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Unfortunately the first article doesn't list the herbal supplements causing liver problems, but the earlier NY Times article mentions green tea extracts as one of them. From Science Daily:

Liver injury caused by herbals, dietary supplements rises in study population

Liver injury caused by herbals and dietary supplements increased from 7% to 20% in a U.S. study group over a ten-year period, research shows. According to the study, liver injury caused by non-bodybuilding supplements is most severe, occurring more often in middle-aged women and more frequently resulting in death or the need for transplantation than liver injury from bodybuilding supplements or conventional medications.

In response to the need for research in this area, the National Institutes of Diabetes and Digestive and Kidney Diseases (NIDDK) supported the establishment of the Drug-Induced Liver Injury Network (DILIN) in 2003 to track cases of liver injury caused by medications (excluding acetaminophen (Tylenol®)), herbals, and dietary supplements. Herbals and dietary supplements were identified as the second most common cause of liver injury in the first DILIN report.

The present study examines hepatotoxicity due to supplements compared to medications, enrolling 839 patients with liver injury from 8 U.S. DILIN referral centers between 2004 and 2013 While bodybuilding supplements caused prolonged jaundice (median 91 days) in young men, no fatalities or liver transplantations occurred. Death or liver transplantation occurred more frequently among cases of injury from non-bodybuilding supplements, 13%, than from conventional medications, 3%. Liver injury from non-bodybuilding supplements was more common in middle aged women.

From NY Times (Dec. 2013):

Spike in Harm to Liver Is Tied to Dietary Aids

But the supplement business is largely unregulated. ... But a federal law enacted in 1994, the Dietary Supplement Health and Education Act, prevents the Food and Drug Administration from approving or evaluating most supplements before they are sold. Usually the agency must wait until consumers are harmed before officials can remove products from stores. Because the supplement industry operates on the honor system, studies show, the market has been flooded with products that are adulterated, mislabeled or packaged in dosages that have not been studied for safety.

The new research found that many of the products implicated in liver injuries were bodybuilding supplements spiked with unlisted steroids,and herbal pills and powders promising to increase energy and help consumers lose weight.

 More popular supplements like vitamins, minerals, probiotics and fish oil had not been linked to “patterns of adverse effects,” he said.

Since 2008, the F.D.A. has been taking action against companies whose supplements are found to contain prescription drugs and controlled substances, said Daniel Fabricant, the director of the division of dietary supplement programs in the agency’s Center for Food Safety and Applied Nutrition. For example, the agency recently took steps to remove one “fat burning” product from shelves, OxyElite Pro, that was linked to one death and dozens of cases of hepatitis and liver injury in Hawaii and other states.

A second trend emerged when Dr. Navarro and his colleagues studied 85 patients with liver injuries linked to herbal pills and powders. Two-thirds were middle-aged women, on average 48 years old, who often used the supplements to lose weight or increase energy. Nearly a dozen of those patients required liver transplants, and three died

But one product that patients used frequently was green tea extract, which contains catechins, a group of potent antioxidants that reputedly increase metabolism. The extracts are often marketed as fat burners, and catechins are often added to weight-loss products and energy boosters. Most green tea pills are highly concentrated, containing many times the amount of catechins found in a single cup of green tea, Dr. Bonkovsky said. In high doses, catechins can be toxic to the liver, he said, and a small percentage of people appear to be particularly susceptible.

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Two write-ups about the same large study.The good news is that there is no one diet that works - the key is to stick with the diet. From Science Daily:

Comparison of named diet programs finds little difference in weight loss outcomes

In an analysis of data from nearly 50 trials including about 7,300 individuals, significant weight loss was observed with any low-carbohydrate or low-fat diet, with weight loss differences between diet programs small, findings that support the practice of recommending any diet that a patient will adhere to in order to lose weight.

Bradley C. Johnston, Ph.D., of the Hospital for Sick Children Research Institute, Toronto, and McMaster University, Hamilton, Ontario, and colleagues conducted a meta-analysis to assess the relative effectiveness of different popular diets in improving weight loss. 

The meta-analysis included 59 articles that reported 48 randomized clinical trials (7,286 individuals; median age, 46 years; median weight, 207.5 lbs.). In the diet-class analysis adjusted for exercise and behavioral support, all treatments were superior to no diet at 6-month follow-up. Compared with no diet, low-carbohydrate diets had a median difference in weight loss of 19.2 lbs. and low-fat diets had similar estimated effects (17.6 lbs.).

