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Science Research Weekly
By Mark R WilliamsonScience
Science Research Weekly episodes
- Episode 14: Of Space Rats and Shiny Apps
Get ready for space rodents microbiomes; 100-year biobatteries; huge, hot exoplanets; reasons why your Shiny App failed; and ways to use statistics to get funding.
References:
- Specific host metabolite and gut microbiome alterations are associated with bone loss during spaceflight
- Moisture-Enabled Germination of Heat-Activated Bacillus Endospores for Rapid and Practical Bioelectricity Generation: Toward Portable, Storable Bacteria-Powered Biobatteries
- Direct imaging and astrometric detection of a gas giant planet orbiting an accelerating star
- Application of Equal Local Levels to Improve Q-Q Plot Testing Bands with R Package qqconf
- The joy of sets
- what is the mann-whitney u test?
- Shiny User Adoption Fails: 9 Reasons Why Nobody Uses Your App
- DHHS: Data Integration and Statistical Analysis Methods
- NOSI: RNA Modifications in Cancer Biology
- NOSI: Synthetic Biology for Biomedical Applications
- MS: Biostatistics/Informatics Junior Faculty Award
R-packages:
- GLMMselect: Bayesian Model Selection for Generalized Linear Mixed Models
- kdry: K's "Don't Repeat Yourself"-Collection
- asmbPLS: Predicting and Classifying Patient Phenotypes with Multi-Omics Data
6 min - Episode 13: Crazy Ants, Crazier Viruses
Get ready for chimeric crazy ants, viruses abounding in protists and infants alike, solar system generation in R, an awesome Python list, and a couple of nifty niche funding opportunities. Science On.
References:
- Obligate chimerism in male yellow crazy ants
- Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses
- Expanding known viral diversity in the healthy infant gut
- Make “Solar System” Plots With {ggsolar}
- Awesome Python
- Microsoft PowerToys
- NOSI: Assembling the Addiction Organelle Interactome
- NIAID: Mechanisms of Neurotropic Virus-mediated Disease
R-packages:
- fakir: Generate Fake Datasets for Prototyping and Teaching
- betaNB: Bootstrap for Regression Effect Sizes
- npclust: Nonparametric Tests for Incomplete Clustered Data
- SQI: Soil Quality Index
6 min - Episode 12: Snowstorms and Dolphins
Get ready for toxic birds, correlation for days, a flipper-tastic multi-tool, blazing fast Shiny development, and Department of Defense cancer grants as far as the eye can see. Science On.
References:
- Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge
- A Morphological and Spatial Analysis of Volcanoes on Venus
- Multiple mutations in the Nav1.4 sodium channel of New Guinean toxic birds provide autoresistance to deadly batrachotoxin
- A social niche breadth score reveals niche range strategies of generalists and specialists
- intRinsic: An R Package for Model-Based Estimation of the Intrinsic Dimension of a Dataset
- Python 3.11.3, 3.10.11 and 3.12 alpha 7 are now available
- Why Use Rank Correlation?
- Weak or strong? How to interpret a Spearman or Kendall correlation
- awesome-flipperzero
- ChatGPT: Made this Shiny App in 10 Minutes
- 6 new books added to Big Book of R
- DoD: Peer Reviewed Cancer, Idea Award
R-packages:
- lessSEM: Non-Smooth Regularization for Structural Equation Models
- AICcPermanova: Model Selection of PERMANOVA Models Using AICc
- rtlr: Print Right-to-Left Languages Correctly
- softbib: Software Bibliographies for R Projects
- Mmcsd: Modeling Complex Longitudinal Data in a Quick and Easy Way
- rrandvec: Generate Random Vectors Whose Components Sum Up to One
7 min - Episode 11: Cue the Sci-Fi Dystopia Film Score
Get ready for atomic nuclei views, artificial organelles, AI article generation, PyCon, Simpson's paradox, building your favorite technologies from scratch, and funding to maintain ENCODE. Science On.
