HealthTechnologies

Can Software help Health care?

2011-12-09T08:25:00.000-08:00

Apps, apps and more apps. Software is everything and everything runs on software.

Almost every industry in the U.S. has been disrupted by software. The health care field is not one of them.

Easily accessible consumer information makes everyone a little bit doctor. Emerging portable diagnostic devices will strengthen the transition. Are we up to it?

Not yet.

A large majority of people want to own their health information. Many want to store it online and have better control over it. Yet, most people don't want any extra work associated with updating and maintaining it. As public health record (PHR) expert Jim Tate said:

My 'dream PHR' continues to evolve. What I want now is a elegant interface which gives me a real time dynamic look into my record located somewhere in the stratosphere. I don’t want to have to do anything. Please don’t ask me to input anything or make more than 2 or 3 decisions. Make it simple, intuitive, powerful, and available on the internet and I will use it. Maybe."

Yes, we are inherently lazy, always trying to find shortcuts and reduce the amount of work to get a task done. Why spend time creating and maintaining our own records when a doctor can do it for us? Or even better, why not just live and enjoy life before we get sick?

Problem is, most of us at various stages throughout life suffer from subtle conditions like food sensitivities or allergies that doctors can't easily diagnose. They're relatively minor in severity, but if managed properly our lives would be a lot better off. So maybe all we need is a doctor who's just a mobile app away, always ready to answer our questions for free.

But will these legions of online doctors have enough insight into our everyday lives to know what we eat, what we breath, and what it is we're not saying to form an expert opinion?

Not likely. Even if we could wear mobile devices - always on, always connected, counting our steps, cataloging our night sweats, and equipped with miniature cameras to photograph what we eat - would the doctors be able to process all that information to form a useful diagnosis?

Aurametrix is an advanced analysis tool that correlates our symptoms, reactions and feelings based on what we enter into the system about our diet, exercise and conditions. Results from early usage of the tool show that even occasional sparse information - entered on days we feel better or worse than average - if properly evaluated can provide a snapshot of our health with sufficient insight to connect the dots to better health. It's a form of collective intelligence that's already providing interesting discoveries without the need for us to know all the details. For example, it already knows what our foods consist of, how our daily activities or feelings align with past events, and that there are commonalities among many different things.

The future is already here but are we ready for the future?

REFERENCES

Archer N, Fevrier-Thomas U, Lokker C, McKibbon KA, & Straus SE (2011). Personal health records: a scoping review. Journal of the American Medical Informatics Association : JAMIA, 18 (4), 515-22 PMID: 21672914

Kim J, Bates DW. Analysis of the definition and utility of personal health records using q methodology. J Med Internet Res. 2011 Nov 29;13(4):e106.

Geissbuhler A, Kimura M, Kulikowski CA, Murray PJ, Ohno-Machado L, Park HA, Haux R.
Confluence of disciplines in health informatics: an international perspective. Methods Inf Med. 2011 Dec 6;50(6):545-55.

Macedo LG, Maher CH, Latimer J, McAuley JH. Feasibility of using Short Message Service (SMS) to collect pain outcomes in a low back pain clinical trial. Spine (Phila Pa 1976). 2011 Dec 3.

Lo Piparo E, Worth A, Manibusan M, Yang C, Schilter B, Mazzatorta P, Jacobs MN, Steinkellner H, Mohimont L. Use of computational tools in the field of food safety. Regul Toxicol Pharmacol. 2011 Aug;60(3):354-62. Epub 2011 May 12.

Benito PJ, Neiva C, González-Quijano PS, Cupeiro R, Morencos E, Peinado AB. Validation of the SenseWear armband in circuit resistance training with different loads. Eur J Appl Physiol. 2011 Dec 6.

Yoshiaki Sugawara,Chie Sugimoto, Sachiko Minabe, Yoshie Iura, Mai Okazaki, Natuki Nakagawa, Miwa Seto, Saki Maruyama, Miki Hirano and Ichiro Kitayama. Use of Human Senses as Sensors. Sensors. 2009, 9(5), 3184-3204; doi:10.3390/s90503184

Danger, Will Robinson!!! or injury prevention with sensors and algorithms

2010-12-17T16:55:00.000-08:00

Health is determined by many factors including:

Behavior (Physical Activity, Eating habits, Tobacco or substance abuse, responsible sexual choices, etc)
Mental Health
Injury and Violence
Environmental Quality
Preventative measures such as immunization
Access to Health Care

All these factors are quantifiable, predictable and preventable. Injuries are most likely to be perceived as “accidents” and “acts of fate”, but they depend on the same determinants as other health factors: individual behavior, social and physical environment. The likelihood of injuries - unintentional ones and those caused by acts of violence - can be computed from physical location (estimations for USA¹ are a good example), gene-environment interactions², prior medical history, and physical traits³.

There are many ways to prevent injuries - just say "no" to risky behaviors, wear preventative gear while playing sports or fall-optimized shoes for elderly, watch out for others engaged in similar activities... Yet, sometimes we forget to watch, don't have access to histories of others or get diverted. Would a body sensor or a gadget with smart software be able to warn us about potential accidents ahead to help prevent accidents? What would it need to measure?

Software and devices automatically detecting and reporting accidents already exist:

Halo Monitoring's fall detection system, for example, consists of a chest strap and belt clip with motion sensors, heart rate and skin temperature monitors. Although the system detects falls only after they happen, a study showed that just the fact of wearing it increases alertness of seniors and reduces the number of falls. Although fall detection systems are not as advanced as telematics for cars - like OnStar or mbrace that "intelligently integrate the driver, the vehicle and the environment" - capabilities such as this will be provided in the area of next-generation health management systems like Aurametrix.
Unprecedented accumulation of data - such as snapshots of driving behavior or 1.2 million person-years of hip fracture observations (Kanis JA) allows development of smarter software able to predict injuries. Logistic regression models (Kononen et al., 2011) predict seriousness of auto accidents, first-principles mathematical models (such as AHAAH for the ear) connect forces with injuries, neural net and other data mining approaches foretell which juvenile offenders are likely to return to crime (source of "intentional injuries"), or allow to calculate risk of fractures based on milk intake, personal history of accidents and body mass index. Self-quantifiers such as René Ghosh are able to figure out how to use their own data to predict future injuries. Using simple math (Riegel equation bringing all running logs on to a comparable level) and trend analysis, he tied his accidents to wanes following waxes in running performance. Researchers keep refining the variables predicting injuries. Swanenburg et al., for example, predicted multiple falls for those with a history of multiple falls (odds ratio, 5.6) and use of multiple medications (odds ratio, 2.3). And there is another simple measurement of standing position helpful in prediction. Frequent fallers, indeed, have a narrower stance width than non-fallers.

In the always-connected smart-sensor-equipped future, things such as Intel's magic carpet - picking up the weight, angle and pressure of steps - will be a commodity. Gene tests predicting injuries will be integrated with data coming from our carpets, clothing, footwear and location information. And this may be sooner than you think.

References

1. Centers for Disease Control and Prevention (CDC), National Center for Injury Prevention and Control. Web-based Injury Statistics Query and Reporting System (WISQARS); 2010 Mar 4 Available from: http://www.cdc.gov/injury/wisqars/index.html

2. Husted JA, Ahmed R, Chow EW, Brzustowicz LM, Bassett AS. Childhood trauma and genetic factors in familial schizophrenia associated with the NOS1AP gene. Schizophr Res. 2010 Aug;121(1-3):187-92. PMID: 20541371

3. Swanenburg J, de Bruin ED, Uebelhart D, & Mulder T (2010). Falls prediction in elderly people: a 1-year prospective study. Gait & posture, 31 (3), 317-21 PMID: 20047833

4. Kononen DW, Flannagan CA, Wang SC. Identification and validation of a logistic regression model for predicting serious injuries associated with motor vehicle crashes. Accid Anal Prev. 2011 Jan;43(1):112-22. PMID: 2109430

5. Price GR. Predicting mechanical damage to the organ of Corti. Hear Res. 2007 Apr;226(1-2):5-13. Epub 2006 Sep 15.PMID: 16978813

You are the Chosen One, at least by your bacteria

2010-10-12T19:45:00.000-07:00

Host genomics is not the main decision-making factor for bacteria immigrating into human body, but it is an important factor. Two papers recently published in the Proceedings of the National Academy of Sciences help to understand why you are chosen and how the choosers make their decisions.

Benson et al studied microbes of mice C57BL/6J, HR and their offspring. BL6 is a common inbred line prone to diet-induced obesity, type 2 diabetes, and atherosclerosis. They also develop age-related hearing loss, if are not following recommended dietary allowance. High runner (HR) mice is lean and fit and loves to exercise - it's in the genes.

Noninvasive 16S RNA sequencing (Roche 454) showed that the abundance of microbes in "core measurable microbiota" depended on 530 host SNPs, mostly those located in 13 quantitative trait loci and was influenced by 5 more QTLs.

Some of the genetic regions appear to determine what kind of bacteria immigrate and strive in the host, other regions influence the immigration rate, attracting a wide variety pf or specific nationalities. Supplementary material elaborates on sources of variation and genotype frequencies at given SNP locations.

How are bacteria making their decisions to colonize or not to colonize?

In another PNAS article, Ben-Jacob and Schultz explain why microbes could be smarter than humans. We may think that our decisions are well thought and sophisticated, but we are, indeed, influenced by other people and our over-interpretations of other people's reactions. Bacteria can assess the noisy and stressful environment around them more objectively and rationally. They anticipate possible drastic changes in the environment and find the best decisions by providing every bacterium with the freedom to choose its own fate. This may look like throwing dice, but the colony manages the odds and effectively programs the effect of the noise on the gene circuit performance.

Our genes may be shaping microbial communities that could, in their turn, control our physical and mental health. Yet our lifestyle choices could break the patterns and let us decide what types of bacteria we want to live with.

And for those whose fight against unwanted microbes is too hard, there may be light in the end of the tunnel: Personal Genomes project has just announced a new collaboration with Rob Knight and Noah Fierer that will enable to explore the microbial diversity of various habitats of the human body and correlate it to the genotype.

References

Andrew K. Benson,, Scott A. Kelly,, Ryan Legge,, Fangrui Ma,, Soo Jen Low,, Jaehyoung Kim,, Min Zhang,, Phaik Lyn Oh,, Derrick Nehrenberg,, Kunjie Hu,, Stephen D. Kachman,, Etsuko N. Moriyama,, Jens Walter,, Daniel A. Peterson,, & Daniel Pomp10.1073/pnas.1007028107 (2010). Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Proceedings of the National Academy of Sciences of the United States of America, Published online before print October 11, 2010
Ben-Jacob E, &; Schultz D (2010). Bacteria determine fate by playing dice with controlled odds. Proceedings of the National Academy of Sciences of the United States of America, 107 (30), 13197-8 PMID: 20660309

Predicting catastrophic health events - noninvasively and short term

2010-08-15T13:25:00.000-07:00

"I've just picked up a fault in the AE35 unit. It's going to go 100% failure in 72 hours". These were famous words of the almighty computer HAL in "2001: A Space Odyssey". Few of us believe too much in software forecasts - be it weather, earthquakes or computer hard disk failures. Yet, we all know that sometimes it works. And such systems are very valuable, assuming they continuously improve.

Word cloud generated from QS #15 intros

Wellness is always a common theme of the many presentations and experiments of Quantified Self enthusiasts - citizen scientists quantifying everyday life in order to improve it. "Health" was the most frequent word among the two-word introductions of QS #15 attendees, followed by variations of sleep and happiness, and ways to measure and understand it.
Are health failures predictable? Nobody argues they are, although most available services - such as genomic testing - provide only long term predictions. Biomarkers that scientists are interested in are obtained through invasive or costly interventions - like blood proteins or intracranial electroencephalograms. Technologies such as Mobile Cardiac Outpatient Telemetry™ (MCOT™) developed by CardioNet are based on real time EKG focused on heart rhythm abnormalities that can't be detected in small 24 or 48 hour windows. These relatively rare events are correlated with symptoms and used for diagnostics.

Your husband just died, … here’s his black box
(from Gordon Bell's presentation)

Perhaps in the future every one of us will leave a black box holding all the truth about our health, helping next generations to better maintain, test and repair their bodies. Many lives have already contributed to the understanding of causes and effects such as the link between cholesterol levels, diet and heart attack. But what about the short term prediction horizon, like the 72-hour window of HAL or 30 seconds to 15-to-45 minutes warning by seizure dogs?
Could computer luminary Gordon Bell predict his heart attack if he wore his heart monitor strap while bicycling? A cardiologist would say "no way", but maybe sometimes it's better to keep quantifying and experiment despite of what medical establishment has to say?
Data from the Women’s Health Initiative study (129,135 postmenopausal women observed over a period of nearly eight years) show that a woman’s resting heart rate may be a good indicator of her risk for a heart attack. Hsia and others (2009) found that women whose resting heart rate is more than 76 beats per minute are significantly more likely to have a heart attack than women with resting heart rate less than 62 beats a minute. This risk factor is particularly strong for women between the ages of 50 and 64, less so for women over the age of 65. (Trial NCT00000611)

Of course, women have different kinds of heart attacks than men do. They are more likely to die from a spasms of heart and the blood vessels leading to the heart, and are more likely to complain of fatigue and sleep disturbances in the weeks and months leading up to a heart attack. Sleep disturbances and decreased physiological differences between day and night are increasing heart attack and stroke risks for males too, at least for shift workers. Exercise tests - known for their false positive results - have better cardiovascular prognostic value for smokers with high cholesterol than healthy men.

Finger arterial pulsatile volume changes or finger blood flow - related to blood pressure - is another medium-to-long term predictor of pending cardiac events. A simple, noninvasive finger sensor test called EndoPAT can predict major cardiac events such as a heart attack or stroke for people who are considered at low or moderate risk.

