Taylor

Giant sea stars are melting away — and now scientists know why Canadian scientists say they’ve finally identified what is likely causing giant colourful sea stars in the Pacific Northwest to literally waste away: It's bacterium from the same family that causes ch...

After years of work, a team of researchers with support from The Nature Conservancy have identified the causative agent of Sea Star Wasting Disease! Big implications for my work & an inspiring example of the amazing things we can do w/ science...plus I'm quoted in it ;)
www.cbc.ca/player/play/...

Introducing the Data Explorer in Positron!

Quickly view raw data files (CSV, Parquet, etc.) or dataframes from your #Python / #RStats sessions with a data grid, summary panel, and filter bar.

Learn more: positron.posit.co/data-explore... #Positron

Nested Date scales in ggplot2: > scale_x_datetime(date_breaks = "2 month", date_labels = "%b-%Y", > guide = ggsurveillance::guide_axis_nested_date())

Nested Date Scale example. Measles Cases per Month as an epicurve.

📦 My R package {ggsurveillance} now supports nested date scales. All thanks to the fantastic {legendry} package by @teunbrand.bsky.social

🔗 ggsurveillance.biostats.dev/
🔗 teunbrand.github.io/legendry/

ggplot rules supreme

#rstats #ggplot #DataViz

The Case for Sustaining Wastewater Surveillance Capabilities in the U.S. The National Wastewater Surveillance System (NWSS) was launched in 2020 to connect independent, local wastewater efforts to form a robust, sustainable national system. But the funding will run out in ...

In addition to the obvious public health benefits:

“recent research estimates that a system such as the NWSS could generate net benefits of nearly $1,500 per person in the first year of a new pandemic”

www.rand.org/pubs/comment...

Yet again, wastewater monitoring plays a critical role in outbreak surveillance

The title of the paper: "A minimum data standard for wildlife disease research and surveillance" - and an example data table

NEW! 🎉 We need wildlife disease surveillance to predict epidemics, but data sharing is rare - we found that only 2-3% of studies share raw data. So, we spent three years developing a data standard and R package to help get wildlife disease data into FAIR repositories. www.nature.com/articles/s41...

YSPH VMOC Special Report - Measles Outbreak Southwest US 5-25-2025.pptx YSPH VMOC Special Report - Measles Outbreak Southwest US 5-25-2025.pptx - Download as a PDF or view online for free

Measles update as of May 25:

📍 Mexico: Three children have died this month.

📍 Canada: Ontario now reports more cases than the entire U.S. Alberta’s case count continues to climb rapidly.

📍 North Dakota: Grand Forks County has confirmed its first cases (2), linked to international travel.

Most applications in R run pretty quickly. But these days, many R users are faced with huge datasets and/or long-running applications, making parallel computation attractive. 🧵 1/

Inhaled bacteriophage therapy shows promise in cystic fibrosis patients

In a small study, CF patients treated with the therapy saw a reduction in multidrug-resistant lung bacteria and improved lung function.

www.cidrap.umn.edu/a...

What's new in R 4.5.0? Here we summarise some of the more interesting changes that have been introduced in R 4.5.0.

New version of R is out!

Our Data Scientist, Russ Hyde, has put together a quick review of the key features and changes in R 4.5 — from new language features to graphics updates and more.

📝 Read the full blog post here: www.jumpingrivers.com/blog/whats-n...

#rstats #Rprogramming #opensource

U.S. measles cases as of March 30, 2025 Map shows how many cases are in each state. 1-2 cases: AK, WA, MN, MI, KY, N, FL, VT, RI. 3-9 cases: CA, OK, PA, NY, NJ, MD, GA. 10-49 cases: NM, KS, OH. 50 or more cases: TX This count includes both confirmed and suspected cases. SOURCES: CORI, state and local health departments, news outlets, YALE ESF-8 Virtual Medical Operation Center

As of March 30, there are approximately 529 measles cases across 20 states. Experts project that the Southwest outbreak, which has spread from West Texas to New Mexico, Oklahoma, and Kansas, could last up to a year as cases continue to rise.

Read this full thread for what to know. ⬇️ 1/11 🧵

CDC A(H5N1) Bird Flu Response Update February 26, 2025 CDC provides an update on recent developments in the multistate outbreak of avian influenza A(H5N1)

Great to see the CDC providing an update on the #birdflu outbreak.
Key points
1/ The CDC has sequenced the H5N1 viruses from recent human cases in Wyoming and Nevada. The data are now publicly available on GISAID:
Wyoming: EPI_ISL_19749443
Nevada: EPI_ISL_19726293
www.cdc.gov/bird-flu/spo...

Texas Measles Outbreak Nears 100 Cases, Raising Concerns About Undetected Spread - KFF Health News Health officials expect a measles outbreak in West Texas to exceed 100 cases because of low vaccination rates and undetected infections. Vaccine misinformation and new laws may make such situations mo...

🚨Texas measles outbreak nears 100 cases, w/16 hospitalizations. Officials suspect it's spilled just across the border to New Mexico.

