Twisted tree of life award: throwback PR from an ingrained Oregon State

Just got pointed to this PR:  Unwanted impact of antibiotics broader, more complex than previously known — ScienceDaily

It has one of the worst microbe-evolution sections of text I have seen in a long long time:

Mitochondria plays a major role in cell signaling, growth and energy production, and for good health they need to function properly. 

But the relationship of antibiotics to mitochondria may go back a long way. In evolution, mitochondria descended from bacteria, which were some of the earliest life forms, and different bacteria competed with each other for survival. That an antibiotic would still selectively attack the portion of a cell that most closely resembles bacteria may be a throwback to that ingrained sense of competition and the very evolution of life.

Yup.  That antibiotics that target bacteria also affect mitochondria is a throwback to that ingrained sense of competition and the very evolution of life. 

Can anyone – anyone – please – please – tell me what that means?

For this, I am giving the folks from Oregon State a coveted Twisted Tree of Life Award.

At #UCDavis today: Jorge Rodrigues talk on “Disrupting the spatial structure of microbial communities in the largest tropical forest in the world”

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. Jorge Rodrigues

(Dept. of Land, Air and Water Resources)

"Disrupting the spatial structure of microbial communities in the largest tropical forest in the world"

Wednesday, February 11, 2015

4:10 pm

1022 Life Sciences

Rodrigues 2-11-15.doc

Postdoc jobs in microbial bioinformatics in Iddo Friedberg’s lab at Iowa State

The Friedberg Lab is recruiting postdoctoral fellows to several newly funded projects. The lab is relocating to Iowa State University in Ames, Iowa as part of a university-wide Big Data initiative. Iowa State is a large research university with world-leading computational resources, and a strong highly collaborative community of bioengineering, bioinformaticians and life science researchers.

The successful candidates will be joining the lab at the College of Veterinary Medicine, Department of Veterinary Microbiology. Areas of interest include: bacterial genome evolution, gene and protein function prediction, microbial genome mining, animal and human microbiome, and biological database analysis.

These are bioinformatics postdoc positions, and the successful applicants would be required to perform research employing computational biology skills.

Requirements: A PhD in microbiology, bioinformatics, or a related field. A strong publication record in peer-reviewed journals. Strong programming skills; strong oral and written communication skills in English; Strong domain knowledge of molecular biology. Salary is competitive and commensurate with experience. The Friedberg lab is a computational biology lab equipped with high-end cluster computers and bioinformatics support.

Ames, Iowa is constantly ranked as one of the best places to live in the US, and has received numerous awards for being a progressive, innovative and exciting community with high affordability and high quality of life.

Candidates should send a C.V. and statement of interest as one PDF document, and have three letters of reference sent independently by their authors to Dr. Iddo Friedberg at Friedberg.Lab.Jobs. Screening of applications begins immediately and will continue until the positions are filled. The positions are expected to start on or after June 2015.

All offers of employment, oral and written, are contingent upon the university’s verification of credentials and other information required by federal and state law, ISU policies/procedures, and may include the completion of a background check. Iowa State University is an Equal Opportunity/Affirmative Action employer. All qualified applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, genetic information, national origin, marital status, disability, or protected veteran status, and will not be discriminated against. Inquiries can be directed to the Director of Equal Opportunity, 3350 Beardshear Hall, (515) 294-7612

This will be excellent: S. Tringe at #UCDavis- Microbial diversity and greenhouse gas dynamics in San Francisco Bay wetlands

Susannah Tringe

Research Scientist, Department of Energy Joint Genome Institute
Title: “Microbial diversity and greenhouse gas dynamics in San Francisco Bay wetlands”

Tuesday, 4:10 – 5:30PM

February 3, 2015

1022 Life Sciences Building

The entire CPB Seminar schedule is available here: http://cpb.ucdavis.edu/Seminars.html.

Quick post – wanted – input on best practices for sample processing & storage for microbiome studies

Over at microBEnet I have a post that may be of interest to many readers: Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? | microBEnet: the microbiology of the Built Environment network.  Basically I am hoping to get a discussion going about the ins and outs of sample processing and storage for microbiome studies.  We have been having lots of discussions in my lab and with collaborators about this and thought it would be better to just get everyone involved.

