Researchers create powerful new method to analyze genetic data

 June 12, 2012 in Genetics University of Texas Medical Branch at Galveston researchers have developed a powerful visual analytical approach to explore genetic data, enabling scientists to identify novel patterns of information that could be crucial to human health. The method, which combines three different "bipartite visual representations" of genetic information, is described in an article to appear in the Journal of the American Medical Informatics Association. The work won a distinguished paper award when it was presented at the AMIA Summit on Translational Bioinformatics in March 2012. In the paper, the authors use their technique to analyze data on genetic alterations in humans known as single-nucleotide polymorphisms, or SNPs. Among other things, the frequencies of particular SNPs are associated with an individual's ancestral origins; for the study, the researchers chose to examine SNP data from 60 individuals from Nigeria and 60 individuals from Utah. "We selected SNPs that we already knew differentiated between the two groups, and then showed that our method can reveal more about the data than traditional methods," said UTMB associate professor Suresh Bhavnani, lead author on the JAMIA paper and a member of UTMB's Institute for Translational Sciences. "This is a fresh way of looking at genetic data, a methodological contribution that we believe can help biologists and clinicians make better sense of a variety of biomarkers." Like many kinds of biomedical data, Bhavnani said, datasets describing individuals and their SNPs are particularly suited to visual representations that are bipartite: that is, they simultaneously present two different classes of data. In the case of the Utah-Nigeria SNP data, Bhavnani and his colleagues started with what is known as a bipartite network visualization — an intricate computer-generated arrangement of colored dots and black, gray and white lines. "In the bipartite network you see both the individuals and their genetic profiles simultaneously, and cognitively that's really important," Bhavnani said. "You can look at the individuals and know immediately which SNPs make them different from others, and conversely you can look at the SNPs to see how they are co-occurring, and with which individuals they are co-occurring. This rich representation enables you to quickly comprehend the complex bipartite relationships in the data" The bipartite network visualization of the Utah-Nigeria individual-SNP data has distinct clusters on its left and right sides that correspond to the Utah and Nigerian subjects and SNPs. It also accurately portrays a genetic phenomenon called admixture, in which an individual possesses SNPs that are characteristic of individuals from Utah as well as from Nigeria. Admixed individuals are placed on the edges of their clusters, relatively close to the center of the visualization. The identification of admixed individuals, and the implicated SNPs could help in the design of case-control studies where there is a need for the selection of homogenous sets of individual from different ancestral origins. To produce an even more detailed picture of the individual-SNP information, the researchers applied two other bipartite visualization techniques to the data: the bipartite heat map, and the bipartite Circos ideogram. In the heat map, rectangular cells laid out in a spreadsheet-like arrangement and colored white, gray, or black helped precisely define the boundaries of the clusters by clarifying individual-SNP relationships. In the Circos ideogram, individuals and SNPs placed around the perimeter of a circle and linked with curved lines, enabling the researchers to more closely examine the admixed individuals' ties to SNPs in the clusters associated with both Utah and Nigeria. "The network representation is very powerful because it gives you the overall structure of the data, but to really understand the complex relationships, you need these additional bipartite representations," Bhavnani said. The JAMIA paper, according to Bhavnani, represents a proof of concept for the researchers' novel combination of methods, which can be applied to a wide range of biomedical questions. "You can think of anything – for example you could examine cases and controls in Alzheimer's disease, or you could compare children who are prone to ear infections and those aren't prone," Bhavnani said. "Whatever your disease or trait of interest is, our approach can handle it."  

永泰度量衡: 醫療用電子秤市場!

