Jesse Shapiro
@bjesseshapiro.bsky.social
📤 1810
📥 790
📝 523
Macrobe qui aime les microbes
http://www.shapirolab.ca/
pinned post!
Now out & nicely formatted in
@isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs,
@gmdouglas.bsky.social
&
@cyanophage.bsky.social
along with co-PIs
@lbobay.bsky.social
& Samuel Chaffron. A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
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Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
https://doi.org/10.1093/ismejo/wraf275
2 months ago
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Jesse Shapiro
Norm Wilner
about 13 hours ago
Humanity: Pretty awesome, sometimes.
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Jesse Shapiro
The Institute for Bird Populations
about 12 hours ago
Birders never stop birding
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Melanie Blokesch
1 day ago
Excited to share our new paper out today in
@science.org
🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky
#phagesky
www.science.org/doi/10.1126/...
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https://www.science.org/doi/10.1126/science.aed0645
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Madhu Pai, MD, PhD
about 24 hours ago
Things are rough these days, but I found some joy in watching this young man reach this wonderful milestone, with a team that is getting Montreal very excited for the future!
www.nhl.com/canadiens/ne...
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Cole Caufield scores 50th goal of the season | Montréal Canadiens
Canadiens forward becomes seventh player in franchise history to hit the milestone
https://www.nhl.com/canadiens/news/cole-caufield-scores-50th-goal-of-the-season
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Colin Carlson
2 days ago
New in
@science.org
‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓
www.science.org/doi/10.1126/...
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Daria Van Tyne
3 days ago
My lab at Pitt is looking for a Research Scientist to help us make phage therapy for patients with antibiotic-resistant infections. Please share and apply!
cfopitt.taleo.net/careersectio...
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Research Scientist
Click the link provided to see the complete job description.
https://cfopitt.taleo.net/careersection/pitt_temp_external/jobdetail.ftl?job=26001943&tz=GMT-04%3A00&tzname=America%2FNew_York
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Thank you to this recommendation letter writer for breaking the monotony of reviewing grad school applications today
3 days ago
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public health guy
4 days ago
i keep thinking about an iranian girl who was featured in the new york times a few months ago. she said she didn’t know how she would be able to evacuate because she couldn’t carry her cats.
add a skeleton here at some point
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Jess Harwood Art
4 days ago
Jealous
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Jesse Shapiro
Madhu Pai, MD, PhD
4 days ago
We are watching pictures that show us how we are citizens of a small, precious planet, even as mad men amongst us are threatening to wipe out entire civilizations My mind is struggling to make sense
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Will Ratcliff
4 days ago
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
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The fitness costs of reproductive specialization scale inversely with organismal size
https://www.pnas.org/doi/epdf/10.1073/pnas.2536055123
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Jesse Shapiro
HappyToast
10 days ago
Everyone remember to hide when the astronauts comes back.
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Jesse Shapiro
Martin Humphries
11 days ago
This 👇
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André Picard @picardonhealth
11 days ago
BREAKING NEWS: Stephen Lewis, former Ontario NDP leader and global AIDS advocate, dies at 88. He was one of Canada greatest orator's. Often referred to as the best Prime Minister the country never had.
www.theglobeandmail.com/canada/artic...
via
@theglobeandmail.com
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Stephen Lewis, former Ontario NDP leader and global AIDS advocate, dies at 88
Lewis died in hospital Tuesday after battle with cancer
https://www.theglobeandmail.com/canada/article-stephen-lewis-dies-ndp-avi-lewis/
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José R Penadés
11 days ago
This paper started as an idea
@albertomarina.bsky.social
had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up. Grateful (and slightly humbled) to be part of this. Thanks Alberto!
www.cell.com/cell/fulltex...
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Phages communicate across species to shape microbial ecosystems
Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...
https://www.cell.com/cell/fulltext/S0092-8674%2826%2900271-0
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Jesse Shapiro
Nandita Garud
11 days ago
I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications!
www.nature.com/articles/s41...
. (1/n)
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Mark Mandel
12 days ago
Apply to be an editor at an ASM Journal! Open call for editors at mBio, mSphere, mSystems, and Microbiology Spectrum. This is a very fulfilling way to share your expertise and give back to our society journals.
@asm.org
journals.asm.org/asm-call-for...
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ASM Journals Open Calls for Editors
A list of current and upcoming open calls for editors at ASM Journals.
https://journals.asm.org/asm-call-for-editors
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Jesse Shapiro
Vaughn Cooper
12 days ago
Now out in AEM
@asm.org
! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy
journals.asm.org/eprint/FBU9M...
