Biomedical Computing on a Budget

The Numbers and Your Wallet

 - Let’s face it. How many Health Professionals are MBAs? Not even all IT Pros are MBAs! And in the current economic world, ROI (return on investment) is key.  So what is one to do? Do we pennypinch in all areas of our life? Some say no. But the majority of you reading this blog are probably feeling the “ouch” of the recession. Even big IT firms are restructuring, retrenching and recalculating all their moves in their day-to-day operations. 

 - Even a number of hospitals have suspended normal operations.  And when I say "normal" I mean feeling free and easy and generous. As a matter of fact, even malpractice insurance premiums are becoming competitive. Just a few weeks ago I learned that the small clinic practice setting has become a viable option for MDs. I have been working in a medium sized diagnostic facility for easily 10 years and I don’t regret it. We still had budget diagnostic packages being offered without sacrificing Quality of Service (QoS). ROI in the health profession is not just about big bucks, but rather, a commitment to care for those who need us. I’m not going to get into a discussion about the budget deficit and my suggestions. It’s getting downright complicated. Or so it seems. The bottom line is: where do we want to spend our hard earned cash. If we all started having to drive a Ferrari to work, then of course our overhead would shoot up. And who takes the heat? The guy next door whose wife is about to give birth and he’s out of work. 

 - It’s not just a financial crisis we have to deal with. It’s also a crisis of moral and ethical behavior. We must remember, we are called to serve. We start with that, stay with that, and live with that. No easy matter at all. The temptation to “me first” is compelling. Why? Because we’re all in the same financial boat-  more or less.  Admittedly, some have quite a fancier boat. No problem with that at all. Just don’t pass the cost to the patient. No I’m not an ordained minister. And neither am I a Navy Seal! Just your friendly neighborhood mad scientist -internist-cardiologist with a laptop. Let’s keep a good sense of humor. It’s a survival skill. So, just a word: keep focused on what really matters. And if you have happened to get lost in the professional-financial forest, try hacking your way through with some kind words and acts, and give thanks to your Creator. Not tomorrow. Today.

 - The Numbers Frenzy

To those of you who are currently working in the area of Health Statistics, well, there are some free tools available from the National Center for Health Statistics. You can visit the resources page here There is also a good epidemiologic tool know as OpenEpi  now in version 2.3.1 Check it out here.   available in English, French, Spanish and Italian. So even if you’re in the European Union, this tool may work for your needs. More free statistics software can be viewed here Since we’re dealing with budget issues, make sure to read the fine print. If you’d like an interesting free online data visualization tool check out Tableau Public available here.

  

 - Like I said, we’re ever confounded by the gamble of Health Technology and money. Different people have all sorts of suggestions. With the explosion of mobile computing people have asked who will pay for the development and adaption of mobile devices in the Medical arena. Businesses have done reasonably well and they’re thinking, when will it be the same in the hospital, clinic or research institute. Somebody’s going to have to pay for this. But who? Will this mean an additional increase in health expenditures? We have enough problems already. But then again, if we were going to go for the “people care” paradigm, then that means it is essential to break the boundaries and reprioritize costs for patients, health professionals as well as clinics and hospitals. And since the research has to go onward we better think of solutions ASAP! Cures have to be found and patients need our utmost attention and QoS. Healthcare can’t take a back seat behind Defense spending. Quite frankly, someone I know once told me that it paid more to blast people out of existence than to cure them. Is this what we’re coming to? I am optimistic though, that things will get better. We just have to keep focus and ride the storm while it’s still roaring. Maybe, once policy makers get their acts straight, we will progress. Will the business model work for healthcare? At any rate, each of us has a voice and we better tell government leaders to be straightforward with their service priorities instead of the self-embellishment that serves no purpose other than to anger their constituents. Those of us in the healthcare galleon should row our individual oars and steer forward and do what we do best: serve and show the world we care. Like I always say, mediocrity is a capital offense. Go and make the world a better place, regardless of your place in the grand drama of things.  And if eHealthcare is your calling, then do it with a passion. Enjoy your work and work at what you enjoy. We in the healthcare business are at a crossroads. The world is watching. Let’s keep people healthy!  Meanwhile, the medical community is pioneering new modes of healthcare delivery based on the continuous management of disease rather than expensive episodic care. Costs decline as quality and access of care improve.

