Science Research Weekly

Science Research Weekly

By Mark R WilliamsonScience
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Science Research Weekly episodes

  • The Birds Are Up to Something (Season 3: Episode 14)

    Get ready for neoavian phylogenetics, marvelous metafluids, the search for dark photon dark matter, normalization and scaling in R, Highcharts for interactive and animated charts, and a grant on rare diseases. Science On.


    References:

    • A region of suppressed recombination misleads neoavian phylogenomics
    • Shell buckling for programmable metafluids
    • First Results from a Broadband Search for Dark Photon Dark Matter in the 44 to 52 μ eV Range with a Coaxial Dish Antenna
    • Add a second axis to a SAS graph
    • 6 New books added to Big Book of R
    • A Practical Guide to Data Normalization in R
    • Scaling Your Data to 0-1 in R: Understanding the Range
    • R Highcharts: How to Make Animated and Interactive Data Visualizations in R
    • NCATS: Preclinical Proof of Concept Studies for Rare Diseases


      • R Packages:

      • CoreMicrobiomeR: Identification of Core Microbiome
      • scimo: Extra Recipes Steps for Dealing with Omics Data
        • 5 min
      • Starquaking in My Boots (Season 3: Episode 13)

        Get ready for the smallest starquake, migraine risks in young stroke, tardigrade biostasis, too many colors spoiling the graph, Bioconductor Conference 2024, and a subset of Department of Defense grants on human health. Science On.


        References:

        • Protective effect of PDE4B subtype-specific inhibition in an App knock-in mouse model for Alzheimer’s disease
        • Expanding the frontiers of cool-dwarf asteroseismology with ESPRESSO
        • Association of Traditional and Nontraditional Risk Factors in the Development of Strokes Among Young Adults by Sex and Age Group: A Retrospective Case-Control Study
        • Labile assembly of a tardigrade protein induces biostasis
        • CRTFASTGEEPWR: A SAS Macro for Power of Generalized Estimating Equations Analysis of Multi-Period Cluster Randomized Trials with Application to Stepped Wedge Designs
        • too many colors spoil the graph
        • Bioconductor Conference 2024
        • DoD Peer Reviewed Medical, Investigator-Initiated Research Award
        • DoD Peer Reviewed Medical, Discovery Award
        • AAAAI Foundation Award to Sustain Research Excellence


          • R Packages:

          • CvmortalityMult: Cross-Validation for Multi-Population Mortality Models
          • flexOR: Flexible Odds Ratio Curves
          • glmMisrep: Generalized Linear Models Adjusting for Misrepresentation
          • biopixR: Extracting Insights from Biological Images
            • 8 min
          • Your Brain on Cosmology (Season 3: Episode 12)

            Get ready for leafhopper cloaking technology, the question of a dark matter-less universe, life at the extremes of inactive hydrothermal vents, not caring about the Levene’s test, and a grant on brain changes across longer time spans. Science On.


            References:

            • Geometric design of antireflective leafhopper brochosomes
            • Testing CCC+TL Cosmology with Observed Baryon Acoustic Oscillation Features
            • Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity
            • Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping
            • Two-dimensional materials by large-scale computations and chemical exfoliation of layered solids
            • assumptions of linear models are about errors, not the response variable
            • Here is why I don’t care about the Levene’s test
            • NIH: New Approaches for Measuring Brain Changes Across Longer Timespans (R01)
            • NIH: New Approaches for Measuring Brain Changes Across Longer Timespans (R21)


              • R Packages:

              • xega: Extended Evolutionary and Genetic Algorithms
              • tidyrates: Tidy Epidemiological Rates
              • calmr: Canonical Associative Learning Models and their Representations
              • ggbrick: Waffle Style Chart with a Brick Layout in 'ggplot2'
                • 4 min
              • Gastronomical Gallivanting (Season 3: Episode 11)

                Get ready for bile acid modification, Pizza Pi, pre-print propensity using R, and a grant on misfolding proteins. Science On.


