Sit less, Move more

I am typing this standing in front of my computer. My tall chair is aside. 

About a year ago, I realized that I felt better when I stood while working. It turned out I was not alone in this discovery; more and more people are opting for a vertical approach to work, and the benefits are becoming increasingly evident.

We're all familiar with the age-old advice to "eat less and exercise". But this may not be enough. As shown in a recent study, exercise does not counteract the ill effects of sedentary lives, we should keep moving (or at least squatting) throughout the day too.  New York Times article about the study (The men who stare at screens) immediately got up-votes from over 100 hackers - those who spend hours staring at screens to code, along with 100+ comments from those staring at screens to read and comment on the news.  Stand up while you read this, asked NYT earlier this year. Prolonged sedentarity affects not only cardiovascular and metabolic health, blood clotting, diabetes and cancer. Countless hours of sitting could cause many other ailments reducing the quality of life such as skewed microbial ecology accompanied by strong body odor, diminishing overall quality of life.

Health promotion efforts targeting physical inactivity should emphasize both reducing sedentary activity and increasing regular physical activity for optimal health.

The lead author of the 2010 study says: "Stand up. Pace around your office. Get off the couch and grab a mop or change a light bulb the next time you watch ‘‘Dancing With the Stars.’’ A five-minute stroll is recommended every half hour.

Stand-up desks and treadmill desk were available years ago, a web site just stand was created for office workers who sit long hours each day, but either the desks are not very usable yet, lobbying your boss for a stand-up workstation is still tricky or most people just like sitting too much. Let's hope this will change.

References

Warren TY, Barry V, Hooker SP, Sui X, Church TS, & Blair SN (2010). Sedentary behaviors increase risk of cardiovascular disease mortality in men. Medicine and science in sports and exercise, 42 (5), 879-85 PMID: 19996993 DOI: 10.1249/MSS.0b013e3181c3aa7e

Dunstan DW, Barr EL, Healy GN, Salmon J, Shaw JE, Balkau B, Magliano DJ, Cameron AJ, Zimmet PZ, & Owen N (2010). Television viewing time and mortality: the Australian Diabetes, Obesity and Lifestyle Study (AusDiab). Circulation, 121 (3), 384-91 PMID: 20065160 
DOI: 10.1161/CIRCULATIONAHA.109.894824

Katzmarzyk PT, Church TS, Craig CL, & Bouchard C (2009). Sitting time and mortality from all causes, cardiovascular disease, and cancer. Medicine and science in sports and exercise, 41 (5), 998-1005 PMID: 19346988 DOI: 10.1249/MSS.0b013e3181930355

Healy GN, Dunstan DW, Salmon J, Shaw JE, Zimmet PZ, Owen N. (2008). Television time and continuous metabolic risk in physically active adults. Medicine and Science in Sports and Exercise 40, 639-645.(PMID: 18317383) 

Khaw K-T, Wareham N, Bingham S, Welch A, Luben R, et al. (2008) Combined Impact of Health Behaviours and Mortality in Men and Women: The EPIC-Norfolk Prospective Population Study. PLoS Med 5(1): e12. doi:10.1371/journal.pmed.0050012 (PMID: 18184033)

Beasley R, Raymond N, Hill S, Nowitz M, Hughes R. (2003) eThrombosis: the 21st century variant of venous thromboembolism associated with immobility. Eur Respir J.  21(2), 374-6. (PMID: 12608454 )

Aurametrix is developing next-generation systems for Personal Health Management. Better solutions for a healthier world

Additional references post-initial publication:

Gao W, Sanna M, Chen YH, Tsai MK, Wen CP. Occupational Sitting Time, Leisure Physical Activity, and All-Cause and Cardiovascular Disease Mortality. JAMA Network Open. 2024 Jan 2;7(1):e2350680-.