 - Patient Numbers

 - As personalized Medicine grows, data capture will have to evolve too. And big numbers will be our challenge. And as we manage all those numbers well we will then see that our efforts will have paid off. Patients will be as smart as can be, and we will have to deliver top quality improvements in data analysis and consolidation. There will have to be a central body or umbrella organization that will enforce common grounds for handling information, akin to the UN/WHO ICD system. All health professionals should participate in training and supervision, and of course, as we deal with our own clients we shall be able to render care to the best of our abilities. Everybody will know the basics of coding, operating and managing the information warehouse. With the explosion of cloud technology, we will have to be tech savvy. But it’s not the tech that’s the goal: it’s the patient we care for. We need to see the big picture. I read once and I remember it well. As a painter steps back from his work to see the big picture, we will likewise need to step back once in a while and see that we are involved in a huge ecosystem where everybody is a player. And we need to play right. Self-directed education is blossoming and we need to get interested in things that we typically shrug off as “not my thing.” Take responsibility for your own education. Let’s all be mature. Like I told a resident once, “we’re not in kindergarten anymore.“ Enough  with the excuses. We have reached an inflection point between the insular ‘sick care’ non-system of the past and the collaborative, proactive, true ‘health and wellness’ system of the future. As we have come to better understand the phenotypic, genotypic, environmental, and lifestyle factors that determine our health, it has become clear that disease and wellness are inherently personal. It should be. The patient also has to learn to take responsibility for his or her education and growth. There is such a thing as patient autonomy. But rather than burden the patient with forms, and more forms, we must guide them safely along the way. Do not underestimate the patient’s capacity for self-care. Of course, at times they need a helping hand. Individualizing treatment for a given patient is a truly daunting, data-driven task. Finding a treatment based on a patient’s genes, proteins, and environment is essentially a signal-detection exercise.

 - In my previous post, I mentioned the need to not only capture the signal, but also get the sense out of it. This will ultimately require data volumes and manipulation techniques unprecedented in information science and technology.  Businesses, banks, insurance firms and even the governments are doing it. eHealthcare must tread the same path of growth. From trial and protocol design all the way to the task of prescribing, all of this may have to be coordinated in a group run. The last mile has always been the hardest: obviously multifactorial, involving structural problems with our care delivery systems, reimbursement policies, etc.  Eventually, patients want a secure network of ‘friends’ around their illness and they want their doctors to ‘like’ them. Regardless of the approach, ‘liking’ our patients—and our patients liking us in return—will be a really large Big Data problem. I dare say that there are some of us healthcare professionals who are in their comfort zones and find it hard to accept the tech issues. Actually, I think that it’s basically a fear of the unknown which can be daunting indeed. Then goes the thinking, “I did fine without it. Why bother with all that now?” My answer is ”Because it behooves us as professionals.” It’s not a threat, but rather, a challenge which we embarked on when we decided to become a doctor, a nurse, and whatever branch of medical service.

 - This is the reason why I include facts, figures, data, and number crunching methods in my discourse- this blog. Just a short while back, somebody told me that she couldn’t get her laptop to work. So I told her, “You need to do such-and-such.” She responded, “I’m not a techie.” So I responded, “You don’t need to be a techie. Just know your machine and start off with the essentials.” Know your machine and what you are doing with it, and, to it. After we overcome that inertia, everything else will come easier. We live in exciting times. Technology is a three-course dinner at the best restaurant. Let’s not get stuck at the soup phase. Let’s savor everything. Artificial intelligence, neuro-linguistic programming, and statistical, decision based systems will then come easy as pie.

 - Back to the Math Exercise

 - Jean Louis Marie Poiseuille  (22 April 1797 – 26 December 1869)

was a French physician and physiologist.   

Source: http://depa.fquim.unam.mx/filtracion/fundamentos.html

 Poiseuille’s law.

This law is important in cardiovascular physiology. However it is  a feature in hydraulics, fluid dynamics, and electrical currents as well. So kindly take a good look at it and see the unifying characteristics of flow. It is very relevant to understanding cardiovascular pathology and eventually diagnosis and clinical investigation.

This concerns the voluminal laminar stationary flow of an incompressible uniform viscous liquid (so-called Newtonian fluid) through a cylindrical tube with constant circular cross-section. In other words, it applies to non-turbulent flow of liquids through pipes. It can be successfully applied to blood flow in capillaries and veins, to air flow in lung alveoli, for the flow through a drinking straw or through a hypodermic needle.

 - Gotthilf Heinrich Ludwig Hagen (March 3, 1797 - February 3, 1884) was a German physicist and hydraulic engineer.

 

In the previous post, we talked about the 

Hagen-Poiseuille’s Law.

For purposes of clarity, I'm including the formula again here.

