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?