Secret microbiome forensic study reveals #deflategate culprit

Chicago. January 31, 2015.

I had the incredible luck to be on an assignment in the midwest this week visiting the lab of Jock Giblet, one of the world’s experts in the new and merging superfield of microbiome forensics.  Giblet  has been at the forefront of forward thinking on using foreheads and foreskins and other microbiome rich samples to do forensics.  His lab has already been involved in hundreds of criminal investigations where microbial forensics was used to do important things like (1) show that microbes were on people involved in crimes (2) that analysis of microbes can be used to reveal who was last in a room (making a few assumptions like, you know who was in the room and what their microbes look like and who was not in the room) and (3) the microbes could be considered as possible instigators of various crimes.

Anyway – I was there to interview Giblet about his latest amazing work on the how microbiome analysis can be used to cheat at card games.  But he was distracted by something.  He called me into his spacious yet somehow very dark and depressing office and said “Can I let you in on a secret?”  Of course I said yes.  Alas, for him, he never said “Can this be off the record?” so I am reporting to you what I then found out, along with some secret recordings I made with my awesome Google Glass recording device.

Over the next 24 hours I witness Giblet and members of his microbiome lab then do a top secret microbiome driven analysis of the deflategate controversy.   It was so exciting to be witness to this edge cutting research.  Below is a description of what I witnessed.

1. Giblet and team travel to the airport to collect footballs from the NFL

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The footballs lined up waiting to be picked up

2. Giblet brings footballs back to the lab and also collect wan assortment of other materials for control experiments

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Aerial of the Top Secret Lab where Dr. Giblet works

3. They then set up a microbiome analysis in their top secret lab with some key samples for testing and as part of the experiment

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Another kind of football
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A key control – a Patriots softball
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Yet another kind of football
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A regulation football
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A football collected at halftime from the Patriots game
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New, sterile examples of the suspected tampering tools

4. It was here that I was able to finally activate the video recording on my Google Glass.  It only worked sporadically but I did get some video of the Giblet lab in action carrying out a microbiome forensic study.  Basically, they used these really complicated secret sampling devices that came hidden in a tube:

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Top secret microbiome sampling device

And they used this to collect microbiomes from multiple sources including hands,  the suspected deflation devices (before and after handling), and the balls before and after handling.  Here is what I could get:

After doing some test samples the then got the footballs from the NFL that they had picked up at the airport and sampled them too.  They also spent a lot of time on the phone discussing some sort of sampling of the hands of all employees of the Patriots and the other team.  And while we were sampling the footballs someone showed up in the lab with a bag of more of these special sampling devices labelled with names of various people.

They then took all the special sampling devices and “got the fu#*(#@ DNA out of them, for sure”.  It was exciting to watch.

5. Sequencing

The DNA from the sampling devices was then dripped into a small device that plugged into a laptop computer via a USB port.  It looked a bit like a thumb drive.   Dr. Giblet spent a lot of time looking at the screen, typing some stuff, and crying and cursing.  He then said “Screw these minions.  I am going back to the Illuminati” and he carried a box of samples out the door, cursing, in a strange accent.  I am not sure how he was connected to the Illuminati but nevertheless, he returned eight hours later (I was getting really impatient, and hungry, sitting there waiting for him, still wearing my Google Glasses).  And he looked happier.  And he said “Booyah – we have data”.

He then explained to me how he had taken the DNA out of the microbes in the samples and did some special chemistry and got out a file with information that would help determine what microbes were in each sample.

6. Analysis

Dr. Giblet and two other people who seemed to be employees of his, then sat in front of an old IBM computer doing something.  I am not sure but I think their names were Jane Jane and Sir Robert.  Very interesting people I note.   Anyway, the cursed a lot, typed a lot, kept talking about some sort of chime they kept hearing.  These were smart people I think.  But really secretive and talking in code all the time.  In fact, they kept asking Sir Robert to do more code, though I note, I had no idea what he was saying anyway.

Nevertheless, after 10 more hours they finally woke me up (I had fallen asleep on the lab floor) and said “We have the answer.”  And then they had me sit in front of a computer to look at some pictures.  By this point my Google Glasses were really acting up.  The best pics I  could get are shown below.

