Best Pics from Nimbus Fish Hatchery

Went to Sacramento for a Doctor's appointment and then had a 2 hour Zoom call. Decided to do the call while walking around the Nimbus Fish Hatchery which I have never been to. I heard that people had seen a rare duck there so went on over. And it was awesome. I then messaged a grad student in my lab, Alonna Wright who lives nearby and she came over for a walk after lunch. Here is a link to a slideshow of some of the pics I got

Some thoughts on Omicron and COVID19 in the last week or so

 

Some recent Tweets and threads from me on Omicron and related topics

I am dismayed by the people, including leaders, who are treating #Omicron as "mild" & therefore not a big deal ignoring the unvaccinated & unboosted, long covid, at risk groups and that it is not "mild" for everyone, just on average has less severe effects to the vaccinated

— Jonathan Eisen (@phylogenomics) January 5, 2022

If you are citing something written by Monica Gandhi on COVID please read this and other threads pointing out just how many times she has been wrong wrong wrong and wrong. https://t.co/XJcJ2kytlt

— Jonathan Eisen (@phylogenomics) January 6, 2022

Looking for guidance on how to wear / test / optimize the fit of KN95s and N95 masks.

— Jonathan Eisen (@phylogenomics) January 6, 2022

Honestly, disappointed in @Bob_Wachter calling this "new". We knew this >1 month ago. https://t.co/8UqtflU7WF

— Jonathan Eisen (@phylogenomics) January 6, 2022

Repeat after me.

It is not the flu.
It is not the common cold.
It is not mild.
It is not something to just let rip.

It is something we can and should keep fighting. https://t.co/any0vRZWwr

— Jonathan Eisen (@phylogenomics) December 31, 2021

And the @ucdavis #COVID #s and positivity rates are going up up up up up up up. https://t.co/VsqgJYyw0C

And remember, many people are away right now so, well, the #s when people return will likely be very much higher pic.twitter.com/x6cE3sKnbB

— Jonathan Eisen (@phylogenomics) January 1, 2022

Tribute to EO Wilson

 

When I was a senior at @harvard in 1990 I started an "Environmental Issues" journal as part of activities leading to the 20th anniversary of Earth Day. I hoped to get EO Wilson to be our faculty sponsor. I phoned his office and arranged a meeting with him via his assistant 1/n https://t.co/0fyvH0ykky

— Jonathan Eisen (@phylogenomics) December 27, 2021

Video and slides of my talk for the Microbiome Virtual International Forum posted

I gave a talk last week for the Microbiome Virtual International Forum. https://www.microbiome-vif.org/ Title: Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically underappreciated)" 

 See the Youtube video:  

 Slides:

Evolution of microbiomes and the evolution of the study and politics of microbiomes (or, how can something be both ridiculously overhyped and horrifically under-appreciated) from Jonathan Eisen

Also see this Twitter thread for some more info:

OK so I gave a talk for the @MicrobiomeVIF tonight https://t.co/4fJ4n6AJE6. I think it went, well OK, but it was really hard for a few reasons ... 1/n

— Jonathan Eisen (@phylogenomics) December 8, 2021

Slideshow of Otters at the UC Davis Riparian Preserve

Made a slideshow of the otters I saw at the UC Davis Riparian Preserve yesterday. See

Videos of Talks from the JGI "NeLLi (New Lineages of Life)" Meeting Now Available

Recently the DOE JGI Hosted the "NeLLi" meeting on New Lineages of life.  See agenda here: https://usermeeting.jgi.doe.gov/2021-nelli/2021-nelli-agenda/ 

There were a whole series of interesting talks in this program and now the videos are available on Youtube. 

See Youtube Channel or the embedded video link below.

Wall Street Journal Podcast on the Downfall of uBiome, part 1 and 2

Part 1 of "The Journal" podcast featuring story by Amy Marcus et al on the downfall of uBiome.  Includes interviews with multiple people including myself.

What went wrong at uBiome, Part 1. 

