Wednesday, August 29, 2012

How to Overlining Words in Microsoft Word

Tips: Windows

Tuesday, August 28, 2012

Fifty Shades of Brown

Fifty Shades of Brown: The Evolving View of Fat
Source: Circulation

This is an editorial article of a PVAT (Perivascular adipose tissue) study supports fat is friend not foe. I have learned decades ago in my medical school that the BAT (brown adipose tissue) which is major thermogenetic fat for an infant, especially cold area of world without heat. Now, researchers find that adults also have the BAT a little bit here and a little bit there.

"...
The relationship between increased body mass index and risk for diabetes mellitus or cardiovascular disease is well established. Such observations have driven considerable interest into the nature of adipose tissue and what mechanisms might help explain how adipose tissue and specific aspects of adipocyte biology influence cardiometabolic disorders. For example, adipocytes are now recognized as a source of mediators released into the circulation, like the adipokines resistin and adiponectin, which can modulate inflammation, insulin sensitivity, and atherosclerosis. Other molecules released from adipocytes like free fatty acids and reactive oxygen species can also exert both local and distant effects that may be integral to the development of diabetes mellitus, atherosclerosis, and their complications. To an increasing extent, adipose tissue is now understood as an organ playing important physiological and pathological roles. Both the absence of fat, as with certain lipodystrophies, and excess adiposity are associated with diabetes mellitus, with mechanisms that appear to include infiltration of inflammatory cells into adipose tissue and the release of systemic mediators.
..."

Wednesday, August 08, 2012

How to calculate confidence interval of incidence rate under the Poisson distribution


How to calculate the confidence  interval of incidence rate under the Poisson distribution


Incidence rate (IR) = # event (N) / person-time at risk (T)

The exact Poisson confidence interval (CI) (Ulm, 1990): 
                   (1- α) % CI of N =
                   (1- α) % CI of IR = 


If N is large, 95% CI of N = 
                    95% CI of IR =  = 

You may use PQRS or use an online calculate like GraphPad QuickCalcs, or Quantile Function Calculator to get a quantile of the chi-square distribution.


The Online OpenEpi, a nice Epidemiologic Calculator, provides different ways to get these confidence intervals. I noticed, if N = 0, the calculator gives N = 0.5 to avoid unrealistic results.


Stata can give exact Poisson CI:
     .cii T N, poisson

Wednesday, August 01, 2012

Recipes

Recipes

Thursday, July 12, 2012

Special issue on lipotoxicity

Editors: A. Vidal-Puig & R.Unger

“It was sometime in March 2009 when our colleague Fritz Spener first proposed a special issue of BBA Molecular and Cell Biology of Lipids focused on the concept of lipotoxicity and its relevance as an integrative pathogenic mechanism of the metabolic syndrome. Although we might have hesitated a little initially, this did not last long as we realised that: a) ours would be a unique, high quality publication addressing the topic in depth and globally; b) this is an important area of research with enormous implications for metabolic disease and, in our opinion, its relevance is underestimated and relatively unknown among both the biomedical community and general public; and c) the great opportunities offered by new technologies and experimental models to understand the role of lipotoxicity in common metabolic diseases makes this a very timely issue. And also, of course, we expected strong support from the “lipotoxic community”. Certainly we have not been disappointed. In fact our colleagues have provided enormous support and their generosity has made this issue viable. Our only regret is that we have not been able to involve as many of the key experts as we wanted due to space constrains and the time scale of the project, and we hope this will not be the cause of any lost friendships!”


Here is the special issue: Special issue on lipotoxicity.

This issue isn’t new. I have got the similar hypothesis after I attended a lecture by J. Denis McGarry in 2001 (In memory of Dr. John Denis McGarry. His article "What if Minkowski Had Been Ageusic?"  is on the wall of my office all the time). I put this special issue on my blog to remind me keeping work on this hypothesis.

Tuesday, July 10, 2012

In Dieting, Magic Isn’t a Substitute for Science



By GINA KOLATA
 "Is a calorie really just a calorie? Do calories from a soda have the same effect on your waistline as an equivalent number from an apple or a piece of chicken?"

Thursday, July 05, 2012

Studies of Human Microbiome Yield New Insights

Studies of Human Microbiome Yield New Insights
Source: NYTimes.com by Carl Zimmer
"For a century, doctors have waged war against bacteria, using antibiotics as their weapons. But that relationship is changing as scientists become more familiar with the 100 trillion microbes that call us home - collectively known as the microbiome.
...". Read full article here.
There is also a story about Zhao Liping combines traditional Chinese medicine and studies of gut microbes to understand and fight obesity on the Nature: My Microbiome and Me.

