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Emanuel Gonçalves

@emanuelvgo.bsky.social
218 followers 223 following 4 posts

Assistant Professor Instituto Superior Técnico (IST) and INESC-ID web.tecnico.ulisboa.pt/emanuel.v.go…

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Reposted by Emanuel Gonçalves
Endpoints News @endpts.com · 14/09/2026
BioNTech's gotistobart added 8.5 months of survival over chemo in previously treated lung cancer, ahead of a pivotal readout due by year's end.
endpoints.news
BioNTech spells out survival win for gotistobart ahead of pivotal readout
BioNTech's gotistobart showed 18.5 vs 10.0 month survival vs chemo in lung cancer Phase 3, cutting death risk 44%. BNTX shares rose 3%.
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Reposted by Emanuel Gonçalves
Pedro Beltrao @pedrobeltrao.bsky.social · 09/09/2026
I made a presentation to other faculty about recent progress in general AI, to facilitate the discussion around the impact for research and teaching in biology. It could be that the slides are useful for others trying to do that same. Feel free to re-use. docs.google.com/presentation...
docs.google.com
generalAI_for research_intro.pptx
Recent AI developments and what they mean for us Quick primer on general AI models* State-of-the-art in AI agent capabilities AI agents in biology (examples) Discussion - what does this mean for our r...
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Reposted by Emanuel Gonçalves
Inigo Martincorena @imartincorena.bsky.social · 03/09/2026
Big paper alert! This project has been years in the making. A comprehensive description of somatic mutation rates and signatures across 53 tissues or cell types using NanoSeq. A large collective effort led by Mimy Pham, Mike Stratton and @r-rahbari.bsky.social. www.biorxiv.org/content/10.6...
biorxiv.org
A comprehensive atlas of somatic mutation rates and mutational signatures in normal human cells
Over the course of a lifetime, somatic mutations accrue in normal human cells, causing variation in cell phenotype and engendering somatic evolution with outcomes ranging from the adaptive immune syst...
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Reposted by Emanuel Gonçalves
Saez-Rodriguez Group @saezlab.bsky.social · 20/08/2026
Our tool MetaProViz is now out in Molecular Systems Biology: doi.org/10.1038/s443... Since our preprint we: - advanced our feature processing workflow - added metabolite-sets to MetSigDB - added metabolite-set visualization to aid functional analysis
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Reposted by Emanuel Gonçalves
Jesse Boehm @boehmjesse.bsky.social · 05/08/2026
Hot off the press in Nature! After 10 years, 2,780 patients and 300+ scientists, today we announce the Human Cancer Models Initiative (HCMI) release of 665 organoids and other next generation models! All models and data available to accelerate cancer drug discovery! @nature.com rdcu.be/fx3I3
rdcu.be
A compendium of next-generation patient-derived models for diverse cancers
Nature - The international collaboration of the Human Cancer Models Initiative presents a comprehensive resource of next-generation cancer models from 2,780 donors with 25 cancer types and...
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Reposted by Emanuel Gonçalves
Molecular Systems Biology @molsystbiol.org · 14/07/2026
authors developed computational framework VEFill to impute missing deep mutational scanning (DMS) scores for variant effect prediction ➡️ link.springer.com/article/10.1...
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Reposted by Emanuel Gonçalves
Pedro Beltrao @pedrobeltrao.bsky.social · 08/07/2026
The @qedscience.bsky.social "impact" score generated a lot of discussion on ranking preprints, including ideas on multi-dimensional rankings that are user specific. Besides describing the ideas, we can now prototype them (with Claude in this case). Here is Salient salient-sgeu6fs5ua-uc.a.run.app
salient-sgeu6fs5ua-uc.a.run.app
Rising — Salient
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Reposted by Emanuel Gonçalves
Pedro Beltrao @pedrobeltrao.bsky.social · 25/05/2026
new lab preprint - Protein function prediction is a well established problem but proteins exist in different post-translationally modified forms. Here, @julianvangerwen.bsky.social built a ML model to predict the biological process regulated by individual phosphosites www.biorxiv.org/content/10.6...
biorxiv.org
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Pedro Beltrao @pedrobeltrao.bsky.social · 06/07/2026
My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...
nature.com
Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386
The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry
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Wolfgang Huber @wkhuber.bsky.social · 01/07/2026
EMBL's new AI unit is recruiting. We are seeking a machine learning scientist to establish their independent research group bridging innovations in machine learning/AI with modern biology. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
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Saez-Rodriguez Group @saezlab.bsky.social · 25/06/2026
🧵 New preprint: Logic models can simulate cancer signalling & screen drug targets in silico, but they need perturbation data & hand-curated networks patients lack. We present FICUS for building dynamic logic models directly from patient omics. 📄 doi.org/10.64898/202...
