New technique uses virtual slides to view tissue in 3D

Researchers at the University of Leeds say their digital scanning system produces high-res images that can be rotated.

Today, pathologists and researchers must cut super-thin slices of tissue samples to view them on a microscope -- a labor-intensive process that renders 3D images created from hundreds of 2D sections prohibitively expensive.

Not to mention tedious to construct. Imagine if a single scene in Halo was presented as a series of 2D images one must perfectly align before getting the lay of, say, a single battleground.

A 3D rendering of cirrhotic human liver tissue infected with hepatitis C.

(Credit: University of Leeds)

Now, computer scientists and medical researchers at the University of Leeds in the United Kingdom say they've devised a novel workaround in the form of a digital scanning system that produces 3D views of tissue samples with almost no extra labor.

Read more.

Source: CNET (by Elizabeth Armstrong Moore)

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Key Patent in the United States further consolidates Visiopharm as innovation leader in Quantitative Digital Pathology

Hoersholm, Denmark - April 23, 2012 -- Visiopharm A/S, a global leader in Quantitative Digital Pathology, announced today that the United States patent and Trademark office will issue the patent “Feature-based registration of sectional images” (Application No. 12/514,918).

The patented technology, which is now protected in both Europe and in the United States, enables perfect alignment of whole slide images at any magnification, independently of tissue type and staining. This is a central capability for the next generation of quantitative bio-marker analysis, and for time- and cost efficient Whole Slide stereology

Next generation of quantitative bio-marker analysis: High-precision alignment of digital slides has direct application for automating the analysis of biomarkers. The rate limiting step for the application of Quantitative Digital pathology in research and diagnostics has been robust and reliable tumor identification and classification. With this technology, it is now possible to implement automated Virtual Double Staining. This is done by aligning two serial sections stained for different markers by immunohistochemistry; any nuclear, membrane, or cytoplasmic biomarker of interest may be stained for in each of the slides. Advanced analysis software is used for automated alignment of slides; the tumor cells are found in one slide, e.g., by means of a cytoplasmic marker, and the expression of the bio-marker of interest, such as Estrogen receptor or Ki67, is quantified in the other slide, within the cells identified with the cytoplasmic marker.

Visiopharm

With the Virtual double staining approach, we can use standardized and optimized staining protocols for both of the markers used without the difficulties that we experience with physical double staining due to, e.g., conflicting protocol requirements and overlapping chromogenes. This could be an important step towards deploying automated and standardized image analysis in clinical pathology. We are currently involved in a number of collaborative studies where this technology is applied and refined for different markers, different reagent vendors, different scanners, and different tumor types. We are basing the development of these methods on our standardized and optimized staining protocols, and expect to publish some of this work later in 2012”, stated Professor Mogens Vyberg, Director of NordiQC.

The technology is fully integrated as part of Visiopharm image analysis and stereology solutions. 

“This patent is very important to Visiopharm. We strongly believe this will become central to improve quality and automation, while at the same time reducing the costs associated with tissue based diagnostics and research. The results we are obtaining with our collaborators are very encouraging in terms of developing fully automated diagnostic tests and validating the value of this approach.”, adds Michael Grunkin, CEO of Visiopharm.

Time- and cost efficient Stereology: For the vast majority of scientific applications, highly automated Whole Slide Stereology can now replace Classical labor-intensive, manual, and high-maintenance complex hardware configurations for microscope-based stereology systems. The ability to automatically align Whole Slide Images of serial sections for an entire study is essential to automating the physical disector, and the sampling of perfectly aligned disector pairs. The technology is implemented in the Autodisector™, which is making Whole Slide Stereology a time- and cost-efficient option also in high-throughput environments.

According to Johnnie B. Andersen, Honorary Associate Professor at the Stereological Research Lab, and Stereology expert at Visiopharm, “Apart from automation, Whole Slide Stereology has demonstrated numerous significant advantages to researchers. Based on thin sections, the classical problems with lack of staining penetration in thick tissue sections are completely eliminated. Working with thin sections also eliminates practical problems that frequently originate from shrinkage and collapse of thick sections. Eliminating these critical issues will save researchers countless hours of futile lab work, when preparing tissue sections for important scientific studies. Loss of critical study data for those reasons can be very expensive. Finally, the combination of slide scanning and Whole Slide Stereology makes stereological data fully traceable, which is mission-critical in highly regulated environments”.

About Visiopharm

Over the past 10 years, Visiopharm image analysis and stereology software has become the preferred Quantitative Digital Pathology solution for leading biopharmaceutical companies, clinical researchers, and academic researchers all over the world. Visiopharm has more than 300 deployed systems worldwide and a large network of distribution and support partners, and is featured in over 400 scientific publications.

Source: Visiopharm

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Tonight at Observatory: Fire and Smoke: A Conversation on Death and Ritual Offering with Tibetan Buddhist Tsering Phunstok

Tonight at Observatory; hope to see you there!

A Discussion on Death & Impermanence Followed by a Ritual Offering with Venerable Tsering Phunstok from Dharamsala, India
Date: Monday, April 23rd
Time: 8:00
Admission: $8
(Please note: All admission fees from tonight's event will be donated to support Venerable Tsering Phunstock, his monastery, and health projects in India)
Presented by Morbid Anatomy

What can a monk tell you about the secret of life? And how does understanding impermanence and preparing for death expand upon the secret of life? Tonight’s conversation between Venerable Tsering Phunstok– a practicing Tibetan Buddhist monk residing in India– and artist Shannon Brunette will investigate Tibetan Buddhist perspectives on death and impermanence in modern life, as well as the life of the Tibetan monk as it relates to the most basic tenets of Buddhist practice and beliefs regarding death, karma and reincarnation through conversation. Questions will also be taken from the audience.

After the talk, Ven. Tsering Phunstok will conduct a traditional Tibetan fire and smoke offering. The Smoke Offering (Sang) is a ritual practice of making vast offerings to pacify obstacles and raise awareness. It is a practice of connecting with the forces of life and establishing an open relationship with existence. It is traditionally used to create harmony, resolve karmic debts, generate vitality, success, prosperity and health in our life, in our land and in our local community. In this purifying ritual edible food, poison-less trees, flowers, fruits, grains, clothes as well as other things are burned to create a smoke cloud offering. This is an offering for both the living and the dead – and for all spirits.

