Gut bacteria promoting colorectal cancer (40 minute biostatistics)

A couple of studies have been published recently, and quite a bit written about them, which link the abundance of types of bacteria found in the mouth with incidence of colorectal cancer.

These finding result from the observation that the oral bacterium Fusobacterium nucleatum is often found in high abundance in colorectal carcinoma tissue samples.

Gram-negative stained culture of F. nucleatum. Image Courtesy of J. Michael Miller, Ph.D.,(D)ABMM of National Center for Zoonotic, Vector-borne, and Enteric Diseases. Picture submitted by him to American Society for Microbiology

Image & caption nicked from: http://microbewiki.kenyon.edu/index.php/Fusobacterium_nucleatum

I've not read up on the science and microbiology in any depth, but I got the feeling that it would be interesting to plot and summarize some of the public health data available on two variables relating to Oral health and Colorectal cancer incidence.

Hence I pulled down some data from the web and made some charts.

US state by state data sets are often complete, with up-to-date and freely available for many observable values.

After a bit of google searching, I came up with these 2 sets from CDC:

The US Centers for disease control and Prevention have data for colorectal cancer for 2009 here;
http://apps.nccd.cdc.gov/uscs/cancersrankedbystate.aspx

[Age-Adjusted Invasive Cancer Incidence Rates and 95% Confidence Intervals by State (Table 5.4.1M) *†Rates are per 100,000 persons and are age-adjusted to the 2000 U.S. standard population (19 age groups - Census P25-1130). Rates are per 100,000 persons and are age-adjusted to the 2000 U.S. standard population (19 age groups - Census P25-1130).]

and the data available for download

The CDC.gov site also carries summary data from the BRFSS survey, which is the "Behavioral Risk Factor Surveillance System", which collected data for 2008 asking adults 18+, whether they "had visited a dentist or dental clinic in the past year": http://apps.nccd.cdc.gov/nohss/ListV.asp?qkey=5&DataSet=2

The two data sets can be merged, and then scatter plot and correlations, and best fit plotted. (assuming linear association and normally distributed data etc etc)

here is the summary data:





TODO:

characterize the association... and consider any other ideas..




August 2013

http://www.cell.com/cell-host-microbe/abstract/S1931-3128(13)00255-2

 http://www.sciencedirect.com/science/article/pii/S1931312813002606


2011


http://genome.cshlp.org/content/22/2/299.full

http://genome.cshlp.org/content/22/2/292.full




genome sequence for Fusobacterium nucleatum SubspeciesPolymorphum
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000659

Sherlock Puzzle (Series 2 Episode 1) "This email will save the world"

I was catching up on the Sherlock series 2 the other day on iplayer.

During the "A Scandal in Belgravia" episode Lara Pulver's character Irene Adler shows Sherlock an email containing a code. Irene Adler then says to Sherlock "go on then, impress a girl".. or words to that effect.

Given that I was developing a soft spot for Irene Adler, that was effectively a challenge I wasn't going to miss, so I copied it down, and had a crack at deciphering it.



Fortunately at that point they did a little slow-motion sequence with overlaid animation of letters appearing in front of Benedict Cumberbatch's head, and I was able to pause it before they gave the answer away.

Any apps which would implement a pairwise comparison of "product features" in head to head playoff elimination format?

I have this massive list of "product features" for an app that I am working on, and I am having trouble just making sense of which to look into first.

I thought it would be cool to have an app that would present all the items successively in "pairwise comparison" format, to enable to determine an "implied priority"

A 1000Minds presentation of two contenders in a pairwise comparison format;

The idea being that initially you would start with a rough list and then successively present pairs of these items (e.g. "add X widget feature" vs "improve Y process") to the stakeholders.

If twitter is Ham-radio for normals, then differencebetween.info is ...?

My pet thesis is that there is absolutely nothing new about the internet (I mean as opposed to smoke signals and hieroglyph), except for 2 things:

1) maintaining the persistent weak links in networks and 2) integrated search (or probably more accurately ubiquitous, pandemic indexes... meaning the pulling out, and structuring of data into information from disparate sources)

Hence I take an interest in things that I think are really just something old, dressed up in jQuery or social media, and presented as new.

(I particularly hate the application of the word "cloud" to everything in tech and calling it new. "Hey, come and see our new "cloud" app"... what that thing this is your old desktop app with some marketing guff and a "cloud-" prefix..)

a very funky book

I bought this item from AbeBooks.co.uk for 0.92GBP plus shipping. for a total of 4.46.

I think the previous owner had it stored in some pretty dank conditions. It's got a quite severe musty funk to it.

Having a baby is...

"...a bit like sitting in the airport waiting for a plane. It's a bit scary, a bit boring, a lot can go wrong, and in reality you have little control over the situation" [anon.]


(And no. I'm not having a baby.)

