[Press release] Loyola website helping cancer researchers make sense of a deluge of genetic data

From the 12 December 2013 Loyola University press release

MAYWOOD, Ill. – A newly improved Internet research tool is helping cancer researchers and physicians make sense out of a deluge of genetic data from nearly 100,000 patients and more than 50,000 mice.

The tool, called the Gene Expression Barcode 3.0, is proving to be a vital resource in the new era of personalized medicine, in which cancer treatments are tailored to the genetic makeup of an individual patient’s tumor.

Significant new improvements in the Gene Expression Barcode 3.0 are reported in the January issue of the journal Nucleic Acids Research, published online ahead of print.

Senior author is Michael J. Zilliox of Loyola University Chicago Stritch School of Medicine. Zilliox is co-inventor of the Gene Expression Barcode.

“The tool has two main advantages,” Zilliox said. “It’s fast and it’s free.”

The Gene Expression Barcode is available at a website designed and hosted by Loyola University Chicago Stritch School of Medicine. The website is receiving  1,600 unique visitors per month.

Knowing how a patient’s cancer genes are expressed can help a physician devise an individualized treatment. In a tumor cell, for example, certain genes are turned on (expressed) while other genes are turned off (unexpressed). Also, different types of cancer cells have different patterns of gene expression. Genes are expressed through RNA, a nucleic acid that acts as a messenger to carry out instructions from DNA for making proteins.

Research institutions have made public the genetic data from nearly 100,000 patients, most of whom had cancer, and more than 50,000 laboratory mice. In raw form, however, these data are too unwieldy to be of much practical use for most researchers. The Gene Expression Barcode applies advanced statistical techniques to make this mass of data much more user-friendly to researchers.

The barcode algorithm is designed to estimate which genes are expressed and which are unexpressed. Like a supermarket barcode, the Gene Expression Barcode is binary, meaning it consists of ones and zeros – the expressed genes are ones and the unexpressed genes are zeros.

Zilliox co-invented the Gene Expression Barcode, along with Rafael Irizarry, PhD. (At the time, Zilliox and Irizarry were at Johns Hopkins University.) Zilliox joined Loyola in 2012, and Irizarry now is at the Dana-Farber Cancer Institute. Zilliox and Irizarry first reported the Gene Expression Barcode in 2007. In 2011, they reported an improved 2.0 version. The Barcode already has been cited in more than 120 scientific papers, and the new 3.0 version will make it even easier and faster for researchers to use, Zilliox said.

The Gene Expression Barcode is supported by funding from the National Institutes of Health and Loyola institutional funds.

In addition to Zilliox and Irizarry, co-authors of the article describing the Barcode 3.0 version are Matthew McCall of the University of Rochester, Harris Jaffee of Johns Hopkins University, Susan Zelisko of Loyola University Chicago Stritch School of Medicine and Neeraj Sinha and Guido Hooiveld of Wageningen University.

In the paper, the authors thank Joseph Koral, Baimei Guo, Corey Sartin and Ron Price of Loyola’s Informatics and Systems Development for their computational support.

The article is titled “The Gene Expression Barcode 3.0: Improved Data Processing and Mining Tools.”

The Loyola University Chicago Health Sciences Division (HSD) advances interprofessional, multidisciplinary, and transformative education and research while promoting service to others through stewardship of scientific knowledge and preparation of tomorrow’s leaders. The HSD is located on the Health Sciences Campus in Maywood, Illinois. It includes the Marcella Niehoff School of Nursing, the Stritch School of Medicine, the biomedical research programs of the Graduate School, and several other institutes and centers encouraging new research and interprofessional education opportunities across all of Loyola University Chicago. The faculty and staff of the HSD bring a wealth of knowledge, experience, and a strong commitment to seeing that Loyola’s health sciences continue to excel and exceed the standard for academic and research excellence. For more on the HSD, visit LUC.edu/hsd.