Buddhists believe that giving without seeking anything in return leads to greater spiritual wealth; Buddhists call this generosity and giving D?na. All admission fees from tonight’s event will be donated to support Tsering, his monastery and health projects in India. We are asking that you share your generosity further at the completion of the ritual offering.

Venerable Tsering Phuntsok
has been a practicing Buddhist monk since entering the Palyulchoekhorling Nyingmapa Buddhist monastery in Bir, India, in 1987 at age 16. For the first 17 years he studied and practiced in the Nyingmapa tradition of Tibetan Buddhism, receiving training in meditation, Buddhist scripture and philosophy, tantric ritual, lama dancing and music. He has received many tantric empowerments and sutra teachings from His Holiness the Dalai Lama and many other High Lamas, including late H.H. Penor Rinpoche. In the last several years he has worked on health related projects for his monastery as well as overseeing his nephew and nieces. He currently makes his residence in Dharamsala, India in the foothills of the Himalayas; his home is less than a minute walk from the Temple and residence of the H. H. Dalai Lama. Currently, he facilitates cultural exchange programs between the Tibetan community and US university students who come to Dharamsala to volunteer with Lha Charitable Trust, a local social work agency devoted to improving the lives of Tibetan refugees and local Indians.

Shannon Brunette
has lived and worked in Brooklyn, NY since 1998 and her beloved hometown is St. Paul/Minneapolis, MN. She received her Masters of Fine Arts at the School of Visual Arts in 2006. Currently, she is exploring a new body of work relating to cultural exchange opportunities, from Alaska video artist-in-residence focusing on climate change to a 5-week international fellowship in exchange with the traditional craftspeople of Orissa, India to volunteer work in Dharamsala with Lha Charitable Trust. Utilizing film and video as a tool to investigate the past, present and future through a poetic and complex interplay between images, to offer an opportunity for reflection and meditation. Shannon captures vignettes from mundane to beautiful and editing in a collage-like style, she explores the nature of fragmented memory, triggered by temporality and impermanence.

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Top articles in medicine in April 2012 (part 3)

Here are my suggestions for some of the top articles in medicine in April 2012:

Botulinum Toxin for Prophylaxis of Migraine and Tension Headaches: not so great - JAMA http://j.mp/IecqxB

Varicocele Is Associated with Erectile Dysfunction: 3.3% of ED patients have it vs. 1.2% of controls http://goo.gl/R8nPi

Evaluation of nail abnormalities: subungual melanomas, account for 50% of melanomas in persons with dark skin http://goo.gl/ryWVo

Sunscreens & Vitamin D: the overwhelming majority of dermatologists recommend to get your vitamin D from food, not from the sun http://goo.gl/BcFtP

Heat waves that last for more than a week can be deadly, particularly for the elderly. For every 1 degree C increase in summer temperature, death risk of the elderly with chronic conditions rises 3-4% http://goo.gl/2sYh1

Personal vs. Professional: How Doctors Manage Their Social Media Profiles - University of Chicago Medicine blog http://goo.gl/JNyu1

45% of women overestimate the effectiveness of the Pill and condoms for pregnancy prevention (study) http://goo.gl/1QcXW

FDA approves fast-acting Viagra rival: Avanafil (Stendra) starts working in 15 min, the fastest of the 4 ED drugs http://goo.gl/Joskq

More than 40% of people in the U.S. live in counties with unsafe levels of air pollutants http://goo.gl/G2bG8

20% of Americans have gone out on a date with someone they met online. New to Online Dating: Here are 11 Tips http://goo.gl/ulviK

Most Peaceful, Least Peaceful U.S. States - For 11th year in a row, Maine is the most peaceful state in America http://goo.gl/ZTr4X

Damage control on physician-rating websites - "We've all got a megaphone now," says CEO of physician-rating site http://goo.gl/ouxiI

7 steps to responding to angry patients - "RAPSAND" acronym builds "emotional muscle" in staff members http://goo.gl/IXcWP

The articles were selected from my Twitter and Google Reader streams.

Posted at Clinical Cases and Images. Stay updated and subscribe, follow us on Twitter and connect on Facebook.


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Morbid Anatomy Coming to Chicago: "A Journey into the Curious World of the Medical Museum," The Chicago Cultural Center, Thursday, May 3, 6 PM








For those of you in and about Chicago, I would love to see you this Thursday, May 3, at The Chicago Cultural Center where I will be giving a lecture entitled "A Journey into the Curious World of the Medical Museum" as part of a series of events supplementing the amazing looking  Morbid Curiosity exhibition. The images above--drawn from my exhibitions The Secret Museum and Anatomical Theatre--constitute a tiny sampling of the many images I will be showing in the presentation.

Full details follow; very much hope very much to see you there.

A Journey into the Curious World of the Medical Museum
An Illustrated Lecture by Joanna Ebenstein
_______


The Chicago Cultural Center
78 E. Washington Street Chicago, IL 60602
Thursday, May 3, 2012
6 o’clock PM

Abounding with images and insight, Ms. Ebenstein’s lecture will introduce you to the Medical Museum and its curious denizens, from the Anatomical Venus to the Slashed Beauty, the allegorical fetal skeleton tableau to the taxidermied bearded lady, the flayed horseman of the apocalypse to the three fetuses dancing a jig. Ebenstein will discuss the history of medical modeling, survey the great artists of the genre, and examine the other death-related arts and amusements which made up the cultural landscape at the time that these objects were originally created, collected, and exhibited.

Joanna Ebenstein is a New York-based artist and independent researcher. She runs the popular Morbid Anatomy Blog and the related Morbid Anatomy Library, where her privately held cabinet of curiosities and research library are made available by appointment. Her work has been shown and published internationally, and she has lectured at museums and conferences around the world. For more information, visit http://morbidanatomy.blogspot.com

You can find out more by clicking here.