 

Part 2 has now been posted

 

Some recent posts of interests from my lab blog and MicroBEnet

So I have been lax in blogging these days as I spend a lot of time on Twitter. And when I do write blog posts, I don't always post here - I also post blog posts to a few other places including my lab blog and the microBEnet blog. Here are a few moderately recent posts from these places

Lab Blog

• The tale of the blue soy products – from contaminated soy milk to a new publication
• The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies (talk video and slides)
• New paper from the Eisen lab (with many others) on Global biogeography of chemosynthetic symbionts

microBEnet blog

• Metagenomic Binning / Assembly
• Wanted: Workers for the COVID19 Mass Testing Operations for UC Davis and Healthy Davis Together 
• Compiling Information about COVID19 transmission, masks, filtration, schools, etc.
• Wanted – science driven guidelines for deciding if and how to keep open / reopen schools re: #COVID19

Some thoughts on the CDC new mask guidance

 

See this thread 

I am with @kprather88 here. Really vexed by what @CDCDirector and @CDCgov have done here. I mean, I get the general idea of trying to return to normal and encourage vaccination. But here are some thoughts for why I am still a bit vexed. https://t.co/tTzdFYoTqU

— Jonathan Eisen (@phylogenomics) May 14, 2021

Made into a thread reader thread here: https://threadreaderapp.com/thread/1393025234303741954.html 

Compiling some of my Twitter comments about the evolution and origins of SarsCoV2/ COVID19

 News Stories Quoted in

• UC Davis Aggie: Emerging SARS-CoV-2 variants raise concern for the future of the pandemic
• 9/15/2020. Newsweek. Fact-check: Does a New Study Give Evidence that the Coronavirus Was Made In a Lab?
• May 17, 2020. Newsweek: Scientists Shouldn't Rule Out Lab As Source of Coronavirus, New Study Says
• April 27, 2020. The controversial experiments and wuhan lab suspected of starting the coronavirus pandemic. Newsweek. 

Twitter Threads

---

Relating to the lab vs natural origin theory of #SarsCOV2. I would like to call attention to the history of the anthrax attack investigation. Circumstantial evidence, that seemed so strong to so many people, was used to falsely accuse multiple people. https://t.co/olpDu8sKT9

— Jonathan Eisen (@phylogenomics) March 27, 2021

---

Reading: Why the COVID lab-leak theory in Wuhan shouldn't be dismissed

By ⁦@alisonannyoung⁩ in ⁦⁦@USATODAY⁩ . #covid19 https://t.co/u42TxLOcHe

— Jonathan Eisen (@phylogenomics) March 22, 2021

---

This is a fascinating deep look into theories about the origins of #B117 #SARSCoV2 variant:

A lone infection may have changed the course of the pandemic https://t.co/jKNgWth63T

By @mattsreynolds1 w/ comments from @EvolveDotZoo, @LauringLab @firefoxx66 @GuptaR_lab @jcbarret

— Jonathan Eisen (@phylogenomics) February 10, 2021

---

Worth reading / rereading - on the risks of gain of function research from 2014 from The Cambridge Working Group #covid19 #GainOfFunction https://t.co/PfTd32nNHe

— Jonathan Eisen (@phylogenomics) May 19, 2020

---

Yes, as I told @newsweek it is theoretically possible that a Chinese lab accidentally released #SARSCoV2 https://t.co/90qFnFcKJc but preponderance of evidence so far supports all natural events and the evidence actually supporting "lab release" is shown in this pic #Covid19 pic.twitter.com/TyqAiFnQuf

— Jonathan Eisen (@phylogenomics) May 3, 2020

---

Reading: Scientists shouldn't rule out lab as source of coronavirus, new study says https://t.co/cZIyRXczrY - personally I do not find the analysis in this new paper remotely convincing 1/n

— Jonathan Eisen (@phylogenomics) May 17, 2020

New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

See Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum 

Paper based on PhD thesis work of Katie Dahlhausen and wrap up of analysis led by Laetitia Wilkins. 