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Apparently these graphs showed that the culprit behind the NFL DeflateGate controversy was none other than Jock Giblet himself.  That is, the samples from the Patriots’ footballs most resembled samples from Giblet’s hands.  He swore to his friends and colleagues that it was not him and that he would never do something like that.  But as they called 911 they said “Sorry Jock. We will miss you.”

Then they shuffled me out the door too.  They never noticed the Google Glass, but I have been cut off from my sources so not sure what happened to Jock after he was taken away.

#UCDavis Biodiversity Museum Day Feb 8

Just recieved this:

Dear MSOs, CAOs,

Please distribute widely.

On Sunday, February 8, six UC Davis natural history museums will once again open their doors to the public for tours and family-friendly activities. The museums are: The UC Davis Center for Plant Diversity (herbarium), the Botanical Conservatory, The Bohart Museum of Entomology, The Anthropology Collections, the Paleontology Collections, and the Museum of Wildlife and Fish Biology.

Attached is a map of where the museums are on campus. The UC Davis Botanical Conservatory is behind Storer Hall and the Center for Plant Diversity is in the Sciences Laboratory Building.

More information can be found at this link:

http://ucanr.edu/blogs/blogcore/postdetail.cfm?postnum=16535

2015 UC Davis Biodiversity Day Map-1.pdf

John Fryxell seminar at #UCDavis 1/29: “Spatial food-web dynamics in the Serengeti ecosystem”

STORER GS3 LECTURE

Ecology and Evolution Seminar Series

Thursday, January 29, 410 pm, Giedt Hall 1003

“Spatial food-web dynamics in the Serengeti ecosystem”

John Fryxell, University of Guelph

Dr. John M. Fryxell
Professor

Research

My research focuses on interactions between behavior and consumer-resource dynamics. A mix of theoretical and empirical approaches is used to consider the dynamics of specific systems. Theoretical questions of interest include herbivore and carnivore movement in relation to resource availability and predation risk, optimal diet, patch selection, and dispersal patterns in heterogeneous environments, the effect of social interference and territoriality on consumer-resource interactions, and impacts of harvesting by humans on fish and mammal populations.

Empirical work has been concentrated on 3 different terrestrial ecosystems over the past decade: large herbivores and carnivores in Serengeti National Park (Tanzania), woodland caribou, wolves, and moose in boreal forests of northern Ontario (Canada), and mustelid carnivores and other small mammals in boreal forests of northern Ontario. In each case, my graduate students and I conduct detailed field and experimental studies of behavioral ecology of both predators and prey. Theoretical models are then used to assess the implications of behavioral strategies on population and community dynamics and model predictions are then tested against long-term observational data from terrestrial ecosystems.

Kevin McCann and I recently initiated a collaborative research program on spatial food web dynamics of phytoplankton and zooplankton populations in massive aquatic mesocosms in the new Limnotron facility at the Biodiversity Institute of Ontario. Initial experiments relate to resource- vs predator- and ratio-dependent functional and numerical responses, responses of predator and algal populations to pulsed versus continuous nutrient influx, resource- and density-dependent diffusion patterns by zooplankton and phytoplankton, and spatial pattern formation in relation to population fluctuations.

An ongoing applied research interest relates to sustainable harvesting of fish and mammal populations. Key questions relate to long-term stability of harvested populations due to dynamic variation in harvester effort, effects of bioeconomic dynamics on long-term stability of fish stocks and prices, and spatial processes in harvested populations with and without no-harvest reserves.

ESTEME Event film showing at #UCDavis 1/29: Makers: Women in Politics

Just got this announcement:

Please join us for our next Equity in STEM and Entrepreneurship (ESTEME) event happening on Thursday, January 29th at 5:30PM in GBSF auditorium! We will be having a special event featuring local broadcast and television station KVIE to debut our next film showing of Makers: Women in Politics! Refreshments will be provided!