AngelMed Guardian System (inventor: Dr. Tim Fischell) is an early warning system - telling 24 hrs to a week before if heart attack is coming. Average time between the cardiac event and hospital arrival is 3 hrs, and about 5 hrs before the surgery starts. By that time 90% of muscles could be dead, so 5 or 10 minute warnings could save lives. Unfortunately, Guardian is highly invasive - sized as an iPod, it is implanted directly into the patient's chest, monitoring electrogram waveforms and other crucial heart-signal data 24-7.

Many portable oximeters and ECG are already in the market - and even though consumers are complaining about noise and difficulties in getting readings of diagnostic intervals, the technologies will continue to improve and self-quantifiers will be finding solutions for better health.

REFERENCES
Hsia, J., Larson, J., Ockene, J., Sarto, G., Allison, M., Hendrix, S., Robinson, J., LaCroix, A., Manson, J., & , . (2009). Resting heart rate as a low tech predictor of coronary events in women: prospective cohort study BMJ, 338 (feb03 2) DOI: 10.1136/bmj.b219

Mayo Clinic (2009). High resting heart rate could predict heart attack in women. Mayo Clinic women's healthsource, 13 (7) PMID: 19498326

Collaboration 2.0

2010-07-17T19:30:00.000-07:00

Information technology is letting people around the world come together in unprecedented ways. Wikis, blogs and microblogs like twitter, crowdsourcing and crowd-task-solving sites continue to flatten the planet.
Scientific innovation used to be a very private endeavor, with narrowly specialized scientists delving deeply into specific research areas. The Internet changed some of this giving rise to Wikipedia - now orders of magnitude larger than the Encyclopedia Britannica, and similar wiki resources for gene annotations, RNA libraries, radiology images, open-source software and other content.

Science funding agencies may appear to be crowdsourcing solutions too - as they employ broad calls for proposals and utilize peer reviews to evaluate the proposed ideas. Their models , however, are not very effective in triggering societal impacts. They impede collaboration in many ways as the researchers are not truly working together and the feedback is not constructive. Reviewers are experts but not direct stakeholders of proposed projects . They add management overhead (Latour, 1996).

One may argue that science is highly competitive and will always be driven by egos and desire for personal vs collective success. Yet, as Johnston and Hauser note, these very human needs could be met by more efficiently designed open source models, extending beyond snapshots of consensus, enabling to capture specific contributions of each participant and permanent record of the life history of the project from conception to completion.

The ease of discovery declines every year - scientists have to search for smaller asteroids, heavier chemical elements and more complicated connections. This has to be matched with either exponential increase in the number of scientists or more innovative collaboration.

People take pleasure in synchronized activities - such as singing or marching together, folding proteins or syncing their brains in a conversation. Could scientists have meaningful conversations on unimaginable scales, conversations including citizen scientists and people whose health needs could be solved by science?
Some researchers are already using help from crowds collecting their donations to support research - like the recently started open-source research project to develop cure for neglected tropical disease schistosomiasis.
Or the Open Source PCR project supported by the public.

Recent call for collaboration asked for a framework to exchange and disseminate information, produce guidelines and summarize finding for Participatory health research (PHR) addressing local health issues. Government agencies are using twitter and expect crowds to supply epidemiological metrics to test health policy efficacy.

Meanwhile, many are already utilizing google docs in the quest for collaborators and exchange of ideas. See for example this Folder of Useful Google Docs including:

Startup Ideas - Front page linking to Editable Table
Innovators - Form to Submit Your Data to appear in this Table (see HN Yellow Pages Thread)
Entrepreneurs looking for Co-founders - Front page linking to Editable Table
Seed accelerators and their companies
Startups Hiring - Form for Employers displaying info in this Table
Software Contractors - Editable Table (HN Contractors Thread about it)

Or check this call for collaborations in the microbiome and metabolome spaces, to solve neglected medical conditions.

Scientists, let's unite and start collaborating in even more creative ways!

References

Johnston SC, & Hauser SL (2009). Crowdsourcing scientific innovation. Annals of neurology, 65 (6) PMID: 19562693
Wright MT, Roche B, von Unger H, Block M, & Gardner B (2010). A call for an international collaboration on participatory research for health. Health promotion international, 25 (1), 115-22 PMID: 19854843

Auer S, Braun-Thurmann H. Towards bottom-up, stakeholder-driven research funding — open science and open peer review: Available at: http://www.informatik.uni-leipzig.de/~auer/publication/OpenScience.pdf. Accessed May 21, 2009

Lawrence PA (2009) Real Lives and White Lies in the Funding of Scientific Research. PLoS Biol 7(9): e1000197. doi:10.1371/journal.pbio.1000197

Marsh A, Carroll D, & Foggie R (2010). Using collective intelligence to fine-tune public health policy. Studies in health technology and informatics, 156, 13-8 PMID: 20543334

Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, & Su AI (2010). The Gene Wiki: community intelligence applied to human gene annotation. Nucleic acids research, 38 (Database issue) PMID: 19755503

Latour, B. 1996. Aramis, or, The love of technology Harvard University Press, Cambridge, Mass
Butler, D. (2010). Open-source science takes on neglected disease Nature DOI: 10.1038/news.2010.50
Facebook page, Just giving fundraiser page.

Scientific collaboration:

Innocentive - crowdsourcing scientific solutions to organization's problems
Science Commons - generic license agreements
TekScout - crowdsourcing R&D solutions
YourEncore - crowd of retired veteran scientists and engineers
Biocrowd - social network for bioscience professionals
Eureka medical - medical open innovation platform

Idea Generation and Solving:

AddictLab - creative think tank
Brain Reactions - post questions and get ideas/feedback on them
Fellowforce - innovation challenge board covering many disciplines
iBridge Network - platform for university innovation
IdeaConnection - idea marketplace and problem solving
Idea Crossing - organize innovation quests
IdeaMagnet - powering idea generation
Ideawicket - open innovation portal
Innovation Exchange - open innovation market place
WhyNot - idea exchange
IdeaBlob - monthly contest for entrepreneurial ideas
Bodyshock - call for ideas to improve health in the next decade
Incuby - online community for inventors
Cofundos - open-source software ideas

Crowd-Task-Solving and Freelance

World4brains, collaboration instead of competition for best ideas, advice and solutions - innovative payment system rewards all valuable input given
TaskRabbit, linking over-stretched consumers with runners for errands, tasks and other to-do’s
oDesk - global marketplace for remote work
Elance - freelance marketplace
Guru - freelance community
Ki Work - sourcing online work
Amazon Mechanical Turk - micro-task crowdsourcing
HumanGrid - small online tasks solving

Crowd-Funding

A Swarm of Angels - crowdfunding a film
Kickstarter - fund ideas and endeavours
Kiva – crowdfunded micro-loans
IndieGoGo - a collaborative way to fund ideas
WePay - ways to collect and manage money

Sit less, Move more

2010-07-14T17:00:00.000-07:00

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

About a year ago I discovered that life is better if I stand while working some of the time. Then I found out that other people discovered it too, and more keep discovering.

We hear it often: 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 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 - the men who stare at screens to write software, along with 100+ comments from those staring at screens to read 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.

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.’’

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

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

2010-07-03T16:03:00.000-07:00

Microbes bring us the great variety of tasty food, 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.
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.
And 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

2010-06-24T16:00:00.000-07:00

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 Pers onal Br ain 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?

To Ruby or Not to Ruby?

2010-05-04T14:25:00.000-07:00

Ruby on App Engine Meetup (May 4, 2010) proved that Google App Engine is not all about Python and Java, although at present only the last ones are benchmarked and discussed by google app engine developers (try yourself)

Python is usually fast enough for what you want it to do (and faster than Ruby), while requires a third of the code of an equivalent Java program and is much easier to read. Both Python and Ruby are easy to learn.

Pythonistas think that Ruby syntax is ugly and inheritance distasteful. The philosophy of Ruby is similar to Perl: there is more than one way to do the same thing. This is great for some people, it leads to the creativity and richness of Ruby libraries like Hpricot and Rake. Ruby tries to take the best of Perl, Smalltalk and Lisp but has elements of a C/Java-like syntax. Rubyists are convinced that they have found the most enjoyable interpreted language. Ruby is younger than Python but already has a strong and loyal community and best web tools. Many programmers, however, don't like having too much power to change the syntax and keywords. This can be dangerous if they are not careful.

Arguments on what language is better resemble disagreements between cultures and ethnicities. For a programmer, it's always fun to learn something new that may be useful in the future. For a startup founder, it's always good to know what is fun and a good investment. Right choices of programming languages, web frameworks and platforms will lead to rapid development, the ability to attract talent, and offer a great expansion potential.

The Java language is an old favorite in the enterprise. There will be a large pull of candidates to work on Java projects, but this language won't make your startup the most attractive shop in town. Python and Ruby will.

The Python community has the Django framework while the Ruby language is paired with the Rails framework. DSL Sinatra is also good. What's the difference between the Ruby and Python developer crowds? RoR favors convention over configuration which means that any Rails programmer can drop immediately into any Rails application and have a very good idea of where to get started. Expect rapid development and prototyping and support from community working on updates and plugins. Ruby/Rails developers tend to be expensive but worth it. Complementary Javascript experience is perfect - for dynamic web pages and nice visual effects. PHP developers tend to be a little cheaper than Django and RoR, but watch out for bad coders in this crowd. All hosting providers can deliver a low cost PHP server environment, but there are great platforms for Ruby and Python - such as Heroku (that recently raised $10 million in Series B funding) and Google App Engine that let you develop for free.

The May 4th meetup was not on Ruby vs other languages. It was about Google App Engine.
Most Rubyists in the audience were using Heroku for their applications, some will now try to pioneer Google App Engine - or will they?..

One interesting observation was the "City” versus “the Valley" comparison of preferred languages: Ruby seems to be the City's favorite! Could it be due to cultural differences? Some even think it's as bad as PC vs Mac world - see this short clip.
There were no Java people in the audience and very few programmed in Python or wanted to learn it. Almost no one tried Google App Engine.

Matthew Blain presented BulkLoader, a minimal library providing a unified interface for loading, accessing and events notification for different types of content (Try the Bulk Loader sample at: http://bulkloadersample.appspot.com/)

John Woodell, Sr Web Developer at Google (twitter: @johnwoodell, e-mail woodie at google), gave the main talk -about running Ruby on the App Engine. Sarah Allen wrote a nice blog about this talk: h ttp://www.ultrasaurus.com/sarahblog/2010/05/jruby-on-google-app-engine/. Another blog post summarizes the sources discussed:
http://jruby-appengine.blogspot.com/2010/05/google-app-engine-0012-gems-released.html

Check out his SlideShare Presentation:

App Engine Meetup

A few pointers and links from this talk:

Hello world, using standard Ruby: http://code.google.com/p/appengine-jruby/wiki/GettingStarted
Google App Engine for JRuby http://jruby-appengine.blogspot.com/
jRuby on Google App Engine: http://code.google.com/p/appengine-jruby/
Google Group – http://groups.google.com/group/appengine-jruby
JRuby and Java Duby
http://en.oreilly.com/rails2010/public/schedule/detail/11230

Zero Configuration needs. Scalable services via standard APIs. Built-in application management console
Schemaless App Engine datastore: No writing to the filesystem. No relational database. No more than 30 seconds per request. Datastore API + DataMapper
Most common tasks: backups and cross-app migration.

A big Rails advantage is that it values convention over configuration and lets to avoid lengthy configuration of files. Load everything at once then initialize it. This helps to free more time to focus on business logic. Google App Engine does not work like that yet, but this is on roadmap.

Key Ruby App Engine Developers (check also this map):

John Wang - iPhone, Android, and Web Developer at Fresh Blocks in Honolulu, (Twitter: @johntwang Github: jwang) Provided RESTful JSON with Google’s Datastore to iPhone and Android apps.

Joshua Moore, Assurance Manger at Armorize Technologies (Twitter: @codingforrent, GAE blog). Coauthored the rails_dm_datastore gem, gave presentations on using jRuby on GAE. Rails 2.3.5, Datamapper, HAML, helped to find datamapper bugs

Leonardo Gallucci, IT Consultant and Software Integrator (Twitter: @leonardog). Wrote tutorial on getting started with Ruby on Rails on Google App Engine (it runs on GAE).

Vladimir Sizikov (github: vvs) . Developed jruby launcher: http://github.com/vvs/jruby-launcher

Sasaki Takeru, a hacker from Japan (Twitter: @urekat). Showed how to run Rails without Ruby Gems. Rails 2.3.5 01/21

Anagiotis Siatras, a Microsoft .Net/Gae+Rails consultant from Greece (Twitter: @azazeal)
Developed taxster.gr. See his useful Ruby tips at http://azazeal.xelixis.net/

More Links:

Open source health gadgets

2010-04-28T11:31:00.000-07:00

Sports Watch
How would you like to have a 3-axis accelerometer, pressure sensor, temperature sensor, RF wireless, and an LCD screen in a development package? You can actually have it - as a wristwatch offered by Texas Instruments. for just $49.

The package includes a USB programming and emulation dongle so that you can develop your own firmware. It uses Texas Instrument’s SimpliciTI and BM Innovations’ Blue Robin RF protocols that enable developers to establish wireless links right out of the box. The firmware transforms it into a sports watch with heart rate monitor, it is written for Windows but could be adopted for other platforms too.

First hackers that got hold of the package used it to wirelessly unlock doors with the buttons and accelerometer. You could utilize other functionalities as well, and jog around while configuring your Linux.

Peripheral nerve stimulator

The jfish peripheral nerve stimulator is a device used in anaesthesia or intensive care to assess the degree of neuromuscular blockade (normal communication between motor nerves and skeletal muscle can be blocked by a drug). The device can detect both the magnitude and type of neuromuscular blockade. Itis developed by Daniel Jolley, a doctor and anaesthetic registrar, at The Austin Hospital in Melbourne, Australia. His device uses Texas Instruments' MSP430 line of microcontrollers - ultra-low power 16-bit RISC mixed-signal computers-on-a-chip. Check the document ‘The science and use of the peripheral nerve stimulator‘ for how to use the stimulator.