                References:

                • High-quality semiconductor fibres via mechanical design
                • Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes
                • The underappreciated diversity of bile acid modifications
                • Newsletter March 2024 - Genie Builder Beta Launch - Create Web Apps and Dashboards Easily
                • Pizza pi
                • My Simple Understanding of Total Effect = Direct Effect + Indirect Effect (via Mediator)
                • Mastering Random Sampling in R with the sample() Function
                • Pre Self: what fraction of a journal’s papers are preprinted?
                • NIH: Exploring Proteogenomic Approaches to Unravel the Mechanisms of Mis-Folded Protein Accumulation in Tauopathies


                  • R Packages:

                  • glmpermu: Permutation-Based Inference for Generalized Linear Models
                  • corrmeta: Correlated Meta-Analysis
                    • 4 min
                  • Vertebrates and Hat Tricks (Season 3: Episode 10)

                    Get ready for low-oxygen Europa, low-mutational nematode genomes, museum-loads of 3D scanned vertebrates, A Steve’s Data Tips and Tricks hat trick plus one, and a NSF grant on AI and math. Science On.


                    References:

                    • Oxygen production from dissociation of Europa’s water-ice surface
                    • Environmental radiation exposure at Chornobyl has not systematically affected the genomes or chemical mutagen tolerance phenotypes of local worms
                    • Decoding chromatin states by proteomic profiling of nucleosome readers
                    • Scientists CT scanned thousands of natural history specimens, which you can access for free
                    • A Beginner’s Guide to Renaming Data Frame Columns in R
                    • How to Rename Factor Levels in R (With Examples)
                    • How to Add New Level to Factor in R
                    • Filtering Rows in R Where Column Value is Between Two Values
                    • NSF: Artificial Intelligence, Formal Methods, and Mathematical Reasoning


                      • R Packages:

                      • DiscreteDatasets: Example Data Sets for Use with Discrete Statistical Tests
                      • rexer: Random Exercises and Exams Generator
                        • 5 min
                      • Ask the Genie for Some Cake (Season 3: Episode 9)

                        Get ready for the brightest quasar of them all, biomolecule chirality mysteries, a Biomedical Engineering roadmap, the release of R’s Angel Food Cake, the release of JuliaHub’s Genie Builder, and Shiny for clinical trial reporting. Science On.


                        References:

                        • The accretion of a solar mass per day by a 17-billion solar mass black hole
                        • Symmetry breaking and chiral amplification in prebiotic ligation reactions
                        • Grand Challenges at the Interface of Engineering and Medicine
                        • R 4.3.3 is released
                        • Unveiling Genie Builder: Create Low-Code Apps on JuliaHub
                        • On using flexible distributions to fit data
                        • Using colors to visualize groups in a bar chart in SAS
                        • What Good is Analysis of Variance?
                        • Escape the Spreadsheet Inferno: Switch to Shiny for Clinical Trial Reporting
                        • Demystifying the melt() Function in R


                          • R Packages:

                          • pctax: Professional Comprehensive Omics Data Analysis
                          • clusEvol: A Procedure for Cluster Evolution Analytics
                          • volker: High-Level Functions for Tabulating, Charting and Reporting Survey Data
                            • 5 min
                          • The Birds and the Beta-amyloids (Season 3: Episode 8)

                            Get ready for blazing computer processing speeds, a link between fine particulate matter and Alzheimer’s Disease, mammalian gene insertion with bird retrotransposons, experimental confirmation of altermagnets, The Journal of Statistical Software Volume 108, a free R/Shiny eBook, and an NSF grant on acceleration of protein design. Science On.


                            References:

                            • Simultaneous and Heterogenous Multithreading
                            • Association of PM2.5 Exposure and Alzheimer Disease Pathology in Brain Bank Donors—Effect Modification by APOE Genotype
                            • Harnessing eukaryotic retroelement proteins for transgene insertion into human safe-harbor loci
                            • Observation of New Isotopes in the Fragmentation of 198 Pt at FRIB
                            • Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2
                            • Journal of Statistical Software Volume 108
                            • On using the range to estimate the variability of small samples
                            • measures of model fit for linear regression models
                            • Level Up Your R/Shiny Team Skills with Our Free Ebook
                            • Enhancing Your Plots in R: Adding Superscripts & Subscripts
                            • NSF: Ideas Lab: Use-Inspired Acceleration of Protein Design
                            • NSF: Plant Genome Research Program


                              • R Packages:

                              • fluidsynth: Read and Play Digital Music (MIDI)
                              • aberrance: Detect Aberrant Behavior in Test Data
                              • ggbrace: Curly Braces for 'ggplot2'
                                • 7 min
                              • Eeny, Meeny, Mimas, Moe (Season 3: Episode 7)

                                Get ready for a mini Mimas ocean, microbes for low-cost molecular biology, Ordovician fossils from France, a 3D-printed titanium metamaterial, Emacs for R, and a NASA omnibus funding announcement chock full of opportunity. Science On.