Images top to bottom, as drawn from my recent photo exhibitions The Secret Museum and Anatomical Theatre:

  1. "Anatomical Venus" Wax wodel with human hair and pearls in rosewood and Venetian glass case, "La Specola" (Museo di Storia Naturale), Florence, Italy, Probably modeled by Clemente Susini (around 1790)
  2. "Slashed Beauty" Wax wodel with human hair and pearls in rosewood and Venetian glass case, "La Specola" (Museo di Storia Naturale), Florence, Italy, Probably modeled by Clemente Susini (around 1790)
  3. "Anatomical Venuses," Wax Models with human hair in rosewood and Venetian glass cases,The Josephinum, Workshop of Clemente Susini of Florence circa 1780s, Vienna, Austria
  4. The Mütter Museum : Philadelphia, Pennsylvania, Pathological model; 19th Century?
  5. Wax Model of Eye Surgery, Musée Orfila, Paris. Courtesy Université Paris Descartes
  6. Wax Anatomical Models in Rosewood and Venetian Glass Boxes, The Josephinum, Workshop of Clemente Susini of Florence circa 1780s, Vienna, Austria
  7. Wax moulages; Probably by Carl Henning (1860-1917) or Theodor Henning (1897-1946); Early 20th Century; Federal Pathologic-Anatomical Museum (Pathologisch-anatomisches Bundesmuseum): Vienna, Austria, Austria
  8. Plaster Models in Pathological Cabinet, The Museum of the Faculty of Medicine at the Jagiellonian University, Krakow
  9. Skeleton and hand models for "la médecine opératoire" Musée Orfila, Paris. Courtesy Université Paris Descartes

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This Monday at Observatory: Organization and Productivity for Creative Types: A Workshop with Oliver Burkeman of "The Guardian"

I am very excited about Monday's upcoming organization for creatives class with journalist Oliver Burkeman, of London's Guardian. There are a few slots still left... if you are interested, please RSVP to morbidanatomy [at] gmail.com. Hope to see you there!

Organizational workshop for creative types with Oliver Burkeman of The Guardian
Date: Monday, April 30th
Time: 7:30-9:30 PM
Admission: $20

*** Limited class size; Must RSVP to morbidanatomy [at] gmail.com to be added to class list
This class is part of The Morbid Anatomy Art Academy

Do you hunger to climb the corporate ladder with ruthless efficiency, leaving your rivals in the dust as you pursue your relentless quest for wealth and power? Hopefully not, but that doesn't mean you can't borrow some tactics from such people and apply them to your own ends; to that end, today's class--taught by Oliver Burkeman, compulsive to-do-list-maker and journalist for London's Guardian--will teach creatives, freelancers, and artists how to plan and manage multiple projects, better plan their time, and, in general, feel less overwhelmed by juggling a variety of projects at one time.

Burkemanhas spent much of the last few years researching and reporting on self-help culture, including the fascinating history of the "how to succeed" publishing genre, and motivational gurus from Dale Carnegie to Stephen Covey, and sifting the wheat from the chaff. (There's a lot of chaff.) Drawing on this research, this workshop will explore some fundamental principles of getting organized, managing multiple projects, overcoming procrastination, time management, and being both more productive and less stressed in the kinds of sprawling artistic/creative/freelance lives that don't get much attention in The Seven Habits of Highly Effective People. No cringe-inducing motivational speeches will be given; no Magic Systems for Instant Success will be promoted. Instead, we'll plunder from the world of the grinning gurus the bits that actually work – so that you'll leave equipped with a toolkit of immediately useable ways to do the stuff you're already doing, and the projects you're planning, with greater efficiency and ease.
The class will begin with an illustrated lecture and conclude with a workshop segment where students will be guided in an application of the principles; participants are encouraged to come to class with a project to organize.

Oliver Burkemanin a writer based in Brooklyn with an unhealthy interest in filing systems. He writes features and a weekly column on psychology for the (London) Guardian. His book The Antidote: Happiness for People Who Can't Stand Positive Thinking will be published by Faber & Faber in the fall.

More here.

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Stem cell division to evaluate clinical trials

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Calcutta News.Net Friday 27th April, 2012 (IANS)

The Directorate General of Health Services has established a stem cell division to evaluate proposals concerning stem cell research, Health and Family Welfare Minister Ghulam Nabi Azad said here Friday.

Speaking in the Lok Sabha, Azad said the stem cell division was established within the Biological Division in Central Drugs Standard Control Organisation for the internal evaluation of all proposals, including stem cell concerning with clinical trial and marketing authorisation.

"Till recently, there was no mechanism in place to take note of the cases violating these guidelines or take action against the agencies found violating these guidelines," said Azad.

The Indian Council of Medical Research and the Department of Biotechnology have jointly formulated guidelines for stem cell research and therapy to help experts and scientists working in the field conduct research responsibly and ethically sensitive manner.

However, in view of the recent development in the field, the guidelines will be revised this year.

More here:
Stem cell division to evaluate clinical trials

President's Council on Fitness, Sports & Nutrition Announces 2012 Lifetime Achievement Award Recipients

WASHINGTON, DC--(Marketwire -04/27/12)- In honor of National Physical Fitness and Sports Month, the President's Council on Fitness, Sports & Nutrition (PCFSN) will pay tribute to the 2012 Lifetime Achievement Award winners at their annual meeting on May 1, 2012.

Presented annually since 2007, the Lifetime Achievement Award is given to individuals whose careers have greatly contributed to the advancement or promotion of physical activity, fitness, sports, and nutrition-related programs nationwide. Recipients are selected by members of PCFSN based on the span and scope of an individual's career, the estimated number of lives they have touched, and the impact of their legacy.

2012 PCFSN Lifetime Achievement Award Recipients

Linn Goldberg, M.D. - Dr. Goldberg is Professor of Medicine and Chief of the Division of Health Promotion & Sports Medicine at Oregon Health & Science University. His groundbreaking programs for young athletes (ATLAS for boys and ATHENA for girls) utilize exercise and nutrition alternatives to prevent the use of alcohol, performance enhancing and illicit drugs.

Thomas McKenzie, Ph.D. - Dr. McKenzie is Emeritus professor in the San Diego State University School of Exercise and Nutritional Sciences. Dr. McKenzie has authored or co-authored over 170 publications and co-founded SPARK -- a nationally recognized research-based public health organization dedicated to improve health through physical activity. In March 2012, he was awarded a Hall of Fame Award from the National Association for Sport and Physical Education.

Jacki Sorensen - Sorensen is the originator of Aerobic Dancing -- the complete fitness program that combines health and toning benefits of jogging with the fun of dancing. Sorensen is the President and founder of Jacki's Inc.

