Michal Galdzicki
@mgaldzic.bsky.social
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📥 307
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I work on data at Arzeda the protein design company.
reposted by
Michal Galdzicki
samuel mehr
3 months ago
this is wild - i was aware of Mary-Claire King's absurdly important discoveries on BRCA / inherited breast cancer but I had no idea that her first PhD paper (King & Wilson 1975, Science, not bad lol) is the "99% of protein coding shared btwn chimps and humans" result
www.science.org/doi/abs/10.1...
add a skeleton here at some point
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Chaitanya K. Joshi
4 months ago
RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations
@simonmathis.bsky.social
and team!!! ❤️ bioRxiv preprint:
www.biorxiv.org/content/10.1...
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Boltz-1 update Boltz-1x introduces inference-time steering for much higher physical quality, CUDA kernels for faster, more memory-efficient inference and training.
www.biorxiv.org/content/10.1...
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Boltz-1: Democratizing Biomolecular Interaction Modeling
Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce Boltz-1, an open-source deep learning model incorporating...
https://www.biorxiv.org/content/10.1101/2024.11.19.624167v3
8 months ago
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Michal Galdzicki
bioRxiv Molecular Biology
8 months ago
BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design
https://www.biorxiv.org/content/10.1101/2025.04.06.647261v1
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Michal Galdzicki
Jim Haseloff
8 months ago
...where a powerful toy slingshot can be used to mount the LoRa node in a tree for better line-of-sight communications with other devices.
www.instructables.com/Meshtastic-S...
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Michal Galdzicki
Guilhem Faure
10 months ago
🚀 Thrilled to share our latest work from Zhang Lab, now published in Science (
www.science.org/doi/10.1126/...
) We introduce TIGR-Tas, a PAM-free, compact, modular RNA-guided DNA-targeting system in prokaryotes & their viruses. More details coming soon 👀
#TIGR
#RNA
#GeneEditing
#CRISPR
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Michal Galdzicki
bioRxiv Genomics
10 months ago
Sequencing by Expansion (SBX) -- a novel, high-throughput single-molecule sequencing technology
https://www.biorxiv.org/content/10.1101/2025.02.19.639056v1
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Wait-a-minute 3 in 1 COVID, Flu A, and B tests are already available from Amazon. Is the RSV one coming? I missed the memo.
a.co/d/4s5izkO
10 months ago
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Michal Galdzicki
Phil Plait
11 months ago
This is pretty cool: Scientists have isolated the gene that may be responsible for the reason grapefruit interferes with some meds. It's not the solution, but it's a start. I love grapefruit but it messes with one of my meds, so this makes me happy.
www.scientificamerican.com/article/why-...
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Why Grapefruit Interferes with Medication, and What to Do about It
Could gene editing produce a tasty citrus fruit that doesn’t interfere with prescription drugs?
https://www.scientificamerican.com/article/why-grapefruit-interferes-with-medication-and-what-to-do-about-it/
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Arzeda has been awarded DARPA funding to advance AI-driven protein design—even with limited data! We're pushing the boundaries to create next-gen proteins for national security, sustainability, and beyond.
#AI
#ProteinDesign
www.prnewswire.com/news-release...
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Arzeda Awarded DARPA Funding to Advance AI-Driven Protein Design for National Security
/PRNewswire/ -- Arzeda, the industry-leading Protein Design Company™, today announced it has been selected for an award from the Defense Advanced Research...
https://www.prnewswire.com/news-releases/arzeda-awarded-darpa-funding-to-advance-ai-driven-protein-design-for-national-security-302358060.html
11 months ago
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Speculative writeup and the webinar Feb 20
web.cvent.com/event/e77566...
add a skeleton here at some point
11 months ago
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Michal Galdzicki
Rob Carlson
11 months ago
From the dependably insightful
@aukehoekstra.bsky.social
.
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Michal Galdzicki
Dietram A. Scheufele
12 months ago
Our inability to reliably study algorithmic info ecosystems, and why it matters for
#scicomm
. Pre-publication version of our forthcoming PNAS piece led by Nicky Krause and Isabelle Freiling :
osf.io/preprints/so...
(a 🧵)
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Michal Galdzicki
Nick Tsergas
about 1 year ago
You guys remember TweetDeck? Bluesky has it, and it's free. Check out 🔗
deck.blue
by
@gildaswise.com
for a multi-column interface. 2/10
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Michal Galdzicki
Howard Salis
about 1 year ago
NEW paper 🚨! We engineered TNT sensors in soil bacteria for long-term detection of explosive in natural soil, enabling geospatial detection of contaminated soil. This work (led by Erin Essington) included new sensors, circuits, modeling, & a 28-day testing workflow. 1/
www.nature.com/articles/s41...