永田牌（NAGATA） 電子體重秤受市場青睞  2012/06/11            ■張傑■ 以自創品牌「永田牌」（NAGATA）行銷市場50多年的永泰度量衡公司，近年來推出專業用電子體重秤系列，不僅通過國際品質ISO9001、醫療器材品質 ISO 13485 認證及CE安規、歐洲EC認證，且產品行銷40餘國，頗受市場青睞。  該公司總經理鄭雅容表示，由於「永田牌」（NAGATA）深耕市場多年，早期以工業用秤起家，品質精準穩定且非常耐用，深受市場喜愛，有鑑於醫療院所磅秤需求，近年來針對不同使用者開發設計包括身高體重秤、扶手秤、嬰兒秤、座椅秤、輪椅台秤等，產品種類齊全，提供買方最適合選擇。  尤其是電子座椅秤，備受矚目，該產品結合了美學、科技及精確穩定性能，採人體工學設計ABS塑鋼座椅，秤重高達200kg並提供200%安全超載保護，確保身體虛弱或行動不便的老弱婦孺的秤重安全，材質容易清潔沒有發泡PVC材質藏污納垢問題。  輔以貼心設計的推動手把及橡膠車輪，可安靜移動座椅秤到任何診間。後方煞車輪確保病人秤重平穩安全。可調整角度液晶LCD數字顯示器置於扶手側，方便醫護員記錄及病人讀取，且扶手可向上舉起至定點、腳踏板可摺合，方便病人進出。  鄭雅容指出，廠內不僅設置有安規測試儀器、磅秤溫控性能實驗室，更擁有全台灣唯一2 噸吊式法碼設備，產品遍及國內各大工廠及醫療診所、學校單位，預估2012年醫療用秤前景看好，醫療用電子秤市場約可成長20%。

Outdoor physical activity ups quality of life for teens

June 12, 2012 in Pediatrics  Over a five-year period, adolescents in the highest tertile of physical activity have a higher health-related quality of life compared with their less-active counterparts, while the converse is true for screen viewing time, according to a study published online June 11 in Pediatrics. (HealthDay) -- Over a five-year period, adolescents in the highest tertile of physical activity have a higher health-related quality of life (QoL) compared with their less-active counterparts, while the converse is true for screen viewing time, according to a study published online June 11 in Pediatrics. Bamini Gopinath, Ph.D., of the Westmead Millennium Institute in Sydney, Australia, and colleagues conducted surveys of teenagers to assess the correlation between physical activity and sedentary behaviors with health-related QoL. A total of 2,353 adolescents were initially surveyed and 1,216 were resurveyed five years later, together with an additional 475 new recruits. The Pediatric Quality of Life Inventory (PedsQL) was used to evaluate health-related QoL. After multivariable adjustment, the researchers found that adolescents in the highest versus lowest tertile of time spent in outdoor physical activity had a significantly higher total PedsQL score, while those in the highest versus the lowest tertile of television viewing had a significantly lower total PedsQL score. Teenagers who remained in the highest versus the lowest tertile of physical activity over the five-year study period had significantly higher scores in the total, physical summary, and social domains. Significantly lower scores were seen in total, physical summary, psychosocial summary, emotional, and school domains for those in the highest versus the lowest tertile of screen viewing time. "These findings reiterate the need for public health policy and interventions that promote less time in recreational screen viewing and more time in physical activity, which could have a beneficial influence not only on weight and fitness but also on general well-being during adolescence and beyond," the authors write.WHO's cancer agency: Diesel fumes cause cancer June 12, 2012 by MARIA CHENG in Cancer Diesel exhaust causes cancer, the World Health Organization's cancer agency declared Tuesday, a ruling it said could make exhaust as important a public health threat as secondhand smoke. Cancer Treatment - Multi-disciplinary and one-stop svc for the management of cancer. - www.hksh.com The risk of getting cancer from diesel fumes is small, but since so many people breathe in the fumes in some way, the science panel said raising the status of diesel exhaust to carcinogen from "probable carcinogen" was an important shift. "It's on the same order of magnitude as passive smoking," said Kurt Straif, director of the IARC department that evaluates cancer risks. "This could be another big push for countries to clean up exhaust from diesel engines." Since so many people are exposed to exhaust, Straif said there could be many cases of lung cancer connected to the contaminant. He said the fumes affected groups including pedestrians on the street, ship passengers and crew, railroad workers, truck drivers, mechanics, miners and people operating heavy machinery. The new classification followed a weeklong discussion in Lyon, France, by an expert panel organized by the International Agency for Research on Cancer. The panel's decision stands as the ruling for the IARC, the cancer arm of the World Health Organization. The last time the agency considered the status of diesel exhaust was in 1989, when it was labeled a "probable" carcinogen. Reclassifying diesel exhaust as carcinogenic puts it into the same category as other known hazards such as asbestos, alcohol and ultraviolet radiation. The U.S. government, however, still classifies diesel exhaust as a likely carcinogen. Experts said new diesel engines spew out fewer fumes but further studies are needed to assess any potential dangers. "We don't have enough evidence to say these new engines are zero risk, but they are certainly lower risk than before," said Vincent Cogliano of the U.S. Environmental Protection Agency. Experts in Lyon had analyzed published studies, evidence from animals and limited research in humans. One of the biggest studies was published in March by the U.S. National Cancer Institute. That paper analyzed 12,300 miners for several decades starting in 1947. Researchers found miners heavily exposed to diesel exhaust had a higher risk of dying from lung cancer. Lobbyists for the diesel industry argued the study wasn't credible because researchers didn't have exact data on how much exposure miners got in the early years of the study; they simply asked them to remember what their exposure was like. A person's risk for cancer depends on many variables, from genetic makeup to the amount and length of time of exposure to dangerous substances. A U.S. group that represents diesel engine makers says major technological advances in the last decade have cut emissions from trucks and buses by more than 95 percent for nitrogen oxides, particulate and sulfur emissions. Some experts said the new classification wasn't surprising. "It's pretty well known that if you get enough exposure to diesel, it's a carcinogen," said Ken Donaldson, a professor of respiratory toxicology at the University of Edinburgh who was not part of the IARC panel. He said the thousands of particles, including some harmful chemicals, in the exhaust could cause inflammation in the lungs and over time, that could lead to cancer. But Donaldson said lung cancer was caused by multiple factors and that other things like smoking were far more deadly. He said the people most at risk were those whose jobs exposed them to high levels of diesel exhaust, like truck drivers, mechanics, or miners. "For the man on the street, nothing has changed," he said. "It's a known risk but a low one for the average person, so people should go about their business as normal ... you could wear a mask if you want to, but who wants to walk around all the time with a mask on?" 