 

A Formula for Vascular Resistance: Standard Fluid Dynamics

The Hagen–Poiseuille equation, a physical law that gives the pressure drop in a fluid flowing through a long cylindrical pipe. The assumptions of the equation are that the fluid is viscous and incompressible; the flow is laminar through a pipe of constant circular cross-section that is substantially longer than its diameter; and there is no acceleration of fluid in the pipe. The equation is also known as the Hagen–Poiseuille law, Poiseuille law and Poiseuille equation. Actual fluid flow is turbulent (i.e., not laminar) for velocities and pipe diameters above a threshold, leading to larger pressure drops than calculated by the Hagen–Poiseuille equation

 - Study the units used for the calculations, and  consider the reasonable limits of the variables. Remember, math is the relationship between objects, whether numbers or words. Functions are intrinsic in calculus. When you start coding, you will come across OOP (Object-Oriented Programming). So get used to this principle. As you start working with different programming languages this knowledge will come in real handy. C, C++, Java, even Python (and all the hybrids) will deal with objects, classes, data structures and algorithms.

 - Get some scratch paper and work it out. If you've got a whiteboard, you can draw out the process. If you've got the latest 10.1 tablet with pen, try doing it. It'll be fun and engaging. Can you imagine, up to 60% of a healthcare individual's time is spent on documentation. Work smart.

 - I hope you do the exercise. Next time we'll talk about viscosity and the characteristics of the flow vessels. Also, we'll be taking a view of diagnostic procedures used in evaluating these elements. PhD not required...

"See One. Do One. Teach One."
-anonymous

 - Take some time to check out the following resources on Big Data

1) Infographic on Big Data from Autonomy (an HP company):

2) Roel Castelein (Global) - Big Data: The Third Wave:

 - The weekend is just around the corner. Take time to step back and look at the big picture. You're part of it.

 - Stay safe!

 - Fernando Yaakov Lalana, M.D.

Markers, Medals and Math:

Pushing the Envelope

 - Markers

 - “OK for me, but not OK for you.” Before we go to today’s agenda, I’ll just talk a bit about the ractopamine issue mentioned in my previous post. The Member States of Codex Alimentarius Commission adopted maximum residue limits for the amount of ractopamine, the animal growth drug, allowed in the tissues of pigs and cattle. The Codex Commission reached a decision through a vote, carried out in accordance with the Commission’s rules and procedures. The limits were approved with 69 votes for, 67 against, and seven abstentions. The decision was made after the assessment was carried out by the Joint Expert Committee on Food Additives (an arm of the FAO/WHO) and reached after a rigorous process of scientific assessment to ascertain that the proposed levels of residues have no impact on human health.

 - Without going into statistical elaborations and disrespecting committee members, or committee rules, we notice that it was not an overwhelming vote. Will a 2-vote difference (among 143 individuals) make the score and tell us that it’s totally “safe” to ingest ractopamine-fed animal products? We’re dealing with world health- our health. And yet we single-out and penalize an Olympic athlete for using performance enhancing drugs. Why the disparity in decision making? Honestly, this is a bit absurd. One might argue that the two situations are different from one another. However, I believe that the WHO, and whoever is deciding for our health outcomes, should adopt a policy that is consistent in all settings. Not, “OK for me, but not OK for you.” I’ll leave you with that food for thought.

For more information please contact:

Glenn Thomas
WHO, Geneva
Mobile: +41 79 509 0677
E-mail: thomasg@who.int

 

 - Biomarkers of Human Health

 

 - A biomarker, or biological marker, is an indicator of a biological state. It is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. It is used in many scientific fields. This marker can be found in a specific tissue, organ, or throughout the body. It is an index of either health or disease. It is meant to detect the smallest unit of a certain molecule, or process (as in the electrocardiogram) in the body. 

 

 - While we know of blood cholesterol levels and traces of zinc in the skin and nails, growth of the knowledge and the technology to asses these elements is expanding remarkably. Now, with the growth of genomics and Medical Information Technology, we are delving deeper, not only with one person’s health, but also with the likelihood of disease in his or her offspring. It is not sufficient to identify a molecule’s presence. We are also measuring their specific levels. Laboratories are currently facing the recession, and because of this we have to work smarter. For example, we could use mathemathical modeling and organ simulation in order to minimize animal or human experimentation whenever feasible. Chemical reagents and the sundry materials of the lab are getting way expensive. It would be possible to buy special computer programs for our particular area of study. If the program is not available, well, we can code one. A bit of study and a bit of practice go a long way. Oh yes, time is gold. If we can plan our experiments well beforehand (with the proper tools), we could save on energy and even possible mistakes.We should make use of the ELN (Electronic Laboratory Notebook) to log all our observations througout the experiment. It is a way of maximizing our observations and calculations thereby enabling us to see the minutiae as well as the bigger picture.

