Some Kind of Caliper, But for What?

A friend brought this caliper by our engineering dept wondering if we knew what it was for. We speculated that it was a one off caliper for a very specific QA check on a plate or some kind of card stock, possibly. The throat is about 2 feet deep and the max thickness measurement is approximately 2 i

SNPs for breast cancer risk? It Depends.

I hold in my hot little hands a copy of the NEJM, March 18th edition. In it there is an article which isn't even released yet.


Entitled
"Performance of Common Genetic Variants in Breast-Cancer Risk Models"

Remember when we did this for heart disease risk? FAIL WHALE.....

Do you think it will happen again?

The Study

10 common genetic variants


I had to create a couple of pages on SNPedia for this list FYI.....

The Methods:
Cases and controls-WHI, ACS CPSII Nutrition Cohort, Nurses Health Study, Prostate/Lung/Colorectal/Ovarian Cancer Screening Trial, and Polish Breast Cancer Study.

Cases-Woman who had received diagnosis of invasive breast cancer.

Risk Models Used-A hybrid of the Gail model.....I.E. Not exactly the Gail Model.
1. First degree relatives with breast cancer
2. Age at Menarche
3. Age at first live birth
4. Number of Breast Biopsies

They acknowledge that they were unable to get atypical hyperplasia and Mammographic density. Both of which have improved Gail.

So, This Gail is a little hobbled and not the best predictive model.......

The studied models- 5 logistic regression models
I don't have the supplementary tables and methods yet.

The nongenetic model-Gail Model
The Demographic/Genetic Variant Count Model-included number of alleles.
The Demographic/Genetic Individual Variant-Accounted for individual effects of each SNP
The Inclusive Model-Gail, Genetics Demographics
The Demographic Model
And Random....

When we do these sorts of statistical analyses we look for a couple of things.

A. Number of people reclassified and how?
B. The Area Under the ROC Curve


Results-

1. The Inclusive Model Yielded and AUC of 61.8%
2. The Nongenetic Model yielded an AUC of 58%
3. The Genetic Individual Variant Yielded an AUC of 59.7%
4. The Genetic Variant Count Yielded an AUC of 58.8%
5. Breast Biopsy BY ITSELF Yielded an AUC of 56.2%

That is a 3.8% difference in Yield from Genes and without Genes integrated into the weaker Gail Model.

Lastly, they asked. Well, does this Inclusive Model do a good job of discrimination of High risk vs. low risk.

The Answer- It determines lower risk better than Gail. It does not determine higher risk better.

The authors of this study have stated that

"As in Diabetes and cardiovascular disease, the addition of the common SNPs added little to the predictive value of the clinical models. On the basis of theoretical models, Gail has shown that increases in the AUC similar to those observed here and not sufficiently large to improve meaningfully the identification of women who might benefit from tamoxifen prophylaxis or screening mammography"

Take Home

The addition of these factors only creates a minimal statistical increase that is of no useful clinical benefit.

The Sherpa Says: If the press says "gene tests fail to improve risk assessment" You can be assured that the DTCG industry is no longer the darlings. If instead they say "Improvement in risk model" well, then you have chance to woo them back! It Depends.......

How can MDVIP use Navigenics Test for Medicine?

I have been harping on this say what you mean. Say what you do. Theme lately.


I am a board certified doctor who practices personalized medicine. I see patients and apply the principles or pharmacogenomics, risk prediction and prevention tailored to each individual patient. I do this by taking a 3 generation pedigree, using current clinical risk models and pharmacogenomic or other genetic tests when indicated. That's me.

I have this nagging pain about MDVIP, Ed Goldman and Navigenics.

Some MDVIP members are using Navigenics tests for medical risk prediction. Navigenics is ok with this because hey, they're doctors.


The contents of our Site, including any risk estimates or other reports generated by the Services (collectively, "Your Report") and any other information, data, analyses, editorial content, images, audio and video clips, hyperlinks and references (collectively, "Content"), are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis, or treatment.

The part I want to focus on is "Are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis or treatment"

It seems to me that this will be the more popular language in a Terms of Service for DTCG.
Notice that nowhere does it say, "This report is not intended to diagnose or treat"

I think that while it is nice to not say that, when in fact people are using it to diagnose, it is even goofier to say that it is not intended to substitute for a professional's diagnosis. Ok, so are you saying

1. This is not to be used for diagnosis/medical advice
2. This is to be used for diagnosis, but the professional's diagnosis trumps ours
3. This test is meant to be used by professionals to aid them in diagnosis and treatment

I am really confused here. Is this a medical test or not. Just come right out and say it!

The Sherpa Says: Say what you do, do what you say you do. Isn't that what the Common Framework of Principles is About?

Core Cutting a Building Floor Slab

Dear all,

Is it advisable to do core cutting in slab. After complition of civil work we realised that we have to cut 300mm bore (core) to transfer material from 4th floor to 3rd floor. Our slab thickness is 500mm.