At 12-month follow-up, the estimated average weight losses of all diet classes compared with no diet were approximately 2.2 to 4.4 lbs. less than after 6-month follow-up. The diet classes of low fat (16 lbs.) and low carbohydrate (16 lbs.) continued to have the largest estimated treatment effects.

Weight loss differences between individual diets were minimal. "Our findings should be reassuring to clinicians and the public that there is no need for a one-size-fits­ all approach to dieting because many different diets appear to offer considerable weight loss benefits. 

From Medical Xpress:

Any diet works, if you stick to it, study finds

At six month follow-up, people on low-carbohydrate diets lost 19 more pounds than those who were not on a diet, while those on low-fat diets lost 17 more pounds than those on no diet. After 12 months about two to three pounds of that difference was gone, and there was no difference between low-carbohydrate and low-fat diets.

Behavioural support in a diet made a difference at six months, enhancing weight loss by about seven pounds, while exercise was significant at 12 months, improving weight loss by about four and half pounds.

Eating more tomatoes is doable, tastes delicious, and reduces prostate cancer risk! From Science Daily:

Fighting prostate cancer with tomato-rich diet

Men who eat over 10 portions a week of tomatoes have an 18 percent lower risk of developing prostate cancer, new research suggests. With 35,000 new cases every year in the UK, and around 10,000 deaths, prostate cancer is the second most common cancer in men worldwide. Rates are higher in developed countries, which some experts believe is linked to a Westernised diet and lifestyle.

To assess if following dietary and lifestyle recommendations reduces risk of prostate cancer, researchers at the Universities of Bristol, Cambridge and Oxford looked at the diets and lifestyle of 1,806 men aged between 50 and 69 with prostate cancer and compared with 12,005 cancer-free men.

The NIHR-funded study, published in the medical journal Cancer Epidemiology, Biomarkers and Prevention, is the first study of its kind to develop a prostate cancer 'dietary index' which consists of dietary components -- selenium, calcium and foods rich in lycopene -- that have been linked to prostate cancer. Men who had optimal intake of these three dietary components had a lower risk of prostate cancer.

Tomatoes and its products -- such as tomato juice and baked beans -- were shown to be most beneficial, with an 18 per cent reduction in risk found in men eating over 10 portions a week. This is thought to be due to lycopene, an antioxidant which fights off toxins that can cause DNA and cell damage. 

The researchers also looked at the recommendations on physical activity, diet and body weight for cancer prevention published by the World Cancer Research Fund (WCRF) and the American Institute for Cancer Research (AICR). Only the recommendation on plant foods -- high intake of fruits, vegetables and dietary fibre -- was found to be associated with a reduced risk of prostate cancer. 

If taking Clostridia as a probiotic for food allergies works, it would be amazing for food allergy sufferers. Very exciting research. From Time:

The Bacteria That May One Day Cure Food Allergies

Every round of antibiotics a person takes will wipe out strains of bacteria inside the body, some of which are eliminated forever. Considering how early and how often antibiotics are administered to kids—coupled with our increasingly antimicrobial lifestyles—we’ve become more prone to allergies and other ailments, the hygiene hypothesis goes. There’s no cure for food allergies, just lifestyle adjustments and abstention. But Nagler and her team may have the germ of an idea for treatment using gut bacteria, according to a new mice study published in the Proceedings of the National Academy of Sciences.

The team dosed two groups of mice with peanut allergens. One group of mice had been bred to be entirely without gut germs; the other group had sparsely populated gut bacteria due to treatment with antibiotics. Both groups of mice had higher levels of the allergen in their bloodstream compared to mice with healthy gut-bacteria populations.

After giving those same mice a mix that contained the bacteria strain Clostridia, their allergen levels plummeted. Infusing the mice with another group of intestinal bacteria, Bacteroides, didn’t help—so the researchers think the effect is special to Clostridia. “These bacteria are very abundant and they reside very close to the epithelial lining, so they’re in intimate contact with the immune system,” Nagler says.

Next, they’ll transfer gut bacteria from food-allergic infants and healthy infants into germ-free mice, Nagler says. “If we give back Clostridia to a mouse that has the bacteria of an allergic child, can we now reverse susceptibility in that mouse?”

This is a more in-depth article of the research. From Science Daily:

Gut bacteria that protect against food allergies identified

The presence of Clostridia, a common class of gut bacteria, protects against food allergies, a new study in mice finds. The discovery points toward probiotic therapies for this so-far untreatable condition. Food allergies affect 15 million Americans, including one in 13 children, who live with this potentially life-threatening disease that currently has no cure, researchers note.