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Nature Biotechnology @natbiotech.nature.com · 19/05/2026
Zero-shot de novo peptide sequencing with open posttranslational modification discovery - @uwcheritoncs.bsky.social go.nature.com/4ujx08d
go.nature.com
Zero-shot de novo peptide sequencing with open posttranslational modification discovery - Nature Biotechnology
RNovA is an open-search de novo peptide sequencing model.
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Simon Fisher @profsimonfisher.bsky.social · 10/04/2026
Stunning illustration of how advances in cellular genomics can disentangle links between gene variants & clinical outcomes. Here, saturation editing revealed distinct neurodevelopmental disorders involving the same non-protein-coding gene. 🙌 @nickywhiffin.bsky.social @gregfindlay.bsky.social & co🧬🔬🧪
nature.com
Saturation editing of RNU4-2 reveals distinct dominant and recessive disorders - Nature
Saturation genome editing of RNU4-2 identifies the functional and clinical impact of variants across the entire gene and delineates variants that cause a new recessive neurodevelopmental disorder distinct from ReNU syndrome.
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Reposted by Emanuel Gonçalves
Stein Aerts @steinaerts.bsky.social · 09/04/2026
We launched a new Group Leader vacancy in our Center for AI & Computational Biology - VIB.AI @vibai.bsky.social - with a Professorship at Ghent University. Join us with your most creative AI+Biology research plan! Apply before 31st May vib.ai/en/group-lea...
vib.ai
Group leader vacancy
We are looking for a Group Leader in applied artificial intelligence in (bio)medical research at VIB.AI & UGent, Belgium
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Reposted by Emanuel Gonçalves
Wolfgang Huber @wkhuber.bsky.social · 04/03/2026
The time to register for this is now! It's a great opportunity for biological / biomedical researchers who want to get better in analysing their own data.
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Reposted by Emanuel Gonçalves
Manuel Kaulich @manuelkaulich.bsky.social · 24/02/2026
Our thoughts, impressions, and presentations of the "2nd EuroDepMap symposium" in Milan (Nov 2025) are online at @febsletters.bsky.social. febs.onlinelibrary.wiley.com/doi/10.1002/...
febs.onlinelibrary.wiley.com
FEBS Press
Held on 20 November 2025 at Human Technopole in Milan, the 2nd European Cancer Dependency Map Symposium convened experimental and computational scientists to discuss how cancer dependency mapping in ...
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Reposted by Emanuel Gonçalves
Saez-Rodriguez Group @saezlab.bsky.social · 12/02/2026
Happy to share new work led by @miraburtscher.bsky.social, together with colleagues from @savitski-lab.bsky.social, @saezlab.bsky.social (shout-out to @martingarridorc.bsky.social), @zimmermannlab.bsky.social and others. Original post + paper below! 👇
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Reposted by Emanuel Gonçalves
Monica Bettencourt-Dias @monicabettencourt.bsky.social · 23/01/2026
📣 Please spread: we’re hiring a Lab Manager! It is a critical position in our new lab. As our lab moves to Barcelona and joins the @crg.eu, we’re looking for a Lab Manager to help build the lab and set the lab atmosphere. 🔗 Apply here 👉 recruitment.crg.eu/content/jobs...
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Britta Velten @brittavelten.bsky.social · 10/12/2025
A new lab preprint is up: Work led by our MSc student Jan Sprengel comparing Interventional Causal Structure Learning Algorithms for Gene Regulatory Network Inference from single cell CRISPR perturbation screens 👇 www.biorxiv.org/content/10.6...
biorxiv.org
Comparison of Interventional Causal Structure Learning Algorithms for Gene Regulatory Network Inference
Background: Causal structure learning offers a promising approach to studying gene regulation in cells, aiming to provide deeper mechanistic insights than purely association-based methods. Theoretical...
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Reposted by Emanuel Gonçalves
David Ochoa @d0choa.bsky.social · 12/01/2026
🚀 Announcing the Official @opentargets.org MCP! We've partnered with @anthropic.com to give AI seamless access to high-quality genetic and target-discovery data. Open for the entire community to accelerate therapeutic development. Read more at blog.opentargets.org/official-ope...
blog.opentargets.org
Introducing the official Open Targets Platform Model Context Protocol
We have released the first iteration of a dedicated MCP server to bring our systematic target discovery capabilities to Large Language Model (LLM)-based workflows.