References:
- Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei
- Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts
- Tomography of ultrarelativistic nuclei with polarized photon-gluon collisions
- Core cellular and tissue-specific mechanisms enable desiccation tolerance in Craterostigma
- Chatting and cheating: Ensuring academic integrity in the era of ChatGPT
- Journal of Statistical Software Volume 106
- Quick PyCon US Update
- JuliaHub & Julia Ranked #12 in the Debut of Redpoint’s Open-source Top 25
- Simpson's paradox and confounding variables
- 15+ Awesome Javascript Projects For Beginners In 2023
- February 2023: “Top 40” New CRAN Packages
- REDCapDM: a package to access and manage REDCap data
- Top five(ish) sources of ecological data
- Build your own X
- DOD: Young Investigator Program
- NHGRI: Maintenance and Integration of the ENCODE Data Resource
- NIDCR: Research Grants for Analyses of Existing Genomics Data
- NIDCR: Small Research Grants for Analyses of Existing Genomics Data
R Packages:
- lenght: Allow Misspellings of Length Function
- c2z: A Reference Manager
- ecan: Ecological Analysis and Visualization
- Vicus: Exploiting Local Structures to Improve Network-Based Analysis of Biological Data
12 min - Episode 10: Sticks and Cones May Break My Bones
Get ready for super microscopes, tardigrade blood stabilization, broken stick modeling, an R version codenamed ‘Already Tomorrow’, a ‘pinecone’ made of Python, and a pitch-style competition for infectious disease funding. Science On.
References:
- Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second
- Natural and engineered mediators of desiccation tolerance stabilize Human Blood Clotting Factor VIII in a dry state
- Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota
- Electrochemical degradation of PFOA and its common alternatives: Assessment of key parameters, roles of active species, and transformation pathway
- Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites
- Journal of Statistical Software Volume 106
- R 4.3.0 scheduled for April 21
- dummy coding in spss glm–more on fixed factors, covariates, and reference groups
- Partial correlation: controlling for confounding variables
- Pynecone
- A suite of tools to scrape and parse search engine results
- NIH: Molecular Transducers of Physical Activity Bioinformatics Center
- NIH: Instrumentation Grant Program for Resource-Limited Institutions
- NSF: Synthesis Center for Understanding Organismal Resilience
- ACS: Postdoctoral Fellowships
- HFSP: Cross-Disciplinary Fellowships
- IDSA: IDea Incubator
R Packages:
- crayons: Color Palettes from Crayon Boxes
- baseq: Basic Sequence Processing Tool for Biological Data
- reappraised: Statistical Tools for Assessing Publication Integrity of Groups of Trials
- ridgregextra: Ridge Regression Parameter Estimation
11 min - Episode 9: Robot Parade!
Get ready for self-healing soft robots, modular NASA robots, Shiny recaps, Statistical Rethinking training, statistical kindergarten, and the NIH Pioneer Award Program. Science On.
References:
- Optical tweezers throw and catch single atoms
- The connectome of an insect brain
- A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes
- A self-healing electrically conductive organogel composite
- Engineering breakthrough in softbotics
- Mix-and-match kit could enable astronauts to build a menagerie of lunar exploration bots
- The Young Supernova Experiment Data Release 1 (YSE DR1)
- Observation of a critical charge mode in a strange metal
- 6 predictions for AI and data in health care and life sciences
- Use the metalog distribution in SAS
- R 4.2.3 is released
- ShinyConf 2022 – Short Recap
- Statistical Rethinking (2023 Edition)
- Introduction to data analysis with {Statgarten}.
- WebR IS HERE!
