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I constantly say "testosterone affects everything." I could just as easily say "blood flow affects everything." Decreased blood flow, for example, has been linked to both dementia and Alzheimer's.  Many tissues require good blood flow to deliver nutrients. The point is that clearing out your arteries can be a key factor in improving endothelial health and thus boosting your overall health and energy.
Here are the 4 more-or-less natural ways that I know of to actually partially reverse arteriosclerosis:
1. Low Fat Diet. The most famous way to clear out your plaque is through a Low Fat Diet. And this makes sense because modern oils, lards, butters and margarines are all a modern invention and very new in the history of mankind. Therefore, it is no surprise that a Low Fat Diet works so well, because it is simply a reflection of how man has eaten the vast majority of his time here on planet earth. As I often point out, wild game is actually generally low in fat - generally very close to the level used in the studies (10-15% of total calories).
In fact, it is tragic that a Low Fat Diet is called "low fat", because it is really not low in fat at all. The typical person on a Low Fat Diet will consume between 20-30 grams of fat per day which is plenty. Furthermore, even foods like grains, legumes and beans will supply a significant amount of saturated fat, more than enough to trigger ample production of cholesterol for the body's needs.
Before I go on, let me just briefly go over the research evidence for the decreased evidence seen from undergoing a Low Fat Diet.
How does a Low Fat Diet clear out arteries? What is interesting is that the research shows it does it by hitting almost every major pathway that leads to arteriosclerosis:
a) Lowered Cholesterol. A Low Fat Diet brings saturated fat consumption down to more natural levels and this, in turn, almost immediately drops cholesterol into the range where there is no heart disease. (Actually, it is possible to have a heart attack with cholesterol below 150, but it is much less common.)
b) Increase LDL Particle Size. Many of the experts consider the baddest of the bad boys are the very small LDL particles. LDL, as many men now know, is the "bad cholesterol" of the lipid world. However, it is really the small particles that do the most damage according to one school of thought. Well, one study showed that a Low Fat Diet increased LDL particle size.  Of course, this makes sense since we know a Low Fat Diet reduces total cholesterol so dramatically.
c) Decreased Oxidation.. Again, small, bad cholesterol particles need to be oxidizied in order to do their damage to arterial walls. The above study showed very significant decreases in oxidation levels as well from a Low Fat Diet. 
d) Decreased Blood Pressure. Hypertension is a plague in modern society and high blood pressure damages arteries, capillaries and surrounding tissues throughout the body, especially as the years and decades go by. A Low Fat Diet has been shown to decrease blood pressure levels significantly in a number of studies and I document this in my link on How to Lower Your Blood Pressure. (See #2.)
e) Diabetes Reversal and Blood Sugar Control. Dr. Neil Bernard, in his book Dr. Neil Bernard's Program for Reversing Diabetes, outlines how easily a Low Fat Diet can actually reverse diabetes. He shows how it can lower glycated hemoglobin levels and normalize blood sugar. This also helps heal and restore your arteries (and about a 100 other tissues.) The key here is to make sure that you eat low glycemic Low Fat foods, i.e. not cheating with sugars and some of the higher
Finally, remember that if you eat Low Fat, you in good company. Most of the supercultures, who enjoy incredible longevity with perfect blood pressure and virtually no heart disease, hypertension or cancer, eat an almost Low Fat Diet. They don't follow perfectly the formula outlined by Esselstyn and Ornish, but quite close. I outline this in my review of the book Healthy at 100.
NOTE: This is how I eat myself and I outline the research of this way of eating in this link on The Many Benefits of a Low Fat (Ornish) Diet. I do tweak a Low Fat Diet, though, to include more protein for building muscle and a few other things.
2. Pomegranate Juice. It is hard to believe but just a little pomegranate juice could actually clear out arterial plaque, but this is exactly what one study showed.  The group of pateints in this study had advanced arteriosclerosis. However, almost anyone reading this article wondering how to clear their arteries is likely in that category or close. And in those with more normal narrowing of the arteries, other research showed that pomegrante likely slowed arterial plaque buildup even if it didn't actually clear it the arteries.
In fact, pomegranate juice is a wonder worker for your arteries in many ways: it lowers blood pressure, boosts nitric oxide, protects against oxidized LDL and lower cholesterol levels. In short, it does everything you could possibly want a foood or supplement to do to protect your cardiovascular system. (Talk to your physician if you're on any medications as it can alter absorption rates of other medications.) For more information, see my links on The Power of Pomegranate Juice and The Benefits of Pomegranate Extract.
3. Gum Disease. One small study showed that by reversing gum disease patients actually reversed arteriosclerosis. This may seem implausible at first, but researchers have noted that "infections" of the mouth raise inflammation levels throughout the body and correlate to heart disease.  Again, keep in mind that this is one study and the fact that it was small and on patients with some periodontal disease. Read my links on How to Control Inflammation and Inflammation and Erectile Dysfunction for some related information.
4. Track Your Plaque Program. Cardiologist Dr. William Davis runs the Track Your Program and has a web site devoted to not only tracking your plaque but reversing it as well. His basic strategy focuses on some of the same ones mentioned above: reducing inflammation, reducing certain kinds of LDL and one more: increasing HDL. I do not know of any studies proving his techniques nor do I know their success rates. However, I mention the program because a) his practice is widely accepted in a manner similar to Dr. Esselstyn and b) his strategy may appeal more to those who want some fat in their diet.
The Paleo and Low Carb crowds have adopted Dr. Davis, because he dislikes grains and thinks cholesterol is not a good marker for cardiovascular outcomes. However, he actually goes against many of their core "doctrines". For example, he is NOT a fan of saturated fat and actually goes on record saying that he prefers monounsaturated and polyunsaturated fats.  He also is defiitely not a low carb or high fat promoter either.
From what I can tell, Dr. Davis is somewhat of a moving target and includes a wide range of protocols, including elimination of wheat, megadosing niacin, higher dosage fish oil, etc. All of this seems a tad "unnatural" to me, but if you absolutely want to have fat in your diet and reverse heart disease, then his program may be just what you are looking for. (Also, you may be interested in Review of Wheat Belly by Dr. Davis.)
CAUTION: If you have a medical condition or are on any medications, please discuss any changes with your doctor first. Certain supplements, foods and even juices can alter absorption rates of certain medications for example. Play it safe.
1) Arteriosclerosis, Thrombosis, and Vascular Biology. 1996, 16:201-207, "Effects of Diet and Exercise on Qualitative and Quantitative Measures of LDL and Its Susceptibility to Oxidation"
2) Clin Nutr. 2004 Jun;23(3):423-33, "Pomegranate juice consumption for 3 years by patients with carotid artery stenosis reduces common carotid intima-media thickness, blood pressure and LDL oxidation"
3) The American Journal of Cardiology, Oct2009, 104(7):936-942, "Effects of Consumption of Pomegranate Juice on Carotid Intima–Media Thickness in Men and Women at Moderate Risk for Coronary Heart Disease"
4) Neurology, Oct 1 1977, 27(10):905, "Cerebral blood flow, oxygen utilization, and blood volume in dementia"
5) Journal of the American Geriatrics Society, Oct 2007, 55(10):1613–1617, October 2007, "Assessment of Endothelial Function in Alzheimer's Disease: Is Alzheimer's Disease a Vascular Disease?"
7) FASEB J, 2009 Apr, 23(4):1196-204. "Treatment of periodontal disease results in improvements in endothelial dysfunction and reduction of the carotid intima-media thickness.
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