OpenECG
Open source hardware and software solution for electrocardiography was presented at the
34th Annual Conference of the International Society for Computerized Electrocardiology
The device is battery powered, it can also use an isolation transformer plus defib protection in front of the op-amps on the front-end.

OpenEEG
Many EEG-based gadgets - like Zeo personal sleep coach - are in the market. OpenEEG p roject can assist your brain-computer interface, bi-directional serial communication or neurofeedback experiments. The modularEEG is currently the most popular of all the designs Check online documentation for more. Then, go to the SourceForge page and download the ModularEEG project zip-file. You will find schematics, board layouts and parts lists that can be ordered from various distributors.

What a paradise for Hackers - they can design gadgets and let other people manufacture them. The open source hardware companies are predicted to be making over one billion in revenues by 2015. Most of them are offering educational electronics, but some of the packages could be utilized for health gadget development. See this talk presented at O'Reilly's foo camp east 2010.

Open source hardware $1m and beyond - foo camp east 2010 from adafruit industries on Vim eo.

Aurametrix is working on low-cost personal diagnostic devices to improve individual health

AWS for Startups: what's up there in the Cloud

2010-04-14T10:21:00.000-07:00

gSounds great, isn't it - computing services that don't need any infrastructure on your end, almost instantaneous delivery of whatever server and storage capacity you need, suite of just-right software, middleware, virtualization, security, and management tools? The "cloud" label is placed on almost every Internet-based application, adding to the large crowd of cloud computing vendors.

In a previous article, we talked about new and established players offering cloud services. This one is about cloud computing pioneer Amazon and AWS Start-Up Event in Silicon Valley (hashtag: #awsstartup_sv). See also presentation slides from their 2009, 2008 and 2007 start-up events on slideshare.net.

The April 14th event was held at Plug and Play Tech Center

Dr. Werner Vogels, Amazon CTO, gave an overview of cloud computing. Here are a few notes taken from his talk:

Design for Automation is important, but things that are out of your control should not be automated. Examples are Human interfaces and Delete operations.

Every task should be decomposed into simpler form.
Ordering pipeline, for example, consists of cart - order - process - store - archive components that need storage and other functionality. If you decompose the pipeline into individual pieces, you will find that most of that storage is needed for particular tasks.

Good things about key value stores is that we know how to scale them. We can't do it with relational databases.

Database administration could be monotonous, overstressed, expensive. Should be more automated and scalable. Need DBA as a service.

Developer should decide how to implement services to obey regulations, failure jurisdictions, break transparency, avoid performance failures

Need evolution not revolutions.

A Virtual Private Cloud with secure VPN connection; a number of devices to have traffic routed through - such as spam, etc

Design with Security in Mind. For example, anonymous access time limit; other limits defined in scripts

Let your customer benefit.

During the past 2 years Amazon reduced pricing 6 times. Amount of bandwidth increased by orders of magnitude more than Amazon itself consumes (see this older slide showing the history of usage growth).

Amazon customers built great applications on top of AWS.

E.g., Cloudmmo - instance cloud, or cloud middleware to reduce infrastructure costs, technology risk and development time

Innovate for your customers

For example, innovate on cloud pricing models: on-demand instances; reserved instances, spot instances

Stax - elastic cloud app for J2EE

Heroku - ruby platform. maps ruby apps to amazon instances; SQL DB

Salesforce.com toolkit to build new cloud-based applications

Tibco's software helps to innovate by connecting applications and data in a service-oriented architecture, providing intelligence tools to make smarter decisions. They have templates that can be launched to cloud.

RightScale® providesfully automated management platform for Amazon EC2 cloud deployments.

Synteractive consulting and automation solutions provider, incl. CloudAdvantage

Also Netflix, Pfizer, eHarmony, Lilly, Malbec..

Pfizer uses Ec2, eHarmony uses MapReduce to find better matches.

Playfish, Intuit, CloudTest by SOASTA

Intuit - everyone files taxes at the last possible moment, need AWS to scale

Lots of companies use clouds for testing and simulations. Intuit simulates submitting tax forms -- if too many at a time

Ribbit; SimpleGeo; Siemens; twilio

Dr. Vogels' contact is werner at amazon or check him on twitter: @Werner

AWS Customer Presentations included VC-backed startups @tubemogul, @rberger, @satyar73, @zynga

Adam Rose (adam at tubemogul.com) founded online video analytics startup Illumenix wich later merged with TubeMogul. The company helps in video delivery using IP and the Internet - deploying uploads and providing analytics, real-time viewership and engagement tracking.

See also useful tips from Nicolas of TubeMogul.

Robert Berger of Runa presented his company's experience with Elastic Compute Cloud, opschef and HBase, along with a few other useful AWS tips. His slides had a bit too large font size, at least for those in the front row. Guy Kawasaki says that optimal font size should be about half of the age of the oldest person in the audience. Centenarians would be certainly happy with this presentation.

A few notes I took were about Javascript for every page, every consumer, one or more AJAX calls; step function, Physical Layer; load every time a new merchant is added..

The company uses Opscode Chef for their tasks, helping to treat "Hardware"as Software .. which took under 5000 lines of ruby code

We are Living in "interesting" times with Amazon. The biggest problem is managing complexity of all the moving parts.

It's impossible to manage horizontal stacks - that's why to use Opscode Chef

there are lots of Learning Curves to Climb

Useful monitoring is hard but not critical

Satya Ramachandran of Jovian Data talked about the reasons to move to the cloud. He discussed HBase on AWS and how it may be dangerous, especially becouse of Hadoop namenode SPOF. if it went down, expect big problems

EC2 can surprise you if deploy multiple versions of horizontally scalable code

JovianData is a paltform as a service to optimize analytics of large data.

NoSQL does not solve application provision challenges

billions of impressions

10 users run 400 reports; 40% of them in hundred milliseconds

JovianData helps to avoid expensive data processing; Reduce Disk IO - by using their propriatory partitioning scheme - by materializing expensive groups (usage-based automatic view materialization).

3 main concerns:

Capital expenditure - long approval times

Over Provisioning - cluster up but nobody is using it

Application Isolation - one person runs unique report, another side section, how to isolate them to not let them run into one another

Biggest mistake - take entire image; 15 terabyte system monthly cost $30K

Role Based Clusters - example - double click services; data cleansing and creating models/ All model creation at night, than hybernated -- Hybernate Model

just kill 20 to 30 nodes; duplicate selectively then kill the nodes

ex: campaign manager needs to run lots of reports/ Classic Tera Scel won't be able to provision in minutes

Satya's advice was - If you are not getting 10x performance improvement - do not move in the clouds.

Aurametrix' comments - and if you do not need 10 or 100x improvement in performance, don't go in the cloud either. AWS is still a bit pricey for webapps and early-stage startups. Neither of the presenting startups fit the bill. A traditional VPS is a better solution if you only have hundreds or thousands of users or beta-testers. GAE is great for experimenting. Back to Satya's talk:

Dynamic Provisioning; using EC2 should be able to reduce performance by 100

Jayme Cox, talked on why Zynga chose AWS.

Zynga is conencting the world through Games. It's hosting 5 of the top 10 Facebook games

they use S3 - simple storage

Jayme Highly recommends RightScale

Scaling services without scaling Sys Admin Team

plan for success - could have 100K users

Horizontal scaling important

The 4 presenting startups also participated in

the Customer Q&A Panel along with the moderator from AWS

The first question was about overall experience with AWS.

1 (Satya): - experience's been pretty good

2 (Adam) - mixed feelings - no free customer support, hard to get the right person listening to you if .. It would cost you 600 dollars check if this session was Amazon customer support -- - worse than with Microsoft.

3 (Robert) - did not expect any support, now that in production; couple of glitches, hard to tell; looks to me Amazon is stepping up, town executives; Alex is great; I would not mind paying per support if it is instance based.. sometimes you are in a crisis and need support.

4 (Jayme) - found AWS to be extremely responsive form feature request. good at taking feedback.

Another Q - can you imagine your company in the pre-cloud era

4 - it's a complete nightmare. life is easier now

3 - my background is in infrastructure building, hard to imagine

2 - we are still somewhat split, not managing everything ourselves, are somewhere in the middle. We do not have this huge massive traffic yet, but if your app fits this bill you need power

1 - completely different; 100 nodes, 200 nodes;

Questions from the Audience

-What monitoring services you each use

#1 - wanted to build on commodity clusters; used RightScale to some extent; but mostly own

2 - same as previous panelist. Used Ganglia and Nagios - but mostly self-built technology

3- ScoutApp and Pingdom, outsourced monitoring, nice way to quickly get some monitoring. On the path of implementing Naglios.. Some Ganglia, use other staff too.

4- also use Pingdom for external monitoring; Naglios for learning; extensively put own code in the application. Use CloudWatch.

3 - using EBS store

2 - same, data pipeline that does all the data crunchinh

1- moved from Hadoop - as it is too primitive..

A reminder to the reader - among the many open-source and commercial monitoring tools, Nagios is used for alerting and notification, SNORT for intrusion detection, Ganglia, Cacti and Scout, are used for performance monitoring.

Q - what steps have you taken to reduce the risk of IP loss. Are you running any intellectual property staff? What assurances do you have to make to the board of directors or VCs to reduce the cloud-associated risk.

As there was a delay in responce from the panelists, Moderator stepped up and told about user agreement polices - whatever data you put on amazon is your data.

No, said the asker form the audience - VCs want to have better assurances...

3 - I do not care if someone downloads everything we have, we won't loose anything anyway.

Moderator - I've been in the field talking to customers; on overall VCs like AWS, they like when you spend on cloud computing versus hardware and operations. What assurances as a VC do you want?.. encrypting the data before storing in the cloud; just encrypt all of the transit data; follow all steps to secure data. Check some of the best practices.

4 - Farmfille - Zynga - our clusters may be faraway from that .. user is the slowest point in that chain

Question from the Audience - how large are your cloud-administration teams

4 - a handful of people

3 - I am the team, looking for someone/; another 4 people are in the development team

2 - 1.5 people

Two more Amazon talks after the break, at 3:45pm

Jinesh Varia, an AWS Evangelist, talked on Architecting Cloud Apps –

Jinesh often helps developers on 1:1 basis in implementing their own ideas using Amazon’s services, so his talks had many useful tips. His updated slides will be available online soon.

Jinesh - who can be contacted as jvaria at amazon or @jinman at twitter - wants to know how you are designing your architectures. He will help with Cloud Best Practices and a Complete Buffet of Amazon Services. Notes from his talk:

Most Applications NEED:

1. Compute

Amazon EC2 instances -- on-demand, reserved, spot

Physical infrastructure - Geographical Regions, Availability Zones, Edge Locations - mix and march

Amazon Virtual Private Cloud

on-demand provisioning, scalability in minutes; efficiency of experts

no contracts or long-term commitments

building scalable apps -- :

increased resources - proportionate increase in performance

hands heterogeneity

1. Design for failure - as W. Vogels says - everything fails, all the time - assume it and design backwards. App should continue to funcion even if the underlying physical hardware fails, removed, replaced

load balancer - how to replace?

-- use elastic IP addresses for consistent and re-mappable routes

-- multiple AZs (available zones)

-- real-time monitoring (Amazon CloudWatch)

-- Amazon Elastic Block Store (EBS) for persistent file systems

2. Build Loosely Coupled Systems

Independent components

design everything as black box

de-coupling for Hybrid models

Load-balance clusters

Use Amazon SOS as Buffers

Tight vs Loose coupling using queues

3. Implement Elasticity

Very cloud-specific

Bootstrapping instances

Your role is a database node.. don't assume health or fixed location of components use designs resilant to reboot and re-launch. Bootstrap your instances

Use auto-scaling - free

Use elastic load Balancing on multiple layers

Use configurations in SimpleDB to bootstrap instance

Automate Everything

Cloud is good for standardized tasks --

Java Stack, RoR stack - you can pick and choose/. important how you design Amazon machine images. -- approaches to design AMIS:

-- 1 inventory of fully baked AMIs - Frozen Pizza Model

-- 2 Golden AMI approach - bundle when you need it

-- 3. more control,

4. Build security in every layer --

cloud - losing a little bit of physical control

5. Don't fear constraints

IOPS - miltiple read - read load across multiple sunchronized slaves; write load -> master

adding caching layers, to get throughput

6. Think Parallel

decompose into simplest jobs, load balancer or massive distr tasks - hadoop -

7. leverage storage -- which storage to use when -- deatailed in the white paper - table --

S3. EC2. EBS. RDS - relational can't be heavy weight with lost of images/ Put images and blobs on S3; metadata on simpleDB

Scale Up or Down on Demand

failover - purposely terminated 2-3 instances to see if it maintains min threshold

app with lower dependences, once you build and moved it in the cloud, you'll have more confidence.. Start small, experiment with architectures, through out ..

@simon @junman

Steve Riley, an AWS Evangelist, talked on Security in the AWS Cloud

He can be reached as steriley at amazon or @steveriley on twitter. Check his blog at stvrly.wordpress.com

His very interactive talk started from asking the audience -

How many don't worry about security? 3 raised hands were more than Steve expected

How many believe that .they won't have to worry about security in the near future?