"fact patterns" - is that new, or did I miss the birth of that phrase? (draft)

From reddit (regarding mandatory sentencing in the US):

As a lawyer I'll say that when it comes to the legal (criminal or civil), honesty is not always the best policy. But silence usually is.

People unfamiliar with the system often mistake truthful statements, arguments of honest mistake or justification, acceptance of responsibility, etc., as doing the "right thing" and pay dearly for doing it.

This issue is especially troubling in instances where the legal system has set up a no-tolerance rule, mandatory reporting, or otherwise deprive responders of "discretion." This happens a lot on the criminal side: domestic abuse (i.e., mandatory arrest), some sex and gun crimes, vehicle-alcohol laws, etc. The domestic abuse one in particular, while well-intentioned, can result in some very bizarre fact patterns for police.

It appears that this guy/gal is a lawyer-speaking, but using the phrase to
mean "sequence of events", or more likely a kind of predictable cascade of institutional response to... (well the fact that I can't define it, suggests it has utility, because I certainly know what they are getting at)

they continue...

For a great many otherwise honest, good people, the first run-in with the legal system, they learn that trying to be helpful, doing the right thing, etc. is some times the wrong thing for them personally.

 The closest definition I am thinking of, is that it functions in a much more precise way as does "story" in something like "it was the same [familiar] story"

ginger steps on venus.

So this joke showed up in my google+ feed at Funny Jokes+ and was reposted at Remo malash+, Haley Falconite+ and others. My first thought was why is Blondie getting all the abuse. I doubt ginger would last long on the surface of venus!

Given that the surface pressure on Venus is ~92x of the Earth, and that spacesuits are designed for low pressure environments. I think something like a deep sea submersible would be required to survive, making it difficult for "ginger to walk on venus" without being squished.

Chef: ERROR: RuntimeError: Please set EDITOR environment variable

I've just setup a workstation on windows, and I'm getting the following error when I try to edit a data bag;

$ knife data bag edit tomhodder tomhodder
ERROR: RuntimeError: Please set EDITOR environment variable

tldr; SOLUTION: use a text editor that understands windows paths ("C:/Users/whatever/file"), rather than unix ("/C/Users/whatever/file"), e.g. export EDITOR=notepad

Is the brain's "embarrassment" architecture single register in working memory?

At various points in my life I am plagued by what could be described as persistent unwanted thoughts. Basically something comes to mind, and is difficult to dislodge maybe for an hour or so, but sometimes much longer. I have strategies I like to use to deal with this, such as to actively get up and do something else to trigger a frame change.

A similar recollection-of-cringe-worthy incident occurred just now, but something slightly unique took place which I thought I would throw out for discussions.
 

Chef web app developer training - Part 7 continued even more... checks/real life (draft)

The purpose of this series of tutorials is to take web app developers through the basic knowledge necessary to create and maintain the cookbooks used to deploy web applications.

Here I demonstrate that searches on data bags are applicable to other indexes and lists of objects in the chef server architecture.

Chef web app developer training - Part 7 continued even more (draft)

here are some checks that you have setup the data bag correctly;

Chef web app developer training - Part 7 continued (draft)

The purpose of this series of tutorials is to take web app developers through the basic knowledge necessary to create and maintain the cookbooks used to deploy web applications.

Here we are going to create a data bag which we will shortly be consuming in a cookbook recipe.

We are going to create a databag on class01 named for your favourite sports team and add some players to it.

Chef web app developer training - Part 7 (draft)

The purpose of this series of tutorials is to take web app developers through the basic knowledge necessary to create and maintain the cookbooks used to deploy web applications.

The prerequisites for Part 7 are to have a working setcloud configuration for "class01" and your own hosted chef organization e.g. "tomhodder". ("knife cookbook list" etc, should work)

The purpose of Part 7 is to cover "data bags", what they are and how they work.

Chef developer training - Part 6 continued (draft)

Here we run some checks to ensure the settings are correct

Chef developer training - Part 6 (draft)

The prerequisites for Part 6 are to complete part 5

Chef web app developer tutorial - Part 5 continued (draft)

Check that the environment variables are correctly loaded

 

Chef developer training - Part 5 (draft)

The purpose of this series of tutorials is to take web app developers through the basic knowledge necessary to create and maintain the cookbooks used to deploy web applications.

The prerequisites for Part 5 are to complete part 4, and to have available the configuration values for both "class01" and your own organization e.g. "tomsorg".

The purpose of this part of the tutorial is to make it super easy to switch between different chef-servers, and organizations. The developer workflow will be to typically have a dev or test organization, and some other production target chef-server.

Chef web app developer training - roundup of parts 1-4

These are the requirements to complete for each part of the session; (replace tomhodder with your opscode username where appropriate)

Chef developer training - Part 4 (draft)

The prerequisites for Part 4 are to complete part 3, and to have a username associated with opscode.