Register here: makerspolitics.eventbrite.com

ESTEME’s mission is to serve as a leadership training program that teaches valuable skills to emerging graduate student leaders. Moreover, ESTEME serves the local community by raising awareness surrounding equity and access, hosting workshops to increase leadership skills, and leading outreach to K-12 schools to encourage young girls in STEM. ESTEME is led by a powerhouse team of students from the Biotechnology Program at UC Davis. If you are interested in participating as a volunteer and in future event planning, please email esteme.ucd.

Makers series flyer-politics 012315.pdf

Trials and tribulations with the "UC Care" medical plan & w/ UCSF, UC Davis health systems

The University of California healthcare options are, well, less than ideal right now, in my opinion.  Here is a little story about my recent experiences.

September 2014.

Forced to switch to the UC Care health plan because UC cancelled the health plan that allowed me to be a part of the Sutter Medical Group. Sutter has always been awesome. Wonderful care. Wonderful people. Rapid scheduling of appointments. And I was very sad to be forced to switch. I kept my primary care physician at Sutter but realized I would have to switch for many other things.

I was not pleased to be pushed into the UC Care plan because my experience with the UC Davis Medical Group has been beyond disappointed in the past.  For example see this: U. C. Davis Medical Group – their time is MUCH more important than yours.  Admittedly, I had not been to people in the UC Davis group in a while, so — maybe things had changed.

Plus I was pleased to note that the UC Care said I should choose their plan if “You want direct access to all providers without a referral.”  Why yes, that sounded good.  Hah hah hah.  Silly me.

September 2014.

Of course.  Just as I switched medical groups I had a serious health issue in need of attention.  Called UC Davis Nuerology  to make an appointment with the specialist recommended by a colleague.  They told me I needed a referral. I told them I had UC Care health plan which says I do not need a referral. They said that it did not matter what plan I had, I needed a referral. So I asked my doctor for a referral.

October 2, 2014.

Meanwhile I wrote to one of the people in the UC Davis Neurology Department where I wanted an appointment to ask how I should make an appointment and told him that I had been referred to him by a UC Davis MD (trying to pull some sort of nepotism here). He connected me to his assistant and I sent her the info she asked for.

October 13, 2014. 

I had not heard back from his assistant so I wrote to her again.

I am writing to see if you got this information I sent Oct 3 and if there is any more information you need from me. Thanks

I again did not hear back.

October 19, 2014.

I received a letter in the mail from UC Davis “reminding” me I had an appointment in Neurology scheduled for December 17, 2014.

Now, I guess it was nice to have an appointment.  But I note – they never called me to ask when would be good for an appointment. They never contacted me at all. And this was clearly less than ideal – an appointment in two months.

So I called them to ask – how did this get scheduled? They said they must have scheduled it with me. I told them, no, nobody even contacted me. I then asked – is there anything sooner? Nope. I then asked – what if I cannot make that date and time (I was scheduled to be away). They then said that would cause a significant delay in the appointment. What the $*@#$8? This is not the first time I have had trouble scheduling appointments with UC Davis physicians but this was absurd. I then asked – is there anything I need to do in advance? They said nope. So I waited. Two plus months. For an appointment for which I needed a referral even though I had signed up for UC Care.  Oh – and – I guess just to prove they had no clue what they were doing – they spelled ny name wrong (Johnathan).

December 17, 2014.  

I had my appointment with the neurology specialist.  He was very nice.  Seemed pretty knowledgeable.  He had some disconcerting misconceptions about me and I tried to correct them but he did not seems to be paying attention.  He did not do any of the more complex tests I had seen in the literature that were standard in the literature I had seen for my condition.  He did not even order any such tests.  He concluded the visit with a possible diagnosis and then said he needed to order a series of blood tests to test some alternative possibilities.  They decided I did not need a follow up appointment and that we would wait to see what the blood tests showed before deciding what to do next.  I told them I was not fasting and asked if that mattered and they said no (one of the reasons I ask in advance about blood tests is that freuqently they need me to be fasting and it is easier to do that early in the AM … but nevermind that … they said it was not needed).

December 22, 2014

I signed up for Mychart.ucdavis (based on the recommendation from the printout I got when I left the doctor’s office)– an online system to communicate with the UC Davis Medical Group.

December 23, 2014

I got an email saying there were test results in Mychart.

