Went on a brief trip to Monterey, CA last week. Took lots of pics. Here are some of the better ones. Also see postings with identifications at iNaturalist.
Sunday, June 05, 2022
Monday, May 16, 2022
Videos about using the UCSC Genome Browser for analysis of SarsCOV2
These look pretty useful and thought I would post here. Text is from the UCSC Youtube channel
This 5-part video series is for virologists and public health researchers interested in leveraging the UCSC Genome Browser and web interface to UShER (Ultrafast Sample placement on Existing tRees). These tools are a 'one-stop shop' to understand SARS-CoV-2 through genome annotations as well as track variants by placing your samples in a phylogenetic tree with millions of other SARS-CoV-2 sequences. Use the SARS-CoV-2 Genome Browser: http://bit.ly/sarscov2browser Visit our SARS-CoV-2 Genome Browser and UShER quick start page with videos, scripts and more: http://bit.ly/ucsccovidbrowser COVID-19 Research at UCSC: https://genome.ucsc.edu/covid19.html 'The UCSC SARS-CoV-2 Genome Browser' publication: https://www.nature.com/articles/s4158... 'Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic' publication: https://www.nature.com/articles/s4158... UShER documentation, installation, source code:: https://github.com/yatisht/usher https://usher-wiki.readthedocs.io/en/... COVID-19 Genomic Epidemiology Toolkit module "Realtime Phylogenetics with UShER: https://www.cdc.gov/amd/training/covi... Learn more about the UCSC Genome Browser: http://genome.ucsc.edu https://twitter.com/genomebrowser Learn more about the UCSC Genomics Institute: https://twitter.com/ucscgenomics https://genomics.ucsc.edu/
Saturday, April 23, 2022
Endosymbiosis Animations for "Biodiversity and the Tree of Life"
Note - I added music - Mussorgsky - Night on Bald Mountain for drama ... I also posted it to Facebook:Endosymbioses are so cool:
— Jonathan Eisen (@phylogenomics) April 20, 2022
Some of the images / animations I will be using today in BIS2C at @ucdavis (I made a little movie and added music here but will have richer explanations for class) pic.twitter.com/92Eb7PMTjL
OK - updated with modifications based on corrections/comments from @Sergiophyceae @mcsymbiont & @DanStarrUCDavis (note, again, these are extracted from slides with lots of other details including comments about which things don't always happen ...) pic.twitter.com/LNGO8Zs94E
— Jonathan Eisen (@phylogenomics) April 21, 2022
Tuesday, April 05, 2022
A good bye to my beloved Clover
Our adopted cat Clover is pretty sick right now and likely on her last legs. We (my family, and the family of @LoranWyman who were her previous caretakers) are very sad. I compiled some of my Tweets about her here https://t.co/JqY1Mijips
— Jonathan Eisen (@phylogenomics) April 3, 2022
Sadly, Clover is gone. I am 💔. I loved her very very very much. https://t.co/xQ1QXMQ658
— Jonathan Eisen (@phylogenomics) April 3, 2022
Monday, March 28, 2022
The ongoing saga with the UC Health Insurance Pharmacy "Benefits" Via Navitus
See this thread in an easier to read format here: https://threadreaderapp.com/thread/1500934973775249412.htmlDear @UofCalifornia @ucdavis
— Jonathan Eisen (@phylogenomics) March 7, 2022
This is NOT OK.
I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting "as of January 1, 2022". Letter was dated in February and was received after March 1, 2022.
This is NOT OK.
See this thread in an easier to read format here https://threadreaderapp.com/thread/1506297722776657920.html And then I got told Navitus was going to be instructed to cover my insulins by UCOP but the message clearly was not recieved.Well, in case you missed it. Two weeks ago I posted about the disastrous and dangerous and incompetent new University of California pharmacy benefits "system" which warned me, two months after the fact, that they were cutting off coverage of my insulin 1/n https://t.co/QuTBaQBsaQ
— Jonathan Eisen (@phylogenomics) March 22, 2022
And finally and thankfully today I was told my insulins would be covered.Well - good news for me - I have been told that Navitus has been instructed to cover the insulin I have been using. More coming soon when I get confirmation and details.
