH. Science On.


                References:

                • A modular platform for bioluminescent RNA tracking
                • 3D Printed Cellulose-Based Fungal Battery
                • Redox-activatable inhalable mucoadhesive proteinic nanotherapeutics for targeted treatment of lung cancer
                • New Silurian aculiferan fossils reveal complex early history of Mollusca
                • Electrical signaling and coordinated behavior in the closest relative of animals
                • Repetitive injury induces phenotypes associated with Alzheimer’s disease by reactivating HSV-1 in a human brain tissue model
                • Hornworts reveal a spatial model for pyrenoid-based CO2-concentrating mechanisms in land plants
                • Diverse plant RNAs coat Arabidopsis leaves and are distinct from apoplastic RNAs
                • Two decades of bacterial ecology and evolution in a freshwater lake
                • Top 10 posts from The DO Loop in 2024
                • Your Classifier Is Broken, But It Is Still Useful
                • Little useless-useful R functions – Vanishing sentences
                • NIH: Trailblazer Award for New and Early Stage Investigators
                • NSF: Enabling Discovery through GEnomics

                • R Packages:

                  • ellmer: Chat with Large Language Models
                  • utf8ify: Format Text Using Unicode
                  • creepyalien: Puzzle Game for the R Console
                  • 12 min
                  • Expect the Unexpected (Season 3: Episode 47)

                    Get ready for mass-shifting quasiparticles, deep sea predatory amphipods, tiny asteroids, cancer-related datasets in R, and a systems biology grant for better crop production. Science On.


                    References:

                    • Semi-Dirac Fermions in a Topological Metal
                    • Insect Mitochondrial Genomics: A Decade of Progress
                    • A new large predator (Amphipoda, Eusiridae) hidden at hadal depths of the Atacama Trench
                    • JWST sighting of decameter main-belt asteroids and view on meteorite sources
                    • 7 New Books added to Big Book of R [7/12/2024]
                    • NIH: HEAL Initiative-Early-Stage Discovery of New Pain Targets Within the Understudied Druggable Proteome
                    • NSF: Chemical Evolution of the Solid Earth and Volcanology
                    • NSF: Life and Environments Through Time
                    • DOE: Systems Biology Research to Advance Bioenergy Crop Production

                    • R Packages:

                      • OncoDataSets: A Comprehensive Collection of Cancer Types and Cancer-Related Datasets
                      • TransProR: Analysis and Visualization of Multi-Omics Data
                      • warehouseTools: Heuristics for Solving the Traveling Salesman Problem in Warehouse Layouts
                      • 6 min
                      • Messy Disease Busting (Season 3: Episode 46)

                        Get ready for mosquito busting, tuberculosis busting, the Tapestry whole exome sequencing study, the Journal of Statistical Software Volume 111, a messy R package, and a grant for tissue engineering on the International Space Station. Science On.


                        References:

                        • Chromobacterium biopesticide overcomes insecticide resistance in malaria vector mosquitoes
                        • How fast are viruses spreading in the wild?
                        • Environmental fungi target thiol homeostasis to compete with Mycobacterium tuberculosis
                        • A Large-Scale Decentralized Whole Exome Sequencing Study for Clinical Practice, Research Discovery, and Genomic Education
                        • A dry Venusian interior constrained by atmospheric chemistry
                        • Journal of Statistical Software Volume 111
                        • A historical method of generating random normal variates
                        • Positron vs RStudio – is it time to switch?
                        • Introducing the {messy} package
                        • NCCIH: Natural Product Mid Phase Clinical Trial
                        • NSF: Tissue Engineering and Mechanobiology on the International Space Station

                        • R Packages:

                          • messy: Create Messy Data from Clean Data Frames
                          • RCNA: Robust Copy Number Alteration Detection (RCNA)
                          • epiparameterDB: Database of Epidemiological Parameters
                          • 7 min
                          • Tumors and Gas Giants (Season 3: Episode 45)

                            Get ready for cancer growth rates, the interior of Uranus and Neptune, the November Juliahub Newsletter, and a grant on biomedical informatics. Science On.


                            References:

                            • High-density sampling reveals volume growth in human tumours
                            • Phase separation of planetary ices explains nondipolar magnetic fields of Uranus and Neptune
                            • Juliahub Newsletter November 2024
                            • NLM Research Grants in Biomedical Informatics and Data Science

                            • R Packages:

                              • autoslider.core: Slide Automation for Tables, Listings and Figures
                              • evolved: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries
                              • scatterbar: Scattered Stacked Bar Chart Plots
                              • TimeDepFrail: Time Dependent Shared Frailty Cox Model
                              • 3 min

                              About Science Research Weekly

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                              A weekly overview of helpful scientific research topics and the successor of the podcast Statistics Weekly. Every week, I will cover 3 topic areas: Research Articles, Research Tools, and Research…