January 2, 2015.  

I still had not heard anything from the doctor’s office.  I wrote to him via the MyChart system asking if he had any update based on the test results.  I called too.  No response.

January 6, 2015.

I finally got a message from my doctor.  It had my name wrong, again, in a different way (John).  The message was short, had one useful thing in it and then said he “You need to check in with your PCP– I have instructed our staff to contact your outside PCP and transmit labs to him and to contact you.”  So much for seeing a specialist directly and communicating with them.  Oh, and he ended the message with “Good we checked labs and caught this now before your travels.”  What the $&##?  I had no travel plans.  This had nothing to do with travel.  He spelled ny name wrong.  They had me listed as having type II diabetes, when I have type I.  And they wanted me to communicate with my primary care physician instead of him.  Such excellent care.  Oh, and he made a comment about my vitamin B levels being too high when I had told him I was taking a specific prescribed vitamin therapy and that I had taken some that AM (this would likely screw up the blood test – I think to know if vitamin levels are off one has to NOT have recently taken vitamin pills).  Jesus Christ what a sham.  In fact, when I told him I was taking this vitamin prescription, he said something to the effect of “random vitamins don’t usually help” and I said “it is not random it is actually prescribed and there are clinical trials showing it has some benefits” but he had never heard of it nor did he seem to care.

January 7, 2015. 

I decided, I needed to see another specialist.  So I went back to a recommendation from another colleague for someone to see at UCSF.  So I checked out the protocol for making an appointment at UCSF and I filled out an online form to request such an appointment.  In the request system it asked for the preferred method of contact for me, and I said email.

January 8, 2015 

A day or so later,  I received an email from their system which said I had an encrypted message regarding my appointment request.  I had to create a new log in to a new system in order to read the message about my appointment request.  The message started with the following:

This email is to acknowledge receipt of your online appointment request for a new patient appointment. We have been unsuccessful in reaching you by phone. Before an appointment can be approved for scheduling we will need the following required documents to start the review process:

·         Referral along with reason or diagnosis
·         Pertinent clinical notes or records
·         Pertinent test results
·         Front and back copy of insurance card and authorization if required by insurance
·         Patient demographic information

What?  Why did they ask for my preferred means of contact if they were then going to call?  Oh well, at least this got through.  I called to ask some questions and only got a machine so I left a message.
Janaury 12, 2015
Appointment with my primary care physician.  He told me they had not received any information from the UC Davis specialist.  But he agreed that it might be good to see a specialist who gave a shit (my words, not his).  So he said they would make a referral to UCSF for me.  I gave them the printout with the information requested from UCSF.  
Janaury 17, 2015. 
Got an email saying my doctor had sent over the referral information to UCSF.  Called UCSF on MLK day and alas they were not open.  But I left another message asking what I had to do to make an appointment.
January 19, 2015.  
My wife took down a message and gave it to me saying UCSF had called about making an appointment.
January 22, 2015.
I called UCSF Neurology.  It took a long long long time to get through to a person.  When I finally did, I said I was calling to set up an appointment.  The person was immediately somewhat rude.  I gave my name and DOB and the person said I had no referral and my record there was empty.  I said I had been called by UCSF and they had left a message saying I should call about an appointment.  Now, mind you, I am not sure why UCSF had called me – it could have been about setting up an appointment or it could have been just to return my call.  But regardless, I told the receptionist that my doctor’s office had told me they had contacted UCSF and that I should call.  The person repeated that they had no record of anything in my file – no calls to me – nothing.   This sounded so weird that I said “Is this definitely the file for Eisen – E-I-S-E-N.” and the person snapped back “I do not make spelling mistakes” or something like that.  Nice.  Eventually, the person transfered me to someone else who actually offered to help and to call my doctor’s office.  They then said they could call me back after this.  I asked what number they had and the number they said was not one I recognized.  Weird.  But I gave them the correct number and then hung up.

After I hung up I started to get pissed off.  What was the deal here? I signed up for this UC Care health insurance beause I was supposed to be able to make appointments with specialists without referrals.  And I am a UC Professor – with an appointment in a medical school.  I probably get treated better than the random person.  What a scam.  And then I remembered how badly UC Davis Medical Group treated my wife many years before.  And how good the treatment we received from Sutter has been.  So I posted something to Twitter.

