Fungal Fruiting Bodies and Fanatics

Fungal Fruiting Bodies and Fanatics, a book review

Source: Science

 …”Mushrooms are the sex organs of fungi. They are ballistics experts that emerge when the fungus is ready to reproduce, launch spores by the billion, and vanish. Or rather, they puff up and deflate. The sudden appearance of mushrooms on a lawn or under a log, like many illusions, is achieved with extensive advance setup and hydraulics. After a spore germinates, it sends filaments out underground in all directions in search of food and other fungi. When two fungal colonies—or three or more, as fungi are substantially less constrained than animals—of the same species meet, their cells merge and their DNA combines in the mushroom version of mating. New spores are produced, and the cells of the future mushroom are organized around them. This process occurs at the tips of the filaments, accounting for mushrooms' quirk of appearing in rings. When the conditions are right, water rushes in and pressurizes the assembly, swelling the cells and inflating the mushroom. In many species, that takes only a few hours, the spores are soon released, and the mushroom shrivels by sundown. Others survive a week or more, and some tougher forms may last for months. “…

full text: here

Exercise: 八段锦

Exercise: 八段锦 (Baduanjin)
from Wikipedia


Full Article in Chinese
...
八段锦(Ba Duan Jin)是一种在中国古代发明的健身方法，由八种肢体动作组成，内容包括肢体运动和气息调理。八段锦有人认为是气功的一种。也有演變成中国武术一种。


八段锦和五禽戏、太极拳等，都是中国民间广为流传的健身方法。1982年6月28日，中国卫生部、教育部和当时的国家体育委员会发出通知，把八段锦等中国传统健身法作为在医学类大学中推广的"保健体育课"的内容之一。2003年中国国家体育总局把重新编排后的八段锦等健身法作为"健身气功"的内容向全国推广。


"八段锦"这个名字，一般认为有两层意思：1、表示这是一种集锦多种练习方法的功法；2、源自一种名为"八段锦"的织锦，表示练习时动作连
...
Full Article in English
...
The Baduanjin (simplified Chinese: 八段锦气功; traditional Chinese: 八段錦氣功; pinyin: Baduànjin qìgong) is one of the most common forms of Chinese qigong used as exercise. Variously translated as Eight Pieces of Brocade, Eight Section Brocade, Eight Silken Movements and others, the name of the form generally refers to how the eight individual movements of the form characterize and impart a silken quality (like that of a piece of brocade) to the body and its energy. The Baduanjin is primarily designated as a form of medical qigong, meant to improve health. This is in contrast to religious or martial forms of qigong. However, this categorization does not preclude the form's use by martial artists as a supplementary exercise, and this practice is frequent.
...

BMJ Basic Concepts for Reading Health Articles

Basic Concepts for Reading Health Articles by BMJ

• How to read a paper
• Epidemiology for the uninitiated
• Academic medicine
• Statistics at square one
• Photographs of twentieth century doctors

How to do a trend analysis in Stata

Tips - Stata: How to do a trend analysis in Stata

• -nptrend- performs the nonparametric test for trend across ordered groups.

    .nptrend exposure, by(grp)
    also see How can I test for a trend across a categorical variable?

• -vwls- estimates a linear regression using variance-weighted least squares.

    .vwls prev year,sd(se_prev)

• Does Stata provide a test for trend?

• Usually, after an analysis like regression you can test trend, I use -contrast- and orthogonal polynomial coefficient contrast to examine the linear or higher order trend.
• I also use other software like Joinpoint Regression Program, a handy tool by NCI, for trend analysis.

Where can we find the citation number of our published article?

Where can we find the citation count of our published articles?

Usually I use Web of Knowledge by Thomson Reuters Science:

• Go to the Web of Knowledge.
• Click on the tab of Web of Science.
• Click on the sub-tab of Advance Search.
• Use your name and some restrictions (e.g. AU=(Cheng, YJ) AND OG=(XYZ))
• Double-check and exclude the articles not published by yourself.
• Click the Create Citation Report on the up-right corner of the first article (if you still cannot find it, press Ctrl-F, and type create citation on that webpage).
• Click and you get and play around the report.