Charles Sterling, Ed.D. - Sterling is Chairman of Youth Initiatives at The Cooper Institute and Chairman of the FITNESSGRAM Board of Trustees. Dr. Sterling is best known professionally as the founder of the widely-used FITNESSGRAM, a health-related testing and feedback system for youth.

Pat Summitt - Summitt is Hall of Fame University of Tennessee Head Women's Basketball Coach Emeritus. Summitt has won more games than anyone else in NCAA college basketball history, winning eight national titles and 1,098 games at Tennessee.

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President's Council on Fitness, Sports & Nutrition Announces 2012 Lifetime Achievement Award Recipients

New avocado rootstocks are high-performing and disease-tolerant

Public release date: 27-Apr-2012 [ | E-mail | Share ]

Contact: Iqbal Pittalwala iqbal@ucr.edu 951-827-6050 University of California - Riverside

RIVERSIDE, Calif. Avocado, a significant fruit crop grown in many tropical and subtropical parts of the world, is threatened by Phytophthora root rot (PRR), a disease that has already eliminated commercial avocado production in many areas in Latin America and crippled production in Australia and South Africa. Just in California the disease is estimated to cost avocado growers approximately $30-40 million a year in production losses.

Research on developing PRR-tolerant rootstocks to manage the disease has been a major focus of avocado research at the University of California, Riverside since the 1950s. The latest research now comes from a team that has released three rootstocks, available for commercial propagation by nurseries, that demonstrate superior tolerance to PRR.

The research, scheduled to appear soon in the journal HortScience, describes the three avocado root-rot-tolerant varieties: Zentmyer, Steddom, and Uzi.

Zentmyer is an extremely vigorous and highly durable variety that is PRR-tolerant under most conditions. But it is not recommended for locations, such as some parts of California, where salt is a problem and often does not yield consistently under non-root-rot condition. Steddom has both a high PRR-tolerance and good salt tolerance. Uzi is highly tolerant to PRR, and its yields are high and usually consistent.

The Zentmyer rootstock is named after George Zentmyer, a pioneer avocado pathologist at UC Riverside and a collector of avocado germplasm (hereditary material). Steddom is named after a former graduate student at UCR. Uzi is named after an Israeli scientist.

"With the release of these high-performing rootstocks, avocado growers worldwide will have more options in choosing PRR-tolerant rootstocks to determine which ones perform better under their own growing conditions," said Greg W. Douhan, an assistant professor of plant pathology and microbiology, who led the research.

A rootstock is the part of the plant that produces the root system. For many fruit trees it is often genetically different than the scion the top portion of the plant that is grafted to the rootstock. The scion gives rise to leaves, stems, flowers, and fruit.

Commercial avocado trees are propagated by grafting scions of desirable cultivars onto various rootstocks with the most popular avocado cultivar being the Hass avocado. While avocados can be grown from seeds, their fruit quality and yield potential can vary dramatically. Therefore, it is more advantageous for avocado growers to have both a scion and rootstock that has the most desirable characteristics, enabling the best "plants" to be grown for profitability and consumption.

Excerpt from:
New avocado rootstocks are high-performing and disease-tolerant

Drug-Resistant ‘Superbugs’ Go Undetected

Nature | Health

Poor training in use of tests is part of the issue. Microbiology companies could help by revealing the exact composition of their test media, which might help improve understanding of tests' limitations

April 27, 2012

By Daniel Cressey of Nature magazine

Efforts to detect and halt the global spread of drug-resistant bacteria are being hindered by a poor understanding of the limitations of crucial laboratory tests. Because infected patients need to be isolated quickly to avoid spreading infections, the failure to identify antibiotic-resistant pathogens is increasing the risk of untreatable outbreaks, microbiologists argue.

This month at the European Congress of Clinical Microbiology and Infectious Diseases in London, Herman Goossens, director of the Laboratory of Medical Microbiology at the Vaccine and Infectious Disease Institute of the University of Antwerp in Belgium, presented data about one type of commercial kit often used to identify particular drug-resistant pathogens.

The tests contain mixtures of chemicals that encourage some bacteria to grow and discourage others. Samples from stools or rectal swabs are streaked across the growth medium on a plate and then left overnight. The next day, different-colored growths indicate the presence of different species of resistant bacteria.

Under the radar

One type of bacterium that is causing concern carries genetic mutations that cause it to produce carbapenemase enzymes, which confer resistance to carbapenem antibiotics. Health agencies around the world have reported a surge in infections involving carbapenem-resistant bacteria over the past decade. Another worrying mutation produces extended-spectrum -lactamases (ESBLs), which are resistant to cephalosporin drugs.

An example of the difficulties with identifying these bacteria, Goossens says, is a common test for carbapenem-resistant bacteria using plates made by CHROMagar, a microbiology company based in Paris. The plates detect only high levels of carbapenem resistance, meaning that laboratories may fail to detect bacteria with low but clinically important levels of resistance, he says.

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Drug-Resistant 'Superbugs' Go Undetected

lobSTR algorithm rolls DNA fingerprinting into 21st century

Public release date: 27-Apr-2012 [ | E-mail | Share ]

Contact: Nicole Giese Rura rura@wi.mit.edu 617-258-6851 Whitehead Institute for Biomedical Research

CAMBRIDGE, Mass. (April 27, 2012) As any crime show buff can tell you, DNA evidence identifies a victim's remains, fingers the guilty, and sets the innocent free. But in reality, the processing of forensic DNA evidence takes much longer than a 60-minute primetime slot.

To create a victim or perpetrator's DNA profile, the U.S. Federal Bureau of Investigation (FBI) scans a DNA sample for at least 13 short tandem repeats (STRs). STRs are collections of repeated two to six nucleotide-long sequences, such as CTGCTGCTG, which are scattered around the genome. Because the number of repeats in STRs can mutate quickly, each person's set of these genetic markers is different from every other person's, making STRs ideal for creating a unique DNA fingerprint.

The FBI first introduced their STR identification system in 1998, when STRs were the darling of the genetics community. However, other identifying genomic markers were soon discovered and gained in popularity. Around the same time, high throughput sequencing allowed researchers to process vast amounts of DNA, but using methods that were ineffectual in repeated DNA, including STRs. STRs were mostly forgotten by geneticists, and innovations to study them stalled.