Full citation:

Dahlhausen KE, Jospin G, Coil DA, Eisen JA, Wilkins LGE. 2020. Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PeerJ8:e10177 https://doi.org/10.7717/peerj.10177

Acknowledgements. We thank Céline Caseys ORCID: 0000-0003-4187-9018 for her idea to search eggNOG annotations against KEGG Class 1.11 Xenobiotics biodegradation and metabolism pathways; Chris Brown ORCID: 0000-0002-7758-6447 for his script to download assemblies in batch from GenBank; Cassandra L. Ettinger ORCID: 0000-0001-7334-403X for valuable comments on the pangenome analysis and help with revising the figures. We also thank Dr. Joseph Gillespie ORCID: 0000-0002-5447-7264, Dr. Raphael Eisenhofer ORCID: 0000-0002-3843-0749 and two anonymous reviewers for comments on the submitted manuscript. Isolate 16S Sanger sequencing was performed at the UC Davis College of Biological Sciences DNA Sequencing Facility.

Green heron at Yolo Bypass

View this post on Instagram

Green heron at #YoloBypass today #nature #birdphotography

A post shared by Jonathan Eisen (@phylogenomics) on Sep 20, 2020 at 7:11pm PDT

Great horned owl at #YoloBypass

 

Went for a walk at Yolo Bypass 8/23/2020 early in the AM and got a nice view of a Great Horned Owl. Here are some pics.

Introducing "Hammerhead Man" - the superhero you did not know you needed.

So I was digging through some old school papers because my daughter asked me what books they had use write reports on in high school and, well, I have a lot of my English papers from high school in a box in a closet.  

And in digging through this box I found a short story I wrote for a creative writing class from freshman year in college, which was taught by Catherine Tudish. 

Now, mind you, I was not in a good place when I wrote this as I was reading from the death by suicide of my father.  And, possibly related to that I truly have almost no memory of writing this, other than the concept of the assignment. But I read it to my kids. And, well, I actually like it.  It has a lot of issues.  But I think it should be expanded on. I may just revisit this.

So - here is the official first release of "Hammerhead Man".  With corrections and comments from Catherine Tudish. 

Brief summary of the gear I use for photography (of mostly birds)

So - many people have asked what gear I use for my photography (mostly of birds). Here is a quick summary. See some of my pictures here: https://jonathaneisen.smugmug.com



Camera: Nikon D500




 Lenses Birding: Nikkor 200-500 f/5.6
 

 Macro: Nikkor 105 mm f/2.8
 


Based on review of Mark Smith.

See more detail in this blog post here. "Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500.

Slides I have used for "Biodiversity and the Tree of Life" at @ucdavis

I have posted the slides I have used so far in remote teaching for "Biodiversity and the Tree of Life" - aka Bis2C - at UC Davis and I thought I would share them here.

Many of the figures are from "Life v 11" by Hillis et al. which is the textbook we have been using for the class. I have been told in the past by the publishers that this was OK to do so I am assuming it is still OK. Hope there are not too many errors ... for some reason Lecture 10 will not upload - working on it

BIS2C_2020. Lecture 6. The Tree of Life. from Jonathan Eisen

BIS2C_2020. Lecture 7. The Domains of Life. from Jonathan Eisen

BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes from Jonathan Eisen

BIS2C_2020. Lecture 9. Form and function from Jonathan Eisen

BIS2C2020 - Lecture 10 - Parasites and Pathogens from Jonathan Eisen

BIS2C_2020. Lecture 11 Viruses and gene transfer from Jonathan Eisen

Lecture 12 - Mutualisms and Microbiomes - BIS2C from Jonathan Eisen

BIS2C_2020. Lecture 13 Organelles and Endosymbiosis from Jonathan Eisen

BIS2C_2020. Lecture 22 Fungi Part 1 from Jonathan Eisen

BIS2C_2020. Lecture 23 Fungi Part 2 from Jonathan Eisen

Today's stay at home activity - virtual tour of the Dali museum

Love that the Dean of the College of Biological Sciences Mark Winey sent out a suggestion to check out this virtual tour of the Dali Museum in his regular message to the college.  And it is pretty cool. Check it out: Visit the museum as you have never done before! | Fundaci� Gala - Salvador Dal�

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Another #NatureAtHome project: Never Home Alone:

This is another nice at home activity relating to Nature.  Rob Dunn and colleagues have been running this  Wildlife of Your Homes project in various ways for many years.  And it is easy to participate in it via iNaturalist. Take pics of bugs or other critters in your home and then post them and add them to the iNaturalist project.  See Never Home Alone: The Wild Life of Homes � iNaturalist.

