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Science Research Weekly
By Mark R WilliamsonScience
Science Research Weekly episodes
- Episode 34: Ribozyme Samurai
Get ready for distractingly dense planets, SAMURI ribozymes, serious clinical sepsis incidence, jittering in R, the Bioconductor 3.18 release schedule, and the NIH HEAL Initiative. Science On.
References:
- A super-massive Neptune-sized planet
- A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells
- The Rhabdodontidae (Dinosauria, Ornithischia), an enigmatic dinosaur group endemic to the Late Cretaceous European Archipelago
- Estimating Sepsis Incidence Using Administrative Data and Clinical Medical Record Review
- Model data from published summary statistics
- Grants For R Language Infrastructure Projects Available Now!
- When to use Jitter
- Insights on R Package Quality and Validation for Clinical Trials
- Bioconductor 3.18 Release Schedule
- NOSI: Quantum Sensing in Biomedical Applications
- NOSI: Research Supplements to Promote Re-Entry, Re-integration into, and Re-training in Health-Related Research Careers
- NIH: HEAL Initiative
- NSF: Postdoctoral Research Fellowships in Biology
R Packages:
- karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels
- phantSEM: Create Phantom Variables in Structural Equation Models for Sensitivity Analyses
- juicedown: 'juice' + 'markdown': Convert 'R Markdown' into 'HTML' with Inline Styles
- procs: Recreates Some 'SAS®' Procedures in 'R'
- webmap: Create Interactive Web Maps Using 'The National Map' Services
7 min - Episode 33: Microbe-Skewering Micro-Spikes
Get ready for allergic disease and the infant gut microbiome, three-eyed arthropods, titanium micro-spikes for killing pathogenic fungus, array thinking in R, and a grant to culture difficult eukaryotic pathogens. Science On.
References:
- Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease
- The early Cambrian Kylinxia zhangi and evolution of the arthropod head
- Apoptosis of Multi-Drug Resistant Candida Species on Microstructured Titanium Surfaces
- Exploring Relationships with Correlation Heatmaps in R
- Plotting Multiple Lines on a Graph in R: A Step-by-Step Guide
- 6 New books added to Big Book of R
- NIH: Research Tools for Difficult to Culture Eukaryotic Pathogens
- NIH: Early-stage Biomedical Data Repositories and Knowledgebases
- Gateway for Cancer Research: Integrative Program
R Packages:
- condensr: Academic Group Website Generator
- ruminate: A Pharmacometrics Data Transformation and Analysis Tool
- phylosem: Phylogenetic Structural Equation Model
6 min - Episode 32: The Kirigami Engineers
Get ready for naked-mole rat longevity transfer into mice, kirigami for engineering, a new antibiotic from microbial dark matter, eDNA for vertebrate biomonitoring, Julia cracking the top 20 programming languages, template files with R, and a Predoctoral to Postdoctoral Fellow Transition Award. Science On.
References:
- Increased hyaluronan by naked mole-rat Has2 improves healthspan in mice
- MIT engineers use kirigami to make ultrastrong, lightweight structures
- An antibiotic from an uncultured bacterium binds to an immutable target
- Vertebrate environmental DNA from leaf swabs
- JuliaHub Newsletter August 2023
- Bootstrap predicted means by using PROC GLMSELECT
- Creating template files with R
- Best Practices for Data Cleaning and Preprocessing
- NIH: Predoctoral to Postdoctoral Fellow Transition Award
- NIH: Research Projects to Enhance Applicability of Mammalian Models for Translational Research
- NSF: Ecology and Evolution of Infectious Diseases
R Packages:
- artpack: Creates Generative Art Data
- syllogi: Collection of Data Sets for Teaching Purposes
- rmass2: Repeated Measures with Attrition: Sample Sizes and Power Levels for 2 Groups
- scriptloc: Get the Location of the R Script that is Being Sourced/Executed
8 min - Episode 31: Are You Not Entertained?