There are also free citation count search engines:

• Google Scholar
• Google Scholar Universal Gadget enables users to search for the total number of citations of author(s). It provides a total citation count, total number of cited publications and Jorge E. Hirsch's H-Index.
• Microsoft Academic Search

Related articles: 

• A plot of my citations in Google Scholar vs. Web of Science using R! is a blog compared the citation search capability of Google Scholar and Web of Knowledge.

Sex-Specific Reporting of Scientific Research A Workshop Sum...

Sex-Specific Reporting of Scientific Research: A Workshop Summary

Editors

Institute of Medicine (US) Board on Population Health and Public Health Practice.

Source

Washington (DC): National Academies Press (US); 2012.
The National Academies Collection: Reports funded by National Institutes of Health.

Excerpt

On August 30, 2011, the Institute of Medicine hosted a workshop, Sex-Specific Reporting of Scientific Research, sponsored by the Office of Research on Women's Health (ORWH) of the National Institutes of Health (NIH). The workshop explored the need for sex-specific reporting of scientific results; potential barriers and unintended consequences of sex-specific reporting of scientific results; experiences of journals that have implemented sex-specific requirements, including the challenges and benefits of such editorial policies; and steps to facilitate the reporting of sex-specific results. Presenters and participants included current and former editors of scientific journals, researchers, and scientists and policymakers from government, industry, and nonprofit organizations. Presentations and discussions highlighted the importance to both women and men of having sex-specific data, the problems with sample size and financial constraints for conducting the research, the appropriateness of sex-specific analyses, and the limitations of journal policies to change experimental designs. During closing remarks, the planning committee chair summarized some of the individual suggestions discussed for advancing sex-specific reporting as: identifying the sex of populations in journal populations, sharing of sex-identified raw data, giving extra credit in review to manuscripts that include sex-specific information, and requiring sex-stratified analyses where applicable.
Copyright © 2012, National Academy of Sciences.

Sections

• THE NATIONAL ACADEMIES
• PLANNING COMMITTEE ON SEX-SPECIFIC REPORTING OF SCIENTIFIC RESEARCH: A WORKSHOP
• Reviewers
• OVERVIEW
• INTRODUCTION
• INCLUSION OF WOMEN IN CLINICAL TRIALS FUNDED BY THE NATIONAL INSTITUTES OF HEALTH
• WHY SEX-SPECIFIC REPORTING IS IMPORTANT
• THE RESEARCHER PERSPECTIVE: COLLECTING, ANALYZING, AND REPORTING SEX-SPECIFIC DATA
• THE EDITOR PERSPECTIVE: IMPLEMENTING JOURNAL EDITORIAL POLICIES
• IMPLICATIONS FOR JOURNALS OF SEX-SPECIFIC REPORTING POLICIES OF JOURNALS
• LOOKING FORWARD
• CLOSING REMARKS
• REFERENCES
• APPENDIXES

PMID:22379657[PubMed]

Books & DocumentsFree full text

Sex-Specific Reporting of Scientific Research: A Workshop SummaryFree full text

Tips - Stata: How to get rate

Tips – Stata: How to get rates by multiple variables for complex sampling designed data (-svy-)

If one wants to get the rates of variable 'dmb20' (0, 1) among adults with 'DM' by 'survey' and 'age3grp', he/she can use different ways to get them, three basic approaches are listed below:  

1. Use –subpop-

.svy, subpop(if DM==1 & age3grp==1): tab survey dmb20, obs row percent ci format(%5.1f)

.svy, subpop(if DM==1 & age3grp==2): tab survey dmb20, obs row percent ci format(%5.1f)

.svy, subpop(if DM==1 & age3grp==3): tab survey dmb20, obs row percent ci format(%5.1f)

2. Use –proportion-

.svy, subpop(if DM==1): proportion dmb20, over(survey age3grp)

3. Use –ratio-

.svy, subpop(if DM==1): ratio (dmb20/DM), over(survey age3grp)

NOTES: The better part of -svy: tab- is using a logit transform to produce confidence intervals of estimates, which makes the confidence interval always between 0 and 1.

However, the one advantage of using 2 & 3 is you can use post estimation commands, such as -testnl- or -nlcom-, flexibly.

we also can use -svy: total- to get the total numbers like use -count- of -svy: tab-, and followed by the post estimation commands.