詹啟賢：生技政策待加強

 中央社  2012-06-12 11:38 AM （中央社記者林孟汝台北12日電）台灣在2002年開始推動生技業，成效卻不如亞洲鄰國，國光生技董事長詹啟賢今天直言，目前生技業碰到瓶頸，「大家走得很辛苦」，政府相關政策措施「有待加強」。 台灣玉山科技協會與國際通商法律事務所今天上午舉辦「全球專利：趨勢與差異」，國光生物科技股份有限公司董事長詹啟賢致詞後受訪時作以上表示。  詹啟賢表示，生技業屬知識密集而又創新的產業，台灣的市場太小，法制一定要與國際接軌，否則生技業「走不出去」。  同時，政府內部的專業人才不足，制定法規只參考國際規範，卻沒考慮台灣的本土特性，很容易扼殺產業。  他認為，生技產業目前碰到了研發、生產設備、法規等瓶頸，「大家走得很辛苦」，政府相關政策措施「有待加強」，政府、法界、業界應多討論，才能讓生技產業蓬勃發展。  詹啟賢直言，政府在生技產業政策上應更明確，現在、未來要做什麼？生物科技很多樣，政府應集中資源輔導，並思考如何串聯上、中、下游的環節；政策確定後就要「一以貫之」，不要搖擺不定。  另外，詹啟賢指出，國家級研發機構所研發出來的成果，應讓產業可以接得上，否則只是將研發成果賣給國外，那就只是「知識販售，而不是產業了」。

