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From beaker to bits: Collaboration creates computational model of human tissuePublic release date: 2-Apr-2012 [ | E-mail | Share ]
Contact: Gabrielle DeMarco demarg@rpi.edu 518-276-6542 Rensselaer Polytechnic Institute
New 'cell graphs' developed at Rensselaer Polytechnic Institute link tissue structure to its corresponding biological function
Troy, N.Y. Computer scientists and biologists in the Data Science Research Center at Rensselaer Polytechnic Institute have developed a rare collaboration between the two very different fields to pick apart a fundamental roadblock to progress in modern medicine. Their unique partnership has uncovered a new computational model called "cell graphs" that links the structure of human tissue to its corresponding biological function. The tool is a promising step in the effort to bring the power of computational science together with traditional biology to the fight against human diseases such as cancer.
The discovery follows a more than six-year collaboration, breaking ground in both fields. The work will serve as a new method to understand and predict relationships between the cells and tissues in the human body, which is essential to detect, diagnose, and treat human disease. It also serves as an important reminder of the power of collaboration in the scientific process.
The new research led by Professor of Biology George Plopper and Professor of Computer Science Bulent Yener is published in the March 30, 2012, edition of the journal PLoS One in a paper titled, "Coupled Analysis of in Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship." They were joined in the research by Evrim Acar a graduate student at Rensselaer in Yener's lab currently at the University of Copenhagen. The research is funded by the National Institutes of Health and the Villum Foundation.
The new, purely computational tool models the relationship between the structure and function of different tissues in body. As an example of this process, the new paper analyzes the structure and function of healthy and cancerous brain, breast, and bone tissues. The model can be used to determine computationally whether a tissue sample is cancerous or not, rather than relying on the human eye as is currently done by pathologists around the world each day. The objective technique can be used to eliminate differences of opinion between doctors and as a training tool for new cancer pathologists, according to Yener and Plopper. The tool also helps fill an important gap in biological knowledge, they said.
Every budding biologist is taught a central concept: there is a relationship between biological structures like cells or organs and their functions. This structure/function relationship is well understood at some levels. For example, we know what individual brain cells are structurally comprised of and the functions they perform in the body. It is when you delve deeper into interactions between millions of different types of cells and dozens of specialized organs that our limited understanding of human biology is quickly brought to light.
"Previous biological analysis techniques simply ground up tissues and looked at things like gene expression. This is like looking at poll numbers after a vote. You don't know who voted for what or why, you only know who won the race," Plopper said. "With this new analysis we can explain how individual cells function in the system while still focusing on the entire system as a whole."
The ability to understand the complex relationship between cells in our tissues required an entirely new way to do biology, according to the scientists.
"We needed to take biology out of the Petri dish and microscope slide and lift it into a different space. We needed to integrate the interactions in the body on multiple scales," Yener said.
Yener and his computational counterparts did this by building a computational model using graph theory that linked several different biological data sets from Plopper and his biology counterparts. The biological data came from tissue samples physically removed from the human body and samples grown outside the body in the lab.
In the diagnosis of cancer, a pathologist removes a section of suspicious-looking tissue from a patient. The tissue sample is then sliced and stained for easier viewing and looked at through the age-old tool of biology, the microscope. This process is called histology. The pathologist is literally looking for cancer. When looking through the microscope, trained pathologists simply know cancer when they see it. They don't know how it came to be or where it is going, just that it is present in the tissue in front of them. In other words, they can see the structure of the cancer, but not know its function. In order to truly know the roots of diseases like cancer, scientists need to know how it arose in the tissue in the first place.
One way of seeing how cancer functions is to literally grow and watch cancerous tissue form in the lab. This process of growing cells in something like a test tube outside of the body is called cell culturing. It is a way to simplify and control the elaborate symphony of what is going on within the body, outside the body. But, a cell culture is only one small part of the symphony of our bodies. It can never tell the whole story.
Therefore, tools like histology and cell culture needed to be combined to get a fuller picture of the transition from healthy cells to full-fledged cancer. But no laboratory experiments exist to make the connection between the two. This is where computation can play a significant role, according to Plopper and Yener. Through computation Plopper and Yener were able to, for the first time ever, quantitatively compare histology samples with lab cultures.
The new computational method uses graph theory. Instead of looking at tissue as a series of cells, graph theory simplifies the system into a series of dots and lines with the dots being the cells and the lines their interactions. The program links and compares the accuracy of data from actual human tissue samples from histology with those grown in the controlled laboratory setting. The result is a new tool that can detect and distinguish cancer and quantify the actual differences between different tissues analyzed.