Difference Between Factor Analysis & Principal Component Analysis | eHow.com

Difference Between Factor Analysis & Principal Component Analysis | eHow.com


Definition of Variables
Confirmatory Variables
Latent Variables
Variance

Tips - Stata: Building complicated expressions the easy way

Tips - Stata: Building complicated expressions the easy way


Step-by-step:

• run a command of analysis
• .db display
• click 'Create...'
• use 'expression builder' to create the complicated formula. It will help to use correct expressions
• click 'ok' and 'submit'.
• then, copy and paste the formula to a 'do' or 'ado' file for further use.

You can find a more detailed article here

Objective measurement of physical activity: best practices and future directions

Objective Measurement of Physical Activity:  Best Practices and Future Directions

source: Medicine & Science in Sports & Exercise


This journal supplement summarizes and builds upon a workshop which convened researchers from diverse sectors and organizations to critically review the state-of-the-science.


The supplement discusses current technologies for objective physical activity monitoring, provides recommendations for the use of these technologies, and explores future directions in the development of new tools and approaches. It presents best practices for using physical activity monitors in population-based research, explores modeling of physical activity outcomes from wearable monitors, and discusses statistical considerations in the analysis of accelerometry-based activity monitor data. It also examines monitor equivalency issues and discusses current use and best practices for accelerometry with particular populations—children, older adults, and adults with functional limitations. 


Open-access, full-text of all articles is available at here.

Tips - Stata: function and extended function to -generate- and -egen-

Tips - Stata: function vs. extended function & -generate- vs. -egen-


Stata provids two kinds of functions: regular functions and extended functions (or called egen function). These functions need to be used with other Stata commands, usually -generate- and -egen-. -generate- is for regular function, or -egen- for egen function and only -egen- may be used to run egen function. some function may look similar but different:

• sum(var) and total(var) (a -egen- function)with -bysort-
• Sum() is a regular function. When you use .gen sum1=sum(var), it will generate a new variable named 'sum1' with cumulative summation of 'var' from top to bottom in order of group.
• However, total() as a egen function used in .egen sum2=total(var), it will generate a new variable named 'sum2' with summation of 'var' of all observation from top to bottom in that group. All the cases in that group have the same values of 'sum2'.
• recode(var,cutpt1,cutpt2,cutpt3,...),  irecode(var,x1,x2,...,xn) and group(varlist) (a -egen- function)

Phys Ed: Exercise as Housecleaning for the Body - NYTimes.com

Exercise as Housecleaning for the Body
source: New York Times
... More striking, when Dr. Levine stuffed both groups of animals with high-fat kibble for several weeks until they developed a rodent version of diabetes, the normal mice subsequently reversed the condition by running, even as they continued on the fatty diet. The autophagy-resistant animals did not. After weeks of running, they remained diabetic. Their cells could not absorb blood sugar normally. They also had higher levels of cholesterol in their blood than the other mice. Exercise had not made them healthier.
In other words, Dr. Levine and her colleagues concluded, an increase in autophagy, prompted by exercise, seems to be a critical step in achieving the health benefits of exercise. ...

Original article published in Nature

YouTube Clips about Orchid Care

YouTube Clips about Orchid Care



Orchid Selection                                          Orchid Care

                      


Repotting Orchid                                         The Orchid Doctor


                      

Series of NCHS Data Evaluation and Methods Research

Series 2. Data Evaluation and Methods Research
Source: NCHS - Vital and Health Statistics Series
Studies of new statistical methodology including experimental tests of new survey methods, studies of vital statistics collection methods, new analytical techniques, objective evaluations of reliability of collected data, and contributions to statistical theory. Studies also include comparison of U.S. methodology with those of other countries.
No. 154 (2012). NCHS Urban–Rural Classification Scheme for Counties. 72 pp. (PHS) 2012-1354.

Making Data Talk: A Workbook

Making Data Talk: A Workbook

Source: National Cancer Institute

Communicating scientific data to lay audiences is difficult. Public health practitioners, researchers, clinicians, and others in the public health field often have the responsibility of communicating "the numbers" to individuals from all walks of life. Making Data Talk: A Workbook, published by the National Cancer Institute's Office of Communications and Education provides key information, practical suggestions, and examples on how to effectively communicate health-related scientific data to the public, policy makers, and the media.