Cloud security scares people, oxymoron

internal logs - customer accidentally destroyed their DB - Amazon was able to recover by looking at HTML logs

Amazon helps to take care of information. Not use Zen, couple of modifications - security functionality comes from it. Security group - defines what traffic is allowed into computer

security group vs firewall. Code implementing security group - worked with 3rd party penetration .. highly qualified eyeballs

if you store confidential info - encrypt it. don;t store keys with Amazon either if afraid. For regulatory reasons may need to require build 3 tier architecture web - application -- database

HTTP-SSH-management from vendor/ Amazon don't provide 3 tiers

WebSG - inbound traffic; AppSG - inbound traffic from corpnet for management purposes; DBSG - Service is a disposable horsepower. IF you use IP addresses, do you need to change security groups - no

configure routing in your corporate network - no direct internet access; available in US East only

Mechanism to enable outbound internet - non trivial feature to turn on - will be added

S3 - objects stored in baskets; key used as the name for the object in the basket.

Permissions on backet do not inherit - need to explicitly assign

Encrypting information- fashionable to bash encryption - not a good solution - if they do not have the key - but what if you lose your key? Encrypting is good with a well undestood process to handle the keys. internally or third party - Red Scale for ex

(Read, Write, Full)

Create File on EBS - encrypt it and add a secrete access key -

AWS Sign In White Authentication Device

SOx - easy, outcome based - if control objectives meating the requirements

HIPAA more of a chalenge - current deployments, how-to-whitepaper derived form a project in production , anonimized

SAS 70 Type II certification

--------------

Concluding comments were on how different customers are leveraging AWS., on other AWS events, including yesterday's SF event - Adobe, Autodesk.. other customers were talking about enterprise side of things.

thestartupdigest.com - helped with the event.

Slides should be available soon at: http://aws.amazon.com/startup_valley/

http://aws.amazon.com

AWS Whitepapers

Overview of Amazon Web Services, Posted 2009-12-08
The Economics of the AWS Cloud vs. Owned IT Infrastructure, Posted 2009-12-07
Overview of Security Processes, Posted 2009-06-01
AWS Security Best Practices, Posted 2010-01-01
Architecting for the Cloud: Best Practices, Posted 2010-01-01
Cloud Architectures, Posted 2007-07-01
Extend Your IT Infrastructure with Amazon Virtual Private Cloud, Posted 2010-01-01
Creating HIPPA-Compliant Medical Data Applications With AWS, Posted 2009-04-01

Overall, it was an interesting event illustrating why “sky-is-the-limit” and cloud computing is a fully-fledged industry.

M-health, or who will take care of me?

2010-04-08T20:42:00.001-07:00

What is the real way to reform Health? asks Eric Wahlgren from DailyFinance, and answers 'Wireless Technology'. The coming convergence of wireless communications, social networking and medicine will transform health care agrees The Economist.

Wireless health (also called mobile health, e-health, m-health or telemedicine) will enable your body parts to make phone calls, your shoes or carpet to consult your doctor , your bed to measure your blood sugar and your phone itself to decide on whether your mental health is deteriorating - based on how quickly you answer the phone and recognize the caller.

No more lies on how much you ate or when you took your last pill. If your heart and other organs are not yet monitored by smart devices, your doctor will listen to your lungs over the phone or check how your knees are doing in 3D.

We are shifting to digital medical era starting from the relatively modest devices to keep you healthy and fit, evolving teletracking, technology, M-health sensors, Telemedicine tools and gadgets, Health 2.0 software tools, and algorithms for health data mining.

There is far more than a list of 101 things to do with a mobile phone in healthcare first compiled a year ago - including simple SMS messaging and GPS-based applications such as Medication Reminders (SMS) and Allergy Alert Service For Asthmatics (SMS and GPS), management of Chronic conditions such as Diabetes, hospital based RFID and the use of technologies such as Bluetooth and ZigBee in health and fitness monitoring.

It's time to take health care off the mainframe says Intel's Eric Dishman in his talk on
behavioral markers, vital sign monitoring and aging care delivery:

The World of Nutritional Omics

2010-04-01T15:42:00.000-07:00

Proteomics and Metabolomics are still lagging behind Genomics, promising to catch up in 5 or 10 years.

Nutriproteomics and Nutrimetabolomics (aka Nutritional Proteomics and Nutritional Metabolomics) may be following the same trend. According to Medline these terms are temporarily forgotten and not yet ready for the prime time.

Nutrigenomics (Nutritional Genomics) is the discipline studying the effects of food on gene expression, thought to bring technologies on tailoring diets to genetic makeups. Many researchers believe that it will also lead to creating foods (so called 'functional foods') that will prevent an individual's genes from expressing disease.

The 2006 report by GeneWatch called nutrigenomics a spin-off from the Human Genome Project created to sell the idea of 'wellness', not for improving health. This report claims that 'Personalized nutrition' is a false solution to the problem of diet-related disease. Most genetic association studies later turn out to be wrong. Genes could contribute to a person's health risks, but the number of other different factors might be overwhelming. According to this report, future health is likely to be much harder to predict than the weather is and basing diets on misleading health predictions could do more harm than good.

With the exception of the major food intolerances (for example, to milk, peanuts, fava beans and alcohol) the body's ability to respond to different diets is complex and likely to be extremely hard to predict from a person's genetic make-up. Aurametrix agrees on this with GeneWatch, but why are the weathermen still employed?.. Aurametrix bases its predictions on the body response to food intake - not only the kind that can be measured by omics technologies, but is acknowledging the importance of genome, proteome and metabolome-based diagnostics.

Like blood pressure and cholesterol levels, but unlike genetic make-up, measurements of gene expression or a person's proteome and metabolome change with time. Researchers are busily tackling transcriptome responses to foods - Dutch ServiceXS, for example, uses microarrays designed by the European Nutrigenomics Organization (NuGo) and manufactured by Affymetrix to study nutrition and genomics.

Nutrition research, on the other hand, is mostly about the isolation and analysis of bioactive components (or nutraceuticals) in foods. At first, it was focused on low molecular weight compounds and single proteins. The rapid growth of molecular biology shifted the focus to DNA, but the great expectations of solving all health-related issues by cracking the genome remained unanswered.

Genes expression does depend on diets, but mRNAs need to be translated into proteins - their sole presence does not guarantee that proteins will be present and working. Genomics fan club defines nutrigenomics as inclusive of all omics disciplines - gene, protein and metabolic profiling, but these are disciplines of their own.

Nutriproteomics studies how diets change expression, modification, distribution and interactions of proteins in the human body. It identifies the protein targets of foods and allows to more accurately than genomics address individual differences in terms of response to diet and food preference. It also helps to assess quality and authenticity of food and is useful for food allergy prevention.
Nutriproteomics addresses not only the qualitative analysis of proteomics interesting to the nutrition scientist, but also protein structures and interactions with other molecules, proteomes specific to body fluids and their localization in tissues.

In our previous blogs, we talked about metabolomics, genomics and molecular dietetics. Nutrimetabolomics focuses on the metabolomic aspect of nutritional phenotype, exploring the human response to different nutritional situations. It is estimated that there are 6,500 individual metabolites produced in the human body. Subtle disruptions in metabolic processes are evident in easily accessed body fluids and vapors. Nutrimetabolomics is nothing short of biochemical oracle for nutrition promising to accelerate the discovery of new markers and diet-related pathways. Quantitative measures of small molecules or metabolites can tell about deficiencies of digestive enzymes, microbiome health, best nutrition methods to improve individual health. Individual metabolic phenotypes do exist and can be defined from multiple measurements after eliminating the daily "noise".

The “Nutritional Phenotype database” (dbNP) was proposed to integrate and interrogate genetics, transcriptomics, proteomics, biomarkers, metabolomics, functional assays, food intake and food composition data, tailored to nutrition research and embedded in an environment of standard procedures and protocols, curated by the Nutrigenomics Organisation (NuGo). dbNP is extensively described in a publication in Genes & Nutrition 2010. It's based on micronutrient data sheets, comprehensive pathways (see examples for folate and selenium in the micronutrient portal ), ontologies and other knowledge engineering and analytic technologies.

Other Links

Aurametrix goal is to provide powerful solutions at your fingertips to help you manage your health. The company is initially focusing on relief for those suffering from digestive problems.

Health Data, Self-serve, Visualization, Semantic Analysis and Collective Intelligence

2010-03-28T12:12:00.000-07:00

Notes from the Biomedical Data Mining Camp Session led by Dr. Irene Gabashvili and other health-related discussions at Data Mining Camp and Transparency Camp 2010.

The title for the session was "Biomedical Data Mining: Successes, Failures, and Challenges" (streamed online from Fireside C).
The topic stemmed from the similarly named last year's session - Biomedical Data Mining : Dimensionality , Noise, Applications - now split into several discussions including Bioinformatics & Genome Sequencing organized by Raymond McCauley, Dimensionality Reduction moderated by Luca Rigazio (HLDA / HDA; LDPP; Core Vector Machines; Sparse Proj SQ; Random Projection and Feature Selection).

Main sub-topics of the biomedical session were:

Reality Mining
Visualization
Imaging
Signal Processing

Reality mining is expected to improve public health and medicine. It was named as one of "1 0 emerging technologies that could change the world". This is not only about mining data pertaining to social behavior - although social factors do impact well-being and social data provides valuable health predictors. It's also about health data collected in real and near real time. Audience asked about ways to collect health data and their limitations. Some of the questions reflected earlier Q&A with the Data Mining Camp expert panel , especially Dr. Michael Walker, author of numerous FDA and CLIA-approved products to diagnose and treat disease. He commented on the need to have tools well beyond the data available to take cell samples every two minutes instead of laboratory testing every few months - in order to allow cellular simulations and obtain parameters for differential equations. Sampling frequencies don't come close to allow this kind of modeling. Irene Gabashvili agreed that first-principles cellular modeling for predicting health won't be possible (although there are engineers that believe a platform for real-time in-vivo measurements of most cells can be developed). Yet, good predictors could be and will be developed - based on sensors measuring macro-level observations and missing value estimators. Genetic information is not enough, we need to capture environmental risk factors. How can we separate genes and environment?, asked one of the participants. Aurametrix' initial focus is on chemicals in our food - and even though some may argue that our taste and satiety mechanisms are dictated by genes, food analytics provides insights into non-genetic components of our health. Other questions were on the time line for body sensor networks and data growth. Jeffrey Nick of EMC estimates that personal sensor data will balloon from 10% of all stored information to 90% within the next decade. Irene Gabashvili thinks that this will happen rather sooner than later, perhaps in the next two years.

Another interesting aspect of reality mining is crowdsourcing or collective intelligence - in order to get useful information from all the data (temporospatial location, GPS, activity, food, symptoms, behavior, communication content, proximity sensing), we need to analyze it not only on individual but also group level. We need to share more, without sacrificing privacy and security. Collective contributions can be reliable - Shamod Lacoui's answer to this is in selecting those who contribute, restricting inputs to domain. It would help to “filter out the dross”, while “saving the best”. It is needed to suppress noise, to infer intelligence from the collection of facts, clicks, steps, whatever one can contribute. This resonates with discussions at the Transparency Camp - one of the useful tools is SwiftRiver - free, open source software platform to validate and filter news. Swift relies on Natural Language Processing, Machine Learning and Veracity Algorithms to track and verify the accuracy of reports and suppress noise (like duplicate content, irrelevant cross-chatter and inaccuracies). Transparency Camp also posed a question on whether there is a need for an FDA-like institution to ensure information safety and healthy information consumption.

Self-serve was a topic of a smaller Data Mining Camp Session. Even though it was aimed at sales reps that need to go beyond Excel spreadsheets to mine private data of their interest, self-service is currently the only option for health care consumers. People need to analyze everyday life for health implications. They need better tools to not focus on metrics that are easy to collect instead of metrics we need to collect.

In order to mine high-dimensional health space, many disparate types of data should be mashed and validated, gaps should be bridged and structured metadata added to data. Randy K erber talked about data formats and approaches to make it happen. Semantic web discussions involved NoSQL experts that mentioned limitations of gaining popularity technologies such as MongoDB, Cassandra and HBase. Another relevant session - on cloud computing - discussed its (sometimes over-rated ?) performance and Hadoop technologies.

Visualization techniques provide one of the most effective methods of extracting knowledge from health data. Remember who invented the pie chart? That's right, it was Florence Nightingale, a nurse who needed a way to better represent her data. one of the most famous examples of visualizing epidemiological data was Dr. John Snow's map of deaths from a cholera outbreak in London, Many other techniques and software tools exist, but maps remain popular - especially google maps API. One of popular tools for epidemiological data is Google Maps API. For example, it embeds Google Maps into healthmap.org with JavaScript.

One of the participants of Biomedical Session developed kidsdata.org (@kidsdata on twitter). It provides insights into geospatial autism statistics and visualizes trends and other useful health-related information.

Another way to display geospatial data is Dynamic Choropleth Maps. Complex networks can be also explored with alluvial diagrams and other approaches. More visualization techniques and tools can be applied to health data - to look at the data in new ways and gain useful insights.

Some of the questions from the audience were on the availability of data. Sources discussed included CDC (see, for example, NHANES laboratory files; eHealth metrics) and Entrez Life Sciences databases.

Signal Detection and Signal Processing for Mining Information was another discussion topic.
Questions were on data mining versus simple tracking and signal monitoring. It was agreed that data mining is the key to health management. Cardionet, body sensors (see posts on teletracking, M-health, Telemedicine: part 1; Telemedicine: part 2; Health 2.0 Software tools, Devices to keep you healthy), SNP detection, telemedicine applications, random and rare electrocardiographic events and other applications were also discussed.

See other materials from Data mining Camp 2010:

ACM Data Mining Camp, March 20, 2010 (sfbayacm.org)
Data Mining Camp Report (Zemanta)
Mining Data mining Camp Impressions (Aurametrix)
My Experience at ACM Data Mining Camp #DMcamp (bytemining.com)

Transparency Camp, March 27-28, 2010 (The Sunlight Foundation)
Notes from Transparency Camp (David “Oso”, Rising Voices)

Mining Data Mining Camp Impressions

2010-03-21T12:33:00.000-07:00

Data Mining Camp organized by Patricia Hoffman and San Francisco Bay Area Chapter of ACM, the Association for Computing Machinery, uses an Open Space Technology (OST) approach - no formal agenda beyond the overall data mining theme. Except the expert panel, sessions are compiled on-the-fly, based on real-time interest and participation.