Now Whitehead Institute researchers have pulled STR identification into the 21st Century by creating lobSTR, a three-step system that accurately and simultaneously profiles more than100,000 STRs from a human genome sequence in one daya feat that previous systems could never complete. The lobSTR algorithm is described in the May issue of Genome Research.

"lobSTR found that in one human genome, 55% of the STRs are polymorphic, they showed some difference, which is very surprising," says Whitehead Fellow Yaniv Erlich. "Usually DNA's polymorphism rate is very low because most DNA is identical between two people. With this tool, we provide access to tens of thousands of quickly changing markers that you couldn't get before, and those can be used in medical genetics, population genetics, and forensics."

To create a DNA fingerprint, lobSTR first scans an entire genome to identify all STRs and what nucleotide pattern is repeated within those stretches of DNA. Then, lobSTR notes the non-repeating sequences flanking either end of the STRs. These sequences anchor each STR's location within the genome and determine the number of repeats at the STRs. Finally, lobSTR removes any "noise" to produce an accurate description of the STRs' configuration.

According to Melissa Gymrek, who is the first author of the Genome Research paper, lobSTR's ability to accurately and efficiently describe thousands of STRs in one genome has opened up many new research opportunities.

"The first and simple next step is to characterize the amount of STR variation in individuals and populations," says Gymrek, who was an undergraduate researcher in Erlich's lab when she worked on lobSTR. "This will provide knowledge of the normal range of STR alleles at each locus, which will be useful in medical genetics studies that would like to determine if a given allele is normal or likely to be pathogenic. Another direction we are looking at is to look at STRs in case/control studies to look for STRs associated with disease. The list goes on, but these are some of the first questions we're looking to tackle."

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lobSTR algorithm rolls DNA fingerprinting into 21st century

Posted in DNA

DNA could exonerate man jailed for 20 years in Palisade murder

Robert Dewey (Colorado Dept. of Corrections)

Robert Dewey has spent nearly 20 years behind bars for the 1994 rape and strangling death of a Palisade woman, and he was expected to die in prison.

But on Monday he could walk free based on new DNA evidence.

Attorneys involved in Dewey's case are reluctant to discuss details ahead of the Monday motions hearing, but his case has been taken up by a team at the state Attorney General's Office that reviews old convictions where DNA is involved.

"We were approached by the defense attorney in this case. It's one that we forwarded to our Justice Review Project for DNA testing," said AG spokesman Michael Saccone. "We look to see whether someone is wrongfully incarcerated."

If Dewey, 51, is exonerated, it will be the first for the Justice Review Project since it was created in 2009.

Mesa County District Attorney Pete Hautzinger could not be reached immediately for comment.

Nearly two decades ago, Dewey was serving a prison sentence for being a felon in possession of a firearm and was scheduled for release in 1995. But before he got out, he was arrested for the June 3, 1994, strangling death of 19-year-old Jacie Taylor.

Prosecutors at the time said he'd been running with a crowd of meth users and had prior convictions for armed robbery and unlawful use of a weapon. Taylor had fallen in with the same crowd.

In the murder case, police found her blood on one of Dewey's work shirts. But his defense attorney at the time argued that semen and other material collected from Taylor's body and apartment did not match Dewey's.

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DNA could exonerate man jailed for 20 years in Palisade murder

Posted in DNA

Attending the Experimental Biology meeting helped me clarify my STEM career path

The other day, I was walking to my car, headed to Animal Care to check on my animals. As I was strolling down the sidewalk I noticed a young lady, African-American. We gave each a cordial nod and said hello as we passed by. Then I heard I heard her call out and I turned around. She the told me how much she enjoyed my lecture in her Evolutionary Biology class, that I had delivered more than two months ago. She said she really enjoyed it and I thanked her. Its always good to hear positive things. (And I find I need more positive feedback lately. It felt good to know I wasnt invisible). She then said that I was the first Black teacher [college] she had. Although I was only a guest lecturer, the experience made her wonder (momentarily) if she should have attended a HBCU Historically Black College or University because felt she like she was missing something, exposure to African-American faculty.

It didnt occur to me that I, a mere post-doc at this great big institution, would be the first Black lecturer that she (or any) student in that senior-level biology class would have had. Surely, all of them no matter their ethnic background- have seen a Black person on that side of the podium before. Right? I guess not.

Her words were poignant; they also struck a chord. I didnt attend a HBCU either; so, I completely relate to her experiences. I had one, 1, African-American instructor in college, my freshman English composition teacher. I attended Tennessee Technological University, a medium-sized university, with about 10,000 students in Cookeville the heart of middle Tennessee in the Cumberland Plateau. There were 3 African-American professors at my college, two in the history department, one in the business school, I think, plus 3 university administrators. It wasnt until I started my doctoral studies at the University of Missouri St. Louis that I had my very first (and last) Black Science Professor Dr. Godfrey Bourne, of Afro-Caribbean heritage. At majority institutions, Black professors are rare and even more rare in science and engineering departments.

Although, this was just one student, her personal account is telling the Higher Education system something very important: Students are crying out for a more representative faculty.

Check out what these Black and Latino Engineering undergrads from Bucknell University say in this CNN Money Report Missing: Minority scientists and engineers

I felt exactly like these students when I was in their shoes. To see someone who looks/sounds like me. Who comes from familiar places and spaces. Who can show me that this path is navigable. But for whatever reason I completely forgot those feelings once I crossed the stage. That was until yesterday.

Perhaps her words were right on time. I was/am still recovering from the Experimental Biology 2012 meeting in San Diego. That meeting was eye opening. I would say hello, introduce myself, tell people what I work on, and without fail they would ask, Whats next? Such a strange question to me. I just started this project, I thought. For a long time I would reflexively respond a tenure-track position. But the truth is, I havent been very excited about becoming a college professor lately, especially if it meant working at a major or medium-sized research institution. Ive been flirting with working at smaller institutions teaching colleges or masters-granting universities. Better, but eh. Even those seemed like incomplete fits. Then as I was talking, interacting and networking with scientists and students outside of my field, things started coming into view.