Wednesday, July 04, 2012

Revolutions: The role of Statistics in the Higgs Boson discovery

The role of Statistics in the Higgs Boson discovery
Source: Revolution Analytics
News is starting to leak that the Large Hadron Collider may have accomplished its primary mission of confirming the existence of the hypothesised and heretofore elusive subatomic particle, the Higgs Boson. And sure, billions of Euros worth of state-of-the-art high-energy machinery and an army of experimental and theoretical physicists probably had something to do with the discovery. But did you know Statistics played a part as well? Check out this explainer video from PhD comics, below (an R chart even appears at the 00:27 mark):
Full text: here

What's in the world is a Higgs Boson? Source: NYTimes.com


The Higgs Boson Explained from PHD Comics on Vimeo.

Monday, July 02, 2012

How to Get Into Stanford with B’s on Your Transcript

How to Get Into Stanford with B's on Your Transcript
Source: Study Hacks by Cal Newport
"Let's try a simple experiment. Imagine that you're an admissions officer at a competitive college, and you're evaluating the following two applicants:
•David — He is captain of the track team and took Japanese calligraphy lessons throughout high school; he wrote his application essay on the challenge of leading the track team to the division championship meet.
•Steve — He does marketing for a sustainability-focused NGO; he wrote his application essay about lobbying delegates at the UN climate change conference in Johannesburg, South Africa.
Who impresses you more?
..."
This is an article recommended by my daughter. You can find the full text here: How to Get Into Stanford with B's on Your Transcript

"...

Lassiter’s Insight

What happened inside your brain when you read the descriptions of David and Steve? According to a clever series of experiments conducted by G. Daniel Lassiter, a psychology professor at the University of Ohio, your first response was to look into the proverbial mirror. Or, as Lassiter describes it, somewhat more formally,  in his 2002 paper on the subject: we have a “pervasive tendency…to use the self as a standard of comparison in [our] dispassionate judgments of others.”
Put another way, to evaluate a person’s accomplishments, we imagine ourselves attempting the same feat, allowing your own capabilities to provide a convenient benchmark for assessing others’.
(In Lassiter’s experiments, students took tests made up of difficult mathematical puzzles. He showed that when a student was asked to rate the intelligence of another student, this judging student used a self-assessment of his own intelligence, combined with how well he did on the test, to construct the rating.)
Let’s walk through the logic here. When you first encountered David and Steve, your brain began to compare them to yourself. In essence, your brain asked: “Could I do that? And if so, what would it require?”
...:

Thursday, June 28, 2012

This is my test run using GoogleVis, a R! package

My test-run using GoogleVis, a R! package

This week, I attended a R! training class instructed by Dr. Aedin Culhane, a wonderful teacher. I was taught that I can use the GoogleVis, a R! package, to draw a moving bubble plot. It's amazing. Here is the output we used in the class.
    R! Codes: library(googleVis)
             M <- gvisMotionChart(Fruits, "Fruit", "Year")
             plot(M)
             cat(M$html$chart, file="tmp.html")
Here is the more information about: Using the Google Visualisation API with R


Data: Fruits • Chart ID: MotionChartIDed077347ee8
R version 2.15.0 (2012-03-30) • googleVis-0.2.16 • Google Terms of Use • Data Policy

Tuesday, June 26, 2012

FW: A Firm Diagnosis of Frailty - NYTimes.com

A Firm Diagnosis of Frailty
Source: NYTimes.com


... After years of observing and working with older patients, Dr. Fried recognized objective hallmarks of frailty, and in the 1990s developed a definition of frailty in people 65 and older that called for the diagnosis when three or more of the following five criteria were present: unintentional weight loss of 10 pounds or more in the past year, self-reported exhaustion, weakness as measured by grip strength, slow walking speed and low physical activity. The presence of one or two of those criteria would identify a person as "pre-frail."

Thursday, June 21, 2012

Update on the alternative to HOMA-IR and HOMA-b


Update on the HOMA-IR and HOMA-b
Source:  iHOMA2
iHOMA2 is an interactive, 24-variable, HOmeostatic Model of Assessment with the baseline default characteristics of the HOMA2 computer model of fasting insulin:glucose interaction. iHOMA2 enables the mathematical functions describing the organs and tissues involved in the glucose and hormonal compartments to be modified using simple visual analogue controls. The model can be used to evaluate therapeutic agents and predict effects on fasting glucose and insulin and on beta cell function and insulin sensitivity.
Here is the main URL for the iHOMA2 website.

I am not a fan of iHOMA2; I post it here as a future reference.

Tuesday, May 15, 2012

Joslin's Diabetes Deskbook, A Guide for Primary Care Providers, Updated 2nd Ed., Excerpt 2: Do You Know the Conditions that May Cause Inaccurate Results from the A1C Test?

Joslin's Diabetes Deskbook, A Guide for Primary Care Providers, Updated 2nd Ed., Excerpt 2: Do You Know the Conditions that May Cause Inaccurate Results from the A1C Test?
By Richard S. Beaser, M.D.