Overal, the unconference - with a new location and almost doubled attendance - was a success - even if judging only by results of twitter sentiment analysis tools (subject of a not-so-successful data mining camp topic) - tweetfeel, twitrratr and twendz.

Obviously, completely ad-hoc sessions could be a bit chaotic - even though organizers briefly presented their topics and rooms were assigned adter counting a show of hands, there were surprises and unmet expectations. Here are sample quotes:

DataJunkie: OMFG Chaos trying to set up and plan which sessions to attend. Idea: have an online vote, and use sim annealing for scheduling. #DMCAMP

ihat: some sessions at #dmcamp have very low signal-to-noise... feature selection referenced tibshirani and boyd. and ppl butchered their work...

Many people preferred traditional formats to round table discussions - tutorials were the most attended sessions, while discussions were either the most or least liked sessions. The arrangement of chairs and the look of the room preset expectations of participants - some organizers did not really plan to present but had to come out with slides or tutorials. Great observation by Dominique Levin:

NextGenCMO Room shape impacts success of un-conference: Circle of chairs works wonders to solicit audience participation at #dmcamp. Circle time!

Another interesting observation was that Linkedin turned to be the most efficient marketing tool for the conference. Twitter and other social networks did not seem to have an impact. The explanation could be very simple though - age group and education level of the target audience.

A winner of retweets was Chris Wensel -(interpreted as "influencer" by twitter data mining tools) - his message "Facebook dropped Cassandra for inbox search and hired HBase person to switch" was retwitted 18 times.

See also:

Data Mining Camp Report (Zemanta)
My experience at ACM data mining camp (R bloggers)
Data on Tab Browsing (presented by Andy Edmonds at Clickstream Session)

and last year's notes:

Bay Area Startups Looking for Cofounders: March 2010

2010-03-11T22:00:00.000-08:00

Starting a company can be a difficult experience. Working alone is hard and a lot less fun than working with co-founders. And even though two is said to be the right number, some data point to an increase in success rates with up to 4-5 co-founders. Co-founders wanted March meetup (organized by Alain Raynaud and Thad) featured startups dedicated to improving many aspects of our lives - from education to work productivity, transportation, energy and health.

Kromink
Srini Reddy is developing online service for high school students. His startup is looking for a web application developer, senior architect, and senior product manager to join the founding team.

Seeyu
David Pol lak is working on the next generation youtube and looking for the 4th co-founder, a web application developer

FiestasMariachi
The audience gave their hearts out in applause for Beto Juarez' performance of Mariachi La Bamba. His vision is a Mariachi website similar to Lawyers.com (see also Alain's post-presentation interview notes and the technical co-founder description). Beto can be reached as BetoIII at gmail and twitter.

Appt izr
Dave is working on the application helping to discover iPhone apps. Looking for one more tech cofoudner to extend bootstrapping time. He can be reached as dli at apptizr. Twitter: @apptizr

Roxolar
Yaya's @roxolar is generating leads for solar energy, the model is similar to lendingtree

Stremfocus
Fred Gibson is looking for a business/marketing cofounder and a coder (Java, Lisp) - the startup is focusing on streamlining workflows based on Steve Blank's Customer Development process. Twitter: @gibsonf1

Gesturelife
Navneet Dalal – with background in machine vision and learning, has an idea on gesture detection using cameras

Life360
Doug gave a brief presentation about this company supported by investments from google and facebook - they won Android Developer Challenge for building one of the top 10 mobile apps and yet are looking for more co-founders.

Crosspath
Ivan presented this early-stage bootstrap making carpooling more accessible form of transportation. Looking for a technical co-founder with 8-10 yrs of experience with web apps

StartupSquare
Tristan Kromer presented MarketResearch Wiki, alternative to Gartner ways to deliver market research and technology insights. The startup needs one more developer/lean co-founder (in addition to 4 technical co-founders). Twitter: @startupSquare

R iseTribe
Matt Howes tries to eat healthier and wants others to do the same. His startup - incorporated in September 2009 - allows members to set goals and track their progress, tapping into the $11 billion self-health market. It integrates with Facebook and Twitter (@risetribe)

Aurametrix
"What if you could have powerful solutions at your fingertips that help you manage your health the way personal finance software manages your money?" asked Irene Gabashvili, who presented her vision for health management systems, including a product in development that focuses on relief for those suffering from digestive problems. Twitter: @Aurametrix

For more startups see:
January minutes
November minutes

Test your genes and loose the weight?

2010-03-06T19:28:00.000-08:00

Do Your Genes Determine Which Diet Means Weight-Loss or General Health Success?
Can nutrition be optimized with respect to your genome?

Commercial genetic tests promising to provide personalized diet recommendations (there were 6 in 2005, not counting companies developing DNA nutri-chips to pinpoint an animal’s nutrition needs) are constantly offered and withdrawn. Interest in genetic testing over the past few years was going down (click on the right figure to see google trends), but continuously published findings cause bursts of interest (click on the right figure to see XRanks by Bing) .
Clearly, genetic variations determine how we absorb, filter, metabolize, store and eliminate nutrients and how these nutrients affect processes in our body. But should we get more vitamin B if our MTR gene carries predisposition to heart disease or have extra calcium and vitamin D if our VDR gene indicates possibly weak bones?
The use of this information may be premature, the gene-vitamin linkages may not be credible, and far inferior to your family health portrait with much higher cost-to-benefit ratio than self-evaluation and self-awareness through personal health management tools.

It Isn't Just What You Eat That Can Kill You, and It Isn't Just Your DNA That Can Save You--It's How They Interact, said a 2005 newsweek article. It is also about other environmental factors, your history of interactions, and microbes you cultivated in your system that determine what food is best for you.

Lactose intolerance, for example, may be derived from genetic tests showing how effective our bodies are in producing the lactase enzyme (the LCT gene). We can determine it in a much cheaper and reliable way, however, by drinking milk and looking at the symptoms. Same about FMO3 variations and trimethylaminuria. A study of lung cancer rates in China found that people at lowest risk were genetically deficient in an enzyme that metabolizes isothiocyanates in cruciferous vegetables, but crucifers don't seem to harm those with a functional enzyme either... except those who gets get intestinal gas from eating them. But this may not be because of the genes, but due to the lack of beneficial gut bacteria.

The weight-loss industry long admitted that one specific diet isn't likely to work for everyone. How do diet programs work? Forget about the ratios of carbs, fiber and protein, the most important factor is to burn off more calories than you're taking in. Behavioral factors rathe r than macronutrient metabolism are the main influences on weight loss, so it's more about mindful eating versus mindless eating. And here genes come into play again. Satiety mechanisms are complex and involve multiple sensors, operating differently according to underlying genetics. that's why a carb-heavy breakfast can leave you hungry in two hours but keep your neighbor full until noon, while high-protein diet makes you fill fuller.

This week (at the American Heart Association’s Joint 50th Cardiovascular Disease Epidemiology and Prevention – and – Nutrition, Physical Activity and Metabolism conference, being held March 2-5 in San Francisco, CA) Stanford University researchers reported that a genetic test can help people choose which diet works best for them. The study involved 133 overweight women, who lost more weight on a diet that matched their genes - either low-carbohydrate or low-fat. Improvements in clinical measures related to weight loss (e.g., blood triglyceride levels) paralleled the weight loss differences.

The findings are also partially based on an earlier paper, called the A to Z weight-loss study published in the Journal of the American Medical Association in 2007 and a small (100-person) unpublished study by Interleukin Genetics.

More than 6,000 genes may be affecting our weight, including multiple genes determining our taste preferences (e.g., to bitter foods, calcium, garlic or coffee) and behavioral predispositions. Genetic testing along with protein- and metabolomic-based diagnostics would provide invaluable data for understanding ourselves. Data-mining tools for health-related factors will allow integrated and holistic analysis and help to personalize diets, fitness and medical treatments.

Organizing the World's information

2010-03-02T18:05:00.001-08:00

"My guess is (it will be) about 300 years until computers are as good as, say, your local reference library in doing search,"says Google's first employee and director of technology Craig Silverstein. "But we can make slow and steady progress, and maybe one day we'll get there." (Inside the Wide World of Google CBS News, March 28, 2004). According to CEO Eric Schmidt, people care a lot about information and the possibilities of the unfolding revolution in technology are greater than many of them even realize: “Imagine the scale of the kinds of questions you could ask that you could not ask before.”

The figure is a great compilation of key Google Facts by PingDom. Among the key technical facts not shown here are far-reaching inventions such as Programmable Search Engine (PSE, see patent application) based on the BigTable database (See Research Publication about it in PDF format) and other systems that could help it become more semantic.

The distributed storage system for managing structured data called Bigtable resembles a database sharing implementation strategies with parallel and main-memory databases. Instead of a full relational data model it uses a simple data model with data indexed using row and column names that can be arbitrary strings. A Bigtable is a sparse, distributed, persistent multidimensional sorted map. The map is indexed by a row key, column key, and a timestamp; each value in the map is an uninterpreted array of bytes, although clients often serialize various forms of structured and semi-structured data into these strings, controlling it through careful choices in their schemas.

PSE and other integration technologies may be providing a higher level of semantic analysis.
These techniques could figure out the meaning of content and “fill in the blanks” when an item of information is ambiguous or missing. The idea is to enrich an information object with additional tags so that queries about lineage (where something came from) and likelihood of accuracy (the “correctness” of an information element) can be used to generate a result.

Another new concept is a probabilistic mediated schema automatically created from the data sources. Semantic mappings between the schemas of the data sources are mediated by schemas with probabilities attached to each - to model uncertainty at its core. A deterministic mediated schema created from the probabilistic ones will be exposed to the user who could use the terminology of this mediated schema to interact with the system.

The Semantic Web is emerging to help us get the most out of the world's information. Many interesting applications are already here. Some of them already acquired by major search players - Bing, for example, is based on semantic technology from Powerset that Microsoft purchased in 2008. This blog article is only about one of the players organizing the world's information. Stay tuned for more.

The Benefits of Exercise

2010-02-17T18:22:00.000-08:00

Image by mikebaird via Flickr

Execise is good. It can halve your risk of developing many major illnesses (including type 2 diabetes, coronary heart disease, osteoporosis, cancers - e.g., it protects against bowel cancer; for older women, it may cut breast cancer risk). Benefits of regular exercise include increasing levels of HDL ('good' cholesterol) and reducing high blood pressure. It promotes bone density to protect against osteoporosis, improves sleep, reduces stress and risk of depression and dementia later in life.

Daily Exercise is good for you

Inefficiencies of Health Care

2010-02-17T10:59:00.000-08:00

Is healthcare cost control possible? Aurametrix addressed some unhealthy aspects of healthcare in other articles, but there is always more to add.

"Despite the rampant inefficiencies and extremely high costs of health care in the United States, it is still possible to make the American health care system even more inefficient and more costly", say Drs. Fodeman and Book in the Wallstreet Opinion journal. What really drives health care spending is it's inefficient structure and business model along with increasing prevalence of chronic disease. Health Care spending is often wasteful failing to improve health outcomes and not bringing any value to the patients. Health care providers seem to be able to charge whatever they like. Existing system insulates both patients and providers from normal market incentives to reduce prices and spending. We recommend to read this article as it provides more insight.

Or watch the video to better see what's wrong with our health care system.

Microbes and Us

2010-01-30T12:18:00.000-08:00

Image via Wikipedia

Who's the True You? A human or a habitat for microbial communities?

Immediately after birth, every macroscopic creature is colonized by myriads of micro-critters that outnumber cells comprising the host.

Guts, ears, nose, skin, mouth, vagina, all environmentally exposed surfaces are home to thousands of species of bacteria, protists, algae, fungi (including yeast, molds, etc) and viruses. The types of microbes vary systematically across body habitats and time, as well as geographical location. Each finger tip is likely to have a distinct set of residents, so are left and right palms. If you are a woman, the number of populating you species is even larger.

Known as microbiota, the trillions of bacteria and other microorganisms could be our little friends. Some of them, dubbed probiotics, help to metabolize calories , provide nutrients, even shape immune responses during health and disease. A common gut bacteria called Bacteroides fragilis alleviates inflammation by restoring a balance of immune cells. It was shown to prevent inflammatory bowel disease in mice. Other bacteria shown to be protective in inflammatory bowel disease includes Lactobacillus casei, Lactobacillus plantarum, Lactobacillus salivarius, Lactobacillus acidophilus, Lactobacillus delbrueckii subspecies bulgaricus, Lactobacillus rhamnosus GG, Bifidobacterium longum, Bifidobacterium breve, Bifidobacterium infantis, Escherichia coli Nissle 1917, Streptococcus salivarius subspecies thermophilus, Bacteriodes thetaiotaomicron, Faecalibacterium prausnitzii, etc.

Many other diseases called autoimmune strike when the immune system gets out of balance. Perhaps some microorganisms could protect us not only from IBD but also from disorders such as asthma, type-1 diabetes, or multiple sclerosis (incidence of which increased more than 3 times in the past years).

Humans are much more similar to one another at the level of the genome than the microbiome. Microbial ratios change with an individual's weight, travels, medications, stress, diet. For early men, changes in bacterial ratios favoring increased fat/energy storage was beneficial - as the periods when food was plentiful would be always followed by times when food is scarce. For a modern man, this is a potential health hazard rather than an advantage.