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An autonomous microbial sensor enables long-term detection of TNT explosive in natural soil - Nature Communications
Engineered microbes can detect harmful chemicals, but may not work well in complex environments. Here, the authors built microbial sensors for detection of TNT explosive and tested their response over...
https://www.nature.com/articles/s41467-024-54866-y
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This is a really cool paper. They developed a reasonably robust circuit to generate patterns.
add a skeleton here at some point
about 1 year ago
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Michal Galdzicki
Jonathan Jacobs
about 1 year ago
🧬🖥🧪 Here are some healthy reminders on just how much Illumina still dominates the
#genomics
space... 😐
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Michal Galdzicki
Jon Lim, MRCP PhD
about 1 year ago
🎨 In case anyone need… The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏! Check it out 👇
bioart.niaid.nih.gov
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Michal Galdzicki
Gabriele Corso
about 1 year ago
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
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Michal Galdzicki
Hana Ayoob
about 1 year ago
The infographic & some extra info here if anyone is interested
www.compoundchem.com/2014/08/21/c...
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Compound Interest: Why Doesn’t Honey Spoil? – The Chemistry of Honey
Honey is something of an oddity, in that, unlike most foods, it doesn’t spoil over time. In fact, the oldest known sample of honey, found in an Ancient Egyptian tomb and dated to approximatel…
https://www.compoundchem.com/2014/08/21/chemistryofhoney/amp/
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Michal Galdzicki
Roland Dunbrack 🏳️🌈
about 1 year ago
Rumors are that they will release model and weights next week.
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Michal Galdzicki
Rob Carlson
about 1 year ago
Arzeda has now produced and sold 10 tons of ProSweet RebM™ stevia, a natural, zero-calorie sweetener, marking a major step forward in sustainable production for the food industry.
#biosky
www.businesswire.com/news/home/20...
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Arzeda, Co-founded by Nobel Laureate David Baker, Drives Industry Innovation with Intelligent Protein Design Technology™ and Delivers Performance Products to Fortune 500 Companies
Arzeda, the leading industrial protein design company co-founded in 2009 by Nobel laureate and University of Washington School of Medicine biochemistr
https://www.businesswire.com/news/home/20241107936695/en/Arzeda-Co-founded-by-Nobel-Laureate-David-Baker-Drives-Industry-Innovation-with-Intelligent-Protein-Design-Technology%E2%84%A2-and-Delivers-Performance-Products-to-Fortune-500-Companies
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Washington's Dream, plants!
youtube.com/shorts/Mz-Er...
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Greenhouse Nursery Trade Gallons Part 2
YouTube video by Smith's Gardentown
https://youtube.com/shorts/Mz-ErXJiT6E?si=YNRkh_DEubGQ4emj
about 1 year ago
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Michal Galdzicki
Jay 🦋
about 1 year ago
Bluesky has grown to 13M users in a year and a half — thank you all for choosing us! We’ve raised a $15M Series A to support our growth and continue to build an open social network that is designed around you, the user.
add a skeleton here at some point
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Michal Galdzicki
Axel Visel
about 1 year ago
New preprint by
@jgi.doe.gov
's Leo Baumgart, Ronan O'Malley and many others Mapping binding sites of 360 TFs across 10 🌿Brassicaceae genomes. 1.1 million TF-target gene assignments in Arabidopsis thaliana alone!
add a skeleton here at some point
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Michal Galdzicki
bioRxiv Synthetic Biology
about 1 year ago
Design of a biomolecular adaptive controller to restore sustained periodic behavior https://www.biorxiv.org/content/10.1101/2024.10.11.617962v1
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Design of a biomolecular adaptive controller to restore sustained periodic behavior https://www.biorxiv.org/content/10.1101/2024.10.11.617962v1
Periodic behavior is a widespread biological phenomenon occurring across various spatiotemporal scal
https://www.biorxiv.org/content/10.1101/2024.10.11.617962v1
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Part 1 had me in stitches
youtu.be/JYqfVE-fykk?...
Part 2 great work
youtu.be/VJ62EfUKI3w?...
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Washington's Dream 2 - SNL
YouTube video by Saturday Night Live
https://youtu.be/VJ62EfUKI3w?si=IOttbM0oSWgGCnG9
about 1 year ago
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Marburg in Rwanda, 20 cases reported
taarifa.rw/rwandas-heal...