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Gabriele Picco @gabrielepicco.bsky.social · 28/12/2025
WRN inhibitors are being tested in patients with MSI cancers. How do tumours adapt to WRN inhibition, and can therapy stay ahead of resistance? Our latest preprint investigates how MSI tumours evolve under pressure from WRN inhibition. Highlights below.
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Traver Hart @traver.bsky.social · 21/12/2025
Merry Christmas, genetic interaction nerds: www.biorxiv.org/content/10.6...
biorxiv.org
Functional modules predict cancer-relevant genetic interactions in mammalian cells
Genetic interactions can reveal gene function and identify cancer-relevant synthetic lethals, but systematic mapping in human cells is constrained by inefficient reagents, vast combinatorial search sp...
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Reposted by Emanuel Gonçalves
Glennis Logsdon @glennislogsdon.bsky.social · 16/12/2025
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
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IRB Barcelona @irbbarcelona.org · 26/11/2025
Yesterday in Valencia Dr. @nlbigas.bsky.social received the 2025 Premio Rei Jaume I in Biomedical Research. Her work on how cancer mutations arise and evolve has earned major recognition! Congratulations, Núria! 🙌 #ReiJaumeI #CancerResearch @cerca.cat @icreacommunity.bsky.social @bbglab.bsky.social
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Pedro Beltrao @pedrobeltrao.bsky.social · 21/11/2025
Finally the scary example. The image of a western blot with a time course experiment, staining a protein of interest, showing the increase of protein over time and a second staining with a control antibody that does not change over time
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Pedro Beltrao @pedrobeltrao.bsky.social · 21/11/2025
The second was about drawing the EGF pathway. I also asked to create an SVG of the EGF pathway drawing which worked but with much lower quality.
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Pedro Beltrao @pedrobeltrao.bsky.social · 21/11/2025
I tried the updated Gemini image generator on scientific related image prompts that have failed in the past and I am really impressed by the quality of the outputs. The first is drawing a diagram for a pocket prediction algorithm using Voronoi diagram, Delaunay triangulation and alpha shapes
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2nd European Cancer Dependency Map Symposium @eurocancerdepmap.bsky.social · 20/11/2025
The last session starts with Lodewyk Wessels from @nkinl.bsky.social sharing the work on perturbation response models!
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2nd European Cancer Dependency Map Symposium @eurocancerdepmap.bsky.social · 20/11/2025
And we finish this session with @epetsalaki.bsky.social showing the potential of using CRISPR data to study context specific signalling and drug responses
Evangelia Petsalaki presenting at the 2nd European Cancer Dependency  Map Symposium
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Reposted by Emanuel Gonçalves
2nd European Cancer Dependency Map Symposium @eurocancerdepmap.bsky.social · 20/11/2025
Next we have @emanuelvgo.bsky.social , presenting the work on Minimal Libraries and use of AI-Synthetic Augmentation of CRISPR-Cas9 Screens for Drug Target Discovery
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Dr Lizzie Coker @lizziecoker.bsky.social · 20/11/2025
@emanuelvgo.bsky.social insisting the metaphors used in @eurocancerdepmap.bsky.social presentations have strong Portuguese representation 😄
Emanuel’s slide depicts a bridge between lab data and patients - but the bridge is carefully labelled as the Ponte 25 de Abril in Lisbon
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2nd European Cancer Dependency Map Symposium @eurocancerdepmap.bsky.social · 20/11/2025
The Synthetic Lethality and Innovations in CRISPR Screening session begins with @manuelkaulich.bsky.social telling us about exciting CRISPR libraries they have developed and how nuclear mRNA processing can mask the CRISPRko phenotypes @eurocancerdepmap.bsky.social
Start of the second session of the 2nd EuroCancerDepMap symposium with a talk from Manuel Kaulich
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Lars Velten @larsplus.bsky.social · 20/11/2025
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
Yes, this is where you would work (the round building, not the boat)
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Reposted by Emanuel Gonçalves
Pedro Beltrao @pedrobeltrao.bsky.social · 16/10/2025
You may have noticed that AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA) but allows it for ligands. We tried to go around this limitation by simply treating one of residues/nucleic acids as a ligand.
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Colm Ryan @colmr.bsky.social · 24/09/2025
Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw
rdcu.be
Synthetic lethality in cancer drug discovery: challenges and opportunities
Nature Reviews Drug Discovery - This Review outlines recent advances in synthetic lethality, from CRISPR-based discovery and machine learning-guided prioritization of gene pairs to new phenotypic...