                                References:

                                • A recently formed ocean inside Saturn’s moon Mimas
                                • Efficient natural plasmid transformation of Vibrio natriegens enables zero-capital molecular biology
                                • The quest for superheavy elements and the limit of the periodic table
                                • The Cabrières Biota (France) provides insights into Ordovician polar ecosystems
                                • Pleural macrophages translocate to the lung during infection to promote improved influenza outcomes
                                • Titanium Multi-Topology Metamaterials with Exceptional Strength
                                • An exact formula for the sampling distribution of the correlation coefficient
                                • NIA Career Transition Award
                                • NASA ROSES: Astrophysics Data Analysis Program
                                • NASA ROSES: New Frontiers Data Analysis Program
                                • NASA ROSES: Exobiology


                                  • R Packages:

                                  • circlesplot: Visualize Proportions with Circles in a Plot
                                  • multe: Multiple Treatment Effects Regression
                                  • valentine: Spread the Love for R Packages with Poetry
                                    • 7 min
                                  • Plankton Power (Season 3: Episode 6)

                                    Get ready for memory B cells that react to allergens, a cosmic chicken and egg questions with black holes and galaxies, the ecological importance of tiny plankton, the spectacular shape of ancient trees, triangular art in Julia, elliptical hearts in SAS, and the 400th entry in the Big Book of R. Science On.


                                    References:

                                    • Type 2–polarized memory B cells hold allergen-specific IgE memory
                                    • Locomotion and the early Mesozoic success of Archosauromorpha
                                    • Which Came First: Supermassive Black Holes or Galaxies? Insights from JWST
                                    • Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides
                                    • The silent majority: Pico- and nanoplankton as ecosystem health indicators for marine policy
                                    • Noninvasive neuromodulation of subregions of the human insula differentially affect pain processing and heart-rate variability: a within-subjects pseudo-randomized trial
                                    • microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data
                                    • Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency
                                    • Enigmatic fossil plants with three-dimensional, arborescent-growth architecture from the earliest Carboniferous of New Brunswick, Canada
                                    • Michael Dickey, our guide through the surprising world of liquid metals
                                    • My First Julia Package – TriangulArt.jl
                                    • Newsletter February 2024 - Next Gen Battery Simulation with JuliaSim
                                    • The elliptical heart
                                    • 9 for SAS9 – Top Tips for SAS 9 Programmers Moving to SAS Viya
                                    • How to Check if Date is Between Two Dates in R
                                    • Big Book of R at 400 [New milestone!]


                                      • R Packages:

                                      • fastTS: Fast Time Series Modeling with the Sparsity Ranked Lasso
                                      • flowchart: Tidy Flowchart Generator
                                      • mulSEM: Some Multivariate Analyses using Structural Equation Modeling
                                        • 9 min
                                      • Great Sharks! (Season 3: Episode 5)

                                        Get ready for a newborn great white shark sighting, an ancient Martian lakebed, a potential new kingdom of viruses, the twin mysteries of correlation and covariance in R, and a clinical trial grant focused on natural products. Science On.


                                        References:

                                        • Novel aerial observations of a possible newborn white shark (Carcharodon carcharias) in Southern California
                                        • Ground penetrating radar observations of the contact between the western delta and the crater floor of Jezero crater, Mars
                                        • Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan
                                        • The name of the variable that contains the largest value in each row
                                        • How to split a large file into smaller chunks using SAS
                                        • Shadow and Substance: Unveiling the Twin Mysteries of Correlation and Covariance
                                        • NCCIH: Natural Product Early Phase Clinical Trial Phased Innovation Award


                                          • R Packages:

                                          • NoviceDeveloperResources2: Further Resources to Assist Novice Developers
                                          • fastglmpca: Fast Algorithms for Generalized Principal Component Analysis
                                          • modelfactory: Combine Statistical Models into a Tibble for Comparison
                                          • unigd: Universal Graphics Device
                                            • 5 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…