Related articles

• Helping cancer researchers make sense of the deluge of genetic data (eurekalert.org)

 

[Press release] Health spending is more efficient for men than for women

From the 12 December McGill University press release

Health expenditures show stronger association with gains in life expectancy for males than for females throughout the industrialized countries of the world

PUBLISHED: 12 DEC 2013

Health care spending is a large – and ever increasing – portion of government budgets. Improving its efficiency has therefore become critically important. In the first-ever study to estimate health spending efficiency by gender across 27 industrialized nations, researchers discovered significant disparities within countries, with stronger gains in life expectancy for men than for women in nearly every nation.

“We were surprised to find a large gender gap in spending efficiency throughout the industrialized countries of the world. The average life expectancy of women rose from 75.5 to 79.8 between 1991 and 2007, while that of men rose from 72.5 to 77.1. The improvement for men had a much stronger association with health expenditures.  In Canada, for example, a $100 increase in health expenditures was associated with a 1.26-month increase in life expectancy for women, compared to a 2.56-month increase for men,” said Douglas Barthold, lead author and doctoral candidate in the Department of Economics at McGill University.

In the United States, a $100 increase in spending was associated with a 0.04 month increase in life expectancy for women, compared to a 0.70 month increase for men. Men fared better in the most efficient countries, like Germany, Switzerland, and Italy, as well as in the least efficient countries, like the USA, Sweden, and Poland. Canada’s overall efficiency ranked 8th out of 27 countries. The United States ranked 22nd.

“Out of the 27 industrialized nations we studied, the United States ranks 25th when it comes to reducing women’s deaths. The country’s efficiency of investments in reducing men’s deaths is only slightly better – ranking 18 out of 27,” said Dr. Jody Heymann, senior author and Dean of the UCLA Fielding School of Public Health.

The researchers examined the relationship between internationally comparable measures of health expenditures, and gender specific life expectancy, while accounting for differences in social expenditures, economic development, and health behaviors. The analysis used country-level data from 27 Organization for Economic Cooperation and Development (OECD) countries during the period 1991 to 2007.

“While there are large differences in the efficiency of health spending across countries, men have experienced greater life expectancy gains than women per health dollar spent within nearly every country,” said Barthold. The exact causes of the gender gap are unknown, thus highlighting the need for additional research on the topic. The study is coauthored by Prof. Arijit Nandi and José Mauricio Mendoza Rodríguez of McGill. The findings are published online in the First Look section of the American Journal of Public Health.

The study was part of the Healthier Societies Initiative at McGill University’s Institute for Health and Social Policy. The Healthier Societies Initiative is a research program funded by Arnold and Blema Steinberg, which informs the public on health care issues related to increasing costs, health quality and access in Canada and other leading economies. A new website, www.healthiersocieties.org, aims to improve health system understanding for the public and policy makers by offering user-friendly interactive visual tools, and allowing comparisons of policies and trends across provinces and nations.

Related articles

• U.S. Ranks Near Bottom Among Advanced Nations In Efficiency Of Health Care Spending (wonderfultips.wordpress.com)
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• Life Expectancy In US Rising Slower Than Elsewhere – OECD (247wallst.com)
• World’s Rich Countries Hit Brake for Health Spending: OECD (medindia.net)
• Nearly a third of 34 OECD states see drop in health spend (irishtimes.com)

 

[Press release] Is smoking cannabis and driving the new drinking and driving?

From the [undated December] Ontario Centre for Addiction and Mental Health

Use of prescription, over-the-counter medications also of concern in CAMH’s latest Ontario Student Drug Use and Health Survey (OSDUHS)

December 11, 2013 – Alcohol consumption and smoking among Ontario students in grades 7-12 is at an all-time low; however recreational use of over-the-counter drugs is on the rise.  Prescription drug misuse and driving after using drugs also remain elevated according to the 2013 Ontario Student Drug Use and Health Survey (OSDUHS) released today by the Centre for Addiction and Mental Health (CAMH). The survey of 10,272 students from across Ontario is Canada’s longest-running systematic study of alcohol and other drug use among youth, and one of the longest-running surveys in the world

Over-the-counter and prescription drugs

The survey shows one in eight (representing 120,000 middle and high school students in Ontario) reported taking a prescription opioid pain medication recreationally in the last year, and the majority of these students said that they got the drugs from home. About one per cent (representing 13,500 students) reported using stimulant drugs (used to treat ADHD) without a prescription. There was an increase in the number of students who reported using over-the-counter cough medication to “get high,” with over 94,000 students (about 10%) engaging in this behaviour. This was the only drug to show an increase in recent years. One in six high school students reported symptoms of a drug use problem; this represents 132,700 students in grades 9-12.