I love research, being in the field, getting dirty. I love outreach, sharing it with non-scientists online and in real life. I love talking about science. I love introducing people to new or over-looked opportunities in STEM. I enjoy teaching and working with students from K-12 to graduate level. But where does someone like me go and earn a decent living? K-12 schools wouldnt allow me to do only do bench research with students. Plus, Ive been uncertain how I would fit in at the university level. I cant tell you how many times Ive been chided for my enthusiasm, bubbly personality, or interests in reaching under-served audiences. Which confuses me because isnt improved teaching and broadening participation a goal? Its as if the very things that bring me joy (and for which institutions are quick to take credit for my hard work when its time to be accountable), AND I also happen to be very good at are also looked down upon by so many. Im good at all of those things; however, my greatest strength is my ability to see connections across the aisles.

Ive been introducing people science for a while now. Ive converted people who once thought science was boring and irrelevant. Im like a wingman. Being a member of scientific communities and many affinity groups means I am able to see and create bridging opportunities between different, often disparate communities. As a result I am able to engage new audiences in discussions about science and diversity. I see collaborative opportunities that no one else sees or even dares to imagine.

I have been trying to inspire a culture change in the sciences and research disciplines, but at the local level. Perhaps, I would do better at the funding agency or professional science society level. Funding agencies (like NSF, NIH) and professional science societies (like AAAS) have incomparable influence on individuals and institutions as it pertains to setting professional ethos and the inclusion of individuals from under-represented groups in the sciences at every stage of the pipeline. Such organizations seem to be an ideal place for someone interested in fostering deep relationships between under-served audiences and STEM. These organizations seem to thrive on new ideas and creative energy.

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Attending the Experimental Biology meeting helped me clarify my STEM career path

VistaGen Secures Key U.S. Patent Covering Stem Cell Technology Methods Used to Test Drug Candidates for Liver Toxicity

SOUTH SAN FRANCISCO, CA--(Marketwire -04/25/12)- VistaGen Therapeutics, Inc. (VSTA.OB - News) (VSTA.OB - News), a biotechnology company applying stem cell technology for drug rescue, has secured a new United States patent covering the company's proprietary methods used to measure and type the toxic effects produced by drug compounds in liver stem cells.

Test methods included in this new patent, (U.S. Patent 11/445,733), titled "Toxicity Typing Using Liver Stem Cells," cover all mammalian liver stem cells -- rat and mouse cells, for example, in addition to human cells. Liver stem cells used in drug testing can be derived from in vivo tissue or produced from embryonic stem cells (ES) or induced pluripotent stem cells (iPS).

H. Ralph Snodgrass, Ph.D., VistaGen's President and Chief Scientific Officer, said, "This patent covers the monitoring of changes in gene expression as an assay for predicting drug toxicities. It is well known that drugs activate and suppress specific genes, and that the changes in gene expression reflect the mechanism of drug toxicities. The specific sets of genes that are affected become a profile of that drug."

VistaGen's new patent also covers techniques used to develop a database of gene expression profiles of drugs that have the same type of liver toxicity. Using sophisticated "pattern matching" database tools, drug developers can analyze these related profiles to determine "gene expression signatures" that are common and predictive of drugs that produce specific types of toxicity.

"Without this database capability, a drug's single gene expression profile could not be interpreted," Dr. Snodgrass added. "The ability to use liver stem cells to differentiate drug-dependent gene expression profiles, and to compare those profiles of drugs known to induce toxic liver effects, provides a powerful tool for predicting liver toxicity of new drug candidates, including drug rescue variants."

Shawn K. Singh, VistaGen's Chief Executive Officer, stated, "Strong and enforceable intellectual property rights are critical components of our plan to optimize the commercial potential of our Human Clinical Trials in a Test Tube platform. This new liver toxicity typing patent further solidifies our growing IP portfolio, and supports the continuing development of LiverSafe 3D, our human liver cell-based bioassay system, which complements our CardioSafe 3D human heart cell-based bioassay system for heart toxicity."

About VistaGen Therapeutics

VistaGen is a biotechnology company applying human pluripotent stem cell technology for drug rescue and cell therapy. VistaGen's drug rescue activities combine its human pluripotent stem cell technology platform, Human Clinical Trials in a Test Tube, with modern medicinal chemistry to generate new chemical variants (Drug Rescue Variants) of once-promising small-molecule drug candidates. These are drug candidates discontinued due to heart toxicity after substantial development by pharmaceutical companies, the U.S. National Institutes of Health (NIH) or university laboratories. VistaGen uses its pluripotent stem cell technology to generate early indications, or predictions, of how humans will ultimately respond to new drug candidates before they are ever tested in humans, bringing human biology to the front end of the drug development process.

Additionally, VistaGen's small molecule drug candidate, AV-101, is in Phase 1b development for treatment of neuropathic pain. Neuropathic pain, a serious and chronic condition causing pain after an injury or disease of the peripheral or central nervous system, affects approximately 1.8 million people in the U.S. alone. VistaGen is also exploring opportunities to leverage its current Phase 1 clinical program to enable additional Phase 2 clinical studies of AV-101 for epilepsy, Parkinson's disease and depression. To date, VistaGen has been awarded over $8.5 million from the NIH for development of AV-101.

Visit VistaGen at http://www.VistaGen.com, follow VistaGen at http://www.twitter.com/VistaGen or view VistaGen's Facebook page at http://www.facebook.com/VistaGen

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VistaGen Secures Key U.S. Patent Covering Stem Cell Technology Methods Used to Test Drug Candidates for Liver Toxicity

Building muscle without heavy weights

Public release date: 26-Apr-2012 [ | E-mail | Share ]

Contact: Nicholas A. Burd nick.burd@maastrichtuniversity.nl Canadian Science Publishing (NRC Research Press)

Ottawa, Ontario (April 23, 2012) Weight training at a lower intensity but with more repetitions may be as effective for building muscle as lifting heavy weights says a new opinion piece in Applied Physiology, Nutrition, and Metabolism.

"The perspective provided in this review highlights that other resistance protocols, beyond the often discussed high-intensity training, can be effective in stimulating a muscle building response that may translate into bigger muscles after resistance training," says lead author Nicholas Burd. "These findings have important implications from a public health standpoint because skeletal muscle mass is a large contributor to daily energy expenditure and it assists in weight management. Additionally, skeletal muscle mass, because of its overall size, is the primary site of blood sugar disposal and thus will likely play a role in reducing the risk for development of type II diabetes."