The most abundant bacterial groups detected by molecular screening are Bacteroides (relatively stable population profile) and the bacteria belonging to the Clostridium coccoides group and the Clostridium leptum group (see this article on the Normal Bacterial Flora of Humans).
A lower proportion of gram-positive anaerobes related to Faecalibacterium prausnitzii, Ruminococcus flavefaciens-Ruminococcus bromii, Eubacterium rectale-Clostridium coccoides, and Eubacterium cylindroides. The most widely promoted prebiotics inulin and fructooligosaccharides (neither is absorbed in the upper gastrointestinal tract) have been suggested to increase the number of bifidobacteria. Dahlia inulin was shown to cause a pronounced increase in the number of bacteria related to R. flavefaciens-R. bromii and E. cylindroides.

Other findings suggest that heavier individuals may have a different makeup of gut bugs than thin ones. The gut microbiota of obese mice has been shown to have significantly more of one main type of bacteria called Firmicutes and fewer of another kind called Bacteroidetes (both types populate human guts as well); in normal mice, the distribution is the opposite.

Bacterial phylotypes Clostridium cocleatum, Clostridium thermosuccinogenes, Coprobacillus catenaformis, Ruminococcus bromii-like, Ruminococcus torques and R. torques were detected in similar amounts in IBS-C and IBS-D patients. C. thermosuccinogenes, however, was quantified in significantly different quantities depending on constipation or diarrhea-predominant cases. Bacteria similar to R. torques was more prevalent in IBS-D patients' intestinal microbiota than in that of control subjects. a R. bromii-like phylotype was associated with IBS-C patients. These findings further emphasized the possible contribution of the gastrointestinal microbiota in IBS. For IBD, novel invasive species of Escherichia coli possibly replacing some Clostridiales were found in inflamed mucosa. The number of E.coli correlated with the severity of Crohn's disease involving the ileum.

Differences in microbiota may depend on genetics, metabolism, environmental exposures during childhood, state of health. Selective increase in novel invasive species of E.coli seems to be involved in the etiopathogenesis to Crohn's disease involving the ileum (different species are implicated in UC). Other bacterial species specific to Crohn's are B. ovatus and B. vulgatus.

Myalgic Encephalomyelitis/Encephalopathy/Chronic Fatique Syndrome may be another condition caused by microbes. People with Cystic Fibrosis, for example, have more microbes enriched in aromatic amino acid metabolism in their airways. Note that this disease causes a distinct acidic breath - the more severe the condition is in an individual, the more acidic his breath becomes. The microbes were especially sensitive to amino-acid starvation indicating that therapeutic measures may be more effective if used to change the respiratory environment, as opposed to shifting the taxonomic composition of resident microbiota.

Altered breath resulting from changed micrflora is a known phenomenon and it can be detected not only by complex mass spec machines, but also by devices used in QA testing of foods (e.g. Cyranose pick up the scent of penzane, isoprene acetone, and benzene in the breath of lung cancer patients) and car air quality sensors to study human "fermentome". Hydrogen Sulfide Urine Test was developed (Kenny de Meirleir's work on testing was never published in a Peer Reviewed Journal) and is available for at-home use. Some people, however, prefer to use their nose instead of spending money for testing kits. Candida overgrowth usually is not associated with excess hydrogen sulfide. Biomed diagnostics offers inexpensive tests for Candida species.
Their InTray^TM Colorex^TM Screen also detects E.coli, Proteus mirabilis, Enterococcus sp., Klebsiella pneumnaiae, Staphylococcus aureus bacteria and Dermatophytes fungi. Many tests are available for urinary tract infections and various metabolites in urine. See also ongoing clinical trials on chemicals in human breath for diagnostics of diseases. The science of Grossology has only just scratched the surface of all the possibilities.

So, even seemingly innocent gut bacteria may be affecting many aspects of health and behavior. One day we may be even allowed to say: I’m sorry, sir, my microbes made me do it.

Even though the vast majority of our microbes are good for us or can be even used for diagnostics of the processes in our bodies, some are there to get us, contributing to skin diseases, body odor, malabsorption, gastrointestinal problems, ear infections and more.

Almost anything we touch or wear could be a breeding ground for bacteria. Remember the heavily reblogged and retwitted statement: "Wearing headphones for just an hour will increase the bacteria in your ear by 700 times"? Well, not exactly 700 times, 11 times and these are mostly our own bacteria that liked heat and humidity created in the ears and started to multiply more actively, but pretty much anything you stick in your ears - stethoscopes, hearing aids, audiological gear - comes out covered in microbes.

Whether you call them thongs, flip-flops or jandals, the simple rubber sandals could be a breeding ground for bacteria too. They allow easy access to oxygen, skin cells and oils, dirt and moisture. Eighty per cent of the population already have Staphylococcus aureus - found on sandals after being work for 4 days - on their skin, in their nose and armpits, yet this microbe aureus could make you pretty sick if it gets into a cut and into your blood, and if your immune system is not robust.

Parade beads could be be contaminated with bacteria too. Gasparilla beads, were shown to be covered with several types of bacteria includinf E. coli and salmonella.

Even cigarettes - besides their harmful toxic chemicals - host a bacterial bonanza —hundreds of different germs, including those responsible for many human illnesses, according to a new study. For example, Campylobacter, which can cause food poisoning and Guillain-Barre Syndrome; Clostridium, which causes food poisoning and pneumonias; Corynebacterium, also associated with pneumonias and other diseases; E. coli; Klebsiella, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, all of which are associated not only with pneumonia but also with urinary tract infections; and a number of Staphylococcus species that underlie the most common and serious hospital-associated infections.

Some of bad bacteria can be even found in bottled water or in Fast Food Soda Fountains (see this article published in International Journal of Food Microbiology). 48% of soda fountains at fast food restaurants contain coliform bacteria. More than 11% of the beverages analyzed contained Escherichia coli and over 17% contained Chryseobacterium meningosepticum. Other opportunistic pathogenic microorganisms isolated from the beverages included species of Klebsiella, Staphylococcus, Stenotrophomonas, Candida, and Serratia.

Anoter source of pathogens is undercooked and spoiled food. Take pork, for example. Five out of 90 samples of retail pork in Lousiana tested positive for MRSA — an antibiotic-resistant staph infection — thanks to antibiotics piglet's ears. MRSA (pronounced “mersa”) stands for methicillin-resistant Staphylococcus aureus whose new strain ST398 is on the rise.

And of course, people could also pass microbes to each other: Epstein-Barr virus (EBV) (causing mononucleosis - infamously known as the kissing disease), Herpes Simplex Virus-1 (causing cold sores) bacterium Streptococcus (causing various infections such as gum disease and strep throat), H.pylori, Candida or other yeast species, Hepatitis B Virus and cytomegalovirus (CMV) are spread via oral transmission from microbe-containing saliva.

How can we control populations of microbes colonizing us? Besides drugs wiping out entire populations - assuming they are not resistant to these drugs, food could help in cultivation efforts too. Example: vinegar. It was shown to reduce counts of not-so-benefitial bacteria. Diluted solutions of various household sanitizers (apple cider vinegar, white vinegar, bleach, and a reconstituted lemon juice product) were tested for their effectiveness in reducing counts of inoculated Escherichia coli and naturally present aerobic, mesophilic bacteria on lettuce. Of the sanitizers tested, 35% white vinegar (1.9% acetic acid) was the most effective in reducing E. coli and other aerobic microbes.

Aurametrix is developing decision support systems to help you evaluate health risks, decide on preventative measures, estimate cost/benefits of performing diagnostic tests, determine your nutrition needs and life style adjustments. Better solutions for a healthier world.

Silicon Valley Meetups and Startups

2010-01-15T07:54:00.001-08:00

View Larger Map

Highlights of January Meetups (that we did not have the time to attend):

Co-founders wanted January meetup

High Note,
Customized Concerts
Contact; Chongkee at HighNoteLive.com
Looking for: Expert ROR developer, Equity only

Phine
Contact: Aaron Tait
Seeking equity compensated founders and investors

sparkler.tv
personalized broadband TV
Contact: sethc at sparkler.tv

Bright Lights
Headlight restoration

Sexy Enterprise XRM
Contact: Sudhir at gqc.com (Sudhir Kshirsagar)
Looking for Equity-based Partner(s)
Money, Brains, Personality, Coffee-powered, FT/Pt (Significant)

EasyLingual
Contact: Sabir Ibrahim
online language learning community

No name company
Contact: mattt314
new communication medium
3 founders developing the prototype
looking for full time engineer founder; equal equity split

Revenzy - a lovechild of eBay and Facebook
plan to IPO in 2012 or 2013
looking for co-founder/China Operations

Bonvoy - that is to Expedia/Orbitz as Generics are to name Brand Drugs
Looking for people who want to disrupt travel space

SaferBuilding
Healthy Home and Office Experts
Rapidly Growing List of Contacts across networks
wanted Lead Architect/Engineer Cash/Equity Package
winston Choe winston.choe@inno-scape.com

(See also November minutes of co-founders wanted group).

The SiliconValley NewTech Meetup Group [SVNewTech] featured the following presenters:
* apptizr.com - iphone app suggestion service that actually works. It's like Netflix for apps on your phone. [David Li]
* iformbuilder.com - Data Collection on the iphone, that is super easy to build and use. Some customers include Hershey Chocolates, Comcast, and a number of Universities. [Chris Reichart]
* thinkcomputer.com - Will be launching a new mobile payments service [Aaron G. & Michael Anderson]
* Expert Talk Series - Putting a Term Sheet together. [Brad Rock, Partner DLA]

Also, check out this SlideShare Presentation from the Semantics in Financial Services meetup organized by Peter Berger and Silicon Valley Semantic Technology Group.

Semantics in Financial Services -David Newman

View more presentations from Peter Berger.

Tele-Tracking and Remote Health Monitoring

2010-01-14T12:47:00.001-08:00

Image by gaspar via Flickr

Medical Care Technologies Inc. (MDCE) today announced completion of version 5.1 of the Trackker(TM) technology for patients suffering with Alzheimer's and Dementia.
The Trackker and its Tele-Health Suite use wireless connections to link a GPS monitor that is worn by the patient and is linked to a 24/7 monitoring service. By programming the GPS to certain safety zones, the service can send a phone or email alert to a caregiver immediately. GPS systems (based on 24 satellites and their ground stations) typically track patients in open areas outside of buildings however, the Patient Tracker system has the ability to monitor the location of patients within and around facilities.
According to the Alzheimer's Disease International, in 2008 there were 30 million people with dementia worldwide. By 2050, it is projected that this figure will have increased to over 100 million and so will numbers of people with Alzheimer's disease. Much of the increase will be in developing countries, especially China, India, and their south Asian and western Pacific neighbours.

Many other remote monitoring systems are commercially available (See, for example, GPS shoes that let mommy know where kids are) Among silvertech offerings, Japanese conglomerate Marubeni’s technology seems to be particularly advanced.

Developed by the Advanced Institute of Wearable Environmental Information Networks, the sensor intended to be worn on the chest measures just 3×3cm and is 5mm thick. Vital signs such as body temperature or heart rate can be monitored remotely and analyzed using special software.

Acciordign to The Nikkei, sensors cost around $350 each, while Marubeni charges $110 monthly for using the software. The company aims at generating $11 million in sales in the first year with the system.

And you may even not wear anything at all in order to be monitored - if you have a tiny chip implanted under your skin. Formerly known as VeriChip, PositiveID ( SVUL) is beginning a study of its Health Link implantable microchip in diabetic, hypertensive and obese patients. The implanted chip can be scanned to access the patient’s online medical records, check glucose and cholesterol levels (see HealthScreenDirect) and is expected to improve disease management. The company’s critics fear the chip will one day become mandatory, leading to a complete loss of medical privacy and healthcare benefits. Credit and Health monitoring may be even integrated. Google and Microsoft are said to be among those possibly testing the chips.

================================================================
This is a continuation of telemedicine/wireless health series by Aurametrix. Previous blogs included Telemedicine: part 1; Telemedicine: part 2; survey of Health 2.0 Software tools, Devices to keep you healthy; Going for the piece of a healthcare pie; On M-Health, wireless health and smart plasters.

Amazon EC2, Google App Engine, Azure and Other Cloud Services

2010-01-13T16:47:00.001-08:00

Image by kevindooley via Flickr

What platform is the best to build an application for cloud computing? Google App Engine? Amazon EC2 and their other hosted services? Microsoft Azure platform? The following tips and recommendations are based on several articles and presentations telling how to navigate the cloud wisely and choose the right platform for particular applications.

The big heralds of Amazon's offering are flexibility, configurability and pay-only-for-what-you-use model. Many pharma companies - Pfizer, Eli Lilly and Johnson & Johnson - have tried and liked AWS. If you are craving control, are already set on a database model and have a ton of data to import, go with Amazon - their command-line access is heavily praised.

Unlike Amazon, Python-centric Google App Engine starts out free, and only costs after you get a lot of traffic and use a ton of computing resources. GAE/J supports Java and JRuby. Google offers ease-of-use and a large degree of automatic configuration, although they do want you to use Google's database vs MySQL or PostgreSQL. If you are a Python and Django junkie and do not like C extensions, go with Google.

Rackspace’s Mosso bills itself as a Web app hosting service. Coders choose what technology stack they want their apps to run on and upload their code. Mosso supports both Windows and Linux, PHP, Ruby on Rails, .Net, Perl, Python, MySQL, and SQL Server. Mosso does not yet support Java applications. SpringSource, on the other hand, offers a comprehensive suite of products for powering the entire build, run, manage enterprise Java application lifecycle.

The Globus Toolkit is a collection of software solutions to many science and engineering applications. Univa UD is utilized in some science and high-throughput engineering environments too.

Microsoft Azure platform is aimed at C#, .NET, Visual Studio, Windows and other Microsoft-tool-loving developers.

Likewise, IBM platform provides access to IBM middleware such as DB2. Informix and WebSphere.

IBM cloud presentation:

I attended this talk earlier last year, it was presented for the Silicon Valley CTO group. Went through it again today.

CommunityOneEast 09 - Running Java On Amazon EC2

View more documents from chris.e.richardson.