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Emmanuele Severi
13 days ago
#microsky
#phagesky
on
#phage
cocktails
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Jesse Shapiro
Canadian Paintings
13 days ago
Mountain Forms Lawren Harris 1926
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Cameron Thrash
15 days ago
Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects
#USC_MEB
#jcampubs
🌊
academic.oup.com/ismecommun/a...
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Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects
Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil
https://academic.oup.com/ismecommun/advance-article/doi/10.1093/ismeco/ycag081/8550906?rss=1&login=false
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Jesse Shapiro
Ben Good
15 days ago
Happy to share the final version of
@oliviamghosh.bsky.social
's paper on inferring low dimensional phenotype-fitness maps from high-throughput fitness measurements across environments. Fun collaboration with
@oliviamghosh.bsky.social
,
@grantkinsler.bsky.social
, &
@petrovadmitri.bsky.social
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Tami Lieberman
15 days ago
"a single antibiotic-susceptible strain ... significantly reduced VRE burden both in vitro and in mouse experiments, whereas multi-strain consortia failed due to competitive interference among consortium members" Great new paper from
@naamagz.bsky.social
et al
www.tandfonline.com/doi/10.1080/...
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Intra-species competition combats vancomycin-resistant enterococci
Vancomycin-resistant Enterococcus (VRE) is a leading cause of multidrug-resistant infections in hospitalized patients, yet no reproducible microbiota therapies exist to selectively displace it. Her...
https://www.tandfonline.com/doi/10.1080/19490976.2026.2647529?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed
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Jesse Shapiro
Olaya Rendueles
16 days ago
So happy to see this finally published in
@plosbiology.org
! This is the first chapter of
@julielebris.bsky.social
PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics w/
@epcrocha.bsky.social
#microsky
@klebclub.bsky.social
Link below- Check out her 🧵 for more details!
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Jesse Shapiro
Gwen Pearson
16 days ago
Yes, seals have lice! Under water, lice close their spiracles and reduce their oxygen consumption to a minimum
www.nature.com/articles/s42...
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Host-parasite coevolution leads to underwater respiratory adaptations in extreme diving insects, seal lice (Lepidophthirus macrorhini) - Communications Biology
Seal lice survive deep-sea dives by closing spiracles, reducing oxygen use, and breathing through their skin. Genomic data suggest they store oxygen via haemoglobin, showing insects can adapt to extre...
https://www.nature.com/articles/s42003-025-08306-2
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Jesse Shapiro
Andrew Hendry
24 days ago
Looking forward to CSEE-SCEE this spring in Toronto?
event.fourwaves.com/csee2026/pages
Considering contributing to our collection of pics from previous meetings. Contact me by email for more info.
@csee-sceemtgs.bsky.social
@csee-scee.bsky.social
@ciee-icee.bsky.social
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Anyone else appreciate the irony of the infinity symbol in the new Doodle logo? (adding insult to injury of the endless calendar polls, their ad-filled website crashes my browser and sends my laptop fan into panic mode every time)
17 days ago
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Jesse Shapiro
Shuaiqi Guo
17 days ago
Our work with the Brun lab on the in situ architecture of the Caulobacter crescentus Tad pilus machine is published in mBio. Amazing collaborative effort led by James Iarocci
@jamesiarocci.bsky.social
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Luiz Pedro Carvalho, PhD
17 days ago
All currently approved antibiotics inhibit essential cellular processes. Ever wonder if we could kill bacteria using the opposite strategy? Here, we demonstrate an alternative antibacterial strategy: lethality through pathway over-activation.
www.nature.com/articles/s41...
(1 out of 3)
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Activation of l-histidine biosynthesis as a new antibiotic strategy against Mycobacterium tuberculosis - Nature Communications
Here, the authors report metabolic activation as a potential antimicrobial strategy against Mycobacterium tuberculosis. They show that supra-physiological activation of L-histidine biosynthesis r...
https://www.nature.com/articles/s41467-026-70510-3
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The Expos are rolling in their grave
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18 days ago
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Montreal to Vancouver, with my dad. Via Duluth, Minnesota, to see where Bob Dylan came from (and why he left; sorry Duluth!)
add a skeleton here at some point
19 days ago
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Jesse Shapiro
Colin Carlson
19 days ago
‼️ New preprint: By solving a paradox in graph theory, we show that specialist symbionts constrain ecosystem structure, drive biodiversity, and face high extinction risk. With
@jbyoder.org
and
@ctrlalttim.com
: 🎉
Specialists drive biodiversity scaling in symbiotic relationships
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Jesse Shapiro
Michel Cayouette
20 days ago
Many great points made in thi article.
www.nature.com/articles/d41...
