Wednesday, July 25, 2012

Antioxidants May Lower Risk of Pancreatic Cancer

The journal Gut (impact factor 10.11) published a prospective study yesterday investigating whether eating antioxidants such as vitamin C (found in fruits and vegetables) and E (found in nuts, seeds, egg yolk), selenium (found in cereals, nuts, fish and meat) and zinc decreases the risk of pancreatic cancer.  They looked at 7-day food diaries of 23,658 participants over 10 years in the European Prospective Investigation of Cancer (EPIC-Norfolk) Study.  The estimates in this study were adjusted for other variables such as age at recruitment, gender, smoking, diabetes, BMI and total energy (smoking and diabetes are two known risk factors for pancreatic cancer).   Interestingly, those with the highest intake of selenium, vitamin C and E reduced the risk of pancreatic cancer by two-thirds. Those with high intakes of selenium and vitamin E had 40% reduced risk.  Those are huge reductions in risk based on these micronutrients.


The American Institute for Cancer Research (AICR) wrote "37,000 Americans will die of pancreatic cancer this year. According to the National Cancer Institute, pancreatic cancer is the fourth leading cause of cancer-related death. It is often not diagnosed until the advanced stages, when treatment is challenging".  With the recent death of Sally Ride, I thought this article discussing pancreatic cancer was particularly relevant.  

Friday, July 13, 2012

War on Cancer

As a statistician applying my research to cancer genetics it is always encouraging to see stories like this that make me feel sometimes all this work isn't for nothing.

The article published last week in the NY Times describes the story of a woman who was diagnosed with a rare form of lymphoma in which white blood cells (T cells) become cancerous and move to the skin.  Faced with a disease with no cure and no standard treatment, she was able to keep the cancer at bay using chemotherapy for five years.  At that point, her health took a turn for the worse and her son who worked at Illumina, which produces some of the latest sequencing technology, decided to quit his job and help his mom full-time by sequencing her genome.  After sequencing her normal and tumor DNA, they found 18K differences (or mutations) with no known significance for disease.  In the analysis of her DNA, the researchers found two genes fused together forcing the growth signals in cancer cells to be reversed: the signal to stop was forcing the cells to grow and the signal to grow was forcing the cells to stop growth.  The researchers decided to give her a new melanoma drug ipilimumab which forces normal T cells to grow, in hopes of stopping the growth of the tumor cells. The drug performed beautifully keeping the cancerous T cells at bay for 8 weeks before the cancer came back and ultimately she passed away a few weeks later.

41 years ago Richard Nixon signed the National Cancer Act of 1971 which started a "war on cancer". The goal was to find a "cure for cancer" by increasing the funding toward cancer research and find more effective treatments.  As defined by PubMed "cancer is the uncontrolled growth of abnormal cells in the body".  Cancer is not just one disease, in fact it is the word we have for hundreds of diseases we label as 'cancer'.  When people talk about "curing cancer", it suggests that once a treatment/cure for one type of cancer is found, it should theoretically be applied to another form of cancer.  In my experience this is definitely not the case.  Every type of cancer is unique in its etiology and treatment.  It is true that some drugs today developed for one type of cancer can be applied to another type of cancer because the target molecule may happen be the same for two different cancers, but this is a separate idea than the finding a "cure for cancer".

I work with several groups of researchers in the Texas Medical Center at University of Texas MD Anderson, Baylor College of Medicine and Texas Children's Hospital who are all trying to exactly this.  They are sequencing the genomes of individuals affected by a particular disease and trying to find the causal mutation or reason for the disease.  My small contribution comes in helping to analyze the results that come out of the sequencing.  Bioinformatics attempts to take in the large amount of sequencing data and make sense of it.  This is by no means easy and will take much longer to properly analyze the data than to just sequence it.  But, even with these small steps I look forward to more success stories like these and seeing further progress being made in the war on cancer.

Tuesday, July 10, 2012

Making a movie out of images .png using ffmpeg

Say you are interested in plotting in three dimensions in R.  This can be quickly done using the rgl package in R.  There are functions called plot3d(), persp3d() and lines3d() which let you plot in three dimensions, light3d() which adds a light to the background, bbox3d() which edits the colors of the 3d box, and view3d() which picks the particular angle of view.  One idea is to quickly write a for loop within R to rotate the image 360 degrees to get a nice little rotation of your 3d image.