Substance use and driving

Eighteen per cent of students reported being a passenger in a car driven by someone who had been drinking alcohol. Four per cent of students with a G-class driver’s license said they had driven a vehicle within one hour of consuming two or more drinks – this is an estimated 12,700 adolescent drivers in Ontario.

Cannabis smoking and driving levels were even higher. Despite the serious impact that smoking cannabis can have on psychomotor skills and the ability to drive safely, one in ten licensed students reported driving a car within one hour of smoking cannabis. This represents 31,500 adolescent drivers in Ontario. Fourteen per cent of students reported being a passenger in a car where the driver had been using drugs.

“The number of students who report using cannabis and driving has remained the same in recent years which tells us that students do not take the potential dangers of driving while under the influence seriously,” said Dr. Robert Mann, CAMH Senior Scientist and OSDUHS Principal Investigator.  “The public health messages around the dangers of drinking and driving seem to have had an impact on our youth but the same can’t be said for cannabis use, which is worrisome.”

Drinking

Alcohol use among Ontario students reached an all-time low with 50 per cent (representing 483,900 students) reporting drinking alcohol in the past year. “Though the overall decline shows promise, we see that the kids who are drinking are doing so in dangerous ways,” added Dr. Mann. “One in five (representing 193,400 students) reports binge drinking at least once in the past month and a similar percentage report blacking out on at least one occasion when drinking alcohol in the past year. Eight per cent report being injured or injuring someone else while they had been drinking.”

New this year

New in this year’s OSDUHS are questions on the use of waterpipes and electronic cigarettes.  Almost 10 per cent (representing 88,400 students) reported smoking tobacco through a waterpipe in the past year. About 15 per cent of high school students (representing 99,800 students) reported smoking electronic cigarettes in their lifetime. For the first time the survey asked students whether they had used synthetic cannabis, commonly known by street names, “K2” or “spice.” Two per cent – representing over 17,000 students – had tried the drug.

“These new numbers give us some insight into the use of alternative and emerging drugs among young people,” said Dr. Hayley Hamilton, CAMH Scientist and Co-Investigator on the OSDUHS. “We see that while cannabis use among students is holding steady since our last survey at around one quarter of students, this new synthetic form has emerged and we will want to track its prevalence in future surveys. The same holds for smoking – while the rate of students smoking has leveled off over the past few years, we see that youth are still smoking cigarettes and tobacco, but in alternate ways.”

Regional differences

• Students in Toronto and Western Ontario reported the nonmedical use of opioid prescription pain medication at higher rates than the rest of the province (15 per cent and 13 per cent respectively)
• Students in the north were less likely to use prescription opioid pain medication (7 per cent) but reported higher rates of hazardous drinking than the provincial average (19 per cent and 16 per cent respectively)
• Students in the east reported higher rates of hazardous drinking than the provincial average (20 per cent and 16 per cent respectively)

For further information, please contact Michael Torres, Media Relations, CAMH at (416) 595-6015 or media@camh.ca

The Centre for Addiction and Mental Health (CAMH) is Canada’s largest mental health and addiction teaching hospital, and one of the world’s leading research centres in the field. CAMH combines clinical care, research, education, policy development and health promotion to help transform the lives of people affected by mental health and addiction issues.

CAMH is fully affiliated with the University of Toronto, and is a Pan American Health Organization/World Health Organization Collaborating Centre.