Get ready the Dinosaur Coliseum, cancer-detecting bioengineer bacteria, embedding Unicode into SAS, a web-crawling Katana, and a Million Dollar Bike ride for rare disease research. Science On.
References:
- Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways
- Vertebrate ichnology and palaeoenvironmental associations of Alaska’s largest known dinosaur tracksite in the Cretaceous Cantwell Formation (Maastrichtian) of Denali National Park and Preserve
- Engineered bacteria detect tumor DNA
- Sustained wet–dry cycling on early Mars
- Add Unicode symbols and format text labels in SAS
- Plot confidence intervals for a regression model in SAS
- Bootstrap confidence intervals for the predicted mean in a regression model
- Mastering Data Visualization: A Guide to Harnessing the Power of R’s par() Function
- GitHub: katana
- NIH/NIA: R43/R44 REDI Award
- NIH/NIA: R41/R42 REDI Award
- NSF: Physics Investigator-Initiated Research Projects
- NSF: Smart Health and Biomedical Research in the Era of Artificial Intelligence and Advanced Data Science
- Air Force: Science and Technology Fellowship
- Marfan Foundation: Innovators Grants
- Million Dollar Bike Ride Pilot Grant Program
- AAI Intersect Fellowship Program
- AHA: AIREA
- McKnight: Scholar Award
R-packages:
- graposas: Graphical Approach Optimal Sample Size
- osmclass: Classify Open Street Map Features
- bulkreadr: The Ultimate Tool for Reading Data in Bulk
- handcodeR: Text Annotation App
- unicol: The Colors of your University
8 min - Episode 30: A Bit of a (DNA) Stretch
Get ready for bacterial circadian clocks, a new form of bacterial transduction, the effect of DNA stretches and twists on mutation rates, web development training materials, and a music-based intervention grant. Science On.
References:
- The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
- Dual pathogenicity island transfer by piggybacking lateral transduction
- Structural underpinnings of mutation rate variations in the human genome
- Enhance Your Plots with the text() Function in R
- GitHub: Web-Dev-For-Beginners
- NIH: Music-based Interventions Toolkit for Brain Disorders of Aging
- NSF: Artic Research Opportunities
- AHA: Institutional Research Enhancement Award
R Packages:
- none
6 min - Episode 29: Greengenes 2, This Time, It’s Personal
Get ready for ancient, icy nematodes, renewable plastics, Greengenes volume 2, linear model transformations in R, and Gut-Brain Communication in Parkinson’s grants. Science On.
References:
- A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva
- Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort
- Biorenewable and circular polydiketoenamine plastics
- Greengenes2 unifies microbial data in a single reference tree
- SatRdays London 2023 – Recordings
- One Weird Trick to Make Ggplot2 Columns the Same Width
- Linear model and Transformations
- GitHub: ClickHouse
- NIH: Secondary Analysis and Integration of Existing Data to Elucidate Cancer Risk and Related Outcomes (R01)
- NIH: Secondary Analysis and Integration of Existing Data to Elucidate Cancer Risk and Related Outcomes (R21)
- NIH: A Consortium for Gut-Brain Communication in Parkinson’s Disease (U01)
- NIH: A Consortium for Gut-Brain Communication in Parkinson’s Disease (U24)
- McKnight Foundation: Neurobiology of Brain Disorders Award
- ASCO: Young Investigator Award
R Packages:
- none
6 min - Episode 28: Fungal Enlightenment
Get ready for fungal genome mining, new R books, and a cancer nanotechnology grant. Science On.
References:
- Size Dependence of the Bouncing Barrier in Protoplanetary Dust Growth
- Near-Infrared Fluorescent Biosensors Based on Covalent DNA Anchors
- Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters
- what is a randomized complete block design?
- Simplify Your Code with R’s Powerful Functions: with() and within()
- 7 New books added to Big Book of R
- GitHub: Cal.com
- NOSI: Lymphatic System in Health and Disease
- NCI: Innovative Research in Cancer Nanotechnology
R Packages:
- MultiClassROC: ROC Curves for Multi-Class Analysis
- UpDown: Detecting Group Disturbances from Longitudinal Observations
4 min - Episode 27: Dog Bites Dinosaur
Get ready for DNA origami, an Elvis-impersonator pterodactyl, self-healing metal, a dinosaur-chomping mammal, the case of the missing dark matter, a lazier way to use Docker, and a grant for theoretical physics hubs. Science On.