Resource for #NatureAtHome: California Academy of Sciences

OK have not been posting much to this blog for a few weeks due to the disruption from the coronavirus but I am going to start posting again when I find things that may be of use for the new world of social distancing, etc.



Today I am posting about the California Academy of Sciences which has a nice page compilation information and resources they have for activities at home: Academy @ Home | California Academy of Sciences



Thanks Cal Academy.

Collecting some of my comments about Sacramento County's poor response to COVID19

Posted this rant on March 9

This does not seem like a good plan: "Sacramento County Announces New Mitigation Efforts COVID-19" https://t.co/5W3Dv4Lqr9 #COVID19 #Coronavirus - especially the plan to shift from containment to mitigation #Sacramento cc: @sacbee_news 1/n pic.twitter.com/dYUwEoUGb1

— Jonathan Eisen (@phylogenomics) March 9, 2020

And then another rant

I think the Sacramento plan is problematic - if they are correct that it is time to ditch containment and move to mitigation then why is their mitigation plan among the weakest announced anywhere ? See https://t.co/mHnvLbdGGG https://t.co/mHnvLbdGGG

— Jonathan Eisen (@phylogenomics) March 10, 2020

And this one

But couldn't you do quarantine for some people but not necessarily for health care workers?

— Jonathan Eisen (@phylogenomics) March 10, 2020

And then Placer and Yolo County came out with their somewhat more aggressive plan

So #Yolo and #Placer counties have announced that they are also stopping containment efforts. I still think this is a bad idea but at least compared to #Sacramento county these counties are at least pushing the mitigation strategy a bit more strongly. See https://t.co/pbtsOMbmGN https://t.co/ZZlO2NtmFX

— Jonathan Eisen (@phylogenomics) March 10, 2020

And more

The Sacramento County plan is a joke - 1) containment is still useful in some cases, they should not ditch it 2) their plan for mitigation (reducing community spread) is the most limited of any place I have seen in the country -see https://t.co/ZZlO2NtmFX

— Jonathan Eisen (@phylogenomics) March 11, 2020

And this

Brutally behind the curve - Sacramento’s public health leader - Q&A: Sacramento’s top health official on what’s being done to stop the coronavirus outbreak https://t.co/enebtjqNkK

— Jonathan Eisen (@phylogenomics) March 15, 2020

And another

So - I went through the #Sacramento County plan for dealing with #COVID19. It is bad. https://t.co/ek99YNBzSw

— Jonathan Eisen (@phylogenomics) March 10, 2020

And this

Really incredibly important and calls into doubt the inane claims from #Sacramento, #Yolo and other local counties that we have to stop contact tracing and other containment actions https://t.co/qp5rE3uACg

— Jonathan Eisen (@phylogenomics) March 11, 2020

And another

Really disappointed in #Sacramento health director’s approach: Sacramento County Health Director Defends Coronavirus Strategy, Says Lack Of Tests Made Containment Impossible - https://t.co/tiWN9gGBkS https://t.co/nqikmcSc67

— Jonathan Eisen (@phylogenomics) March 14, 2020

And another

Really great article by @edyong209 about some of the problems with the UK #covid19 strategy and communications; sadly some similar things have been going on here in #Sacramento area https://t.co/jtdVqkfPel

— Jonathan Eisen (@phylogenomics) March 16, 2020

My posts about #UCDavis and #Covid19

Going to use this page to keep track of some of what I have been posting about what is going on at UC Davis in regard to the coronavirus.  Will add more later ... but just going to use this to keep track.