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Rwanda’s Health Ministry Provides Update on Marburg Virus Outbreak: Six Dead, 20 Infected - Taarifa Rwanda
On Sunday afternoon, the Ministry of Health in Rwanda held a press conference to update the public on the country’s first-ever outbreak of the Marburg virus. Health Minister Dr. Sabin Nsanzimana confi...
https://taarifa.rw/rwandas-health-ministry-provides-update-on-marburg-virus-outbreak-six-dead-20-infected/
about 1 year ago
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Michal Galdzicki
Sebastian S. Cocioba
about 1 year ago
Here are some useful links to my work. Please bookmark for easy access! 💚 Open Laboratory Notebook:
tinyurl.com/ATGCFFE
Open Data Repository:
tinyurl.com/ATGCSWEET
Web Store for Plasmids and Goodies:
atinygreencell.com
Binomica Labs GitHub:
github.com/Binomica-Labs
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Bluesky now has over 10 million users, and I was #1,292,419!
about 1 year ago
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Michal Galdzicki
Diego del Alamo
over 1 year ago
Another group has more or less reproduced AF3, but has built in a way to add spatial constraints for PPI prediction. These constraints lead to huge increases in fraction of models that are correct-ish, without changing fraction that is high-accuracy
chaiassets.com/chai-1/paper...
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Michal Galdzicki
Mike Young
over 1 year ago
🌍 We have just extracted a NEW global network of researchers and a global 100 scientist top ‘influencers’ on Bluesky.
@lassehjorthmadsen.bsky.social
and I show that scientists are in a series of distinct communities:
mikeyoungacademy.dk/communities-...
😀 All 'likes' and reshares appreciated!
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Communities of scientists are emerging on Bluesky - Mike Young Academy
Global network data: The ‘nicer’ alternative to X is fortifying its presence in fields that range from philosophy to chemistry, finance, and beyond.
https://mikeyoungacademy.dk/communities-of-scientists-are-emerging-on-bluesky/
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Michal Galdzicki
Compound Interest | Chemistry infographics
over 1 year ago
Forgot to add that, while Kekulé’s benzene structure has endured, some of his other structural depictions were less successful. For some reason, his “sausage formulae” never caught on…
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Michal Galdzicki
bioRxivpreprint
over 1 year ago
Computational design of highly active de novo enzymes https://www.biorxiv.org/content/10.1101/2024.08.02.606416v1
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Computational design of highly active de novo enzymes https://www.biorxiv.org/content/10.1101/2024.08.02.606416v1
Custom designed enzymes can further enhance the use of biocatalysts in industrial biotransformations
https://www.biorxiv.org/content/10.1101/2024.08.02.606416v1
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Michal Galdzicki
bioRxiv Synthetic Biology
over 1 year ago
Accelerated enzyme engineering by machine-learning guided cell-free expression https://www.biorxiv.org/content/10.1101/2024.07.30.605672v1
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Accelerated enzyme engineering by machine-learning guided cell-free expression https://www.biorxiv.org/content/10.1101/2024.07.30.605672v1
Enzyme engineering is limited by the challenge of rapidly generating and using large datasets of seq
https://www.biorxiv.org/content/10.1101/2024.07.30.605672v1
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Michal Galdzicki
bioRxiv Synthetic Biology
over 1 year ago
Preventing plasmid multimer formation in commonly used synthetic biology plasmids https://www.biorxiv.org/content/10.1101/2024.07.23.604805v1
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Preventing plasmid multimer formation in commonly used synthetic biology plasmids https://www.biorxiv.org/content/10.1101/2024.07.23.604805v1
Plasmids are an essential tool for basic research and biotechnology applications. To optimize plasmi
https://www.biorxiv.org/content/10.1101/2024.07.23.604805v1
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Happy 4th. Transglutaminase fact: they're used to improve the texture of hot dogs
add a skeleton here at some point
over 1 year ago
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Michal Galdzicki
over 1 year ago
Hi all - I have a couple of positions open for lab management and research! Please pass this on to creative and enthusiastic folks who might be interested. (And repost if you don't mind.) Ability to learn/adapt more important than specific skills! Thanks so much.
arizona.csod.com/ux/ats/caree...