— Jonathan Eisen (@phylogenomics) March 23, 2022
I am now interested in what is happening to others out there who have been harmed by the UC / Navitus system.Update - to the saga of the Navitus pharmacy "benefits" plan. I got a call today saying that my Novolog and Lantus insulin would indeed be covered by Navitus. Yay. I am very happy. Now I want to know what is going to happen to others who were harmed by the new plan ... https://t.co/yvtlODyIbz
— Jonathan Eisen (@phylogenomics) March 29, 2022
Wednesday, March 23, 2022
Some links to articles about Diabetes and COVID19
Posting some information about #COVID19 and #type1 #diabetes that might be useful to folkshttps://t.co/q9LrTXyrAy
— Jonathan Eisen (@phylogenomics) March 21, 2022
"Your Guide to Post-COVID Travel with Type 1 Diabetes"
"As masks come off, vulnerable Americans feel left behind"https://t.co/WGDJ1eII6x
— Jonathan Eisen (@phylogenomics) March 21, 2022
COVID-19 Update: The Diabetes Connection, WHO Concerned about BA.2https://t.co/GT9xXPMNX2
— Jonathan Eisen (@phylogenomics) March 21, 2022
Coronavirus (COVID-19) – information for people living with type 1 diabeteshttps://t.co/4L8MAMGtpz
— Jonathan Eisen (@phylogenomics) March 21, 2022
Why Do Diabetics Need to be Cautious About Omicron Variant?https://t.co/IdsokhYIpO
— Jonathan Eisen (@phylogenomics) March 21, 2022
How COVID-19 Impacts People with Diabeteshttps://t.co/iOOeT6N8G9
— Jonathan Eisen (@phylogenomics) March 21, 2022
Rights for Workers with Diabetes During the Coronavirus Pandemichttps://t.co/OjGpLpWEpg
— Jonathan Eisen (@phylogenomics) March 21, 2022
This is also useful: https://t.co/gx3HDCXLpE
— Jonathan Eisen (@phylogenomics) March 23, 2022
In particular this part is important pic.twitter.com/X7EwIJyPNb
— Jonathan Eisen (@phylogenomics) March 23, 2022
This also has some useful information https://t.co/sFFkf8BtWQ
— Jonathan Eisen (@phylogenomics) March 23, 2022
For example says diabetics are at higher risk even when fully vaccinated "Garza-Silva, who is immunocompromised, and Liber, who is diabetic, are among the millions of Californians at greater risk of complications from a COVID-19 infection despite being fully vaccinated."
— Jonathan Eisen (@phylogenomics) March 23, 2022
See also
Independent risk factors of COVID-19 pneumonia in vaccinated Mexican adults
Age, Underlying Conditions Top Factors in Breakthroughs
A Wall Street Journal analysis found that among fully vaccinated people, the ones most likely to be hospitalized with breakthrough infections of COVID-19 are the elderly and those with specific underlying medical conditions.
“In particular, people with diabetes, chronic lung disease, kidney disease and compromised immune systems were at risk of serious outcomes from breakthrough cases,” The Journal reported.
Lots of useful responses to question "What should high risk people do in face of relaxed masking requirements"?
So I posted this to Twitter.
So - hive mind. A question. If you were at high risk for COVID complications if infected, with the ending of indoor mask requirements, would you just try to avoid large indoor gatherings of people even when you wear a good mask?
— Jonathan Eisen (@phylogenomics) March 18, 2022
And got lots of useful resposnes. Rather than compile them here if interested people should browse the responses.
Tuesday, March 22, 2022
The ongoing disaster of the new UC Health Insurance Pharmacy "benefits"
Dear @UofCalifornia @ucdavis
— Jonathan Eisen (@phylogenomics) March 7, 2022
This is NOT OK.
I just got a notice by letter in mail that my insurance will no longer cover the insulin I have been getting "as of January 1, 2022". Letter was dated in February and was received after March 1, 2022.
This is NOT OK.
Well, the saga continues -- just got this from Navitus. They say I "may be eligible" for an extension of 1 bonus month with my prior prescription. Pretty useless to be honest. pic.twitter.com/ASUHvYuUwn
— Jonathan Eisen (@phylogenomics) March 14, 2022
Below is the email from UC. More about this in a bit but I wanted to share the full text for people to see here.