"Currently, biology is a lot of trial and error," Yener said. "With a mathematical model of something like cancerous tissue, you can computationally represent the relationships between cells. That model can then be predictive and eliminate time and energy lost in trial and error."
To non-scientists, interactions between two different types of scientists seems like the norm. But, there are no two groups of scientists more disparate than biologists and computer scientists, according to both Yener and Plopper. For biologists, discovery is in the details. How many genes are being expressed in a tissue? What protein is involved in the disease? Computer scientists seek to represent the larger relationship between different data points. What those data points actually represent is largely irrelevant.
"We have a very unique relationship," Plopper said. "I think it will take my whole career to get people in both fields who currently don't talk to even accept the fact that they should. But if all scientists understand how to generate and use numeric data of some sort, that would really lower the barriers between fields."
Plopper has even created a class, "Cell-Extracellular Matrix Interactions," to develop a new type of data-savvy biologist.
"These discoveries have to come from both fields," Yener said. "Scientists need to trust computational methodologies and that trust will only come when we go back to the basic biology that can be fed into the modeling and tested."
###
[ | E-mail | Share ]
?
AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.
From beaker to bits: Collaboration creates computational model of human tissuePublic release date: 2-Apr-2012 [ | E-mail | Share ]
Contact: Gabrielle DeMarco demarg@rpi.edu 518-276-6542 Rensselaer Polytechnic Institute
New 'cell graphs' developed at Rensselaer Polytechnic Institute link tissue structure to its corresponding biological function
Troy, N.Y. Computer scientists and biologists in the Data Science Research Center at Rensselaer Polytechnic Institute have developed a rare collaboration between the two very different fields to pick apart a fundamental roadblock to progress in modern medicine. Their unique partnership has uncovered a new computational model called "cell graphs" that links the structure of human tissue to its corresponding biological function. The tool is a promising step in the effort to bring the power of computational science together with traditional biology to the fight against human diseases such as cancer.
The discovery follows a more than six-year collaboration, breaking ground in both fields. The work will serve as a new method to understand and predict relationships between the cells and tissues in the human body, which is essential to detect, diagnose, and treat human disease. It also serves as an important reminder of the power of collaboration in the scientific process.
The new research led by Professor of Biology George Plopper and Professor of Computer Science Bulent Yener is published in the March 30, 2012, edition of the journal PLoS One in a paper titled, "Coupled Analysis of in Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship." They were joined in the research by Evrim Acar a graduate student at Rensselaer in Yener's lab currently at the University of Copenhagen. The research is funded by the National Institutes of Health and the Villum Foundation.
The new, purely computational tool models the relationship between the structure and function of different tissues in body. As an example of this process, the new paper analyzes the structure and function of healthy and cancerous brain, breast, and bone tissues. The model can be used to determine computationally whether a tissue sample is cancerous or not, rather than relying on the human eye as is currently done by pathologists around the world each day. The objective technique can be used to eliminate differences of opinion between doctors and as a training tool for new cancer pathologists, according to Yener and Plopper. The tool also helps fill an important gap in biological knowledge, they said.
Every budding biologist is taught a central concept: there is a relationship between biological structures like cells or organs and their functions. This structure/function relationship is well understood at some levels. For example, we know what individual brain cells are structurally comprised of and the functions they perform in the body. It is when you delve deeper into interactions between millions of different types of cells and dozens of specialized organs that our limited understanding of human biology is quickly brought to light.
"Previous biological analysis techniques simply ground up tissues and looked at things like gene expression. This is like looking at poll numbers after a vote. You don't know who voted for what or why, you only know who won the race," Plopper said. "With this new analysis we can explain how individual cells function in the system while still focusing on the entire system as a whole."
The ability to understand the complex relationship between cells in our tissues required an entirely new way to do biology, according to the scientists.
"We needed to take biology out of the Petri dish and microscope slide and lift it into a different space. We needed to integrate the interactions in the body on multiple scales," Yener said.
Yener and his computational counterparts did this by building a computational model using graph theory that linked several different biological data sets from Plopper and his biology counterparts. The biological data came from tissue samples physically removed from the human body and samples grown outside the body in the lab.
In the diagnosis of cancer, a pathologist removes a section of suspicious-looking tissue from a patient. The tissue sample is then sliced and stained for easier viewing and looked at through the age-old tool of biology, the microscope. This process is called histology. The pathologist is literally looking for cancer. When looking through the microscope, trained pathologists simply know cancer when they see it. They don't know how it came to be or where it is going, just that it is present in the tissue in front of them. In other words, they can see the structure of the cancer, but not know its function. In order to truly know the roots of diseases like cancer, scientists need to know how it arose in the tissue in the first place.