Although the causes of food allergy -- a sometimes deadly immune response to certain foods -- are unknown, studies have hinted that modern hygienic or dietary practices may play a role by disturbing the body's natural bacterial composition. In recent years, food allergy rates among children have risen sharply -- increasing approximately 50 percent between 1997 and 2011 -- and studies have shown a correlation to antibiotic and antimicrobial use.

"Environmental stimuli such as antibiotic overuse, high fat diets, caesarean birth, removal of common pathogens and even formula feeding have affected the microbiota with which we've co-evolved," said study senior author Cathryn Nagler, PhD, Bunning Food Allergy Professor at the University of Chicago. "Our results suggest this could contribute to the increasing susceptibility to food allergies."

To test how gut bacteria affect food allergies, Nagler and her team investigated the response to food allergens in mice. ...This sensitization to food allergens could be reversed, however, by reintroducing a mix of Clostridia bacteria back into the mice. Reintroduction of another major group of intestinal bacteria, Bacteroides, failed to alleviate sensitization, indicating that Clostridia have a unique, protective role against food allergens.

To identify this protective mechanism, Nagler and her team studied cellular and molecular immune responses to bacteria in the gut. Genetic analysis revealed that Clostridia caused innate immune cells to produce high levels of interleukin-22 (IL-22), a signaling molecule known to decrease the permeability of the intestinal lining.

While complex and largely undetermined factors such as genetics greatly affect whether individuals develop food allergies and how they manifest, the identification of a bacteria-induced barrier-protective response represents a new paradigm for preventing sensitization to food. Clostridia bacteria are common in humans and represent a clear target for potential therapeutics that prevent or treat food allergies. 

Interesting study that definitely needs follow-up to see if it also applies to women. Nice news for coffee drinkers - that coffee consumption may have protective effects against gum disease. From Medical Xpress:

Coffee drinkers—your gums may thank you

Coffee contains antioxidants. Antioxidants fight gum disease. Does coffee, then, help fight gum disease?  Lead author and 2014 DMD graduate Nathan Ng said, "We found that coffee consumption did not have an adverse effect on periodontal health, and, instead, may have protective effects against periodontal disease."

Coffee consumption was associated with a small but statistically significant reduction in number of teeth with periodontal bone loss. Researchers concluded that coffee consumption may be protective against periodontal bone loss in adult males—the group examined in the study.

I've always recommended that people eat as many unprocessed foods as possible, and that one should always read the ingredient list when buying processed and prepared foods. The Center for Science in the Public Interest strongly urges that people avoid the following food ingredients: aspartame, food dyes, mycoprotein (Quorn), and partially hydrogenated oils (trans fat). The following article may be an eye opener for those who think that the FDA (Food and Drug Administration) carefully regulates what goes into our food. Link to the full article to read all the health concerns with mycoprotein (Quorn), Epigllocatechin-3-gallate (EGCG), and carageenan. From The Washington Post:

Food additives on the rise as FDA scrutiny wanes

The explosion of new food additives coupled with an easing of oversight requirements is allowing manufacturers to avoid the scrutiny of the Food and Drug Administration, which is responsible for ensuring the safety of chemicals streaming into the food supply.

And in hundreds of cases, the FDA doesn’t even know of the existence of new additives, which can include chemical preservatives, flavorings and thickening agents, records and interviews show. “We simply do not have the information to vouch for the safety of many of these chemicals,” said Michael Taylor, the FDA’s deputy commissioner for food.

The FDA has received thousands of consumer complaints about additives in recent years, saying certain substances seem to trigger asthmatic attacks, serious bouts of vomiting, intestinal-tract disorders and other health problems.

At a pace far faster than in previous years, companies are adding secret ingredients to everything from energy drinks to granola bars. But the more widespread concern among food-safety advocates and some federal regulators is the quickening trend of companies opting for an expedited certification process to a degree never intended when it was established 17 years ago to, in part, help businesses.

A voluntary certification system has nearly replaced one that relied on a more formal, time-consuming review — where the FDA, rather than companies, made the final determination on what is safe. The result is that consumers have little way of being certain that the food products they buy won’t harm them“We aren’t saying we have a public health crisis,” Taylor said. “But we do have questions about whether we can do what people expect of us.”

In the five decades since Congress gave the FDA responsibility for ensuring the safety of additives in the food supply, the number has spiked from 800 to more than 9,000, ranging from common substances such as salt to new green-tea extracts. This increase has been driven largely by demand from busy Americans, who get more than half their daily meals from processed foods, according to government and industry records. 

Within the past six months, top officials at the FDA and in the food industry have acknowledged that new steps must be taken to better account for the additives proliferating in the food supply. 

