Author | Lightnews

Brendan J. Kelly @bjklab.bsky.social · 3d

Pseudomonas aeruginosa has big slug energy. #IDsky #MicroSky

ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 4d

Cool 🦠

William Schmidt
Gerard Wong Lab @UCLA
Nature Microbiology

Pseudomonas aeruginosa lays down Psl exopolysaccharide as it crawls

Other cells detect and follow these trails using type IV pili pulling against adhesins like CdrA triggering c-di-GMP & cAMP surges to shift into early biofilm mode

Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation - Nature Microbiology

Opposing forces generated by exopolysaccharide trail binding versus type IV pilus retraction generate a high cyclic diGMP–high cyclic AMP state in Pseudomonas aeruginosa that promotes social motility.

www.nature.com

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Reposted by Brendan J. Kelly

UW Infectious Disease Fellowship Program @uwidfellowship.bsky.social · 8d

A study of COVID therapeutics in immunocompromised individuals on B-cell depleting therapy!!!

Nirmatrelvir/ritonavir significantly more effective than no rx (HR 0.56) molnupiravir w non significant trend to improved outcomes (HR also 0.56)… #IDSky #covid

academic.oup.com/cid/advance-...

Effectiveness of Nirmatrelvir/Ritonavir or Molnupiravir Use in Immunocompromised Patients on B-Cell–Depleting Therapy With COVID-19: A Target Trial Emulation Study

This target trial emulation study assessed nirmatrelvir/ritonavir and molnupiravir effectiveness in COVID-19 patients receiving B-cell–depleting therapy. N

academic.oup.com

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Reposted by Brendan J. Kelly

Kai Kupferschmidt @kakape.bsky.social · 15d

I am fascinated by how viruses evolve - and not just since #SARSCoV2 has shown us at the global stage how consequential virus evolution can be for us.
In my new story in @science.org I got to explore how researchers are probing deeper into the past with old RNA virus genome.
So a 🧪 thread…

On an Arctic archipelago, frozen soil may preserve a hidden history of viruses

Scientists are hunting for ancient RNA in Svalbard’s permafrost, hoping to shed light on the evolution of viral diseases

www.science.org

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Reposted by Brendan J. Kelly

Max Planck Institute for Demographic Research (MPIDR) @mpidr.bsky.social · 18d

💻Join online! 🎧
Süßmilch Lecture at the Max Planck Institute for Demographic Research (MPIDR)
Putting Science Before #Statistics
🗣️Richard McElreath 🐈‍⬛ MPI-EVA Leipzig
📅Oct 21, 2025
🕒3 pm CEST
✏️Sign up now:
https://ow.ly/uxfc50Xb5Yx

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Reposted by Brendan J. Kelly

Rachel M. Wheatley @rachelmwheatley.bsky.social · 23d

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

The Lancet Microbe @lancetmicrobe.bsky.social · 24d

New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA

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Brendan J. Kelly @bjklab.bsky.social · 22d

What could possibly go wrong? #IDSky

Kathleen Bachynski @bachynski.bsky.social · 22d

“Roughly 70 Epidemic Intelligence Service officers — the so-called “disease detectives” who respond to outbreaks around the globe — received layoff notices, according to a person familiar with them. The service was spared during an earlier round of layoffs in February.”

Trump Administration Lays Off Dozens of C.D.C. Officials

www.nytimes.com

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Reposted by Brendan J. Kelly

Aki Vehtari @avehtari.bsky.social · 27d

I'm looking for a doctoral student with Bayesian background to work on Bayesian workflow and cross-validation (see my publication list users.aalto.fi/~ave/publica... for my recent work) at Aalto University.

Apply through the ELLIS PhD program (dl October 31) ellis.eu/news/ellis-p...