 

Microbial sequencing for food applications is gaining momentum, but challenges remain

Microbes bring us a wide variety of foods, transforming texture and intensifying flavors. Jake Lahne, posted a great overview of some of the good microorganisms in cheese - like Penicillium molds in Cabrales cheese shown on the right - that adds to other ingredients such as milk, salt and coagulants.

While modern cheeses are made with preselected cultures, traditional cheeses carry dozens of types of microbes, some highly unusual and uncharacterized.


Lactic acid bacteria, including lactococci and lactobacilli, not only convert the basic milk sugar, lactose, into lactic acid but also make the cheese inhospitable to many spoilage organisms and is the first step towards deliciousness. Streptococci are also important in cheese and yogurt-making, adding flavor to alpine (Emmental, Gruyere, etc) and Italian hard (Grana Padana, Pecorino Romano, etc) cheeses. Lactococcus lactis, Staphylococcus, Trichococcus, and Monascus are strongly associated with the 36 key aroma compounds of Monascus-fermented cheese. Lactococcus lactis was found to be the dominant bacterium while Monascus was confirmed to be the dominant fungus.

Propionobacter shermanii, are able to digest acetic acid and convert it to sharp, sweaty-smelling propionic acid and carbon dioxide. Several species of propionibacteria also inhabit human skin, producing less wanted odors.

Most of the molds that grow on cheese are species of Penicillium, but some cheeses, like St. Nectaire, develop others such as blue mold, P. roqueforti and P. glaucum in blue cheese. Blues include Roquefort, Stilton, Gorgonzola, and Cabrales, and goat cheese Monte Enebro.
White molds, which are found on the outside of all types of soft-ripened cheeses, are subspecies of P. camembertii (also called P. candidum). These white molds produce enzymes that break down the milk proteins and producing garlicky or earthy, also ammonia smells.

Room-clearing ability of Epoisses, Münster, and Limburger owe to the smear bacteria officially known as Brevibacter linens. They need salty (up to 15%), moist environments to grow,and create stinky odor compounds, producing oniony or garlicky, fishy, and sweaty aromas. The aroma of the washed-rind cheeses is often compared to smelly feet - and, yes, brevibacter grow well on human skin.

But it is not only cheese that carries myriads of microbes. There are many other foods. And not all of the bacteria we consume with the foods is good for you.

Genome sequencing was predicted to bring practical benefits to the field of microbial food safety, identifying and controlling emerging microbial pathogens. It is still not as readily available and inexpensive as needed for practical applications, but a few pilot projects have showed a promise.

GenomeWeb's Andrea Anderson recently published this article about academic researchers and public health agencies exploring the use of genomics-based approaches to complement existing food safety and surveillance methods.

Common foodborne pathogens include E. coli 0157:H7, Salmonella, Listeria, and Campylobacter, but there are many more in need of identification. Having effective ways to distinguish between dangerous and neutral microbes is crucial for food safety.

Many identification methods exist, but whole-genome sequencing could give unprecedented wealth of information, allowing predictions about the nature of organisms, their potential sources and associated risk,

In a paper published in the Journal of Food Protection in May, USDA's Ward and his colleagues reported on their findings from a multi-locus genotyping study of more than 500 Listeria monocytogenes isolates collected by the USDA-FSIS from a variety of ready-to-eat foods.
"Integration of PFGE and DNA-sequence-based sub-typing provides an improved framework for prediction of relative risk associated with L. monocytogenes strains from [ready-to-eat] foods," they wrote.