One way of seeing how cancer functions is to literally grow and watch cancerous tissue form in the lab. This process of growing cells in something like a test tube outside of the body is called cell culturing. It is a way to simplify and control the elaborate symphony of what is going on within the body, outside the body. But, a cell culture is only one small part of the symphony of our bodies. It can never tell the whole story.
Therefore, tools like histology and cell culture needed to be combined to get a fuller picture of the transition from healthy cells to full-fledged cancer. But no laboratory experiments exist to make the connection between the two. This is where computation can play a significant role, according to Plopper and Yener. Through computation Plopper and Yener were able to, for the first time ever, quantitatively compare histology samples with lab cultures.
The new computational method uses graph theory. Instead of looking at tissue as a series of cells, graph theory simplifies the system into a series of dots and lines with the dots being the cells and the lines their interactions. The program links and compares the accuracy of data from actual human tissue samples from histology with those grown in the controlled laboratory setting. The result is a new tool that can detect and distinguish cancer and quantify the actual differences between different tissues analyzed.
"Currently, biology is a lot of trial and error," Yener said. "With a mathematical model of something like cancerous tissue, you can computationally represent the relationships between cells. That model can then be predictive and eliminate time and energy lost in trial and error."
To non-scientists, interactions between two different types of scientists seems like the norm. But, there are no two groups of scientists more disparate than biologists and computer scientists, according to both Yener and Plopper. For biologists, discovery is in the details. How many genes are being expressed in a tissue? What protein is involved in the disease? Computer scientists seek to represent the larger relationship between different data points. What those data points actually represent is largely irrelevant.
"We have a very unique relationship," Plopper said. "I think it will take my whole career to get people in both fields who currently don't talk to even accept the fact that they should. But if all scientists understand how to generate and use numeric data of some sort, that would really lower the barriers between fields."
Plopper has even created a class, "Cell-Extracellular Matrix Interactions," to develop a new type of data-savvy biologist.
"These discoveries have to come from both fields," Yener said. "Scientists need to trust computational methodologies and that trust will only come when we go back to the basic biology that can be fed into the modeling and tested."
###
[ | E-mail | Share ]
?
AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.
A number of major hotel chains are expanding their global presence by opening at new locations around the world. Despite the fact that economies are still struggling in many countries, luxury hotels are constantly opening. One example of this can be seen in Starwood Hotel and Resorts Worldwide?s new W Hotel.? The W brand is continuing its recent expansion by opening a new hotel in Paris. The W Paris Opera hotel is set in an historic 19th century building in the French capital, located close to the Opera Garnier, and offers guests luxurious and stylish accommodation. This is the W brand?s first hotel to open in Paris.
Starwood Hotels and Resorts Worldwide have also been extending another of their hotel brands, Sheraton Hotels. This worldwide expansion is set to continue throughout 2012 as 20 new hotels are due to open over the course of the year. New Sheraton Hotels plan to open throughout central Europe, Eastern Europe, North America and Asia in 2013 and 2014 with several new sites including branches in Pakistan and hotels in the Ukraine and Dubai.
InterContinental Hotels Group is another company that is expanding globally by opening more Holiday Inn hotels, particularly in Latin America. The InterContinental Hotels Group views business travellers and families as its target market for its Holiday Inn hotels and this brand is currently re launching itself in a bid to give the group a more contemporary image.
China, in particular, has experienced a steep increase in the number of hotel chains expanding into the country. Large hotel brands such as Hyatt and Hilton have increased their number of hotels in the country, as have other brands such as Crowne Plaza, Holiday Inn and Sheraton. In the future, Ritz-Carlton is planning for around one quarter of its worldwide hotels to be located in China in the near future.
The Hilton hotel group is also planning to increase their number of hotels in China, and aims to reach a total of 100 hotels in the country by 2012. One of the reasons for the recent boom in new high-end hotels being built in China is that governments and businesses across the country want to have a large, grand hotel close by to attract business and to create a strong impression on visiting business contacts. However, other hotel brands that are currently experiencing some success in China include budget chains such as Home Inns and Hotels Management Inc. China?s growing importance as a major economic power and tourist destination is helping to ensure that major hotel chains will continue to expand throughout the country as there is such a potential for profit to be made from business and leisure travellers.
Posted onApril 2, 2012
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WP Timeline Fan Pages Create powerful WP Timeline pages for Facebook - Full Control + Create Unlimited Pages
I understand you have put a lot of time, energy and effort straight into creating then building up your online business. It is now time for you to settle-back and gain from your effort, and make your money online. Nevertheless, are you aware of the most up-to-date trends advertising? Remember, it?s very important to keep abreast of all the newest developments inside the field, if you need to gain a keen edge around your competition.