ELLIS PhD Program: Call for Applications 2025

The ELLIS mission is to create a diverse European network that promotes research excellence and advances breakthroughs in AI, as well as a pan-European PhD program to educate the next generation of AI...

ellis.eu

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Brendan J. Kelly @bjklab.bsky.social · Oct 1

Fantastic discussion of the BALANCE trial -- and randomized trial preparation / design in general. Also, great to hear Communicable and Breakpoints teaming up! #IDSky

CMI Communications @cmicomms.bsky.social · Sep 16

The 2nd #Communicable & #Breakpoints collaboration drops on 19 Sept! Hosts @angelahuttner.bsky.social & @erinmccreary.bsky.social invite BALANCE trial leads Nick Daneman & Robert Fowler to discuss everything from the trial's humble start to its meteoric impact in clinical practice.
#IDSky #clinmicro

Screenshot of Communicable & Breakpoints hosts Erin McCreary & Angela Huttner with guests Rob Fowler and Nick Daneman.

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Brendan J. Kelly @bjklab.bsky.social · Sep 27

"It turns out boredom is the Cadillac of feelings."

Tim Onion @bencollins.bsky.social · Sep 27

This final post from Kaleb Horton is very beautiful and hits hard. This is just so sad. RIP.

2025, So Far

I wish I had a time machine so I could go back in time and talk to my dad in 1988, just before I was born, and tell him what it’s like to live in the future. I’d tell him all the amazing things that a...

kalebhorton.ghost.io

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Reposted by Brendan J. Kelly

Jan Broder Engler @jbengler.de · Sep 18

The new ggplot2 4.0.0 now supports absolute plot dimensions 🤩

#rstats #dataviz #phd

library(tidyverse)

mtcars |>
head(8) |>
rownames_to_column("name") |>
ggplot(aes(x = drat, y = name, fill = name)) +
geom_col() +
theme(panel.widths = unit(50, "mm"), panel.heights = unit(50, "mm"))

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Brendan J. Kelly @bjklab.bsky.social · Sep 18

#IDsky

Sopranos meme with sarcastic congratulations

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Reposted by Brendan J. Kelly

FEMS @femsmicro.org · Sep 17

Happy International Microorganism Day! 🎉

Today, we are celebrating the tiny powerhouses that have a massive impact on our world. From the bacteria in our gut to the fungi that give us antibiotics, these incredible organisms are essential to life.

Let's make some noise for the microscopic!

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Reposted by Brendan J. Kelly

César Sánchez @twistedbacteria.bsky.social · Sep 14

Typhus, a disease once nearly eradicated in the U.S., is on the rise in Texas

"76-year-old Clark contracted #typhus from clearing weeds from her garden"
🦠

flip.it/Zzrht7

Typhus, a disease once nearly eradicated in the U.S., is on the rise in Texas

Texas is seeing an explosion of cases of typhus, a disease that – if untreated – can be fatal. Typhus was almost eradicated from the United States, but now it's making a comeback.

flip.it

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Reposted by Brendan J. Kelly

Nature Microbiology @natmicrobiol.nature.com · Sep 12

#Newresearch

This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.

#MicroSky

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

Learning ecosystem-scale dynamics from microbiome data with MDSINE2 - Nature Microbiology

This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.

www.nature.com

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Brendan J. Kelly @bjklab.bsky.social · Sep 12

Remembering David Rose today. www.bbc.com/news/article...

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Reposted by Brendan J. Kelly

Eurosurveillance journal @eurosurveillance.org · Sep 11

This week's rapid communications describe

➡️A strain of Neisseria gonorrhoeae producing false negative results on Xpert CT/NG assay in England

🔎An atypical sixfold rise in #influenza A(H1N1)pdm09 cases in Denmark during summer

Full issue here 👉 bit.ly/eus2036

#EpiSky #IDSky #MedSky #STISky 🛟🦠🧫⚕️

Image showing the table of content of issue 36 in 2025:

Rapid communication
Detection and characterisation of Xpert CT/NG assay Neisseria gonorrhoeae diagnostic escape mutants, England, June 2025

An interseasonal outbreak of influenza A(H1N1)pdm09 related to a music festival, Denmark, August 2025