February 26

Things blew up at @ucdavis with reports that the 1st community acquired case of COVID19 was at our hospital. I received an email about this that I eventually posted to Twitter (I waited to post until I saw others reporting this)

Email I received earlier today from @ucdavis Medical Center leaders regarding the case of apparently community acquired #COVID19 in #Sacramento at #UCDavis hospital pic.twitter.com/q9qrJq5iWo

— Jonathan Eisen (@phylogenomics) February 27, 2020

Tons of stories came out over the next few weeks about this and I will add some links to them. But eventually, attention went elsewhere as the 1st large clusters of cases that were detected in the US ended up being in other locations.

March 7.

Actions from UC Davis announced regarding COVID19 was, well, better than nothing but pretty limited.

Announcement from @ucdavis re: #ucdavis #COVID19 #Coronavirus #SocialDistancing:

Will help increase social distancing but not going as far as I would like ... I hope this moves very soon from "recommend" to "require" https://t.co/khnnVCZFeN

— Jonathan Eisen (@phylogenomics) March 8, 2020

Important announcement from @ucdavis: not as far as I would like but will help increase social distancing; hope they move from "encourage" to "require" soon ... #ucdavis #COVID19 #Coronavirus #SocialDistancing https://t.co/sqjGXO3fqF

— Jonathan Eisen (@phylogenomics) March 8, 2020

March 10. 

UC Davis expanded actions.

Major new actions from @ucdavis regarding #COVID19 #Coronavirus h/t @TLowePower https://t.co/NLOLw2EaH0

— Jonathan Eisen (@phylogenomics) March 10, 2020

Some of my favorite books about infectious disease, viruses, bioweapons in relation to #Coronavirus #COVID19

I posted some pics of my books I brought home from work to look over in relation to the current coronavirus outbreak and some people asked if I could post a list. So here is a collection. I will update with other books.

I used Amazon links here b/c, well, that was really simple.


Infectious Diseases

 


Biological Warfare

 

General Information about Viruses

 

What's worse than not cancelling your conference during #COVID19? How about a #MANEL #YAMMM during #COVID19.

Well got invited to this meeting "Non-Coding RNAs In Biology & Medicine Conference".  And I looked up the meeting so I could see if the meeting was still on and if yes, to then encourage the organizers to encourage them to postpone the meeting to help reduce the spread of the coronavirus going around.

And alas, the meeting still on - April 2-4, 2020
As a side note, it is around the corner from where I used to work (it is in the same general area as where TIGR used to me).

And, alas, on top of the meeting apparently still being on, it is also what appears to be a MANEL - a meeting with a highly skewed gender balance of speakers.  I say "what appears to be" since I just do not have time right now to do what I frequently do which is to look up people's personal websites to see how they describe themselves in terms of gender.  So I am basing this entirely on names and appearance but it does not look like a good balance.

Not a good look Johns Hopkins and USUHS,

#1 - due to #COVID19 this conference should be cancelled
#2 - due to the apparently extreme gender skew for the speakers, this conference is one I would encourage people to not attend anyway.

Reading Relevant to Contributions to Diversity, Equity and Inclusion Statements (by Prof. Dawn Sumner)

Dawn Sumner, a colleague and friend of mine who is a Professor at UC Davis, sent me this document she has written up on readings of relevance to DEI statements and I thought it would be useful broadly and offered to post it here.  See below:

Reading Relevant to Contributions to Diversity, Equity and Inclusion Statements

By Dawn Sumner

Summary: the state of knowledge on diversity, equity and inclusion in universities, with all their intricacies: “An Inclusive Academy – Achieving Diversity and Excellence” by Stewart and Valian. This is a long read at something over 400 pages. It is very good and presents the issues with nuance and discussions of what unknown.  The library provides free digital access: https://direct.mit.edu/books/book/4114/An-Inclusive-AcademyAchieving-Diversity-and

Chapter 5 is specifically about faculty hiring. It includes a good list of design principles for avoiding bias in hiring. Diversity statements are mentioned as one aspect. It also explains the context for why there is such a huge drop between the available pool of underrepresented candidates and those who actually apply to faculty jobs at UCD.

