Sunday, October 15, 2017

From Google Scholar: Follow Related Research for Key Authors

This seems like it could be useful:



Google Scholar Blog: Follow Related Research for Key Authors


Scholar provides several ways to keep up with research in your area. You can set up keyword alerts, get recommendations related to your publications and follow your colleagues’ profiles.

Today, we are adding another approach to stay up to date in areas of your interest. Now, in addition to following articles by and citations to an author, you can follow research that is related to her work. 
To follow related research for an author, simply go to her public profile, click “Follow” and select “New articles related to this author’s research”. Scholar will automatically scan all new publications for articles related to her research and will send them to you as an email alert. 
This is particularly useful if you are a graduate student or an early stage researcher. By following related research for your advisor, your thesis committee and possibly a few key faculty members in your department, you would be able to see the research landscape from their experienced vantage point.

It is also useful if, like myself, you are an industry or medical professional who isn’t active in the research realm but would like to keep up. By following related research for leading scholars, you will be able to quickly view relevant articles in key areas.
The astute reader has no doubt guessed that this can also be used to get email alerts for research related to your own work -- go to your public profile, click “Follow” and select “Recommended articles”.

Monday, October 09, 2017

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic





This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:
Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue
But it goes way way way downhill from there.  Here are the parts with problems
  •  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
    • Sure, in my wildest dreams I would cure cancer too.  
  • In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
    • Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
  • Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
    • Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
  • The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
    • What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  
No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.


UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See


Friday, October 06, 2017

This week in Science SPAM

I would love it if I could just ignore my Gmail Spam folder.  Alas, every once in a while I find important emails in Gmail Spam.   So alas I cannot ignore it. While digging through today I found a collection of "Science Spam" - that is Spam emails that have some science-y theme.

Here are the ones from this week in my Gmail Spam folder that I identified as being Science Spam.   Most are invites from Spammy journals.  Some are invites from Spammy conferences.  A few are other things.  Do other people get this much science Spam?






Monday, September 25, 2017

Nature Publishing Group continues to deceive about #OpenAccess to genome papers

I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome



That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.


UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall










And more



UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles



Friday, September 01, 2017

Trip to Chaa Creek Lodge in Belize - Day 1

Note - writing this with some help from my daughter.

My family and I went on a trip to Belize in early August 2017 and I am posting some notes and pictures from the trip here.

We chose Belize for a few semi - random reasons.  First, we had wanted to go to Europe but we really only could travel just the week before school started for my kids and we felt like Europe was (1) too far (2) would involve too much jet lag and (3) would involve too many Real Madrid fans.  So we started looking around closer to home.  We wanted to go out of the country (out of the USA - not just out of California, though it really is it's own country).  So - well - we looked at Mexico.  And Central America.  And we settled on Belize.

We decided to spend the whole week of our trip at one place and, since we have been going to Hawaii a bit recently, we decided we did not want to spend our time in a beach-like setting, so we looked for places in the inland rainforesty areas.  My wife spent quite a lot of time searching for possible places and she came up with some candidates and after discussions on the pluses and minuses of all the places and after also asking Twitter and friends and such we settled on Chaa Creek.  An ecolodge of sorts with a slight upscale angle.

More on the place and such later.

Right now I really want to start to get some pictures posted.  So here are some from our travel day.

SMF to Dallas to Belize.

On the plane
I did not take too many (well, more than one) pictures on the actual trip.  But suffice it to say we flew on a plane.


An interesting shirt at a shop at the airport

Waiting for our ride while all the local taxi drivers, well, tried to offer us rides in ways I found to be, well, dubious. 

The ride to Chaa Creek was about two hours long.  I took some pics along the way.  Here are some of them.  Oh - and our driver, Edward, was an FC Barcelona fan.  Yay.

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek 
On the road to Chaa Creek 
On the road to Chaa Creek 
Off to the reception building 
Off to the reception building

Off to the reception building

Off to the reception building

We settled in, got some dinner, and were very hot.  Like really very hot.  Like really really warmer than warm.  It was beautiful.  And interesting.  And hot.  Really really hot.  Or, more relevant.  It was hot and really really humid.  I mean, I grew up in the Washington DC area so I know hot and humid.  But I live in California now, where hot and humid usually do not go together.  We get hot in Davis.  Really really really hot.  But dry. Like really really dry. .


Saturday, August 26, 2017

Crosspost: Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World – microBEnet: the microbiology of the Built Environment network

Crosspost: just pointing people to this post I wrote on microBEnet which may be of interest:

Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World – microBEnet: the microbiology of the Built Environment network

Crosspost: #MoBE17: Microbiology of the Built Environment Research & Applications Symposium – microBEnet: the microbiology of the Built Environment network

Crossposting from microBEnet



#MoBE17: Microbiology of the Built Environment Research & Applications Symposium – microBEnet: the microbiology of the Built Environment network

This meeting should be of interest to many out there. A great collection of speakers and topics. Keynotes by Ed Yong, Susan Lynch and Marc Edwards. Registration deadline is September 1.