Please guide me.

365 Days of Astronomy shoots the Moon | Bad Astronomy

365 Days of Astronomy podcast

My friend Eran Segev, an Aussie skeptic and all-around good guy, submitted a podcast to 365 Days of Astronomy dealing with the venerable Parkes radio dish and its support of the Apollo 11 Moon landing. It’s a good story — it was fictionalized in the very cute movie "The Dish" — and he interviews a couple of the men who were there during the whole thing. And if you listen to the whole thing, they mention a familiar name, too…


A Thermal look at the Great Red Spot

Thermal images from ESO's ground based telescope on top, taken May 18, 2008, and the Hubble optical on bottom, taken on May 15, 2008. Click for a larger version. Image Credit: NASA/JPL/ESO and NASA/ESA/GSFC

A team of astronomers recently took a look at the  Jupiter’s Great Red Spot and the local area around it using a collection of the best telescopes in the world to make a thermal map.  The images show: the Great Red Spot and two smaller storms nicknamed Oval BA and Little Red Spot.

The thermal image was taken in the infrared wavelength range of 10.8 microns, which is sensitive to Jupiter’s atmospheric temperatures in the 300 to 600 millibar pressure range in order to coincide with the altitude of the white, red and brown aerosols seen in the visible-light image on the bottom.

Pretty fascinating stuff.

Here’s the press release and it tells the story:

New thermal images from powerful ground-based telescopes show swirls of warmer air and cooler regions never seen before within Jupiter’s Great Red Spot, enabling scientists to make the first detailed interior weather map of the giant storm system.

The observations reveal that the reddest color of the Great Red Spot corresponds to a warm core within the otherwise cold storm system, and images show dark lanes at the edge of the storm where gases are descending into the deeper regions of the planet. These types of data, detailed in a paper appearing in the journal Icarus, give scientists a sense of the circulation patterns within the solar system’s best-known storm system.

“This is our first detailed look inside the biggest storm of the solar system,” said Glenn Orton, a senior research scientist at NASA’s Jet Propulsion Laboratory in Pasadena, Calif., who was one of the authors of the paper. “We once thought the Great Red Spot was a plain old oval without much structure, but these new results show that it is, in fact, extremely complicated.”

Sky gazers have been observing the Great Red Spot in one form or another for hundreds of years, with continuous observations of its current shape dating back to the 19th century. The spot, which is a cold region averaging about 110 Kelvin (minus 260 degrees Fahrenheit) is so wide about three Earths could fit inside its boundaries.

The thermal images obtained by giant 8-meter (26-foot) telescopes used for this study — the European Southern Observatory’s Very Large Telescope in Chile, the Gemini Observatory telescope in Chile and the National Astronomical Observatory of Japan’s Subaru telescope in Hawaii — have provided an unprecedented level of resolution and extended the coverage provided by NASA’s Galileo spacecraft in the late 1990s. Together with observations of the deep cloud structure by the 3-meter (10-foot) NASA Infrared Telescope Facility in Hawaii, the level of thermal detail observed from these giant observatories is comparable to visible-light images from NASA’s Hubble Space Telescope for the first time.

One of the most intriguing findings shows the most intense orange-red central part of the spot is about 3 to 4 Kelvin (5 to 7 degrees Fahrenheit) warmer than the environment around it, said Leigh Fletcher, the lead author of the paper, who completed much of the research as a postdoctoral fellow at JPL and is currently a fellow at the University of Oxford in England. This temperature differential might not seem like a lot, but it is enough to allow the storm circulation, usually counter-clockwise, to shift to a weak clockwise circulation in the very middle of the storm. Not only that, but on other parts of Jupiter, the temperature change is enough to alter wind velocities and affect cloud patterns in the belts and zones.

“This is the first time we can say that there’s an intimate link between environmental conditions — temperature, winds, pressure and composition – and the actual color of the Great Red Spot,” Fletcher said. “Although we can speculate, we still don’t know for sure which chemicals or processes are causing that deep red color, but we do know now that it is related to changes in the environmental conditions right in the heart of the storm.”

Unlocking the secrets of Jupiter’s giant storm systems will be one of the targets for infrared spacecraft observations from future missions including NASA’s Juno mission.

Pipeline Heat Loss

How many feet of insulation do we need to remove on the 18" line heading to a unit to cool the incoming production 10 degrees c, The following are the assumed numbers:

1) Line size - 18" Sch 40.

2) Flow rate - 60,000 BWPD and 20,000 BOPD

3) Initial temperature - 105 degre

Power Wattage Consumption

I'm trying to calculate the wattage a radar ultra-sonic device takes. The radar instrument is loop powered (4-20ma).

Data sheet only shows 24VDC with max 550 ohms.

P = V*I = 24VDC * 20mA = .48 Watts

Can someone please confirm instrument power consumption?