Check also these videos on Google App Engine

Counting Health Care Costs

2010-01-13T13:54:00.001-08:00

Is control of health care costs possible?

A piechart from this article shows that constantly rising health care costs are mostly due to hospital care (31%). Physician services are the next largest item, comprising one-fifth of the national health spending. Prescription drugs, while accounting for only 10% of total expenditures, have been the fastest-growing segment along with new medical technologies that are often not cost-effective, and provide incremental improvement or just an illusion for consumers that they are better taken care of. Second major contributor to the increase in spending is chronic disease. It actually accounts for 75% of national health expenditures. One of the main reasons for increased disease prevalence is an increase in unhealthy lifestyles. Obesity-related illnesses accounted for 27 percent of the real health care expenditure increase between 1987 and 2001, of which increased obesity prevalence accounted for 12 percent. Non-obesity food-related illnesses are at fault too. Aging of the population also contributes (although rather minimally) to the high growth rate of health care spending. Administrative costs comprise 7% of health care expenditures (~2% Medicare program).

So the primary cost is unnecessary complexity. We need to change the culture of medicine, it's business model to improve the efficiency in delivering care and reduce the cost resulting from the wrong model.

An excellent blog in New York Times yet again explains the reasons on why health care costs so much. Great comments from the readers provide even more insight.

Here are a few excerpts we can't agree more:

"Health care is expensive because of the pervasive entitlement attitude" Joseph R. Antos, the William H. Taylor scholar in heath care and retirement policy at American Enterprise Institute.

"Insurers, pharmaceutical companies, device manufacturers, doctors and hospitals are all able to drive up prices with limited pushback" Jacob S. Hacker, the Stanley B. Resor professor of political science at Yale University.

"People often do not have control over medical expenses, the way they can control expenses when buying a car"
"Another reason normal market forces fail in the health care system is a lack of clear information. Purchasing health care is not like buying a car.", "the price tag is rarely even discussed", "people often do not have control over medical expenses",
David M. Herzenhorn

"The costs of medical care are a hodgepodge of different prices for different patients", "There is no rational process for selecting a cost-effective treatment", M Mackiernan

"How do I "negotiate" my fees when they are pre-set by my insurance company?", "I keep reading that doctors recommend unnecessary tests but how am I to know what's necessary? I'm not a doctor. I just want to feel better and that's why I go to the expert", E. Nowak

"Doctors and patients rarely know the costs and administrators do not want them to know.",

Andy

"Health insurance is not really insurance at all. It is more like a membership fee to a YMCA.", Marci Twain

"The most powerful way we can reduce medical costs is for people to stop getting medical care when non-medical health care will suffice.", Anonymous Commenter

"One element of the increasing cost is the vast overtesting that is performed in teaching hospitals.", "A large fraction of blood tests, procedures, and imaging are simply a waste, but there is no effort to put any brakes on the system.", David Freeman

"Please do not ever think a doctor writes a prescription because it is his best choice, it usually is written because he likes the pharmaceutical rep and she or he has treated the like a king.",
Mark Shryock

"New and fancy machines which offer marginal improvement in actual care but cost more.", PH

"What a mess. It makes me sick--a luxury I apparently cannot afford.", Elliot

"In essence the solution to cost control is in great part in the realm of industrial engineering. Lets get the industrial engineers on board and perhaps in charge.", Rafael Venegas

"The vast majority of xrays scans and tests performed are done to avoid malpractice. .. Americans are radiated so doctors can avoid the awful pressure of lawsuits and you pay for it..", Boly

"In some areas, like implantable medical devices, an increasing number of manufacturers contractually require hospitals to keep prices that hospitals pay secret from the surgeons who tell hospitals which products to buy.", Jeffrey Lerner

"The reason health care in the U.S. is so expensive is because all the players (doctors, lawyers, insurance companies, drug companies, medical equipment companies, patients, et al.) are abusing the system.", G. Stern

"I can't believe a five minute altrasound cost over 1,000 dollars", Linda

"Capitalist theory says that price is set at that point at which providers (suppliers) receive enough money to be induced to make the products and consumers (demanders) are willing to pay for that product. The problem is that the demand for health care is “relatively inelastic.”.. there is no limit on the will of the consumer to pay.", AF

Let me disagree with the last commenter, though. "Thank God", says AF, "I do not have to know the science behind to know the relative effectiveness rates of each type of treatment". A century ago nobody would imagine been able to make a phone call or operate a computer. May be people like to live too much. But better tools will be created to allow them make informed decisions to better their health and their lives at reasonable costs.

Aurametrix is developing decision support systems to help you evaluate personal health risks, decide on preventative measures, estimate cost/benefits of performing diagnostic tests. Better solutions for a healthier world.

Semantic Web

2010-01-05T15:35:00.000-08:00

Image via Wikipedia

The semantic web promises to define the meaning of its content (semantics) making computer programs able to perform all the tedious work of searching, comparing and combining bits and pieces of information - all the tasks we have to do by ourselves in order to find answers to complex questions.

Attempts to make this possible includes languages: Resource Description Framework (RDF), Web Ontology Language (OWL), and Extensible Markup Language (XML); data interchange formats (e.g. RDF/XML, N3, Turtle, N-Triples), and notations such as RDF Schema (RDFS). Some believe that even simpler unambiguous formats will be part of the semantic web.

An early example of a semantic web application, FOAF (an acronym of Friend of a friend) expressed using RDF and OWL is a descriptive vocabulary, an ontology describing people, their activities, and relations to each other. Check, for example, semantictweet.com that allows to turn Twitter accounts into FOAF profiles.

Simpler components of semantic web include meta-tags - an extension of metadata in the form of tags used to describe Web pages' content in the early days of web design. This could be labels with keywords, name of the page author, description or metadata representing sets of facts. Ontologies are often used to generate metadata and mapping between vocabularies.
Zemanta system semantically filters content of the page to automatically tag it or suggest other relevant content. Semantic standards like Common Tag - developed jointly by Zemanta, Metaweb, and Yahoo! - add semantic meaning to tags expressed using RDFa, making Web content more discoverable and decentralized. With Common Tag, content is tagged with unique, well-defined concepts - everything jaguar the animal is tagged with one concept for jaguar the animal vs. the car.

Ontologies defined as "an explicit specification of a conceptualization" are about the kind of things existing in the domain and their relations to each other. There could be no perfect scheme, however. In working classification systems, success is not "Did we get the ideal arrangement?" but rather "How close did we come, and on what measures?" There are no fixed shelves and perfect arrangements. It would not hurt to rearrange things from time to time, add a few secondary links and subdirectories. "This book is mainly about the Balkans, but it's also about art, or it's mainly about art, but it's also about the Balkans." The classification can not be perfect - except very small and specialized domains, stable entities, clear edges, authoritative sources and a lot of money to support the authoritarian system. This will never work for the Web - with many uncoordinated users that don't think alike and are naive classifiers.

Web users have very different tagging strategies too - but all together they are creating value for one another, by connecting similar tags.

Some of most often mentioned examples of semantic web application include Freebase - an open database where anyone can perform complicated queries. It is like a structured version of Wikipedia, combining the advantages of free text and relational databases. It's qualified users can not only add the content but also change the structure itself modifying the definitions of existing types. With many qualified users both the content and structure will evolve over time.

Even though some sources claim that Freebase is built around an exhaustive ontology, it's more like a collection of ontologies or rather tags. Unlike the W3C approach to the semantic web, which starts with controlled ontologies, Metaweb adopts a folksonomy approach, in which people can add new categories (much like tags), in a messy sprawl of potentially overlapping assertions.

See more on the State of Linked Data in 2010:

From the Semantic Web to the Web of Data: ten years of linking up

View more presentations from Davide Palmisano.

An example of a semantic data storage tool able to analyze networks and events in large volumes of structured and unstructured data is AllegroGraph. this RDF graph database can be, for example, used for GeoSpatial and Temporal Reasoning performing complicated queries against news articles scraped from Google

NYCSW GeoSpatial, Temporal Reasoning with AllegroGraph from Morton Swimmer on Vimeo.

On M-Health, Wireless Health and Smart Plasters

2010-01-03T18:05:00.001-08:00

M-health or mobile health is a recent term for mobile devices supporting medical practice. This term is closely related to Telemedicine (coined in the 1970s) and to another recently introduced term wireless health.

Aurametrix wrote about exciting health gadgets and devices in several last year's blogs (such as Telemedicine: part 1, Telemedicine: part 2, Devices to keep you healthy, Going for the piece of a healthcare pie)

Many companies - large and small -make use of wireless sensors to collect clinically-actionable data for point-of-care. Companies including GE, Cinterion, Cardionet, Heatlhsmart, Digi, RIM, Proteus, E-Device, MedApps, are now working in mobile health area offering products and developing prototypes. Check, for example T+ Medical, Turkcell's Saglik365, Orange's Diabeo, Telstra's My-Glucose, Cardionet's MCOT™, and numerous cell phone applications (as some people say, the Phone will become your doctor) such as Allscripts remote. And there will be many more exciting developments - portable wearable devices scanning brain for signs of depression & stress disorders,

Everyday choices determine your health better than genomics. In addition to exciting gizmos and wearable monitors measuring activity, heart rate, sleep patterns, some companies are working on tiny implantable sensors helping to monitor health and health-related behaviors.
Proteus Biomedical is implanting tiny sensors into pills that send signals translatable into messages - such as "just took lipitor at 6:20pm" - sent in a very safe and private way to a wearable plaster, or a smart-band aide. This smart plaster is also picking up information on health-related measurements such as your heart rate, breathing patterns, activity level, stress, respiration
get sends you reminders. Last September Novartis worked with Proteus on a small 20 patient study to track patients’ compliance with their blood pressure drug regimen. This year the companies will work on sensor technology in organ transplantation.

American tech companies, taking notice of the unmistakable demographic trends, have launched a surge in gudgets for aging population - dubbed the silvertech. Emergency alert services have become a proliferating category in silvertech, along with sensor systems for the home, various kinds of long-distance health monitoring and smart medication dispensers that provide reminders and control dosage. Some dispensers signal a caregiver when a dose isn’t taken or a pharmacy when it’s time for a refill.

GE scientists are developing wearable RFID sensors to detect airborne chemical agents - to alert people to the presence of environmental chemical agents in the air. A novel technology based on resonant antenna structures of RFID sensors coated with various sensing films will recognize specific volatile organic compounds (VOCs) and chemical agents with part-per-billion detection limits. The sensor could also be used to analyze a person’s breath. Simply breathing on the sensor could potentially pick up biomarkers that serve as an early signal to the presence of certain diseases such as diabetes or cancer and metabolic disorders.

Non Invasive Health Monitoring with mHealth

View more documents from Bart Collet.

Environmental Mapping: from personal choices to global impact

2010-01-01T17:30:00.001-08:00

Image by manybits via Flickr

In the not-so-far-away-future, we will be surrounded by “smart dust” — tiny digital sensors, strewn around the globe, gathering all sorts of information and communicating with powerful computer networks to monitor, measure and understand the physical world in new ways.

These tiny sensors could be embedded in identification badges or cloth, perhaps using resonant antenna structures of RFID sensors or other systems coated with various sensing films that will recognize specific volatile organic compounds (VOCs), biological and chemical agents with part-per-billion detection limits. Wearable RFID sensors could detect not only airborne chemical agents alerting to the presence of environmental chemical agents, but also breath biomarkers serving as early signals to the presence of certain diseases such as diabetes or cancer and metabolic disorders.

Wondering where it's safe to swim in Europe? An initiative called Eye on Earth - Water Watch created by Microsoft and the European Environment Agency and powered by Bing will help you find out what water you can swim in without wondering if you're going to go home with more than just memories.

Want to keep an Eye on Earth? From plankton blooming off the coast of Ireland, diminishing and increasing populations of plants and animals, satellite images of the planet could give a more vivid understanding of the world that surrounds us. Launched during the recent United Nations Climate Change Conference, the interactive online Environmental Atlas of Europe initially focuses on visuals and stories from European countries.

Microsoft and EEA have previously collaborated on the Eye on Earth platform, which combines scientific information with on-the-ground local observations contributed by millions of users on topics such as water quality at more than 22,000 swimming sites in Europe. The AirWatch application provides real-time data on specific air pollutants from air-quality monitoring stations, as well as user-submitted descriptions of air quality in different areas. Much of the information is available through text messages as well as online. Future plans for Eye on Earth include tracking ground-level ozone, oil spills, biodiversity, and coastal erosion to create what the partnership calls "a global observatory for environmental change." Other available online tools include Danish MapMyClimate that allows people to understand the impact of their consumer habits on the environment; Project2Degrees, emissions-tracking software developed in partnership with the Clinton Foundation that allows city authorities to measure and reduce their emissions; Fiat eco:Drive, a dashboard tool that helps drivers improve their fuel efficiency; and Bend the Trend, a website where users around the world can pledge to make lifestyle changes that will have a positive impact on emissions reduction.

In addition to smart sensors, smart phones can provide more powerful capabilities combining human intelligence and the ability of phones to automatically record pictures and sounds, tagged with keywords, where and when information automatically uploaded to web sites

PEIR, the Personal Environmental Impact Report, is one of many online tools that allows to explore and share how you impact the environment and how the environment impacts you.
This project involves collecting travel, time and location data from mobile phones feed into Web databases to calculate an individual’s personal environmental impact and exposure to pollutants. Another tool - whatsinvasive.com, in cooperation with the National Park Service, uses a smartphone application to identify, photograph and track the advance of invasive plants, like Harding grass and poison hemlock, which can crowd out local species and undermine biodiversity.

Deborah Estrin, a computer scientist at the University of California, Los Angeles and her colleagues at the university’s Center for Embedded Networked Sensing have designed several projects that use cellphones and people in data-gathering and analysis. Cellphones, they say, are versatile data collectors and are becoming more powerful all the time — with cameras, GPS, accelerometers and Internet connectivity. Their work is at the forefront of an emerging field called participatory sensing.