 - Math

 

 - Different computer programs are now increasingly used to assess the significance of certain health data. One such program is MATLAB, a mathematical analysis tool that is used in cases ranging from aerodynamic data to abnormal physiological signals. The book by Steven C. Chapra, “Applied Numerical Methods with MATLAB - for Engineers and Scientists”, is a good resource dealing with computers: MATLAB features, computer uses and their limitations in the scientific field. In this day and age, to eschew information technology is a major offense. This also holds true in the health professions. With the increasing portability of data access, we have to make some notable changes in our diagnostic attitude. Physicians and nurses are tapping into servers and cloud engines to support their skills and acumen. The advent of telemedicine is further strengthening the role of health computing machines in the workplace and wherever the patient may be. 

 

 - It’s not enough, though, to record signals or biologic phenomena. It is also  imperative that we study and make this data relevant to our roles as purveyors of health. How we carry out our analysis will matter in the ways that data is relevant in an individual in a given situation. In other words, it’s not just about collecting and storing data, but rather understanding and making decisions that will impact your health. Statistics, time-series analysis, signal processing, and biophysics simulations are all important analytic processes. While it is true that there may are special departments devoted to these applications, we must be cognizant of their operations. The whole process eventually depends on the algorithms used in the analysis of the data. Whether one is a clever clinical diagnostician or a computer programmer, the formulas we utilize can spell the difference in the diagnosis between a gastric reflux state, and a case of an impending myocardial infarction. Obviously, we may not have time to review calculus and other maths in an acute and potentially catastrophic 50/50 situation. That is why we should take as much time honing our tech skills as we do our daily SOP (standard operating procedures). 

 

 - Actually, all this study is a definite load on the time and energy of health practitioners. That is why we should accept this responsibility and work more efficiently. If not, we will all burn out eventually and that will put us out of reach with the patient After many years dealing with critical cases in the ICU/CCU, it has become second nature to me to make the most reasonable choices in a given situation. But it is not boasting, but rather accepting that our competence relies heavily on our clinical and technical aptitude. Now, we have associations dealing with Medical Information Systems, and we have access to the surmounting knowledge that is paving the way to a better health experience. 

 

 -In the following days and weeks, I will be demonstrating to you certain ways of computer-based math in the diagnostic arena. Our bodies are mysterious temples with many hidden corridors and alleys. It is now our time to unravel bit by bit what stuff we are made of. At the same time, we will be exercising our frontal lobes. It's not just calculating numbers, but rather picturing the process in our minds. Or, pen it at the back of an envelope if you have one. If you've got a mobile device with a stylus, that would be nice. It's good to remember that math is basically the relationships between objects.

 - Stuff for Exercise

 - A Formula for Vascular Resistance: Standard Fluid Dynamics

 - We begin with the Hagen–Poiseuille equation, a physical law that gives the pressure drop in a fluid flowing through a long cylindrical pipe. The assumptions of the equation are that the fluid is viscous and incompressible; the flow is laminar through a pipe of constant circular cross-section that is substantially longer than its diameter; and there is no acceleration of fluid in the pipe. The equation is also known as the Hagen–Poiseuille law, Poiseuille law and Poiseuille equation. Actual fluid flow is turbulent (i.e., not laminar) for velocities and pipe diameters above a threshold, leading to larger pressure drops than calculated by the Hagen–Poiseuille equation. In the blood vessels, you have turbulence at bifurcations or stenosis. The change in flow can give rise to Eddy currents (also called Foucault currents). The term eddy current comes from currents seen in water when dragging an oar breadthwise. These localized areas of turbulence known as eddies give rise to persistent vortices. Any spiral (or, spinning) motion with closed streamlines is vortex flow. In cardiology, eddy currents are important because these areas of spinning can facilitate the formation of thrombi. Blood flow in the opposite direction from normal is regurgitation. Alright, so now we begin our exercise.

  

1) To start: on the left is the first formula to take a good look at;

2) Try to determine the unit of measurement for the variables, such as P, L, and so on;

3) What would be the usual and reasonable limits for each of the variables;

4) Calculate.

Since we are dealing now with blood vessels, remember the characteristics of the vessel,

(e.g. artery or vein) and understand the different agents that may influence the characteristics, (e.g. hormones, blood gases, electrolytes).

 - In the process you will be reviewing anatomy, physiology, biochemistry, and biophysics. Grab your favorite calculator and try it out. We will continue next time...

 - Stay cool! See you.

 - Fernando Yaakov Lalana, M.D.