Low vax rates+undetected infections mean it will grow.

“This is going to get a lot worse before it gets better”

My latest kffhealthnews.org/news/article...

COPENHAGEN, Denmark, February 14, 2025 – Bavarian Nordic A/S (OMX: BAVA) announced today that the U.S. Food and Drug Administration (FDA) has approved VIMKUNYA™ (Chikungunya Vaccine, Recombinant) for injection, the first virus-like particle (VLP) single-dose chikungunya vaccine in the U.S. for persons 12 years of age and older. The FDA approved VIMKUNYA under Priority Review, based on results from two phase 3 clinical trials which enrolled more than 3,500 healthy individuals 12 years of age and older. The studies met their primary endpoints, with results showing that 21 days after vaccination, the vaccine induced neutralizing antibodies in up to 97.8% of the vaccinated individuals and demonstrated a rapid immune response starting to develop within one week. The vaccine was well-tolerated and vaccine-related adverse events were mainly mild or moderate in nature1. VIMKUNYA is a VLP vaccine, which means that it uses virus-like particles designed to mimic the chikungunya virus without the ability to infect cells, replicate or cause disease.

Some great news: the FDA just approved a new chikungunya vaccine for people aged 12 and older.

Home - ProMED - ProMED-mail ProMED is the largest publicly-available surveillance system conducting global reporting of infectious diseases outbreaks. Subscribe today.

If you aren't already subscribed to ProMED I highly recommend doing so to help stay up to date regarding infectious diseases in ppl, animals, and plants promedmail.org

ShinyConf 2025 Registration and Call for Proposals are open! - Posit Join us for ShinyConf 2025, the biggest virtual Shiny event of the year hosted by our partner Appsilon!

ShinyConf 2025! Develop Shiny apps? Submit a proposal by Feb 2nd! Free virtual conf (April 9-11) with workshops, talks & app showcases. Learn more & register: posit.co/blog/shinyco...

#rstats #pydata #RShiny #ShinyforPython

Majestic elk

#CWD prions confirmed in raw, cooked elk meat, water used for boiling, but risk to people unclear

Grilling boosted detection of prions, which the authors say may be because heat helps release prions trapped in tissue.

cidrap.umn.edu/chronic-wast...

Photo: Oregon DOA / Flickr cc

tidymodels Internship for 2025 - Tidyverse The tidymodels team is sponsoring a summer internship in 2025.

The tidymodels team is hiring an intern! Please share with #rstats folks looking for summer opportunities with an interest in data preprocessing for ML.

www.tidyverse.org/blog/2025/01...

An excellent report from the folks at @cidrap-cwd.bsky.social

#OneHealth

CDC says H5N1 bird flu sample shows mutations that may help the virus bind to cells in the upper airways of people The CDC said Thursday that the mutations, detected in a sample taken from a Louisiana patient, may help bind the virus to the upper airways in people.

The #H5N1 #birdflu virus from a severe case in Louisiana shows it was developing mutations that could help it attach to cells in human respiratory tracts, including a mutation seen in a recent severe case in British Columbia, Canada, the #CDC reported today. www.statnews.com/2024/12/26/c...

Chalk up another state with a human case of H5N1: Louisiana. Per the DOH, they “had exposure to sick and dead birds that are suspected to have been infected with H5N1.”

Louisiana hasn’t had any H5N1 detections reported to USDA for cattle or bird flocks, so either wild or unreported domestic here. 🧪

Let me know if you want to be added to the Genomics Technology starter pack go.bsky.app/3oiGMBe

USDA launching mandatory national milk testing program to track H5N1 flu outbreak in cows The USDA is starting a mandatory milk testing program to see how widespread the bird flu virus is on dairy farms

The U.S. Department of Agriculture announced that it is instituting a mandatory milk testing program that should provide a much clearer picture of how widespread the virus is in the country’s dairy industry.

Toward AI-Resilient Screening of Nucleic Acid Synthesis Orders: Process, Results, and Recommendations Fast-moving advances in AI-assisted protein engineering are enabling breakthroughs in the life sciences that promise numerous beneficial applications. At the same time, these new capabilities are crea...

Identifying & mitigating an AI-enabled biosecurity vulnerability. Confidential effort on biosecurity red-teaming leads to distrib. of "patches" that bolster DNA synthesis screening. Article: aka.ms/AAtoa8e Work continues.
@msftresearch.bsky.social

Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections - Nature Medicine Next-generation metagenomic testing increases the accuracy and sensitivity of the etiology of central nervous system infections in hospitalized patients.

Key paper alert

'Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections'

www.nature.com/articles/s41...

'These data justify routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection'

Why a teenager’s bird-flu infection is ringing alarm bells for scientists A strain of avian influenza is showing signs of adaptation to human hosts, but there is no evidence that it can transmit from person to person.

'It’s not the time to panic,” he says. “But this should serve as a warning: this virus has the capacity to switch very quickly into a form that can cause severe disease.”'
www.nature.com/articles/d41...