MoBE 2017
Microbiology of the Built Environment
Research and Applications Symposium
October 10 - October 12, 2017
NAS Building Washington, DC


More detail here.

Registration is free and open until September 1, 2017.

Sponsors Include: Alfred P. Sloan Foundation, NAS, Zymo Corporation, Standards in Genomics Sciences, Microbiome Journal, NASA, US Green Buildings Council




Agenda

Tuesday October 10th
Keynote.
  • Ed Yong (The Atlantic). A science writer’s view of the MoBE field.
Kick-off reception 


Wednesday October 11th
Introduction
  • Lynn M. Schriml (MoBE 2017 symposium chairman, University of Maryland School of Medicine, Institute for Genome Sciences)
  • Paula J. Olsiewski (MoBE Program Director, Alfred P. Sloan Foundation)
Keynote
  • Susan Lynch (UCSF School of Medicine). Chronic Inflammatory Disease and the Built Environment
Session 1: MoBE Science Here and Now
  • Jonathan Eisen (UC Davis). The microbiology of the built environment network (microBEnet) and perspectives on the MoBE field
  • Jessica Green (University of Oregon). Designing healthier spaces and buildings
  • Lisa Brenner (University of Colorado). Mental Health and the Microbiome of the Build Environment
Session 2: Implications of MoBE for Health and Design
  • Elaine Hubal (EPA). Session Chair
  • Shelly Miller (University of Colorado). Building Engineering Controls for Improving Occupant Health: Mitigating Airborne Particles, Toxic Gases, and Infectious Aerosols.
  • Rachel Adams (BIMERC). Sources and quantities of microbes and mVOCs indoors.
  • Karen Dannemiller (Ohio State University). The nexus of housing characteristics, indoor microbial communities, and asthma severity
  • Mark Mendell (California Department of Health, LBNL). Adverse and beneficial effects of the indoor microbiome – current implications for health or design?
Session 3: Public Health and Indoor Microbial Communities
  • Diane Gold, Session Chair
  • Maria Gloria Dominguez-Bello (NYU School of Medicine). Microbial Biogeography of Homes across urbanization gradients
  • Brandon Bubba Brooks (Kaleido Biosciences). The NICU microbiome’s role in neonate gut colonization
  • Jane Carlton (NYU School of Medicine). A city view: ATM's, parasites and wastewater
Session 4: MoBE Insights on Microbial Exposure
  • Tina Bahadori (EPA) Chemical Safety for Sustainability Research Program Leader, Session Chair
  • Eric Alm (MIT). Sewers, microbes and drugs
  • Emmanuel Mongodin (Institute for Genome Sciences, UMSOM). Microbial function and built environments
  • David Mills (UC Davis). Microbiology of food production built environments: dairies and wineries
Panel Discussion: Myth and Reality of MoBE Manipulation
  • Rob Knight (UCSD), Moderator
  • Rita Colwell (University of Maryland)
  • Jeffrey Siegel (U of T)
  • Ilana Brito (Cornell)
  • Jessica Green (University of Oregon)
Poster Session & Reception



Thursday October 12th
Welcome
  • Jordan Peccia (Yale). Gordon Conference Announcement.
Keynote
  • Marc Edwards (Virginia Tech). MoBE, Public Health and the Flint Water Crisis
Session 5 - From MoBE Research to MoBE Applications
  • Scott Kelley (San Diego State University). Session Chair.
  • Jack Gilbert (University of Chicago). From Hospitals to Forensic Applications
  • Richard Shaughnessy (University of Tulsa). From Home to School: Tribal Indoor Air Quality Intervention Study
  • Anders Benteson Nygaard (Oslo and Akershus University College of Applied Sciences). Bacteria in Norwegian kindergartens: Small children and their microbial environments
Session 6: The Building Science – MoBE nexus
  • Richard Corsi (University of Texas at Austin). Session Chair.
  • Richard Corsi (University of Texas at Austin). Building Science ∩ Science in Buildings (or why MoBE > Robots)
  • Amy Pruden (Virginia Tech). Towards Prebiotic/Probiotic Control of the Microbiome in Built Water Systems
  • Betsy Pugel (NASA). Tiny houses: Planetary protection-focused materials selection for spaceflight hardware surfaces
  • Kent Duffy (SRG Partnership). The influences of microbial research on architectural practice
  • Wendy J Goodson (Air Force Research Laboratory). Microbiomes of Military Cargo Aircraft and their Connection to Biocorrosion
Session 7 - NAS Microbiomes of the Built Environment Consensus Study
  • Katherine Bowman (NAS). Session Chair.
  • Joan Bennett (Rutgers University) : NAS MoBE study overview MoBE outcomes, perspectives and future studies
Panel Discussion: Charting MoBE Research Priorities
  • Jonathan Eisen (UC Davis). Moderator.
  • Jordan Peccia (Yale)
  • Norman Pace (University of Colorado)
  • Claire Fraser (Institute for Genome Sciences, UMSOM)
Meeting Closing
  • Paula Olsiewski (Alfred P. Sloan Foundation).