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For the 1.2 million Americans living with HIV, the Affordable Care Act will be utterly life-changing. For some, it will be life-saving.
Just ask Will Wilson, 58, who was diagnosed with "full-blown AIDS" in 2002.
"It will basically mean freedom," said Wilson, a Chicago resident and an advocate for the Illinois Alliance for Sound AIDS Policy.
For the first time, Wilson will be able to purchase private insurance without fear of being rejected for his preexisting condition. The former graphic designer will be able to aggressively re-enter the job market without risking his continuous access to lifesaving HIV drugs that cost him $3,000 a month.
He'll have options he's never had.
This week, the Supreme Court has heard oral arguments on the constitutionality of the Affordable Care Act, specifically the legality of the individual mandate provision and the expansion of Medicaid. It is slated to rule in June on what is widely considered to be the most important Supreme Court case in decades. Many people living with HIV/AIDS and other preexisting conditions will be hoping and praying that the court rules in favor of health care reform.
In January, the AIDS Foundation of Chicago (AFC) signed on to a legal brief -- along with 130 other HIV/AIDS organizations throughout the country -- asserting that the Affordable Care Act is, in fact, constitutional. It's also necessary to stopping the AIDS epidemic in the United States.
"The list of supporters for our brief urging the court to uphold the ACA continues to grow because of the law's enormous potential to impact the domestic AIDS epidemic," said Scott Schoettes, HIV Project Director for Lambda Legal, the legal firm that submitted the brief.
About 24 percent of people living with HIV are uninsured, according to data from the U.S. Department of Health and Human Services. The majority of people living with HIV depend on Medicaid and Medicare for medical treatment.
Those unlucky, uninsured hundreds of thousands -- who are not eligible for Medicaid or Medicare -- often depend on the federal Ryan White funding system, which was never intended to be the primary source of health care funding for people with HIV when it was enacted in 1990. Ryan White provides HIV-related treatment and medication, but it's not insurance. But for many, it's the only limited option.
It's not enough just to be poor. Many uninsured people living with HIV don't qualify categorically for Medicaid, meaning they're not over 65, an infant or a pregnant woman. And they're not yet sick enough to meet the disability category.
That's a tragedy in itself. By the time many people living with HIV become eligible for Medicaid, it's almost too late. They're incredibly sick because they did not have earlier access to the drugs and treatment that could have prevented their decline.
As of 2014, the Affordable Care Act will begin expanding Medicaid to accept all low-income Americans. As a result, low-income adults with HIV will no longer have to wait for an AIDS diagnosis to become eligible for coverage.
Perhaps more importantly for people like Will Wilson, the Affordable Care Act will also prohibit insurers from denying coverage because of preexisting conditions. And no longer will insurance companies be able to charge exorbitant premiums for people with HIV.
Wilson has made his living with odd jobs, most recently a gig as a tour bus guide, since his AIDS diagnosis. He does not qualify for Medicaid. He carefully monitors his wages to remain eligible for the AIDS Drug Assistance Program (ADAP), the Ryan White program that helps low-income people afford costly AIDS drugs.
If Wilson were to pursue private insurance, he would face several daunting prospects, including being denied for his preexisting condition or being charged exorbitant premiums. Even in moving to a group insurance plan, Wilson could be subject to interruptions in his continuous care that could be detrimental to his health.
He looked into the preexisting condition insurance plans -- which are now available but vary in cost state-by-state -- but found the premiums too cost-prohibitive.
"Do I drop out of Ryan White, get denied coverage and then go to the bottom of the list?" Wilson said. "You stay with what's got you covered."
In other words, he's stuck in a broken health care system. Like many others, he's eagerly looking forward to 2014 when he can seek out private insurance that won't deny him or cost him out of the healthcare he desperately needs. So, he waits.
Around the country, HIV/AIDS advocates and organizations are intently focused on how the Affordable Care Act will be implemented. The Ryan White system is expected to be an extremely important safety net for the foreseeable future. Visit the new educational website -- hivhealthreform.org -- for a comprehensive discussion of that transition.
David Ernesto Munar, president of the AIDS Foundation of Chicago, has lived with HIV for nearly 17 years. Speaking from his personal experience and his professional expertise, Munar believes healthcare reform to be critical in preventing new infections and, ultimately, stopping the AIDS epidemic in the United States.
"By expanding coverage and ensuring more preventative services like HIV testing, we can begin to turn the tide against this epidemic," Munar said.
Of course, people with HIV are not alone. There are nearly 50 million Americans with no health insurance, people of all walks with various diseases and ailments, trapped in the forgotten corners of the healthcare system. The Supreme Court will have its say on whether that's right.