For new, novel ingredients — or when approved additives are used in new ways — the law says companies should seek formal FDA approval, which must be based on rigorous research proving the additive is safe. The agency uses the phrase “food additive,” in a narrow legal sense, to apply to substances that get this approval.

But many other additives are common food ingredients — vinegar is considered a classic example. The law allows manufacturers to certify, based on research, that such ingredients are already Generally Recognized as Safe, or GRASFor both types of additives, FDA scientists initially conducted detailed reviews of the company’s research. The agency also published its own evaluation of that research in the Federal Register.

This oversight system shifted dramatically in 1997. In response to a shortage of staff members and complaints from industry that the process was too cumbersome and did not improve food safety, the FDA proposed new rules. The agency told companies that were going the GRAS route — which turned a years-long process into one of months — that they no longer would have to submit their research and raw data. The companies can share just a summary of their findings with the agency.

The changes didn’t work out as planned. For starters, most additives continued to debut without the FDA being notified. Moreover, companies that did choose to go through the FDA oversight process largely abandoned the formal approval route, opting instead for the new, cursory GRAS process, even for additives that could be considered new and novel, according to agency documents and an analysis of those records by the Natural Resources Defense Council.

An average of only two additive petitions seeking formal approval are filed annually by food and chemical companies, while the agency receives dozens of GRAS notifications, according to an NRDC analysis of FDA data. Hundreds of other food chemicals and ingredients have been introduced without notifying the FDA at all, according to agency officials, trade journals and food safety groups.

Companies often bypass the FDA altogether. Under the rules, companies may make their own GRAS determination. Sharing it with the agency and getting it to sign off is voluntary. This is the opposite of what the overisght law intended, the FDA’s Taylor said. 

Even when the FDA approves a new additive or signs off on a company’s GRAS determination, a safe ingredient can turn dangerous if its use becomes more widespread than the agency envisioned. And under the rules, the agency has little way of monitoring this threat after the initial introduction of the additive, called “post-market.”

During the initial review, the FDA sets limits for how much of a chemical or ingredient can be used in a particular product. But the cumulative consumption can soar as the additive is used in more and more types of food and beverages.

Two new studies find problems when vitamin D levels are low. From Science Daily:

Low vitamin D levels linked to increased risks after noncardiac surgery

Patients with low blood levels of vitamin D are at increased risk of death and serious complications after noncardiac surgery, suggests a study. The researchers analyzed the relationship between vitamin D level and surgical outcomes in approximately 3,500 patients who underwent operations other than heart surgery between 2005 and 2011. Only patients who had available data on vitamin D levels around the time of surgery -- from three months before to one month afterward -- were included in the study.

Most patients did not meet the recommended 25-hydroxyvitamin D concentration of greater than 30 nanograms per milliliter (ng/mL). The median vitamin D level was 23.5 ng/mL -- more than 60 percent of patients were in the range of vitamin D insufficiency (10 to 30 ng/mL). Nearly 20 percent had vitamin D deficiency (less than 10 ng/mL).

"Higher vitamin D concentrations were associated with decreased odds of in-hospital mortality/morbidity," the researchers write. For each 5 ng/mL increase in 25-hydroxyvitamin D level, the combined risk of death, cardiovascular events, or serious infections decreased by seven percent.

From Science Daily:

Vitamin D deficiency may reduce pregnancy rate in women undergoing IVF

Women with a vitamin D deficiency were nearly half as likely to conceive through in vitro fertilization (IVF) as women who had sufficient levels of the vitamin, according to a new study. Long known for its role in bone health, vitamin D is a steroid hormone that is emerging as a factor in fertility.

Women who had sufficient levels of vitamin D were nearly twice as likely to conceive as their counterparts with vitamin D deficiency. Since women with sufficient levels of the hormone were more likely to produce top-quality embryos, researchers theorized vitamin D was involved in the production of quality eggs in the ovaries as well as the successful implantation of embryos in the uterus.

A favorite food of financially or time strapped people and students may be problematic. Just looking at the ingredient list and nutritional information should have been a clue. From Science Daily:

Can instant noodles lead to heart disease, diabetes and stroke?

Significant consumption of instant noodles -- ramen included -- may increase a person’s risk for cardiometabolic syndrome, especially in women, research shows. The findings could shed new light on the risks of a worldwide dietary habit. "This research is significant since many people are consuming instant noodles without knowing possible health risks," one researcher said. 

Because ramen consumption is relatively high among Asian populations, the research focused primarily on South Korea, which has the highest per-capita number of instant noodle consumers in the world. In recent years, South Koreans have experienced a rapid increase in health problems, specifically heart disease, and a growing number of overweight adults. Such changes could lead to increased mortality due to cardiovascular disease, as well as increased health care costs.