An important message from UC about your pharmacy benefitsDear Jonathan,We are writing to acknowledge — and apologize for — the problems many members of the UC community are experiencing with Navitus Health, a new administrator of pharmacy benefits for UC employee and Medicare PPO plans, and to let you know what we are doing to fix the problems.Last year, University of California Health (UCH) and UC Systemwide Human Resources selected Navitus Health to administer pharmacy benefits, starting Jan. 1, 2022. This decision was made following an extensive formal bid process, conducted by a committee with representatives from UCH, Systemwide HR, UC faculty with pharmacy expertise and UC’s retiree association.Navitus was selected as the partner that could provide UC with the best overall flexibility, service, and affordability. However, since UC’s transition to Navitus Health, we have heard from too many members who have been negatively impacted by this change.Some members have had to change prescription drugs, been required to complete time-consuming authorization processes and experienced denials by Navitus, causing unnecessary anxiety and frustration. Navitus failed to meet the scheduled target date for mailing a clinical transition letter, causing hardship and worry for faculty, staff, retirees and their family members.Additionally, like many employers Navitus has faced customer service staffing challenges, leading to wait times that far exceed Navitus’ standards and UC performance guarantees. Among other things, this has put undue pressure on benefits professionals at UC locations and in the UC Retirement Service Center and the UCPath Center, as they have worked to provide support that should be handled by Navitus.We take these problems — and our responsibility to ensure that members of UC health plans have access to the prescriptions they need — very seriously. UCH and UC Systemwide Human Resources have been in constant communication with Navitus, and we want to let you know what we are doing to fix these problems.Support with member transitions
- Due to the delay in mailing clinical transition letters, Navitus has provided an extended transition period to the end of April for drugs that are not covered. Extension letters and an email campaign were recently initiated.
- Navitus will call members who need to transition to new medications directly and offer help with authorizations, denials, and appeals. Those who have experienced a denial for a Not Covered/Non-Formulary medication will also receive a phone call offering help.
- UCH, Alliant (a UC consultant) and Navitus will audit and review the protocols Navitus uses for denials to ensure they are in alignment with Navitus internal guidelines, industry standards and Medicare guidelines – and to identify and correct any gaps.
Customer service improvements
- Navitus has committed to adding an additional 35 customer service representatives (an increase from 125 to 160) by the end of April, and hopes to add another 15 staff after that, along with additional support for UC benefits professionals.
- Navitus has also added two more personnel with pharmacy clinical expertise to help UC benefit professionals support members.
- In addition, Navitus is exploring a concierge-type customer service model to ensure UC members receive the dedicated assistance they need.
Again, we sincerely apologize for any difficulties you or your family members have experienced during this transition. We are committed to you receiving the critical health care you deserve, without unnecessary inconvenience or frustration.Sincerely,Cheryl Lloyd Dr. Carrie ByingtonVice President Executive Vice PresidentSystemwide Human Resources University of California HealthPlease do not reply to this message. Replies to this message are routed to an unmonitored mailbox.
Saturday, March 19, 2022
Baby Hummingbirds at Yolo Bypass
So I got a glimpse of a hummingbird nest at Yolo Bypass
Hummingbird sitting in nest at #yolobypass - thanks to @ucdavis Prof. David Rizzo and wife who I bumped into and who pointed it out pic.twitter.com/qHRxfz2Fgl
— Jonathan Eisen (@phylogenomics) March 6, 2022
And this was amazing for me - might be 1st hummingbird I have seen in field on a nest since 1988 when I studied Broad tailed hummingbirds at @RockyMtnBioLab with Bill Calder
— Jonathan Eisen (@phylogenomics) March 6, 2022
And then I went back and got a better look at it , with babies ...Here are a few higher resolution pics (now that I got home) pic.twitter.com/2HXkxJmSKc
— Jonathan Eisen (@phylogenomics) March 6, 2022
And I posted some videos tooFollow up from a few days ago ..
— Jonathan Eisen (@phylogenomics) March 18, 2022
Baby
Hummingbirds
In
Nest
I did not want to disturb so stayed really far away (this is cropped and was taken with a 500 mm lens)
But still -- OMG OMG OMG https://t.co/DboPEDSfkP pic.twitter.com/ceI3HnQa1Z
Friday, February 11, 2022
A field guide to SarsCOV2
Gave a talk on SarsCOV2 to the Yolo County Community of Practice group. I basically discussed how the concept of a field guide can be useful for thinking about SarsCOV2. Here are my slides I will try to post the recording of the talk at some point.
Wednesday, February 09, 2022
Monday, January 10, 2022
Best Pics from Nimbus Fish Hatchery
Friday, January 07, 2022
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.
— Jonathan Eisen (@phylogenomics) December 31, 2021
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
And the @ucdavis #COVID #s and positivity rates are going up up up up up up up. https://t.co/VsqgJYyw0C
— Jonathan Eisen (@phylogenomics) January 1, 2022
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
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