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The problem with Canada’s plan to buy scientific prestige
The government’s plans to poach 100 US researchers might make good economic sense. But what about the existing community?
https://www.nature.com/articles/d41586-026-00743-1
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Jesse Shapiro
Kristian G. Andersen
21 days ago
I have been listening to
@theskepticsguide.bsky.social
since I was a graduate student! It was therefore a great pleasure to join this weeks show to talk about the origin of COVID-19. One of the most succinct and on-point interviews I have done on the topic!
www.theskepticsguide.org/podcasts/epi...
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Episode #1080 | The Skeptics Guide to the Universe
News Items Cannabis Review AI Agent Breaks Out Of Testing Environment Life on Exomoons Strongest Carbon Fiber Bigfoot Hoax Revealed Interview with Professor Kristian Andersen https://www.scripps.edu/f...
https://www.theskepticsguide.org/podcasts/episode-1080
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Jesse Shapiro
/r/Habs
21 days ago
Youppi holds a photo of Montreal Expos legend Rodger Brulotte, the man who helped create the mascot back in 1979
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The only brunch worth brunching
21 days ago
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Jesse Shapiro
Eduardo Rocha
21 days ago
David Botstein wrote one of the most insightful and inspiring papers I’ve read on the evolution of mobile genetic elements. Still very much worth a reading these days. Hard to find people with such diverse, outstanding contributions.
nyaspubs.onlinelibrary.wiley.com/doi/10.1111/...
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Jesse Shapiro
Pleuni Pennings
about 2 months ago
My colleagues at
@sfsu.bsky.social
used 3 decades of data to show that students with low undergrad GPA have equal PhD completion rates compared to students with high GPA.
@sfstatebio.bsky.social
journals.plos.org/plosone/arti...
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Awesome, stupid AI bubble means my students can’t have laptops
22 days ago
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Jesse Shapiro
Sullivan Lab at OSU
24 days ago
🚨NEW PAPER
@isme-microbes.bsky.social
on phage-bacteria dynamics. Collab between us and
@joshuasweitz.bsky.social
labs. "Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics". 👉
doi.org/10.1093/isme...
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Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics
Abstract. Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coe
https://doi.org/10.1093/ismejo/wrag041
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Tami Lieberman
24 days ago
If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship
engineering.mit.edu/novo-nordisk
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Novo Nordisk Fellowship
Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...
https://engineering.mit.edu/novo-nordisk#why
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Rachel Gregor
24 days ago
Coming this August 3-5 to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)!
#Microbiome
#MicroSky
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Jesse Shapiro
Kristian G. Andersen
24 days ago
One week - and that's more than the entirety of the US public health budget up in, literal, smoke. *poof*
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Based on past experience, this will be a super fun meeting! Join online or at our Montreal hub, if you're in easy carpooling/train distance.
add a skeleton here at some point
24 days ago
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Jesse Shapiro
Daria Van Tyne
25 days ago
Two new studies from us using culture-enriched metagenomics to study populations (not just clones!) of some of our favorite superbugs collected from infected patients in the hospital 🧵
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Jesse Shapiro
Stu West
about 1 month ago
New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome
www.pnas.org/doi/10.1073/...
@lauriebelch.bsky.social
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Jesse Shapiro
Gravel Influencer
26 days ago
This is one of those great examples of how bicyclists can never win with drivers.
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Jesse Shapiro
Kristian G. Andersen
26 days ago
The vast majority of labs in the U.S. rely on federal funding to do their research - labs like my own. We're already running on fumes and while top-line budgets have been maintained, for now, research isn't getting funded. Once those fumes are out 👉 🪦.
elizabethginexi.substack.com/p/i-wrote-re...
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I Wrote Research Funding Announcements for NIH for 22 Years. This Year They’ve Published 14
How NIH went from 756 funding announcements to 14 in two years — and what it means for every disease that depends on federal research
https://elizabethginexi.substack.com/p/i-wrote-research-funding-announcements?publication_id=6018767&post_id=191085985&isFreemail=true&r=1a37zq&triedRedirect=true
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In the lab, antibiotics can make integrated viruses (prophages) pop out of bacterial genomes. In this (short!) preprint, we asked a simple question: how much does this happen outside the lab, in the human gut? TLDR: Not much overall, in specific bacterial species. 🧵
www.biorxiv.org/content/10.6...
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Species-specific prophage induction by ciprofloxacin in human gut metagenomes
Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut. Importance Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations. ### Competing Interest Statement The authors have declared no competing interest. NIH Common Fund, https://ror.org/001d55x84 Natural Sciences and Engineering Research Council
https://www.biorxiv.org/content/10.64898/2026.03.11.711154v1
26 days ago
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Jesse Shapiro
Gavin Douglas
26 days ago
New preprint where
@lbobay.bsky.social
and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area.
doi.org/10.64898/202...
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https://doi.org/10.64898/2026.03.09.710665
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