"... With respect to the testing methodology, when HPLC laboratory techniques are used to perform measurements, the number of things that can affect the test results is limited. Using this methodology, the most common factors that can affect A1C measurements are:

  • Hemolytic anemias Carbamylated and acetylated hemoglobins (rare).
  • "Fast" migrating hemoglobins, most commonly hemoglobins D, J, and N, can lower readings.
  • Fetal hemoglobin greater than 25% interferes with hemoglobin A1c measurement and cannot be corrected for.
  • True beta-thalassemia will interfere with some HPLC methods, but the patient has to be symptomatic at the time for the effect to be significant.
  • Severe lipemia in some patients can interfere with measurements. Interference can be reduced by washing red cells and making an offline dilution to report out the A1C value
  • Taking medications such as salicylates can have an effect, though rarely ..."

Monday, May 14, 2012

Fatty Liver Disease in Diabetes: Good and Bad?

Fatty Liver Disease in Diabetes: Good and Bad?


When the enzyme called histone deacetylase 3 (HDAC3) was removed, the mice had massively fatty livers, but lower blood sugar, and were thus protected from glucose intolerance and insulin resistance....


The findings demonstrate that fat itself is not necessarily all bad. "It matters a lot how fat is handled and stored," notes Lazar. "It also highlights the importance of complying with our internal circadian clock. For example, since our body does not anticipate food at night and is preparing to generate more glucose, night-time eating is likely to shoot up blood sugar and thus may contribute to diabetes."


The full text here.
The original article here.

Tuesday, May 08, 2012

Metabolic surgery for type 2 diabetes and obesity related - Nature Medicine

Metabolic surgery for type 2 diabetes
David E Cummings

Clinicians note that bariatric operations can dramatically resolve type 2 diabetes, often before and out of proportion to postoperative weight loss. Now two randomized controlled trials formally show superior results from surgical compared with medical diabetes care, including among only mildly obese patients. The concept of 'metabolic surgery' to treat diabetes has taken a big step forward.

Topic: Guts over glory - why diets fail
Rachel Larder and Stephen O'Rahilly

Losing weight can pose a challenge, but how to avoid putting those pounds back on can be a real struggle. A major health problem for obese people is that diseases linked to obesity, such as type 2 diabetes and cardiovascular disease, put their lives at risk, even in young individuals. Although bariatric surgery[mdash]a surgical method to reduce or modify the gastrointestinal tract[mdash]was originally envisioned for the most severe cases of obesity, evidence suggests that the benefit of this procedure may not be limited to the staggering weight loss it causes. Endogenous factors released from the gut, and modified after surgery, may explain why bariatric surgery can be beneficial for obesity-related diseases and why operated individuals successfully maintain the weight loss. In 'Bedside to Bench,' Rachel Larder and Stephen O'Rahilly peruse a human study with dieters who regained weight despite a successful diet. Appetite-regulating hormones in the gut may be responsible for this relapse in the long term. In 'Bench to Bedside,' Keval Chandarana and Rachel Batterham examine how two different methods of bariatric surgery highlight the relevance of gut-derived hormones not only in inducing sustained weight loss but also in improving glucose homeostasis. These insights may open new avenues to bypass the surgery and obtain the same results with targeted drugs.


Topic: Metabolic insights from cutting the gut
Keval Chandarana and Rachel L Batterham

Losing weight can pose a challenge, but how to avoid putting those pounds back on can be a real truggle. A major health problem for obese people is that diseases linked to obesity, such as type 2 diabetes and cardiovascular disease, put their lives at risk, even in young individuals. Although bariatric surgery[mdash]a surgical method to reduce or modify the gastrointestinal tract[mdash]was originally envisioned for the most severe cases of obesity, evidence suggests that the benefit of this procedure may not be limited to the staggering weight loss it causes. Endogenous factors released from the gut, and modified after surgery, may explain why bariatric surgery can be beneficial for obesity-related diseases and why operated individuals successfully maintain the weight loss. In 'Bedside to Bench,' Rachel Larder and Stephen O'Rahilly peruse a human study with dieters who regained weight despite a successful diet. Appetite-regulating hormones in the gut may be responsible for this relapse in the long term. In 'Bench to Bedside,' Keval Chandarana and Rachel Batterham examine how two different methods of bariatric surgery highlight the relevance of gut-derived hormones not only in inducing sustained weight loss but also in improving glucose homeostasis. These insights may open new avenues to bypass the surgery and obtain the same results with targeted drugs.


Full Text | PDF 

Monday, May 07, 2012

Stata: useful and Interesting user-written ado programs

Stata: Useful and Interesting User-written ado Programs/packages
Manage the ado programs
A list of ado packages I am using (. ssc install -package-)
Other Resources for adding features to Stata by Stata