Research
Progress towards HIV transmission elimination targets: model-based estimation of incidence and the extent of undiagnosed infection, Scotland, 1981 to 2022

Repeated cross-sectional surveys show a decreasing trend in Borrelia burgdorferi sensu lato seroprevalence over a 50-year period, Finland, 1966 to 2017

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Reposted by Brendan J. Kelly

ASM @asm.org · Sep 10

Attention early-career scientists! Apply for ASM’s Young Ambassador Program to gain leadership experience, build your network and inspire the next generation of microbiologists. Applications are due Nov. 1. asm.social/2Ah

ASM Young Ambassadors at ASM Microbe 2025

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Reposted by Brendan J. Kelly

Adam L @lauretig.bsky.social · Sep 10

Simon Wood, the GOAT of generalized additive models & creator of the mgcv #rstats package, has an Annual Review of Statistics essay on GAMs, available open access #statssky #mlsky

www.annualreviews.org/content/jour...

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Reposted by Brendan J. Kelly

UW Infectious Disease Fellowship Program @uwidfellowship.bsky.social · Sep 5

More on the outbreak of Neisseria meningitidis conjunctivitis among military trainees, from the MMWR… #IDSky

www.cdc.gov/mmwr/volumes...

Outbreak of Neisseria meningitidis Conjunctivitis ...

This report describes 41 cases of Neisseria meningitidis conjunctivitis among military trainees living in a communal setting in Texas.

www.cdc.gov

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Reposted by Brendan J. Kelly

Ferric Fang, MD @fangferric.bsky.social · Sep 5

Interesting that an unencapsulated meningococcal strain was responsible. Outbreaks of pneumococcal conjunctivitis have also involved unencapsulated strains (Baumgartner. N Engl J Med, 2003; Crum. Clin Infect Dis, 2004).

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Reposted by Brendan J. Kelly

IDSA @idsainfo.bsky.social · Sep 3

As national medical, scientific, public health and patient organizations, we call for the resignation of HHS Secretary Robert F. Kennedy Jr. to ensure the health of the American people.

Our statement: https://bit.ly/45LeJHi

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Reposted by Brendan J. Kelly

Jason Rasgon @vectorgen.bsky.social · Aug 26

The Center for Infectious Disease Dynamics (CIDD) at Penn State is hiring for a senior-level position in Infectious Disease Modeling. Come join our dynamic group of disease researchers!

Feel free to message me for details

psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

Full or Associate Professor in Infectious Disease Modeling

APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...

psu.wd1.myworkdayjobs.com

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Reposted by Brendan J. Kelly

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Aug 21

In my dept today we discussed deriving estimators from causal models. This can be opaque, but as a simple e.g. instrumental variable Z for estimating X on Y.

Z –a–> X –b–> Y, and X <– U –> Y, where U is unmeasured, a and b are path coefs. We want to know b. U prevents direct approach. >>

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Reposted by Brendan J. Kelly

Grant McDermott @gmcd.bsky.social · Aug 10

I had a blast at #useR2025.

Here are my slides on `tinyplot`. grantmcdermott.com/tinyplot/vig...

(Rendering of the title slide is a bit off on mobile. I'll fix when when I get sec.)

tinyplot –

grantmcdermott.com

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Reposted by Brendan J. Kelly

Samir S. Shah @samirshahmd.bsky.social · Aug 3

Two major points on influenza-associated acute necrotizing encephalopathy

- High mortality (27%)
- Most affected children were unvaccinated & did not have major comorbid conditions

#PedSky #IDSky

JAMA @jama.com · Aug 3

#Influenza-associated acute necrotizing encephalopathy in US children during the 2023-2024 and 2024-2025 influenza seasons showed high morbidity and mortality.

ja.ma/4oinX4Q #MedSky #PedSky

Figure 1. Neuroimaging Findings of Children With Influenza-Associated Necrotizing Encephalopathy

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