- NIH: Director’s Pioneer Award Program
- NIH: Entry-Level Modules for Training the Genomics Research Workforce
- NIH: Enhancement of external environmental exposure assessment for cancer epidemiology research
- Falk Medical Research Trust: Catalyst Awards Program
- CRI: Immuno-Informatics Postdoctoral Fellowship
- ACS: Early Career Postdoctoral-Faculty Bridge Grant
Other Articles:
- LEXpander: Applying colexification networks to automated lexicon expansion
- Surface changes observed on a Venusian volcano during the Magellan mission
- Why is Pumas-QSP So Fast? Some Insights Into Differentiable Simulation Performance
R-packages:
- pharmaverse: Navigate 'Pharmaverse'
- toweranNA: A Method for Handling Missing Values in Prediction Applications
- waspasR: Tool Kit to Implement a W.A.S.P.A.S. Based Multi-Criteria Decision Analysis Solution
10 min - Episode 8: Flash Grants in the Pan
Get ready for technological tribology, tingible translational cell biology, flipping fossils, Volume 14/4 of the R Journal, ebook tips and tricks, and flash grants to fixate on. Science On.
References:
- Novel friction stabilization technology for surface damage conditions using machine learning
- Crevasse refreezing and signatures of retreat observed at Kamb Ice Stream grounding zone
- Apoptotic cell fragments locally activate tingible body macrophages in the germinal center
- Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart
- An abundant sea anemone from the Carboniferous Mazon Creek Lagerstӓtte, USA
- Paleontologists flip the script on anemone fossils
- Python 3.12.0 alpha 6 released
- The R Journal Volume 14/4
- 7 New books added to Big Book of R
- What I’ve learned making an .epub Ebook with Quarto
- DOD: DEPSoR - Research Collaboration
- DOD: Ovarian Cancer CTR Award
- DOD: Ovarian Cancer Clinical Trial Award
- NHBLI: Research Project Grants in Valvular Heart Disease
- NHBLI: Integrative Omics Analysis of NHLBI TOPMed Data
- HHS: Small R01s for Clinical Trials Targeting Diseases for NIDDK
- Biogen: Sponsorships
- AHR: Strategically Focused Research Networks
- CRI: Technology Impact Award
- IAFNS: Live Dietary Microbe Intake and Health Outcomes
- NC Life Sciences: Flash Grants
R-packages:
- BayesFluxR: Implementation of Bayesian Neural Networks
- lorem: Generate Lorem Ipsum Text
- HDRFA: High-Dimensional Robust Factor Analysis
- guildai: Track Machine Learning Experiments
- aihuman: Experimental Evaluation of Algorithm-Assisted Human Decision-Making
11 min - Episode 7: Life, the R-Universe, and Everything
Get ready for an exploration of the R-Universe, simulated octopus tentacles, effects of Vitamin D and exercise on health, fossil wings and fins, statistical conferences to set your calendar by, and a very special 23rd birthday. Science On.
References:
- Energy-shaping control of a muscular octopus arm moving in three dimensions
- Injury primes mutation-bearing astrocytes for dedifferentiation in later life
- Origin of the propatagium in non-avian dinosaurs
- Effectiveness of physical activity interventions for improving depression, anxiety and distress: an overview of systematic reviews
- MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data
- 3D printing of living structural biocomposites
- Network expansion of genetic associations defines a pleiotropy map of human cell biology
- A shape-shifting nuclease unravels structured RNA
- Systematics and Phylogenetic Interrelationships of the Enigmatic Late Jurassic Shark Protospinax annectans Woodward
- Vitamin D supplementation and incident dementia: Effects of sex, APOE, and baseline cognitive status
- JuliaHub Newsletter February 2023
- Bioconductor Conference 2023
- PhyloPic
- R 4.2.3
- R-universe
- January 2023: “Top 40” New CRAN Packages
- Happy 23rd Birthday R!