Ractopamine, Swine and Man

- The United Nations food standards body, the Codex Alimentarius Commission, has decided to set residue limits of the animal growth promoter, ractopamine, which also keeps pigs lean for the slaughter. Cattle are also administered this beta-adrenoceptor agonist. The ractopamine limits set by the Commission are 10 micrograms per kilogram of pig or cattle muscle, 40 micrograms per kilogram in liver and 90 micrograms per kilogram of the animals’ kidneys.

- Known as Paylean for swine and Optaflexx for cattle, 4-[3-[[2-Hydroxy-2-(4-hydroxyphenyl)ethyl]amino]butyl]phenol is banned in the European Union, Republic of China (Taiwan) and Mainland China.  Curiously, in 27 countries, including Japan, South Korea, Mexico, Canada, the United States and many others, have determined that meat from animals fed ractopamine is safe for human consumption.  As a leanness-enhancing agent, orally-given (in animal feed) ractopamine is absorbed, distributed and eliminated rapidly in pigs, cattle, laboratory animals and primates. It notably increases the rate of weight gain, improves feed efficiency and increases carcass leanness in finishing swine.

- In humans, this agent is likewise rapidly absorbed.  In a study with volunteers given a single oral dose of 40 mg, the mean half-life was around 4 hours, and it was not detected in plasma 24 hours after said ingestion. The urinary metabolites were monoglucuronide and monosulfate conjugates, with ractopamine monosulfate being the major metabolite present.

- It is considered safe as a finishing feed for swine over 240 lbs. In studies in rats and mice, acute toxicity was observed  and the oral LD₅₀ in mouse and rat are 3547-2545 mg/kg body weight (male and female) and 474-365 (male and female), respectively.  You can access a European Food Safety Authority opinion here.  LD_n represents “Lethal  Dose” and the subscript, n,  represents the percentage of test organisms killed by a specific dosage of a pathogen (a given substance or type of radiation)  and half will die at LD₅₀. In effect, it is the index indication of the lethality of the pathogen in a “normal individual.”

 - This begs a question: if it is toxic to laboratory subjects (here, rats and mice) then why is it considered safe for man’s consumption?  Why is also there a disparity in the permissions and prohibitions among different countries?  Under 21 CFR 556.570, safe concentrations for total residues of ractopamine hydrochloride are: 0.25 ppm in muscle, 0.75 ppm in liver, and 1.5 ppm in kidney and fat. (ppm=parts per million) By the way, the liver is the target tissue.

- We’re getting into more numbers here. In spite of the observations in the lab, the Joint FAO/WHO Expert Committee on Food Additives has said that it is safe for humans to consume these meats. So let’s see how technology is supposed to help us now. It is not mutagenic, genotoxic, nor considered to be a direct carcinogenic agent. Anyone familiar with the actions of beta-adrenergic agents will know that there will be some irritability, restlessness, tremors, tachycardia, and an increase in cardiac output. Clenbuterol  (another beta-adrenergic agonist) is a growth promoting compound. It is known to have the effect of enhancing weight gain and proportion of muscle to fat.

- Lest we forget, this beta-adrenergic agent is also banned by the international sports body and known controversies concerning athletes with traces of clenbuterol have arisen. And in a case of cycling recently,  I remember that the athlete was basically castigated for using performance-enhancing drugs. Compared to ractopamine, clenbuterol is known to have a much longer half-life in blood than ractopamine and thus has a greater potential for bioaccumulation

  - So what are we going to use as a meter for the safety of humans? Isn’t it possible that the continuous ingestion of meat of animals fed ractopamine may be dangerous for man?  I don’t think we should wait a generation or two to come to some sense of “sobriety” or realization that artificially enhanced food is not in our best interest. The demand for more food worldwide is apparently governing the choices we make. Even genetically modified grass is given to cattle to graze on. The reason for this method of feeding was that there was more meat and more money to be made doing it this way. You may even have already consumed this artificially enhanced food earlier today, or this week.

 - We are not talking about our individual decision to be herbivorous or omnivorous. That will be a subject for another day. What we are arriving at here is to consider, not just our safety (or self-interest), but the welfare of the future generations. I, for one, will not want my own children or grandchildren to ask me later, “why did you allow all this to happen?” Maybe, some of you are quite liberal in your choices, and that’s one’s lawful right. What we must decide is to make the responsible decision today. 

 - If it’s not good for the athlete, it may not be good for you. And mind you, I have had first-hand experience dealing with both national and international sporting events. This reminds me now of the issue of concussions in high-contact sports. I have witnessed athletes stagger even after winning a match. I hope we will not stagger in our choices as well.

 - Stay safe and have a nice day. Bon appétit!

 - Fernando Yaakov Lalana, M.D.