Alzheimer's risk gene and protein: ApoE4 & tau

 Alzheimer's risk gene disrupts brain function in healthy older women, but not men   June 12, 2012 in Alzheimer's disease & dementia A team led by investigators at the Stanford University School of Medicine has found that the most common genetic risk factor for Alzheimer's disease disrupts brain function in healthy older women but has little impact on brain function in healthy, older men. Women harboring the gene variant, known to be a potent risk factor for Alzheimer's disease, show brain changes characteristic of the neurodegenerative disorder that can be observed before any outward symptoms manifest. Customised Knockout Mice - Designed to your specifications. Contact us for a free consultation - www.ozgene.com/knockouts Both men and women who inherit two copies (one from each parent) of this gene variant, known as ApoE4, are at extremely high risk for Alzheimer's. But the double-barreled ApoE4 combination is uncommon, affecting only about 2 percent of the population, whereas about 15 percent of people carry a single copy of this version of the gene. The Stanford researchers demonstrated for the first time the existence of a gender distinction among outwardly healthy older people who carry the ApoE4 variant. In this group, women but not men exhibit two telltale characteristics that have been linked to Alzheimer's disease: a signature change in their brain activity, and elevated levels of a protein called tau in their cerebrospinal fluid. One implication of the study, which will be published June 13 in the Journal of Neuroscience, is that men revealed by genetic tests to carry a single copy of ApoE4 shouldn't be assumed to be at elevated risk for Alzheimer's, a syndrome afflicting about 5 million people in the United States and nearly 30 million worldwide. The new findings also may help explain why more women than men develop this disease, said Michael Greicius, MD, assistant professor of neurology and neurological sciences and medical director of the Stanford Center for Memory Disorders. Most critically, identifying the prominent interaction between ApoE4 and gender opens a host of new experimental avenues that will allow Greicius' team and the field generally to better understand how ApoE4 increases risk for Alzheimer's disease. For every three women with Alzheimer's disease, only about two men have the neurodegenerative disorder, said Greicius, the study's senior author. (The first author is Jessica Damoiseaux, PhD, a postdoctoral scholar in Greicius' laboratory. They collaborated with colleagues at the University of California-San Francisco and UCLA.) True, women live longer than men do, on average, and old age is by far the greatest risk factor for Alzheimer's, Greicius said. "But the disparity in Alzheimer's risk persists even if you correct for the difference in longevity," he said. "This disparate impact of ApoE4 status on women versus men might account for a big part of the skewed gender ratio." Besides age, another well-studied major risk factor is genetic: possession of a particular version of the gene known as ApoE. This gene is a recipe for a protein involved in transporting cholesterol into cells — an important job, as cholesterol is a crucial constituent of all cell membranes including those of nerve cells. And nerve cells are constantly responding to experience by developing or enhancing small, bulblike electrochemical contacts to other nerve cells, or diminishing or abolishing them. For all these processes, efficient cholesterol transport is critical. The ApoE protein comes in three versions, each the product of a slightly differing version of the ApoE gene: E2, E3 or E4. Most people have two copies of the E3 version of ApoE. A small percentage carries one copy of E3 and one of E2, and even fewer two copies of E2. The protein specified by the E4 gene version seems to be somewhat defective in comparison to the one encoded by either E2 or the much more common E3. Thus, while only about 10-15 percent of the population carries one copy of E4 (or, much less commonly, two), more than 50 percent of people who develop Alzheimer's are E4 carriers. But, as it turns out, the heightened risk E4 imposes may be largely restricted to women. To demonstrate this, the scientists first obtained functional MRI scans of 131 healthy people, with a median age of 70, to examine connections in the brain's memory network. They used sophisticated brain-imaging analysis to show that in older women carrying the E4 variant, this network of interconnected brain regions, which normally share a synchronized pattern of activity, exhibit a loss of that synchrony — a pattern typically seen in Alzheimer's patients. In healthy older women (but not men) with at least one E4 allele, activity in a brain area called the precuneus appeared be out of synch with other regions whose firing patterns generally are closely coordinated. The brain-imaging technique Greicius and his colleagues used is known as functional-connectivity magnetic resonance imaging, or fcMRI. Performed on "resting" subjects, who remain in the scanner awake but not focusing on any particular task, fcMRI can discern on the order of 20 different brain networks, each consisting of a set of dispersed brain regions that are physically connected by nerve tracts and whose pulses of activity are synchronized, or in phase. Greicius, Damoiseaux and their associates have previously shown that the synchronous firing pattern of one network in particular, critical to memory function and known as the "default mode network," is specifically targeted by Alzheimer's and deteriorates as the disease progresses. To independently confirm their imaging-based observations, the scientists assessed records from a large public database compiled from the Alzheimer's Disease Neuroimaging Initiative, a multi-site study of healthy aging and Alzheimer's disease. The Stanford study focused on the healthy 55- to 90-year-old volunteers who had agreed to undergo a spinal tap and have their cerebrospinal fluid analyzed. From this database the Greicius team extracted the records of 91 subjects, with an average age of 75, and divided them into four groups representing women with or without a copy of the E4 variant, and men with or without a copy. For each group, they checked recorded concentrations of a protein named tau in these subjects' cerebrospinal fluid. Elevated tau levels in cerebrospinal fluid are a key biomarker of Alzheimer's disease. The results — the CSF of women, but not men, who carried at least one E4 allele was substantially enriched in tau — confirmed the brain-imaging findings. The tau findings constitute another first. "It was only possible to see these differences in tau levels when we separated the patients by gender," Greicius said. Notably, all the men and women participating in the Journal of Neuroscience study were screened for cognitive status. Only those whose ability to think and remember appeared normal for their age were admitted. Thus, the observed changes in brain activity and CSF composition were occurring well before the onset of classic Alzheimer's symptoms such as memory loss, disorientation and dementia. It may someday be practical to substitute fcMRI, which is noninvasive, for a spinal tap as a diagnostic tool, Greicius said.