The authors from McMaster University conducted a series of experiments that manipulated various resistance exercise variables (e.g., intensity, volume, and muscle time under tension). They found that high-intensity muscle contractions derived from lifting heavy loads were not the only drivers of exercise-induced muscle development. In resistance-trained young men a lower workout intensity and a higher volume of repetitions of resistance exercise, performed until failure, was equally effective in stimulating muscle proteins as a heavy workout intensity at lower repetition rates. An additional benefit of the low-intensity workout is that the higher repetitions required to achieve fatigue will also be beneficial for sustaining the muscle building response for days.

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The perspective "Bigger weights may not beget bigger muscles: evidence from acute muscle protein synthetic responses after resistance exercise" appears in the June issue of Applied Physiology, Nutrition, and Metabolism.

For more information contact:

Corresponding author: Nicholas A. Burd (e-mail: nick.burd@maastrichtuniversity.nl).

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Building muscle without heavy weights

MDxHealth and PLUS Diagnostics Enter U.S. Marketing Agreement for ConfirmMDxâ„¢ for Prostate Cancer

IRVINE, Calif., & LIEGE, Belgium--(BUSINESS WIRE)--

Regulatory News:

MDxHealth SA (NYSE Euronext: MDXH), a leading molecular diagnostic company that develops and commercializes epigenetic tests to support cancer treatment, and PLUS Diagnostics today announced that they have entered into an agreement to co-promote MDxHealths ConfirmMDx for Prostate Cancer test in the United States.

PLUS Diagnostics, a leading U.S. anatomic pathology company that offers a full range of multi-specialty services, will build awareness of ConfirmMDx for Prostate Cancer, through its national network of urologists. ConfirmMDx for Prostate Cancer is a laboratory-developed test (LDT), performed at MDxHealths Irvine, California laboratory that assists urologists with identifying men who may safely forego unnecessary repeat biopsies.

We are excited to combine forces with one of the leading anatomic pathology providers in the U.S. PLUS Diagnostics is highly regarded for its extensive pathology expertise and premier testing services, and has built strong relationships with urologists. The national reach afforded by PLUS Diagnostics provides a direct channel into the urology community and will aid in meeting the growing demand for our test, said Dr. Jan Groen, CEO of MDxHealth.

Our company is dedicated to providing our customers with the highest quality tests and services that meet their unique needs for diagnosing and treating their patients. We are impressed with the support of key opinion leaders from prominent academic institutions and the body of published scientific evidence that MDxHealth has generated. We believe this test will improve the standard of care for patients with negative prostate biopsies, said David Pauluzzi, CEO of PLUS Diagnostics.

About ConfirmMDx for Prostate Cancer

Over 650,000 American men receive a negative prostate biopsy result each year; however approximately 25-35% of these results are false negative. Under the current standard of care, prostate biopsy procedures collect 10-12 needle biopsy cores on average, effectively sampling less than 1% of a mans prostate. This approach leaves men at risk of occult cancer, leading to a high rate of repeat biopsies, often on cancer-free men. There is an unmet medical need for a clinically effective diagnostic test to address this dilemma. ConfirmMDx for Prostate Cancer is an epigenetic assay to help distinguish patients who have a true-negative biopsy from those at risk for occult cancer. The test helps urologists rule out prostate cancer-free men from undergoing unnecessary repeat biopsies and, helps rule in high risk patients who may require repeat biopsies and potential treatment. The test is able to detect a proven epigenetic field effect or halo associated with the cancerization process at the DNA level in cells adjacent to cancer foci. This molecular halo around a cancer lesion can be present despite having a normal appearance under the microscope. Thus ConfirmMDx for Prostate Cancer aids urologists in identifying men who may safely forego unnecessary repeat biopsies.

The company expects to launch ConfirmMDx for Prostate Cancer in Q2 2012. MDxHealth and PLUS Diagnostics will begin co-promoting the test immediately.

Please visit the companies at the American Urology Association Annual Meeting, May 19-23 2012 in Atlanta, GA, booths #3831 and #3923.

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MDxHealth and PLUS Diagnostics Enter U.S. Marketing Agreement for ConfirmMDxâ„¢ for Prostate Cancer

Rick Ware Racing Announces the Addition of Adia Nutrition to the 2012 RWR North American Professional Motorsports Tour …

THOMASVILLE, NC and NEWPORT BEACH, CA--(Marketwire -04/26/12)- Rick Ware Racing (RWR), a leading professional motorsports organization, and Adia Nutrition (ADIA.PK - News) ("Adia") today announced a partnership to expand the reach of Adia Nutrition across North America through the RWR POYNT Racing Tour. The partnership kicks off this weekend for the NASCAR Nationwide Series race in Richmond, Virginia with 2011 "Rookie of the Year" winner Timmy Hill in the #41 POYNT.com Ford. Additionally, Adia will be included in the RWR North American Tour for the remainder of the events leading into the first quarter of 2013.

Wen Peng, the CEO of Adia, added, "We are excited to bring the power of probiotics to a much larger audience. We think this partnership will expose us to an entirely new audience and we're excited to be affiliated with Rick Ware Racing."

The tour encompasses over 115 professional motorsports events across North America and includes the NASCAR Sprint Cup Series, NASCAR Nationwide Series, NASCAR Camping World Truck Series, NASCAR Whelan Modified Series, the Grand-Am Rolex Series, the AMA Arena-cross Series and the Summer X Games.

Team owner Rick Ware stated, "We are delighted to be associated with Adia Nutrition. We believe their 'On-the-Go' drink powders and chews are the next step in performance nutrition and Adia as a brand associated with the RWR POYNT tour has the potential to stand-out in this segment."

Drivers and personalities that have been announced for the tour include NASCAR drivers Jeffrey Earnhardt and Chris Cook in the Grand-Am Rolex Series, 2011 NASCAR Nationwide Series "Rookie of the Year" champion Timmy Hill, California based NASCAR and Rolex Series road course driver Kevin O'Connell, NASCAR driver and Hollywood director and stuntman Stanton Barrett, 2009 Trans AM champion Tomy Drissi, eight (8) time NASCAR Whelan Modified champion Tim Brown, 2009 AMA ArenaCross champion Jeff Gibson, and Summer X Games gold medal winner Vicki Golden.

Kevin O'Connell, co-founder of the "Tour" and CEO of General Pacific Partners, stated, "Adia is a fresh, dynamic brand with a management team lead by Ms. Wen Peng. We are confident the introduction of Adia Nutrition to the racing fans of North America will prove to be yet another example of the unusual loyalty and expanding diversity of a unique base of consumers that exists in the racing world."