References:
- DNA-origami-directed virus capsid polymorphism
- Petrodactyle wellnhoferi gen. et sp. nov.: A new and large ctenochasmatid pterosaur from the Late Jurassic of Germany
- Autonomous healing of fatigue cracks via cold welding
- An extraordinary fossil captures the struggle for existence during the Mesozoic
- The massive relic galaxy NGC 1277 is dark matter deficient
- Dates and location for useR! 2024
- JuliaHub Newsletter July 2023
- Standardize regression coefficients for models that include categorical variables
- GitHub: lazydocker
- GitHub: how-web-works
- NSF: Focused Research Hubs in Theoretical Physics
R Packages:
- badgen: Fast and Simple Badge Generator
- forestly: Interactive Forest Plot
- quickcode: A Compilation of Some Frequently Used R Functions
7 min - Episode 26: Living Cameras and Old Universes
Get ready for weird whales, bacterial sample collection via lollipop, hints at life on Mars, living digital cameras, a much older universe, free training on 67 programming languages, and a Housing and Urban Development grant for radon detection and mitigation. Science On.
References:
- Convergent evolution of skim feeding in baleen whales
- At-Home Saliva Sampling in Healthy Adults Using CandyCollect, a Lollipop-Inspired Device
- Microeukaryotic predators shape the wastewater microbiome
- The effects of board games on math skills in children attending prekindergarten and kindergarten: A systematic review
- Oncogene-like addiction to aneuploidy in human cancers
- A mid-Cambrian tunicate and the deep origin of the ascidiacean body plan
- Diverse organic-mineral associations in Jezero crater, Mars
- A biological camera that captures and stores images directly into DNA
- JWST early Universe observations and ΛCDM cosmology
- datasetR – R package for creating datasets
- Unveiling a New Era in Molecular Visualization: Introducing shiny.molstar for Large Molecular Structures Visualization in R
- Array Languages: R vs APL
- exercism
- HUD: Radon Testing and Mitigation Demonstration for Public Housing
- DOD: Toxic Exposures
R Packages:
- grpnet: Group Elastic Net Regularized GLM
- bbmix: Bayesian Model for Genotyping using RNA-Seq
- TOmicsVis: Transcriptome Visualization Process Scheme
10 min - Episode 25: Top Transposon, Maverick
Get ready for metallic 3D prints, Cambrian predators that skipped appendage-day at the gym, the mechanisms of chemical gardens, the mysteries of virus-like transposon ‘Mavericks’, coding cheat sheets, and a rare disease grant. Science On.
References:
- Remote detection of a lunar granitic batholith at Compton–Belkovich
- Metallic gels for conductive 3D and 4D printing
- Raptorial appendages of the Cambrian apex predator Anomalocaris canadensis are built for soft prey and speed
- Pattern selection by material aging: Modeling chemical gardens in two and three dimensions
- Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities
- An Easy Way to Customize Your Shiny App Theme
- CheatSheet for coding in R, Python and Julia
- GitHub: Tkinter-Designer
- NIH: Preclinical Proof of Concept Studies for Rare Diseases
- NIH: Cellular and Molecular Biology of Complex Brain Disorders (R01)
- NIH: Cellular and Molecular Biology of Complex Brain Disorders (R21)
- Jonathan F. Reichert Foundation: ALPhA Immersions Support
- AABB Foundation: Early-Career Scientific Research Grants Program
R Packages:
- esem: Exploratory Structural Equation Modeling ESEM
- protHMM: Protein Feature Extraction from Profile Hidden Markov Models
- ZooID: Load, Segment and Classify Zooplankton Images
8 min
About Science Research Weekly
From the publisher's feed
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…
Funding. Science On.