Dr. Shin, who led the study on behalf of the Baylor Heart and Vascular Hospital (BHVH), found that eating instant noodles two or more times a week was associated with cardiometabolic syndrome, which raises a person's likelihood of developing heart disease and other conditions, such as diabetes and stroke.

Dr. Shin also found that those results were more prevalent in women. He said that can likely be attributed to biological differences (such as sex hormones and metabolism) between the sexes, as well as obesity and metabolic syndrome components. In addition, men and women's varied eating habits and differences in the accuracy of food reporting may play a role in the gender gap.

Another potential factor in the gender difference is a chemical called bisphenol A (BPA), which is used for packaging the noodles in Styrofoam containers. Studies have shown that BPA interferes with the way hormones send messages through the body, specifically estrogen.

This study found a link with coffee consumption and lower rates of tinnitus, so perhaps coffee drinking would help those with tinnitus? Stay tuned. From Science Daily:

Caffeine intake associated with lower incidence of tinnitus

Higher caffeine intake is associated with lower rates of tinnitus, often described as a ringing or buzzing sound in the ear when there is no outside source of the sounds, in younger and middle-aged women. "We observed a significant inverse association between caffeine intake and the incidence of tinnitus among (participating) women," said the lead author.

Specifically, researchers report that when compared with women with caffeine intake less than 150 milligrams/day (approximately one and a half 8-ounce cups of coffee), the incidence of reported tinnitus was 15 percent lower among those women who consumed 450 to 599 mg/day of caffeine. The majority of caffeine consumed among the women was from coffee and the results did not vary by age.

"The reason behind this observed association is unclear," said Curhan. "We know that caffeine stimulates the central nervous system, and previous research has demonstrated that caffeine has a direct effect on the inner ear in both bench science and animal studies. Researchers note that further evidence is needed to make any recommendations about whether the addition of caffeine would improve tinnitus symptoms.

The following is from a presentation from The American Association of Diabetes Educators Annual Meeting August 6-9, 2014 by M.Jardin and C.Kafity. But the coffee and tea statement is different from what I've read elsewhere, specifically that coffee is beneficial, is a source of soluble fiber, and may keep pathogenic bacteria in check. From Endocrinology Today:

Plant-based diet helps grow healthy microbiota, halt diabetes disease process

With research mounting on the onslaught the body’s microbiota take from human eating patterns and the environment, making choices to maintain inner ecosystem health is essential, according to presenters at the American Association of Diabetes Educators Annual Meeting. Choosing a plant-based diet is one way people can increase the diversity of bacteria in their biome, reduce inflammation and begin to reverse the diseases processes involved in obesity and diabetes — often in just a few days.

“We know obesity and diabetes have increased tremendously in the last 20 years and we know that our genes haven’t changed, so that can’t account for the change,” Meghan Jardine, MS, MBA, RD, LD, CDE, RDN, of Parkland Health and Hospital System, said during a presentation. “Many scientists believe the changes in our diet and physical activity can’t really account for the change either, that there’s something else at work here.”

Weighing at least two kilograms in all and accounting for more than 3 times the amount of the body’s human cells, gut bacteria is colonized after birth, stabilized by age 3 years but influenced by a number of external factors, Jardine explained. Areas of influence include nutrition and immune function, both priorities in treating obesity and diabetes.

“Microbiota releases enzymes that digest food so we can absorb nutrients, produces vitamins, combats opportunistic infections and works with the immune system,” Jardine said. “About 70% of our immune systems are in our gut.”

People who consume plant-based diets have “healthy” gut microbiota in terms of global parameters and functional and compositional features, Christina Kafity, RN, BSN,CHC... “Children and elderly individuals who consumed more plant carbohydrates versus the typical standard American diet had rapid, reproducible alterations of the gut microbiota for the better, and this happened within 24 hours to a week,” Kafity said.

Growing good bacteria depends on creating an environment in which they can thrive, Kafity explained, including choosing foods that contain certain fibers intact in plants and probiotics; among them are soluble, insoluble and functional fibers as well as psyllium and inulin.

Intake of cruciferous vegetables including Brussels sprouts, kale and cabbage can help boost healthy microbes and, further, provide glucosinolates to help to reduce inflammation, Kafity said. Yogurt, kefir and probiotics also promote the growth of good bacteria, Kafity noted, while some popular beverages may not be much help. “We’re considering that coffee and teas may actually sterilize the bacteria.”