You can access this book here: Making Data Talk: A Workbook

Reflections, Anecdotes, and Tips on R by Lyndon Walker

Reflections, Anecdotes, and Tips on R by Lyndon Walker

Revolution Analytics Free Webinars on R

Revolution Analytics Free Webinars on R
Revolution Analytics, a company provides the production-grade R and supports the R's popularity, is providing some nice free webinars for free. You can register these webinars here.

• A Backstage Tour of ggplot2 with Hadley Wickham
• Introduction to R for SAS and SPSS Users
• Big Data Analysis Starts with R

Enjoy!

Unraveling the Obesity-Cancer Connection

Unraveling the Obesity-Cancer Connection
By Gary Taubes
Summary
Insulin, a hormone produced in the pancreas, is more commonly known for its role in diabetes. But its reputation may be changing. Insulin and a related hormone known as insulin-like growth factor (IGF) are now at the center of a growing wave of research around the world aimed at elucidating what many scientists consider to be their critical role in fueling a wide range of cancers. Elevated levels of insulin and IGF are also the leading candidates to explain a significant correlation in epidemiology that has gained attention over the past 30 years: Obese and diabetic individuals have a far higher risk than lean healthy people of getting cancer, and when they do get it, their risk of dying from it is greater. And now that obesity and diabetes rates are skyrocketing, the need to understand this link has become far more urgent. ...
Read the full text here

New Ways Calories Can Add Up to Weight Gain

New Ways Calories Can Add Up to Weight Gain

Source: WSJ.com

"Whether you are just starting a New Year's diet or struggling to maintain a healthy weight, a provocative new study offers some timely guidance. It isn't so much what you eat, the study suggests, but how much you eat that counts when it comes to accumulating body fat.

The findings are the latest in a string of studies to challenge claims that the secret to healthy weight loss lies in adjusting the amount of nutritional components of a diet—protein, fat and carbohydrates.

The diet industry has offered dozens of strategies recommending raising or lowering carbohydrates, protein or fat." ...

The original JAMA article and two related articles: 

• Bray (2012) Effect of Dietary Protein Content on Weight Gain, Energy Expenditure, and Body Composition During Overeating
• Livingston (2012) Inadequacy of BMI as an Indicator for Bariatric Surgery
• Sjöström (2012) Bariatric Surgery and Long-term Cardiovascular Events

Thoughts: Hazards of dependence on surrogate endpoints

Thoughts: Hazards of dependence on surrogate endpoints


HK: Professor Yudkin et al. (The idolatry of the surrogate (2011)) offer a very important insight into the use of surrogate endpoints in medical science.   They argue that this practice - so widespread, especially in diabetes care - is tantamount to losing sight of the patient's interest.   It's a very readable piece -- a challenge to much of our work in public health & chronic-disease epidemiology.   It adds to the growing chorus of criticisms directed at the "guidelines" we (used to) cherish.

YC:  I like to read this kind of article.We are fool only when we think surrogate is a real/only cause of the disease. I agree that the hard event is the most important for evaluation of a treatment. However, the authors seem ignoring the whole spectrum of development of science, which is from short range (quick surrogate) to long range (hard event). If a drug even cannot control the level of meaningful surrogate such as glucose and blood pressure, I don’t think that the drug is good for controlling of the hard event beyond the surrogate.


BTW, the example of rosiglitazone exactly demonstrates that the scientists or physicians (maybe I need say good scientists ^_^) didn’t forget the target beyond the glucose and stop digging up more evidences. Anyhow, this is a heads-up for someone.

Selected References of The idolatry of the surrogate (2011):

• ebook: Institute of Medicin (2010).Evaluation of Biomarkers and Surrogate Endpoints in Chronic Disease.
• Yudkin JS, Richter B, Gale EAM. Intensified glucose lowering in type 2 diabetes: time for a reappraisal (2010); Intensified glucose control in type 2 diabetes—whose agenda? Lancet (2011)
• Emerging Risk Factors Collaboration (2010). C-reactive protein concentration and risk of coronary heart disease, stroke, and mortality.
• O’Connor PJ, Bodkin NL, Fradkin J, Glasgow RE, Greenfield S, Gregg E, et al (2011). Diabetes performance measures: current status and future directions.
• Lehman R, Yudkin JS and Krumholz HM (2010). Licensing drugs for diabetes.