Day: 05/31/2015

Scientists identify key to preventing secondary cancers .

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Leading scientists from the University of Sheffield and University of Copenhagen have identified a possible key to preventing secondary cancers in breast cancer patients, after discovering an enzyme which enhances the spread of the disease.

Secondary (metastatic) breast cancer is the main cause of the 12,000 deaths which occur from breast cancer in the UK every year.

The most common site for the disease to spread is the bone — occurring in around 85 per cent of secondary breast cancer patients.

The new research, which was conducted at The Institute of Cancer Research, London, found that the enzyme LysYl Oxidase (LOX) released from the primary tumor causes holes in bone and prepares the bone for the future arrival of cancer cells.

The findings suggest that identifying LOX in estrogen receptor negative (ER negative) breast cancer patients early, could allow doctors to block the enzyme’s activity, preventing bone damage and the spread of tumor cells to the bone (metastasis), halting the progression of the disease.

The researchers also showed that treatment with bisphosphonate, an existing class of drug which prevents the loss of bone mass and is already used to treat diseases such as osteoporosis, was able to prevent the changes in the bone and the spread of the disease in mice.

The pioneering research, co-led by Dr Alison Gartland at the University of Sheffield’s Department of Human Metabolism, could lead to a better prognosis for cancer patients in the longer term.

Dr Gartland said: “This is important progress in the fight against breast cancer metastasis and these findings could lead to new treatments to stop secondary breast tumors growing in the bone, increasing the chances of survival for thousands of patients.

“We are really excited about our results that show breast cancer tumors send out signals to destroy the bone before cancer cells get there in order to prepare the bone for the cancer cells’ arrival.

“The next step is to find out exactly how the tumor secreted LOX interacts with bone cells to be able to develop new drugs to stop the formation of the bone lesions and cancer metastasis. This could also have implications for how we treat other bone diseases too.”

Study co-leader Dr Janine Erler, formerly Team Leader in Cancer Biology at The Institute of Cancer Research, London, who now is Associate Professor at the Biotech Research & Innovation Centre (BRIC) at the University of Copenhagen, said: “Once cancer spreads to the bone it is very difficult to treat. Our research has shed light on the way breast cancer cells prime the bone so it is ready for their arrival. If we were able to block this process and translate our work to the clinic, we could stop breast cancer in its tracks thereby extending patients’ lives.”

The research, funded by Breast Cancer Campaign, Cancer Research UK, Novo nordisk foundation, Danish cancer society, lundbeck foundation, and both universities, is published in the journal Nature.

Katherine Woods, Senior Research Communications Manager at Breast Cancer Campaign and Breakthrough Breast Cancer, said: “By unveiling the role that the protein LOX is playing, these results open up a whole new avenue for research and treatments that could stop breast cancer spreading to the bone. The research also adds weight to the growing body of evidence supporting the role of bisphosphonates in stopping secondary breast cancer in its tracks.

“The reality of living with secondary breast cancer in the bone is a stark one, which leaves many women with bone pain and fractures that need extensive surgery just when they need to be making the most of the time they have left with friends and family.”

She added: “Secondary breast cancer kills 1,000 women each and every month in the UK alone and yet we still don’t know enough about how and why breast cancer spreads to stop it.

“Our newly-formed charity is determined that by 2050, no one will lose their life to breast cancer and we’ll do this by ramping up our research efforts, in this area in particular, doing everything possible to achieve that goal.”

​Hawking warns gifted disabled scientists could be left without financial support — RT News

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Stephen Hawking (Reuters / Suzanne Plunkett)

World-renowned physicist and author Stephen Hawking has expressed concerns over imminent cuts in funding for talented academics with serious medical conditions that could harm their progress in research.

“I wonder whether a young ambitious academic, with my kind of severe condition now, would find the same generosity and support in much of higher education,” Hawking said at a dinner that marked his 50th year as a fellow of Gonville and Caius College at the University of Cambridge.

‘Colonize planets to save the human race’ – Professor Stephen Hawking

“Even with the best goodwill, would the money still be there? I fear not,” the 73-year-old professor added.

Suffering from progressing motor neurone disease (MND), he received support from the college. Hawking said that “Caius [college] gave me a home, literally and figuratively, and is a constant thread running through my life.”

“That fellowship [that Hawking received in 1965] was a turning point in my life, as the college made sure I could continue my research, despite my increasing disability.”

The college’s master, Alan Fersht, replied to the words of Hawking, saying “Stephen questioned whether a young academic in his condition would get the same level of support today? For Caius at least, I can say emphatically ‘yes’. The fellowship is a family, just as our students, our staff and our alumni are all parts of the Caian family.”

Stephen Hawking: Artificial Intelligence could spell end of human race

Fersht went on to say: “In 1965, none of us dreamt that we would be here, 50 years on, to celebrate this day. I say none, but I suspect I actually mean ‘all, but one’.”