About Rick Ware Racing: Rick Ware Racing (RWR) has competed in every NASCAR sanctioned series, ARCA Series, the WMA Motocross Series, AMA Arenacross, Motocross and Supercross Series, Summer X-Games and Rolex Grand-Am Series.

About General Pacific Partners: General Pacific Partners, LLC (GPP) is a southern California based public venture capital group that provides advisory work, direct investment and marketing and branding strategies in early and developmental stage private and public companies.

About POYNT CorporationPOYNT Corp. (about.poynt.com) is a global leader in the mobile local advertising space. Its Location Based Search (LBS) and advertising platform, POYNT (www.poynt.com), enhances a user's ability to connect with the people, businesses and events most important to them. POYNT is available on Android, iPhone, Windows Phone and Nokia devices, along with BlackBerry smartphones and BlackBerry PlayBook Tablets in Canada, the United States, Europe, India and Australia. POYNT Corp. entered the mobile publishing space with the acquisition of an advertising publishing platform in January 2011. Whether through the POYNT Local Search Platform or the Ad Publishing Platform, POYNT Corp. simplifies connecting consumers with businesses, retailers and events. Headquartered in Calgary, AB, Canada, POYNT Corp. trades on the TSX Venture Exchange under the symbol PYN and in the United States on the OTCQX under the symbol PNYTF.

About Adia Nutrition: Adia Nutrition, Inc. (ADIA.PK - News) is a company specializing in probiotics. Currently, Adia offers four flavors of probiotic drink mixes and two flavors of probiotic chews. Adia sells their products across the country in independent pharmacies, health food stores, fitness centers and grocery store chains. For more information, visit our website at http://www.adianutrition.com

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Rick Ware Racing Announces the Addition of Adia Nutrition to the 2012 RWR North American Professional Motorsports Tour ...

New Products from Abbott's EAS® Sports Nutrition Brand Help Athletes Improve Post-Workout Recovery and Meet Fitness …

ABBOTT PARK, Ill., April 25, 2012 /PRNewswire/ --(ABT) When it comes to maximizing recovery and accomplishing fitness goals, exercise enthusiasts identify building muscle or getting lean and toned as main objectives. However, reaching these goals depends as much on proper nutrition habits as on the rigor of training regimens.

Abbott's EAS Sports Nutrition has developed a new science-based line of performance nutrition products that include: EAS Lean 15 powder and bars, EAS Recovery powder, EAS Myoplex 30 bars and EAS Myoplex Original shakes featuring Revigor.

Through ingredients such as Revigor and specially formulated carbohydrate and protein blends, EAS products rapidly deliver needed nutrients to fatigued muscles and help athletes recover and build muscle. Revigor, a source of HMB (beta-hydroxy-beta-methylbutyrate), is an amino-acid metabolite that can help protect and promote muscle tissue growth(2). The line also offers new protein powders to give fitness-focused individuals an easy way to get needed protein at 100 calories per serving.

All EAS products are tested for banned substances and certified by independent laboratories and marked with a "Tested and True" seal.

Fueling Athletic Performance

Athletic pursuits demand nutritional needs beyond a normal diet. Active individuals require specific amounts of carbohydrates, proteins and fats to fuel muscles, build strength and recover after physical activity. Timing of these essential nutrients is critical to future performance.

"Nutrition to enhance athletic performance involves not only what to eat, but when to eat it," said Keith Wheeler, PhD, FACSM, global director, Performance Nutrition, Research and Development at Abbott. "When athletes don't consume important nutrients in the right ratios at the right time, they will deplete their bodies and compromise their ability to perform. The new EAS recovery products are scientifically formulated to rapidly replenish muscles after a workout with needed nutrients."

The benefits of well-timed proper nutrition can include reduced muscle fatigue and exercise-induced muscle damage as well as accelerated repair.

"The key nutritional strategy after training is getting a combination of carbohydrate and protein within the first 30 minutes after a workout," said Amanda Carlson-Phillips, MS, RD, CSSD, vice president of Nutrition and Research, Athletes' Performance and EAS Academy board advisor. "On average, men should aim for 15-30 grams of protein and women should get 10-20 grams of protein in combination with carbohydrate in a 2:1 or 3:1 carbohydrate to protein ratio. The protein is needed to stimulate protein synthesis and provide the building blocks for muscle and the carbohydrates are needed to help refuel the body."

New EAS Products:

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New Products from Abbott's EAS® Sports Nutrition Brand Help Athletes Improve Post-Workout Recovery and Meet Fitness ...

Mead Johnson Nutrition Beats Analyst Estimates on EPS

By Seth Jayson | More Articles April 26, 2012 |

Mead Johnson Nutrition (NYSE: MJN) reported earnings on April 26. Here are the numbers you need to know.

The 10-second takeawayFor the quarter ended March 31 (Q1), Mead Johnson Nutrition met expectations on revenues and beat expectations on earnings per share.

Compared to the prior-year quarter, revenue expanded and GAAP earnings per share grew.

Gross margins dropped, operating margins dropped, and net margins improved.

Revenue detailsMead Johnson Nutrition reported revenue of $986.6 million. The 10 analysts polled by S&P Capital IQ expected to see a top line of $978.2 million on the same basis. GAAP reported sales were 9.6% higher than the prior-year quarter's $899.8 million.

Source: S&P Capital IQ. Quarterly periods. Dollar amounts in millions. Non-GAAP figures may vary to maintain comparability with estimates.

EPS detailsNon-GAAP EPS came in at $0.82. The 13 earnings estimates compiled by S&P Capital IQ forecast $0.78 per share on the same basis. GAAP EPS of $0.80 for Q1 were 13% higher than the prior-year quarter's $0.71 per share.

Source: S&P Capital IQ. Quarterly periods. Non-GAAP figures may vary to maintain comparability with estimates.

Margin detailsFor the quarter, gross margin was 62.1%, 230 basis points worse than the prior-year quarter. Operating margin was 25.2%, 270 basis points worse than the prior-year quarter. Net margin was 16.6%, 40 basis points better than the prior-year quarter.

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Mead Johnson Nutrition Beats Analyst Estimates on EPS