Study: Men & Dogs First Became Best Friends in the Middle East | 80beats

DogReflectionAt some point in evolutionary history dogs diverged from wolves thanks to domestication by humans. But just where did dogs first become man’s best friend? Robert Wayne and his team have many years invested in answering the question, and their newest findings, published this week in Nature, suggest that the answer is the Middle East.

Researchers looked at gene segments from 912 dogs, from 85 breeds, and samples of 225 grey wolves, dog’s close cousins who they evolved from in prehistory, from 11 regions [USA Today]. Dogs and wolves that come from the Middle East, Wayne says, show the most genetic similarity. The researchers propose that dogs were first domesticated there, and then spread outward.

Dogs and wolves are closely related enough that they have interbred at various times, complicating the problem of unraveling dogs’ origin. Wayne’s team suggests that after the domestication of dogs in the Middle East, they interbred with wolves when they reached East Asia, which is how dogs and wolves there came to share some of their genetics.

Indeed, previous research had suggested East Asia as the origin of dog domestication, as breeds from there showed the most genetic diversity. But Wayne says those papers focused on a small subset of DNA called mitochondrial DNA, instead of looking across all 2.4 billion letters that make up the dog genome [NPR]. But Peter Savolainen, one of the scientists arguing for East Asia, says he wasn’t moved by Wayne’s new study. Savolainen says it did not sample dogs in East Asia from south of the Yangtze, the region where the diversity of mitochondrial DNA is highest. Also archaeologists in China have been less interested in distinguishing dog and wolf remains, he said [The New York Times].

So this study won’t be the final word. But what’s not in doubt is the importance of dogs to early human civilization (that is, once the domesticators selected for small body size and other characteristics you’d want to make best friend that doesn’t eat you). Dogs could have been the sentries that let hunter gatherers settle without fear of surprise attack. They may also have been the first major item of inherited wealth, preceding cattle, and so could have laid the foundations for the gradations of wealth and social hierarchy that differentiated settled groups from the egalitarianism of their hunter-gatherer predecessors [The New York Times].

Related Content:
80beats: Where Did Dogs First Become Man’s Best Friend?
80beats: Wolves Have Dogs to Thank for Their Dark Fur
80beats: Hairless Dogs Give Up the Genetic Secret of Their Bald Glory
DISCOVER: The Genetics of… Dogs
DISCOVER: Ascent of the Dog

Image: flickr / mikebaird


Cheesy News Roundup: The Steve Jobs Cheese Head and Breast Milk Cheese | Discoblog

At Discoblog, we do our best to keep the party going. So, even as we lurch back into existence after St. Paddy’s celebrations, we are looking forward to our next big party–which just might be the iPad launch party next month. So, here’s an idea for Apple-themed party food, courtesy Chef Ken at The Cooks Den.

There’s nothing like a cheese plate to make an occasion feel festive. For this recipe, you will need:

* 1 Steve Jobs Cheese Head
* Assorted gourmet cheeses such as brie, camembert or stilton
* Crackers
* Fruit

cheeseplate

Oh! You’re not familiar with the culinary marvel known as the Steve Jobs Cheese Head? Forgive us. Chef Ken created this perfectly crafted head of the Apple CEO from a block of mozzarella; the chef thinks mozzarella works best, since the color of the cheese matches His Steveness’s pasty white pallor. It’s pretty simple to create this cheesy replica of a Jobs head. For step-by-step instructions, go here.

Once your Steve Jobs Cheese Head has been lovingly crafted, place it on fancy plate, arrange crackers, pieces of fruit, and assorted cheeses, and serve to your guests. Chef Ken also suggests serving Jobs’s head as part of a nacho concoction or in a fusion dish he calls iPad Thai. Hey, the Steve Jobs Cheese Head goes with anything.

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But if by some weird chance the Steve Jobs Cheese Head does not grab your interest, you might also consider serving cheese made from breast milk.

This all-natural creation was pumped to existence when chef Daniel Angerer’s wife realized she had a lot of extra breast milk lying around in packets, cluttering the freezer.

But instead of throwing the excess milk out and wasting “gold,” as Angerer terms it, he turned it to cheese, much to the delight of other moms who are now asking for more breast milk recipes.

They want to use their extra milk to make ice-cream, milk shakes, and other stuff that can be fed to fussy eaters.

We aren’t really sure what sort of party would call for the serving of breast milk cheese–but Angerer has helpfully provided detailed instructions from his “Mommy’s milk cheese making experiment” for anyone who wants to follow his example.

Related Content:
Discoblog: NCBI ROFL: St. Paddy’s Day special: Surprise! Drinking makes the Irish more aggressive!
Discoblog: Honoring St. Patrick: Guinness Bubbles Demystified and Why Your Hangover Hurts
Discoblog: A Giant Leap for Cheddarkind: Brits Launch Cheese Into Space
Discoblog: Caution: Your Cheese Grater May Be Radioactive, Study Finds
Discoblog: Cooking with Joel Stein: How to Eat a Placenta

Images: The Cooks Den, Daniel Angerer