OSDUHS is Canada’s longest-running systematic study of alcohol and other drug use among youth, and one of the longest-running surveys in the world. During the 2012-13 school year, 10,272 students from across Ontario in grades 7 to 12 participated in the survey, administered on behalf of CAMH by the Institute for Social Research at York University.

 

Related articles

• Is driving high the new drinking and driving for Ontario teens? (globalnews.ca)
• Is smoking cannabis and driving the new drinking and driving? (medicalxpress.com)
• Prescription drug abuse among youth on the rise: Report (sunnewsnetwork.ca)
• Cough syrup, marijuana use up in Ontario high schools (cbc.ca)
• More Ontario teens drive after using marijuana than after drinking: study (globalnews.ca)
• Is driving high the new drinking and driving for Ontario teens? | Globalnews.ca (kimmiecats.wordpress.com)

 

[News article] New Strain of Bird Flu Packs a Punch Even After Becoming Drug-Resistant

English: Countries that have reported swine flu Tamiflu resistance. (Photo credit: Wikipedia)

 

From the 11 December 2013 ScienceDaily article

 

Researchers at the Icahn School of Medicine at Mount Sinai reported that a virulent new strain of influenza — the virus that causes the flu — appears to retain its ability to cause serious disease in humans even after it develops resistance to antiviral medications. The finding was included in a study that was published today in the journal Nature Communications.

It is not uncommon for influenza viruses to develop genetic mutations that make them less susceptible to anti-flu drugs. However, these mutations usually come at a cost to the virus, weakening its ability to replicate and to spread from one person to another.

Initial reports suggested that H7N9, an avian strain of influenza A that emerged in China last spring, could rapidly develop a mutation that made it resistant to treatment with the antiviral medication Tamiflu (oseltamivir). However, patients in whom drug resistance developed often had prolonged, severe infections and poor clinical outcomes. No vaccine is currently available to prevent H7N9, which infected at least 135 people and caused 44 deaths during the outbreak. In the absence of a vaccine, antiviral drugs are the only means of defense for patients who are infected with new strains of the flu.

“In this outbreak, we saw some differences in the behavior of H7N9 and other avian influenza strains that can infect humans, beginning with the rapid development of antiviral resistance in some people who were treated with oseltamivir and the persistence of high viral loads in those patients,” said lead investigator Nicole Bouvier, MD, Assistant Professor of Medicine, Infectious Diseases at the Icahn School of Medicine at Mount Sinai.

 

 

 

Read the entire article here

 

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[News article] Malnourished Children Still Have Hope Beyond First 1,000 Days

English: World map showing % of children under the age of 5 under height. (Photo credit: Wikipedia)

 

From the 11 December 2013 ScienceDaily article

 

Children who are malnourished during their first 1,000 days (conception to age 2) often experience developmental setbacks that affect them for life.

To that end, philanthropic groups have funded massive global health initiatives for impoverished infants and pregnant women around the world. While money flows justifiably to this cause, programs for children past the 1,000-day mark are seen as having little hope, and garner less support.

But new research from Brigham Young University is finding that global health workers should not give up on impoverished children after that critical time frame.

In a longitudinal study of 8,000 children from four poverty-laden countries, BYU health science assistant professor Ben Crookston and colleagues found that the developmental damage of malnutrition during the first 1,000 days is not irreversible.

“The first 1,000 days are extremely critical, but we found that the programs aimed at helping children after those first two years are still impactful,” Crookston said.

Specifically, the study found that nutritional recovery after early growth faltering might have significant benefits on schooling and cognitive achievement.

The data for the study, which comes from the international “Young Lives” project led by the University of Oxford, tracked the first eight years of life of children from Ethiopia, Peru, India and Vietnam.

Initially, Crookston and his colleagues found what they expected with the data: Children who had stunted growth (in this case, shorter than expected height at 1 year of age) ended up behind in school and scoring lower on cognitive tests at 8 years of age.

However, kids who experienced “catch-up growth,” scored relatively better on tests than those who continued to grow slowly and were in more age-appropriate classes by the age of 8.

 

Read the entire article here

 

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• Malnourished children still have hope beyond first 1,000 days (eurekalert.org)
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