Now, say you are interested converting the 360 different views in R into 360 images with a .png format.  This can be done within the rgl package using the rgl.snapshot() function.  In R, type the following

# Load rgl library
install.packages("rgl")
library(rgl) 


# Plot 3d image
plot3d(x, y, z)

# For loop rotating the 3d image 360 degrees
degrees <- seq(1,360, by = 1) # a sequence from 1 to 360
for(i in 1:length(deg)){
    view3d(degrees[i], phi = 0) # pick the angle of view
    rgl.snapshot(paste(paste("/file_directory/filename", "-", 
        formatC(i, digits = 3, flag = "0"), sep = ""), "png", sep = "."))
}

formatC() is a function that will add -001, -002, -003 etc to each of your images. This will be important in a moment.  

Finally, say you are interested in converting these 360 images to a movie.  I came across a great blogpost that showed me the commands to quickly and painlessly accomplish this.   It requires the use of the ffmpeg command in the terminal. In the terminal, type the following: 

$ cd ./location_of_file/file_directory
$ ffmpeg -f image2 -i filename-0%3d.png video.mpg

This converts the 360 images named 'filename-0001.png', 'filename-0002.png' etc to a video named video.mpg.  I know this won't make sense to most people, but here is what I ended up with: 

video


Tuesday, July 3, 2012

Dark Chocolate Mousse

Recently, I attempted my first chocolate mousse recipe from scratch.  I must admit, it was easier than I thought it was going to be.  I looked around for several recipes including one that replaced the cream and eggs with avocado, but I decided for my first mousse I would keep it classic.


I decided to follow Bobby Flay's recipe which only had four ingredients in it: 6oz dark chocolate, 14oz heavy cream, three egg whites and 1oz sugar.  The recipe was very straight forward.  Start with some high quality chocolate (preferably > 70% cacao):


To melt the chocolate, Bobby suggests using a double boiler, but Ina Garten said on Barefoot Contessa that you can always just put chocolate in the microwave for 20 seconds, take it out, stir, put back in microwave for 20 seconds and repeat.  When it is almost melted (but still has a few chunks) just take it out, stir and the rest of the chocolate will melt naturally (to avoid burning it).  Next, whip the cream until stiff peaks and set aside.


Third, whip the egg whites and slowly add in sugar until stiff peaks. Mix the melted chocolate with the egg whites all at once.  Once everything is mixed, start to slowly fold in the whipped cream into the chocolate mixture.  Separate mixture into four ramekins (or wine glasses) and place in fridge to set up for at least 1 hour.  When ready to serve, top with a few pieces of fruit and some coco powder. Hopefully you will enjoy it as much as I did!  This will definitely be a repeat dessert.



Monday, July 2, 2012

Cooking Whole Red Snapper

The last few weeks have been very busy with research and a bit of traveling.  Lots of changes are happening with me and Chris, but one thing has definitely not changed: our culinary interest in learning about new foods and new recipes.  This weekend we set out on an adventure to learn how to cook an entire fish (yes, head and all).  After watching several videos and reading many, many recipes, we decided to follow Alton Brown's recipe.  He uses striped bass, but we knew we were just going to pick whatever was fresh at Central Market.

To begin, we realized we were going to need a roasting pan of sorts.  The closest thing we had was a flat sheet pan or a small clear 8x8 pyrex pan.  In last minute trip to Bed Bath and Beyond, we picked up a very nice Calphalon Tri Ply 14'' Roaster.


Interestingly it came with a rack and lifters which will be perfect for roasting chickens or our first turkey this fall. :)


Now that the pan had been secured, we set off to Central Market to buy a fish. As a side note, we had also heard that in Houston another great place to buy fresh fish was J & J's Fish Market.  Next time we will probably check that out.  For now, back to Central Market.  The guy behind the fish counter (I believe David was his name) was so nice when we told him we wanted to buy two whole red snappers.  


He offered to de-scale, de-fin and clean up the snapper for us even though it took him a full 5-10 minutes (on a Saturday afternoon in Central Market with a line of people behind you, that was incredibly generous of him for taking the time to do that for us).  


After putting it on ice and getting the fish safely home, we started to chop of the aromatics needed for recipe.  You begin by making a bed of parsley and dill.


Add some sliced onion and lemon to the party.


Add fish on top of the aromatics.


Add more parsley and dill on top of the fish.


Cover with aluminum foil and place in a 500 degree oven for 35 minutes or until an internal temp of 120 degrees.


We served it on a bed of fresh parsley with some lemon.



It turned out to be delicious!  The only troubling thing was the bones.  Not sure if there is a polite way to spit out a bone? :)  Either way, I would definitely recommend this recipe to anyone interested in learning how to cook a whole fish.  We also had a lot of fun along the way.