In another recent paper, Ward and collaborators from Colorado State University used genotyping to show that a virulence-decreasing inlA mutation in L. monocytogenes was more common in isolates from ready-to-eat than from isolates from actual human listeriosis cases.
Honisch presented a poster outlining work done with collaborators from London's Health Protection Agency at the American Society for Microbiology annual meeting in San Diego this May, describing how the team used the Sequenom MassArray platform to do multi-locus sequence typing, or MLST, on hundreds of Salmonella isolates. Honisch told GWDN that the approach is promising, in part, because mass spec is high-throughput and generates very reproducible data.
During a session at the recent ASM meeting, Eric Brown, a microbiologist with the US Food and Drug Administration, explained that the FDA has been exploring the use of Roche 454 sequencing to characterize Salmonella isolates and to find markers for tracing outbreak strains back to their source.
And in Canada, the NML's Gilmour was lead author on a paper appearing in BMC Genomics this February in which researchers used the Roche 454 GS FLX platform to sequence the genomes of two L. monocytogenes strains isolated during a 2008 outbreak of listeriosis in Canada that killed 22 people and caused serious illness in dozens more.
"This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events," Gilmour and his co-authors wrote, "and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole-genome sequences in the context of epidemiology."
Even so, Gilmour said it will take time for whole-genome sequencing to become a standard traceback method — largely due to remaining bioinformatics challenges.
"It's our job to learn how to use those [sequencing] technologies and glean the interesting information or the informative information," Gilmour said. "That's kind of the bottleneck we're at right now, is developing those bioinformatics tools to take that raw data and quickly parse through it and find relevant information."

There is still a long way before genome-sequencing or methods developed based on sequencing results will be standardized and incorporated into practice, but the results look promising and are opening new horizons for health applications.

References

Ward TJ, Evans P, Wiedmann M, Usgaard T, Roof SE, Stroika SG, & Hise K (2010). Molecular and phenotypic characterization of Listeria monocytogenes from U.S. Department of Agriculture Food Safety and Inspection Service surveillance of ready-to-eat foods and processing facilities. Journal of food protection, 73 (5), 861-9 PMID: 20501037

Van Stelten A, Simpson JM, Ward TJ, & Nightingale KK (2010). Revelation by single-nucleotide polymorphism genotyping that mutations leading to a premature stop codon in inlA are common among Listeria monocytogenes isolates from ready-to-eat foods but not human listeriosis cases. Applied and environmental microbiology, 76 (9), 2783-90 PMID: 20208021

St-Gelais D, Lessard J, Champagne CP, & Vuillemard JC (2009). Production of fresh Cheddar cheese curds with controlled postacidification and enhanced flavor. Journal of dairy science, 92 (5), 1856-63 PMID: 19389943

Rossetti L, Fornasari ME, Gatti M, Lazzi C, Neviani E, Giraffa G. (2008). Grana Padano cheese whey starters: microbial composition and strain distribution. Int J Food Microbiol. 2008 Sep 30;127(1-2):168-71. Epub 2008 Jun 12.PMID: 18620769

Flórez AB, Mayo B. (2006) Microbial diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. Int J Food Microbiol. 2006 Jul 15;110(2):165-71. Epub 2006 Jun 27.PMID: 16806553

Aurametrix is developing next-generation diagnostic tools for Personal Health Management. Better solutions for a healthier world

QS#14: There are more questions than answers

Quantifying self: there are more questions than answers

Notes from QS Show&Tell #14 held in the San Francisco Bay Area Tech Museum of San Jose on June 22nd.

Quantifying Productivity

Bill Jarrold used a simple script to record his Unix activity with timestamps on the commands he typed. By quantifying the number of operations per hour he determined that he is usually on the roll at about 3pm, but is slowing down around 10am and midnight. The talk spurred discussions about other ways to analyze productivity - number of builds per time unit? keystrokes? content analysis of the commands? There also were suggestions on using GUI-based tools. For example, CoScripter Reusable History that records everything one does on the web. Or DeliciousDiscovery that analyzes Delicious bookmarks and tags. There are even commercial software tools such as SpyAgent that capture everything a computer user does: keystrokes typed, websites visited, chat conversations, applications ran, emails sent and received, files opened, and more.