In November, voters will have their say, too. Gregory Trotter is a staff writer for the AIDS Foundation of Chicago.
Whether they worry, obsess or panic, if you have a loved one struggling with anxiety it can be almost as painful for you as it is for them. The first impulse is often to reassure??everything will be fine?, ? don?t worry about it?, ?it?s nothing?. Then perhaps you begin to pick up the slack, helping out with more and more to lighten their load and lower their stress. But, over time, this wears on you, especially when you find that it doesn?t really result in much improvement anyway?and may even makes things worse! Eventually, frustrated, you move to cajoling, criticizing or threatening in a desperate attempt to control the anxiety and regain some sense of normality in your life. Sadly, this just leads to more stress, tension and anxiety and, feeling stuck, you may disengage from the relationship altogether.
So, if helping doesn?t work and not helping doesn?t work, what do you do when someone you love is anxious? There is no formula guaranteed to work for everyone, but you may find that some of the concepts below can guide you in developing a plan to cope with your loved one?s anxiety.
Knowledge. Here, the old adage is true?knowledge is power. Learn as much as you can about anxiety and its symptoms, causes and treatments. Share this information with your loved one as well. Understanding the available treatment options for anxiety may be an important first step to recovery for them. And the better you understand what they are experiencing, the better you?ll be able to cope with it.?
Criticism. You might be surprised to learn that criticism is not always a bad thing when dealing with an anxious spouse, child or friend. While high levels of anger, hostility or criticism are almost always detrimental, some studies have found that focused criticism?criticism that is not globally rejecting of the person?may actually result in improved outcomes (e.g., Zinbarg, Lee and Yoon, 2007). Fair criticism directed at specific behaviors may actually work better than unconditional acceptance.
Accommodating. In fact, too much acceptance can often inadvertently lead to a poorer prognosis through accommodating behaviors and reassurance. While giving in to anxious requests can keep the peace in the short-term, in the long-run it feeds into the cycle of anxiety and dysfunction. It is easiest to refuse these traps right off the bat, but if you?ve already fallen prey to modifying your behavior or given in to repeated requests for reassurance it is not too late to make a change and set some limits.?
Limit setting. This is a simple concept but surprisingly hard to implement because setting limits requires patience, strength and consistency. Patience because, despite how frustrated you may be, it works best to decrease rituals or reassurance gradually?a good rule of thumb is by about half every two weeks. Strength because when you set a limit, things will often get a little worse before they get better. In behavioral theory, this is called an extinction burst. It essentially means that when someone is accustomed to their behavior being met in a particular way?like getting a reassuring answer when they voice a worry?it is a shock to suddenly not hear that response and the first reaction will be to try harder, or ask more, to get it. The good news is that if you stay consistent in your new stance, eventually things will improve.
Setting limits is a difficult but necessary part of living with someone with anxiety but it goes without saying that this should never be done as a surprise. Talk to your loved one in advance and let them know that things will be changing and why. It doesn?t hurt to have a supportive, alternative statement prepared for when tough situations come up?something along the lines of ?I love you, so I refuse to participate in this behavior because we know it is harmful to you in the long-run.?
Coaching. If your relationship is a good one and you feel you can manage it, work with your loved one to coach them in their battle with anxiety. If emotions run too deep for you to be objective and supportive when the anxiety is high, help them to identify someone else in their life to play this role. Whether it is supporting and practicing their therapy goals or helping them work through a self-help program, a good coach should be encouraging, not forceful or ridiculing, and can provide an important model for recovery.
Contracting. Though the word has legal connotations, contracting is not just for lawyers anymore. Clearly outlining--in writing--the goals and the plan to reach them can help to organize and commit to the purpose. This would ideally include vows on both sides?what each of you will do to improve the situation. Be as specific as possible and be sure to note the time frame for achieving these goals as well as the contingencies if they aren?t met. ?Then stick to it.
Self-care.?Perhaps the most important point, remember to take care of you. When someone you care about is struggling with anxiety, it is all too easy to focus on helping them and to forget about your own needs. Be sure to stay well yourself?talk to friends for support, get your own therapist, consider joining a support group or an online discussion board.
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References
Zinbarg, R., Lee, J.E. & Yoon, L. (2007). Dyadic Predictors of Outcome in a Cognitive-Behavioral Program for Patients with Generalized Anxiety Disorder in Committed Relationships: A ?Spoonful of Sugar? and a Dose of Non-Hostile Criticism May Help. Behaviour Research and Therapy, 45, 699 ? 713.
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Public release date: 2-Apr-2012
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