- NIH: Translational Research in Maternal and Pediatric Pharmacology and Therapeutics (R01)
- NIH: Translational Research in Maternal and Pediatric Pharmacology and Therapeutics (R21)
- NIH: Genomic Community Resources (U24)
- CDC: Clinical and Applied Research Strategies for the Prevention and Control of Fungal Diseases
- USDA: USDA-ARS Postdoctoral Fellowship in Spatial Statistics for Continental-Scale Soil Health Modeling
- TSC Alliance: 2023 Grant Cycle
- CHEST: COPD Research Grant
- CHEST: Young Investigator Research Grant
R-packages:
- aihuman: Experimental Evaluation of Algorithm-Assisted Human Decision-Making
- reactCheckbox: Checkbox Group Input for 'Shiny'
- treediff: Testing Differences Between Families of Trees
- rutledge: Real-Time PCR Data Sets by Rutledge et al. (2004)
12 min - Episode 6: Boss-Level Antibiotics
Get ready for better arsenic detection, broad-spectrum antibiotics, model-breaking massive galaxies, Julia and Python working in harmony, a hard-to-pronounce R-package on Gaussian mixture models, and Department of Defense lung cancer grants aplenty. Science On.
References:
- Scalable selective absorber with quasiperiodic nanostructure for low-grade solar energy harvesting
- Toward surface-enhanced Raman scattering using electroless substrate for trace arsenic detection and speciation
- Site-specific encoding of photoactivity and photoreactivity into antibody fragments
- Complete Genome Sequence of the Lysogenic Pseudomonas Bacteriophage Fyn8
- A broad-spectrum synthetic antibiotic that does not evoke bacterial resistance
- Discovery of massive early galaxies defies prior understanding of the universe
- Julia and Python better together
- DOD: Multidisciplinary Research Program of the University Research Initiative (MURI)
- DOD: Lung Cancer, Concept Award
- DOD: Lung Cancer, Translational Research Award
- DOD: Lung Cancer, Idea Development Award
- DOD: Lung Cancer, Career Development Award
- NASA: Early Career Faculty
- FDA: Natural History and Biomarker Studies of Rare Neurodegenerative Diseases
- LCRF: Leading Edge Research Grant Program
- UMDF: Research Grant Program
R-packages:
- dataMojo: Reshape Data Table
- ggmapinset: Add Inset Panels to Maps
- bubbleHeatmap: Produces 'bubbleHeatmap' Plots for Visualising Metabolomics Data
- gmmsslm: Semi-Supervised Gaussian Mixture Model with a Missing-Data Mechanism
- rWCVP: Generating Summaries, Reports and Plots from the World Checklist of Vascular Plants
6 min - Episode 5: A Bouquet of Space ROSEs
Get ready for exoplanetary systems, missing Neptunes, a Dungeons & Dragons R package, GIFs for top R packages, Tidvyverse functions to save your day, and a whole host of NASA grant announcements. Science On.
References
- Framework for the architecture of exoplanetary systems
- RNA's 'joints' play key role in our gene expression
- Help! Our Neptune-sized exoplanets are missing
- The ins and outs of an undergrad-run journal
- the difference between the bernoulli and binomial distributions
- Top 9+ Interesting R Project Ideas To Try In 2023
- 10 Tidyverse functions that might save your day
- Putting the top 100 R packages into a GIF
- NSF: Plant Genome Research Program
- NSF: Computer and Information Science and Enginering Core Programs
- NIH: HEAL Initative
- NIH: Aging Research
- NIH: IDeA Networks of Biomedical Research Excellence (INBRE)
- DOD: Ovarian Cancer Early-Career Investigator Award
- DOD: Ovarian Cancer Investigator-Initiated Research Award
- DOD: Ovarian Cancer Pilot Award
- NASA: Research Opportunities in Space and Earth Science (ROSES) 2023
R-packages
- HanStat: Package for Easy Interpretation of Statistical Methods
- hidecan: Create HIDECAN Plots for Visualising Genome-Wide Association Studies and Differential Expression Results
- dndR: Dungeons Dragons Functions for Players and Dungeon Masters
7 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.