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Research Professional II (Multiple Positions)
-Work independently on defined experiments (e.g., set up, scheduling, data acquisition) and report on the findings to the PI.-Have a general understan...
https://arizona.csod.com/ux/ats/careersite/4/home/requisition/19645?c=arizona&source=Higheredjobs
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Michal Galdzicki
bioRxiv Synthetic Biology
over 1 year ago
Induction of Meiosis from Human Pluripotent Stem Cells https://www.biorxiv.org/content/10.1101/2024.05.31.596483v1
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Induction of Meiosis from Human Pluripotent Stem Cells https://www.biorxiv.org/content/10.1101/2024.05.31.596483v1
An in vitro model of human meiosis would accelerate research into this important reproductive proces
https://www.biorxiv.org/content/10.1101/2024.05.31.596483v1
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Michal Galdzicki
over 1 year ago
If you're interesting in the
#H5N1
outbreak in cattle in the US, please have a look at our preliminary analyses just posted. Part 1 of 2:
virological.org/t/preliminar...
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Michal Galdzicki
RCSB Protein Data Bank
over 1 year ago
Bagheera helps Molecule of the Month author David Goodsell create his amazing illustrations. Can you guess which molecule Bagheera is in? #NationalPetMonth #PetsofRCSBPDB
pdb101.rcsb.org/motm...
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Michal Galdzicki
Daniel Bolnick
over 1 year ago
Excited for this live public event with the
@bigbiology.bsky.social
podcast, addressing ecological restoration in Alaskan Lakes! If you know someone in Alaska who might be interested, please share it with them!
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reposted by
Michal Galdzicki
bioRxiv Synthetic Biology
over 1 year ago
MAIA: An open-source, modular, bioreactor for cities https://www.biorxiv.org/content/10.1101/2024.05.03.592196v1
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MAIA: An open-source, modular, bioreactor for cities https://www.biorxiv.org/content/10.1101/2024.05.03.592196v1
This work presents the design and fabrication of MAIA, an open-source, modular, low-cost, and portab
https://www.biorxiv.org/content/10.1101/2024.05.03.592196v1
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Michal Galdzicki
Elinne Becket, PhD
over 1 year ago
And AFTER ALL THAT....
#BlueSoup
isolate has 98.7 ANI with the Pseudomonas carnis genomes from the Marina De León &
@phylogenomics.bsky.social
paper
jgenomics.com/v09p0055.htm
💀 99.2 ANI with P. NBRC 111137; still digging!
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Draft Genome Sequences and Genomic Analysis for Pigment Production in Bacteria Isolated from Blue Discolored Soymilk and Tofu
https://jgenomics.com/v09p0055.htm
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Michal Galdzicki
Torsten Wittmann
over 1 year ago
No videos here ... yet. So, here is a cute AlphaFold2 model of the mEmerald labelled nanocages that we used to determine that there are ~120 DCX molecules bound per µm growth cone microtubule🧪
doi.org/10.1101/2024...
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De novo design of antibody variable heavy chains (VHH's) using RF diffusion
www.biorxiv.org/content/10.1...
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Atomically accurate de novo design of single-domain antibodies
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
https://www.biorxiv.org/content/10.1101/2024.03.14.585103v1
over 1 year ago
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Michal Galdzicki
Rob Carlson
over 1 year ago
Nice list of community science projects here.
www.seattletimes.com/pacific-nw-m...
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Trikafta changed CF from a death sentence to a treatable condition. It overcomes the deficit of a chloride channel caused by a specific inherited mutation in the CFTR gene, discovered in 1989, and only 30 years later this story was possible. How much quicker will this take these days?
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The Cystic-Fibrosis Breakthrough That Changed Everything
The disease once guaranteed an early death—but a new treatment has given many patients a chance to live decades longer than expected. What do they do now?
https://www.theatlantic.com/magazine/archive/2024/04/cystic-fibrosis-trikafta-breakthrough-treatment/677471/
over 1 year ago
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@bioandbaseball.bsky.social
any chance you could share that
www.liebertpub.com/doi/10.1089/...
paper PDF?
almost 2 years ago
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reposted by
Michal Galdzicki
Rob Carlson
almost 2 years ago
Next, an editorial from the Seattle Times on restoring salmon streams. "The course is not cheap, but it is clear: The state must fix the culverts, using the best science possible." WA must stay the course on culvert removal to save salmon
www.seattletimes.com/opinion/edit...
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WA must stay the course on culvert removal to save salmon | Editorial
The Legislature should ensure that the state's efforts to remove culverts that block salmon runs are carried through.
https://www.seattletimes.com/opinion/editorials/wa-must-stay-the-course-on-culvert-removal-to-save-salmon/
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