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Reposted by Emanuel Gonçalves
Mathew Garnett @mgarnett.bsky.social · 20/09/2025
The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data! Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models. Start mining data now: dataminer.depmap.sanger.ac.uk
depmap miner logo
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John Doench @johndoench.bsky.social · 07/09/2025
Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...
biorxiv.org
Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design
The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...
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Eric Topol @erictopol.bsky.social · 02/09/2025
A nasal spray reduced the risk of Covid infections in a double blind, placebo controlled randomized trial jamanetwork.com/journals/jam...
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Nature Cell Biology @natcellbio.nature.com · 28/08/2025
🍹This Perspective discusses recent insights into #vimentin filament structure and function, as well as emerging findings that point to a role in #tumor invasion in #mesenchymal cells analogous to embryonic development and wound healing. 👉https://rdcu.be/eCOQp bit.ly/423dC3c
bit.ly
Vimentin intermediate filaments as structural and mechanical coordinators of mesenchymal cells - Nature Cell Biology
This Perspective presents recent insights into vimentin filament structure and function and discusses emerging findings that point to a role in tumour invasion in mesenchymal cells analogous to embryo...
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Eric Topol @erictopol.bsky.social · 26/08/2025
If this was a drug, it would be a blockbuster prevention vs Alzheimer's disease for APOE4 homozygotes, with 35% reduction of risk!
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Greg Findlay @gregfindlay.bsky.social · 18/08/2025
We recently performed SGE of RNU4-2 and identified functionally impactful variants underlying a new recessive disease. Today, the team led by @rociorius.bsky.social @alexblakes.bsky.social @cassimons.bsky.social & @nickywhiffin.bsky.social provide in-depth analysis of its clinical presentation. 🧵⬇️
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Maria Leptin @marialep.bsky.social · 23/07/2025
Very promising news on the next seven-year EU budget, with a proposed substantial increase for Horizon Europe including the ERC. We are analysing the other parts of this proposal in more detail. @Vonderleyen @EZaharievaEU research-and-innovation.ec.europa.eu/news/all-res...
research-and-innovation.ec.europa.eu
Horizon Europe 2028 - 2034: twice bigger, simpler, faster and more impactful
Research and innovation news alert: As part of the next long-term EU budget 2028-2034, the Commission is proposing to double the budget of the research and innovation framework programme to €175 billi...
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 15/07/2025
Second day of the Royal Soc Future of Science Publishing conference #FutureSciPub. This morning we start with a panel on leveraging digital infrastructure to go beyond traditional journal/article model.
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IorioLab @ioriolab.bsky.social · 06/07/2025
New work out in @natgenet.nature.com from @davidjadams.bsky.social Lab @sangerinstitute.bsky.social (with a contribution from us led by A.Vinceti): CDS2 is a cancer dependency in uveal melanomas with low CDS1 expression: a synthetic lethal axis with broad potential 🔗 www.nature.com/articles/s41...
nature.com
The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types - Nature Genetics
This study employs a functional genomic approach to identify a synthetic lethal interaction between CDS1 and CDS2 in uveal melanoma and other cancers, which may represent a potential therapeutic targe...
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Emanuel Gonçalves @emanuelvgo.bsky.social · 03/07/2025
Não há palavras... talvez cantar seja a melhor recordação! www.reddit.com/r/PrimeiraLi...
reddit.com
From the PrimeiraLiga community on Reddit: Diogo Jota 20
Explore this post and more from the PrimeiraLiga community
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Fyodor Urnov @urnov.bsky.social · 04/06/2025
Here: Baby KJ at home with his mom Nicole. This really happened, folks. Hundreds of people from 8 organizations (led by Rebecca Ahrens-nicklas and Kiran Musunuru) came together to make a bespoke gene editor for this kiddo. He was once in the 7th percentile of body weight. Look at him now! ❤️
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Yasset Perez-Riverol @ypriverol.bsky.social · 02/06/2025
🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets Meet the Team and Labs behind the project 👉 quantms.org/about #OpenSource #Proteomics #ASMS2025
quantms.org
quantms - Quantitative Mass Spectrometry Analysis
A bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS)
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Saez-Rodriguez Group @saezlab.bsky.social · 23/05/2025
Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4
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Eric Topol @erictopol.bsky.social · 21/05/2025
New @nature.com An ingenious way to track DNA replication patterns at the single-cell level that leads to cell heterogeneity and daughter cells that can potentially give rise to cancer www.nature.com/articles/s41...
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