Welcome 2010!

2009-12-31T21:44:00.000-08:00

According to Bill Vaughan, an optimist stays up until midnight to see the new year in. A pessimist stays up to make sure the old year leaves.

Goodbuy 2009 was more frequently twitted as 2010 was sweeping across the globe, but there were no more pessimists left shortly after 2010 arrived on the islands of Western Hemisphere.
2009 was a year to remember but not repeat . Everyone hopes for a better year, so "Happy New Year"will continue to be a trending topic for a while - even if not among the top 10.

Wellcome 2010!

The Power Of Visualization

2009-12-21T15:06:00.000-08:00

Things change, but we don't always understand how. Networks and clustering methods help to uncover changes in complex large-scale systems, but more sophisticated approaches are needed to distinguish between real trends and noisy data, between meaningful structural changes and random fluctuations. A recent PlosOne article demonstrated how bootstrap resampling accompanied by significance clustering provides a solution to this problem. The figure on the right illustrates major shifts in the structure of scientific research, showing how neuroscience emerged from an interdisciplinary specialty to a mature and stand-alone discipline.
The figure was generated by (i) clustering the original networks observed at each time point; (ii) generating and clustering the bootstrap replicate networks for each time point; (iii) determining significance of the clustering for at each time point; and finally to reveal stories in the network data and connect the changes between time points (iv) generating an alluvial diagram.

The technology used to generate biological networks is not and can't be very accurate, "medium" accuracy -for yeast two-hybrid screening of protein-protein interactions, as an example, - is on the order of 50% false positives. A recent article in PNAS titled, "Missing and Spurious Interactions and the Reconstruction of Complex Networks" by Guimera et al. outlines a method to accurately analyze different types of complex networks. It strongly relies on the fact that the nodes in networks can be organized into groups. Group membership governs which nodes can interact.

Many other simpler data visualization tools and methods exist suitable to other specific data-rich applications. IBM's Many Eyes site provides a variety of ways to analyze text, maps, trends and relationships among data points.

Bubble diagrams (also known as bubble charts and spray diagrams) are centered around one (like mind maps) or more concepts. They can then be used to compare and contrast concepts, and identify the common ground and the areas of difference. Diagramic builds such diagrams from spreadsheets and text files.

World Wibe Web makes huge quantities of information readily available."How do you take a big collection of things and make sense out of it?" asks Gary Flake, founder and director of Microsoft Live Labs designing experimental Web tools. The lab's answer to this question is Pivot, a tool recently released to the public - see a demonstration Flake gave at the TED conference in Long Beach, CA.

UI designer Theresa Neil highlights these 28 tools for creating graphs, Gantt charts, diagrammers, calendars/schedulers, gauges, mapping, pivot tables, OLAP cubes, and sparklines, in Flash, Flex, Ajax or Silverlight.

Ajax.org
This platform is a pure javascript application framework for creating real-time collaborative applications that run in the browser.

AnyChart
AnyChart is a flexible Flash based solution that allows you to create interactive and great looking flash charts.

Axiis
Axiis is a Data Visualization Framework for Flex. It has been designed to be a concise, expressive, and modular framework that let developers and designers create compelling data visualization solutions.

BirdEye
BirdEye is a community project to advance the design and development of a comprehensive open source information visualization and visual analytics library for Adobe Flex. The actionscript-based library enables users to create multi-dimensional data visualization interfaces for the analysis and presentation of information.

Degrafa
Degrafa is a declarative graphics framework for creating rich user interfaces, data visualization, mapping, graphics editing and more.

DojoX Data Chart
An addition in the Dojo 1.3 release is the new dojox.charting class. Its primary purpose is to make connecting a chart to a Data Store a simple process.

Chronoscope
If you need to visualize thousands or millions of points of data, check this out. Very well designed and can be navigated with the keyboard or mouse. There's a Javascript API, a Google Visualization API or try it as a Google Gadget on Google Spreadsheets, iGoogle, or Open Social.

Dundas
Dundas provides a wide range of data visualization solutions for Microsoft technologies. They offer a number of data visualization tools including: Chart, Gauge, Map and Calendar for .net and Dashboards for Silverlight.

ExtJs
Ext JS is a cross-browser JavaScript library for building rich internet applications. It also includes charts.

Flex
Flex has built in chart controls: area, bar, bubble, candlestick, column, HLOCC, Line, Pie, Plot.
Flex uses FXG, a graphical interchange format developed by Adobe and is similar in many ways to SVG. Nice article here by James Whittaker looking at FXG and Degrafa. See quick tutorial and article on Creating Visual Experiences with Flex 3.0.

FlexMonster Pivot Table and Charts
Flexmonster provides Pivot table Flex/Flash components rich internet application (RIA) development services.

FusionCharts
Animated flash charts for web apps.

Google Chart API
The Google Chart API lets you dynamically generate charts.

gRaphaël
gRaphaël is a Javascript library to help you create stunning charts on your website.

iLog Exlixir
Enhance data visualization within Flex and AIR applications with IBM ILOG Elixir.

JFreeChart
Creates charts such as bar charts, line charts, pie charts, time series charts, candlestick charts, high/low/open/close charts, wind plots, and meter charts. I wish these charts looked better out of the box, because the features and functionality are good, but the visual design really detracts from the graphs. JFreeChart guys- email me- together we can make the world of JFreeChart a prettier place.

JQuery Plugins

JPowered
The PHP graphing scripts provide a very easy way to embed dynamically generated graphs and charts into PHP applications and HTML web pages.

JSCharts
JS Charts is a JavaScript chart generator that requires little or no coding. JS Charts allows you to easily create charts in different templates like bar charts, pie charts or simple line graphs.

Kap IT Labs Diagrammer and Visualizer
Kap Lab's Diagrammer provides ready-to-use yet highly customizable multi-layout data visualization and diagramming for Adobe Flex and Air.

Visualizer displays data as graphs to better visualize connections. Kap Lab's Visualizer provides ready-to-use yet highly customizable multi-layout data visualization for Adobe Flex and Air.

MilkChart
A simple to use, yet robust library for transforming table data into a chart. This library uses the HTML5 tag and is only supported on browsers other than IE until ExCanvas gets proper text support.

Open Flash Charts
Open source Flash charts.

PlotKit
PlotKit is a Chart and Graph Plotting Library for Javascript. It has support for HTML Canvas and also SVG via Adobe SVG Viewer and native browser support.

Protovis
Protovis composes custom views of data with simple marks such as bars and dots. Unlike low-level graphics libraries that quickly become tedious for visualization, Protovis defines marks through dynamic properties that encode data, allowing inheritance, scales and layouts to simplify construction.

Silverlight
Microsoft Silverlight comes with the bar, line, pie, column, and scatter charts.

Telerik Charts for Silverlight, WFP, ASP.NET
Telerik Charts offers rich functionality and data presentation capabilities.

VisiFire
Visifire is a set of open source data visualization controls - powered by Microsoft® Silverlight™ & WPF.

yFiles for Ajax , .NET or Flex
The yFiles product family means state-of-the-art software components for the visualization of networks and diagrams. Unequaled automatic diagram layout, cutting edge graph analysis, and extraordinary visualization.

A few more resources:

Gephi, the open graph Viz platform

XML/SWF Charts is a simple, yet powerful tool to create attractive charts and graphs from XML data.

Bime, Browser-based business intelligence solution (based on Flex)

75+ tools to visualize your data

Kquery-based Highcharts

Flare is an ActionScript library for creating visualizations that run in the Adobe Flash Player

Microsoft Chart Controls, ASP.NET and Windows Forms Chart Controls for .NET Framework 3.5 SP1

Periodic table of visualization methods (data, information,concept, strategy, metaphor)

Popular and Creative visualization methods

jqPlot Charts and Graphs for jQuery

jQuery Sparklines

AnyChart Flash Chart Component

Chart FX from Software FX has lots of great products for every platform.

Also check out MIT's SIMILE project

Google Vizualisation API with maps and magic-tables

InstantAtlas™ enables information analysts and researchers to create highly-interactive online reporting solutions that combine statistics and map data to improve data visualization, enhance communication, and engage people in more informed decision making.

Dygraph is an open source JavaScript library that produces interactive, zoomable charts of time series. It is designed to display dense data sets and enable users to explore and interpret them.

Mindsetgeometrics allows to build custom charts using predefined SVG files or Adobe Catalyst models.

Seer is a lightweight, semantically rich Ruby on Rails wrapper that provides a seamless interface for the Google Visualization API . It allows to easily create a visualization of data in a variety of formats with a single line of code.

YUI Charts from Yahoo

Silverlight Pivot Grid

AmCharts is a set of Flash charts for your websites and Web-based products. AmCharts can extract data from simple CSV or XML files, or they can read dynamic data generated with PHP, .NET, Java, Ruby on Rails, Perl, ColdFusion, and many other programming languages.

The deadly kiss - on allergens and other things you do not want in your system

2009-12-17T14:03:00.000-08:00

Be careful who you kiss, especially if you have sensitivities to food, chemicals or other substances you do not want to have in your body.

Richard Gasquet was cleared of doping today, on the grounds that cocaine had been passed into his system from a nightclub kiss.

What else could we get from an innocent kiss?

Remember the tragic story of a peanut allergic teenager from Quebec? Christina Desforges went into anaphylactic shock and died after being kissed by her boyfriend who had just eaten a peanut butter sandwich. An almost immediately administered adrenaline shot didn’t help.

Though not widely recognized, food hypersensitivity by inhalation can cause a lot of problems. 8 top allergens (TEMPS WFS: Tree nuts, Eggs, Milk, Peanuts, Shellfish (crab, lobster, shrimp), Fish (bass, cod, flounder), Wheat, Soy) cause 90% of food allergies. Food related allergies have been on the rise in recent years. Whether this is due to the use of baby creams and lotions (e.g., with a peanut oil content) in early childhood, 20th century hygiene, synthetic & fortified foods or other issues of Western civilization, we need to be careful and think about all possible ways of being exposed.

Epstein-Barr virus (EBV) (causing mononucleosis - infamously known as the kissing disease), Herpes Simplex Virus-1 (causing cold sores) bacterium Streptococcus (causing various infections such as gum disease and strep throat), H.pylori, Candida or other yeast species, Hepatitis B Virus and cytomegalovirus (CMV) are spread via oral transmission from microbe-containing saliva. Many sexually-transmitted diseases follow this route too.

Even cigarettes - besides their harmful toxic chemicals - host a bacterial bonanza —hundreds of different germs, including those responsible for many human illnesses, according to a new study. For example, Campylobacter, which can cause food poisoning and Guillain-Barre Syndrome; Clostridium, which causes food poisoning and pneumonias; Corynebacterium, also associated with pneumonias and other diseases; E. coli; Klebsiella, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, all of which are associated not only with pneumonia but also with urinary tract infections; and a number of Staphylococcus species that underlie the most common and serious hospital-associated infections.

One of the best natural defenses in our saliva is the “good” bacteria and supporting it molecular environment that protects us from settlements of pathogenic microbes and prevents their growth. Some people are more susceptible than others, but everybody should be careful... about whom they kiss.

Understanding Your Lab Values: Creatinine test

2009-12-13T15:15:00.000-08:00

Image by scribbletaylor via Flickr

According to a recent study, reported at the annual meeting of American Society of Nephrology in San Diego. primary care physicians are failing to diagnose chronic kidney disease, especially in women.

Study leader Dr. Maya Rao of Columbia University in New York says primary care doctors typically order a blood test called creatinine to measure kidney function, but this alone is not a particularly accurate measure of kidney function.

Glomerular filtration rate (GFR) is the best test to measure your level of kidney function and determine your stage of kidney disease.
You can calculate your Glomerular Filtration Rate (GFR), by entering results of your blood creatinine test, your age, race, gender and other factors.

The distribution of creatinine test results in 6434 people is shown on the right (NHANES 2006 study, weighted for USA demographics, graph by WolframAlpha)

The typical reference ranges in adult males are 0.7 to 1.2 mg/dL according to Wikipedia and 0.6 to 1.2 milligrams (mg) per deciliter (dl) according to medicinenet. In adult females, it's 0.5 to 1.1 milligrams per deciliter (wikipedia) or 0.5 to 1.1 mg/dl (medicinenet). LabCorps lists normal values between 0.57 and 1.00 mg/dL. (see also reference values for other medical tests and Aurametrix blog on liver tests). Men tend to have higher levels of creatinine because they generally have more skeletal muscle mass than women. Muscular young or middle-aged adults may have more creatinine in their blood than the norm for the general population. Vegetarians have been shown to have lower creatinine levels. Creatinine tends to be slightly lower in pregnancy. It increases with height and body weight. While a baseline serum creatinine of 2.0 mg/dL (150 μmol/l) may indicate normal kidney function in a male body builder, a serum creatinine of 0.7 mg/dL (60 μmol/l) can indicate significant renal disease in a frail old woman.

Infants have normal levels of about 0.2 or more, depending on their muscle development. In people with malnutrition, severe weight loss, and long standing illnesses the muscle mass tends to diminish over time and, therefore, their creatinine level may be lower than expected for their age.

A person with only one kidney may have a normal level of about 1.8 or 1.9. Creatinine levels that reach 2.0 or more in babies and 10.0 or more in adults may indicate severe kidney impairment and the need for a dialysis machine to remove wastes from the blood.

In the United States, creatinine is typically reported in mg/dL, while in Canada and Europe μmol/litre may be used. 1 mg/dL of creatinine is 88.4 μmol/l.

Creatinine is a waste product in your blood that comes from muscle activity. It is normally removed from your blood by your kidneys, but when kidney function slows down, the creatinine level rises.

Aurametrix is developing decision support systems to help you evaluate personal health risks, decide on preventative measures, estimate cost/benefits of performing diagnostic tests. Better tools for a healthier world.