https://direct.mit.edu/books/book/4114/chapter/170145/Recruiting-New-Faculty-Developing-a-Diverse-Pool

Morality and Diversity:This article describes 3 moral approaches to diversity, including the intrinsic conflict between 2 of them that reflect the debate we are currently having over DEI statements. The third (new) approach is to focus on the virtues/skills that someone needs to have to do their job well and the values of the organization to shape fair practices that promote excellence. https://link.springer.com/article/10.1007/s10551-012-1434-z

What’s in DEI Statements?Some of the arguments against requiring DEI statements relate to their contents. Here are some analyses of what's in real statements from applicants. (Note that I saw on twitter tonight some complaints about plagiarized DEI statements - so it is certainly true that there are problems.)

short: https://www.insidehighered.com/news/2018/11/19/new-paper-explores-what-faculty-candidates-include-their-diversity-equity-and

longer: https://quod.lib.umich.edu/cgi/t/text/idx/c/currents/17387731.0001.112/--promise-of-diversity-statements-insights-and-a-framework?rgn=main;view=fulltext

           

To me, the combination of using a virtues-and-values–focused framework for considering diversity, placed in the context of understanding how academic processes are discriminatory with an understanding of what’s communicated in diversity statements shows: 1) the potential value of DEI statements; and 2) how they should be used appropriately to help inform the process of finding colleagues who possess the skills (virtues) to promote our values (as we express them).

DEI statements can help us find the best colleagues. Misusing them can be very damaging. We need to work on setting appropriate standards for how to effectively use DEI statements to level the playing field, promote equity, and ensure excellence.

A month of #DailyINat - observations posted to @inaturalist every day for January 2020

I posted a thread to Twitter about this topic. See

OMG I pulled it off. I did daily observations that I posted to @inaturalist for all of January #DailyiNat - see my Calendar - this was not trivial since I was on jury duty for almost three weeks (with some time off in the middle) 1/n https://t.co/Wff4VP9E4t

— Jonathan Eisen (@phylogenomics) February 1, 2020

if you want to see this on Twitter but am reproducing it here.


OMG I pulled it off. I did daily observations that I posted to @inaturalist for all of January #DailyiNat - see my Calendar - this was not trivial since I was on jury duty for almost three weeks (with some time off in the middle) 1/n
https://www.inaturalist.org/calendar/phylogenomics …


____________________________________

In total I made 1841 observations for the month - see https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&subview=table&user_id=phylogenomics&verifiable=any… - might go up a little as I got through a few more pictures #DailyiNat 2/n

____________________________________

My observations were predominantly (97%) of birds (for those who KNow me I am sure you are shocked, shocked by this) https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&subview=table&taxon_id=3&user_id=phylogenomics&verifiable=any… #DailyiNat 3/n

____________________________________

All of these observations were in the general area near #DavisCA and #SacramentoCA #DailyiNat 4/n



____________________________________

Most amazing to me was that I reported >120 species of birds during this time - including a few lifers #DailyiNat https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&subview=table&taxon_id=3&user_id=phylogenomics&verifiable=any… 5/n

____________________________________

Incredibly grateful to @inaturalist @LMGerhart @ReaderMeter @ShannonSkalos @talonDNA @tvanlaarmicro @calacademy and many many others for inspiration and all the people doing IDs to help me out https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&taxon_id=3&user_id=phylogenomics&verifiable=any&view=identifiers… #DailyiNat 6/n

____________________________________

One of my favorite observations during this time: Prairie Falcon - https://inaturalist.org/observations/37667468… my 1st time seeing one #DailyiNat 7/n



____________________________________

Also seen a few ferruginous hawks which are becoming one of my favorite birds - https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&subview=grid&taxon_id=5181&user_id=phylogenomics&verifiable=any… #DailyiNat 8/n

____________________________________

Also fun - my 1st pics of a golden crowned kinglet https://inaturalist.org/observations?d1=2020-01-01&d2=2020-01-31&place_id=any&subview=grid&taxon_id=117100&user_id=phylogenomics&verifiable=any… #DailyiNat 9/n

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