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And finally I got contacted by someone who actually seemed to care.

Not sure where things are going to go – but at least one person associated with a UC Medical Group is trying to help …

UPDATE January 29, 2015

Still no call back from UCSF Neurology despite their promises that they would call my doctor and then call me back as soon as possible.  Unbelievable.

UPDATE January 29, 2015 #2

Wrote an email directly to the Doctor I wanted an appointment with.

UPDATE January 29, 2015 #3

Tried to contact the appointment desk.  Was on hold for 30 minutes before I had to hang up.

UPDATE January 30, 2015

Got through to the appointment desk.  OMG how ridiculous.  They said they needed to transfer me to another department (memory and dementia) because that was where I had the referral (I had asked for an appointment in neurology, I have some peripheral neuropathy).  They said the doctor at UCSF had reviewed my chart and that is where they determined I needed an appointment.  And that I would need to contact my doctor about this.

What the F#*$*#?  Completely insane.

UPDATE February 2, 2015

Lesson of the day.  UCSF doctors and personnel, other than the receptionist I interacted with on the phone, really really really do care about getting things right.  After I posted again about this issue to Twitter and sent an email to my brother who forwarded it to people at UCSF, many people stepped up to try to help.  All of them have been incredibly gracious and concerned and helpful.

And at the same time I decided to get a copy of the referral from my primary care physician just in case there was a mistake from their end.

And, well, there it was.  The referral was to see a neurologist for diabetic related neuropathy issues.  Looked good.  Then I looked at page 2.  And there was a comment about my having a history of dementia and that they could not do an MRI due to my pacemaker.  Well.  WTF?  What chaos.

Certainly this explains why UCSF thought I should see the dementia clinic.  It does not explain why UCSF neurology would never return my calls and was rude on the phone, but, well, it does make me feel like a schmuck for the mistake my doctor’s office made.

UPDATE February 2, 2015 1:45 PM

Finally – a call from UCSF.  Yay. And they are going to contact my docs office and confirm that I do not have dementia.  And then, maybe then, I will get an appointment.

UPDATE February 2, 2015 5:45 PM

Well, I got a call from the UCSF Neurology appointment desk.  The person said they were calling because I had apparently contacted another doctor who contacted them (were they pissed off about this? sounded like it).  And they told me the first appointment was April 19.  Wow.  That is, like, not soon.  Lovely.  I took it.  But am going to see if there is a way to move it up.

UPDATE April 19, 2015

So – I finally had my appointment with a Neurologist at UCSF.  I had to get up so so early for my 9 AM appointment at UCSF Parnassus campus.  I was planning to take the train at 5:45 AM and then somehow wind my way to the UCSF campus.  And my alarm was somehow silenced.  I woked up at 5:30.  And I literally threw stuff in my bag and changed and jumped in my car.  But there was just no way to make it.  And so I decided to suck it up and drive into SF.  Traffic was bad already that early.  And I was pretty wiped when I got to UCSF.  And I was prepared for the worst.

But OMG.  What a difference.  I was treated so incredibly well by everyone there.  The information desk people on the 1st floor were helpful.  The lab people where I went for blood tests afterwards were pleasant and helpful.  The staff in the Neurology Department were friendly and respectful and helpful.  And my doctor.  Wow.  She was just so great.  Yes I do have some neuropathy.  And yes indeed it does completely suck.  And yes it still freaks me out and stresses me out.  But now I finally feel like I am getting excellent medical care.  And that is uplifting, even though my health is imperfect.  Such a contrast compared to the awful experience at the UC Davis Neurology

UPDATE April 21, 2015

Got a call from a UCSF Neurologist to discuss my blood test results.  My doctor was not available so an alternative doctor called me.  And she was phenomenal too.  Spent quite a while on the phone discussing things.  Came up with a plan.  All based on actual science.

UPDATE April 22, 2015

Got my medical report in the mail from UCSF.  Incredibly detailed report about my appointment, recommendations for me, and more.  Another wonderful feature.  I have STILL not gotten any such thing from UC Davis.

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