One needs not only sophisticated screening and recording of performance related measures but also more sophisticated data analysis methods. There is a good discussion on HN about More-Hours-Worked not equal to More-Work-Getting-Done (it started from this post: Something Deeply Wrong With Chemistry). Dependence of productivity on hours worked is bell shaped and very individual. Some may be most productive when working 35 hours a week, others could increase workload to 60 hours. Number of keystrokes may not necessarily correlate with meaningful output either. Remember Jack Nicholson in The Shining? Besides, sometimes we need to think before turning ideas into action. And how could we measure what is going on in the brain?

Quantifying Thoughts

Mark Carranza is probably the most notable collector of thoughts among the Bay area quantifiers. His database has more than one and a quarter of a million thoughts and keeps growing, with more entries than the diary of Samuel Pepis and the collection of Lion Kimbro, the man who wrote down every though he had.
Jim, the second presenter of QS#14 is collecting thoughts too - he has 65,000 of them connected by associations and represented by colorful visualizations. He uses spreadsheets and Personal Brain software to create and display the results. TheBrain's display is organized around a central Thought, surrounded by all its Children, Siblings and Jumps - like an ontology - helping to follow a train of hought, flowing from one to the next or just wandering around. Navigation through the data is interesting although rather chaotic. Questions from QS participants addressed the usefulness of the tool. Does it really help to to leverage the power of visual thinking and understand the context of information before taking action?

Quantifying Stress

Bharat Vasan of PulseTrace Technologies gave a great impromptu talk on how he is using his watch reading real time heart rate from his wrist. Data may be uploaded via USB or wireless connection. One good application is managing stress. Bharat wants to be a good public speaker - and he certainly is, but his pulse rate always skyrockets during a presentation. Of course, some of us don't need to have a watch like this to know if pulse rate is elevated - the tendency to blush lets everybody around to take the readings. Shortness of breath, nausea and sweating may add to the picture. As Jerry Seinfeld said about delivering the eulogy, most people would rather be in the casket than speaking in public. One the other hand, some increase in pulse when talking is rather good and he trick is to use it as energy to fuel the presentation.
Pulse rate is a good measure of stress levels. Other measures would complement it and contribute to meaningful analytics. For example, recovery heart rate, a measure of how quickly ones heart could return to resting state. Standing vs sitting - normally there is 5 to 10 beats difference. Temperature in the room. Coffee or spices in food...

I have not tried the PT100 sensor-based watch, but my complaints about similar monitoring watches include their inability to measure heart rate during running at full speed, sensitivity to humidity, rain, food vapors, limited time intervals between repeated measurements. I also question reliability of measurements in 1-5% of cases.

Quantifying Motion

Indeed, quantifiers are improving their lives not only with spreadsheets and software - gadget usage continues to rise. ("Zeo's broken" was among two-word introductions of meetup participants). There were many Fitbit fans proudly showing their devices and less proudly measurements for the day - Wow, we are becoming ashamed for not stepping enough! Popular motion gadgets do not work for everyone and are generation 1.0 or rather 0.5 - some like swimming instead of running and elliptical trainers instead of treadmills, others are surprised to find that rocking baby in their arms was counted as calorie-burning steps. BodyMedia Fit (GoWear Fit), for example, measures not only acceleration, but also skin temperature and galvanic skin response reflective of physical stress, but is not water proof and can't measure emotional stress. Fitbit is less pricey but also not quite ready to do what most people want. The next talk was devoted to fitbit's corporate competitor - DirectLife.

Alex Bangs, co-founder of Entelos now working on a spinoff - DigitalSelf, likes this little white plastic box and DirectLife program. The device has accelerometers to quantify how much you move. The program starts with a one week assessment to get a good idea of individual's current activity and create a baseline. The plan has daily activity goals that increase slowly week by week (hopefully not as in The Red Shoes by Andersen!). Alex showed how his device was flashing congratulating him with good activity levels for the day. It could be even better, he said, the little box can almost sing a tribute to you if you walked more than your goal. The device fits in the pocket, but can be forgotten at home - which makes every wearer sad as the accomplishments of the day will not be logged and recognized. We love to be tapped on the back and told well done, are not we all?