Back in 2008, Hawking warned that £80m ($122m) of grant cuts could put Britain’s position in the international scientific community under threat. He said, “These grants are the lifeblood of our research effort; cutting them will hurt young researchers and cause enormous damage both to British science and to our international reputation,”according to the Guardian.

Cashews Are A Natural Anti-Depressant

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Two handfuls of cashews is the therapeutic equivalent of a prescription dose of Prozac. Inside you, the essential amino acid L-tryptophan is broken down into anxiety-reducing, snooze-inducing niacin.

Even more important, tryptophan is also made into serotonin, one of your body’s most important neurotransmitters. Serotonin gives a feeling of well-being and mellowness, or as the Australians would say, “no worries.” This is such a profound effect that Prozac, Paxil and similar antidepressants usually either mimic serotonin or artificially keep the body’s own serotonin levels high.

You can do the same thing with your food. And no one can tell us that beans, peas, cheese, nuts and wheat germ are toxic if you eat a lot of them! Plenty of carbohydrates (starches) in your meals help tryptophan get to where it does the most good: in your brain. In order to cross the blood-brain barrier to get in, carbos are required. So cheese and crackers provides a better effect than the cheese standing alone.

An egg or two on toast is better than just the egg. Beans, peas, and nuts already contain carbohydrate, so you are all set there. Consider that five servings of beans, a few portions of peanut butter, or just one big handful of cashews provides one to two thousand milligrams of tryptophan, which will work as well as prescription antidepressants… but don’t tell the drug companies. Some skeptics think that the pharmaceutical people already know. Here are two quotes in evidence: “Pay careful attention to what is happening with dietary supplements in the legislative arena… If these efforts are successful, there could be created a class of products to compete with approved drugs.

The establishment of a separate regulatory category for supplements could undercut exclusivity rights enjoyed by the holders of approved drug applications.” (Source: FDA Deputy Commissioner for Policy David Adams, at the Drug Information Association Annual Meeting, July 12, 1993) Here are 15 other Amazing Health Benefits Of Cashew Nuts Who doesn’t know about cashew nuts? Caju is what we call them in India. We use them mostly in sweets and children love to eat them as they are. They are full of anti-oxidants, vitamins and minerals which are required for the normal functioning of the body. They actually belong to Brazil but Portuguese brought them to India in the 16th century. The kidney shaped or bean shaped nuts have many health benefits, a few of which are presented below: 1. Prevents Cancer: Proanthocyanidins are a class of flavonols which fight against tumor cells by stopping them to divide further.

These proanthocyanidins and high copper content in cashew nuts help fight against cancerous cells and keeps you away from colon cancer. This is one of the major cashew nut benefits. 2. Healthy Heart: Cashews contain low fat content when compared to other nuts and that too in the oleic acid form which is very healthy for heart. They are cholesterol free and the antioxidants present keeps you away from heart diseases. 3. Lowers High Blood Pressure: Cashew nuts lower your blood pressure with the help of magnesium present in them. 4. Helps Hair: Copper is the mineral which helps your hair get that color. So if you take cashews which are full of copper content, you can get that black hair that you always wished for. 5. Healthy Bones: Like calcium, magnesium is also important for bone health which is the main content in cashew nuts. 6. Healthy Nerves: Magnesium is stored on the bones surface which prevents calcium from entering the nerve cells and thus keeps the blood vessels and muscles relaxed. Insufficient amount of magnesium can lead calcium to enter the blood vessels leading them to contract. It also leads to high blood pressure, migraine headache etc. 7. Prevents Gallstones: Daily intake of cashewnut can reduce the risk of developing gallstones up to 25%. 8. Helps in Weight Loss: Even though cashew nuts are considered as fats, it contains good cholesterol. So contrary to popular belief, those who eat cashews at least twice a week gain less weight when compared to those who eat less. 9. Anti-oxidants: Selenium, copper, magnesium etc. act as co-factors for many enzymes. 10. Helps Digestion: Cashew nuts help in growth and development, nucleic acid synthesis and digestion. 11. High on Vitamins: Cashew nuts are rich in vitamins like riboflavin, pantothenic acid, thiamin, niacin etc. These vitamins keep you safe from sideroblastic anemia, pellagra, etc. 12. Healthy Gums and Teeth: As mentioned before, the magnesium content present in cashew nuts is very good for bones. So it gives healthy teeth as well as strong gums to hold them. 13. Pleasant sleep: After menopause, these cashew nuts can give you relaxed and pleasant sleep during nights. 14. Free Radicals: Cashew nuts help our body to utilize iron properly and eliminate free radicals which cause health problems. 15. Macular Degeneration: Cashew nuts have the ability to filter Sun’s UV rays and protect us from macular degeneration. Now that you know the health benefits of Cashew nuts, ensure that you eat a few once every week I am sure you already love them.

The Mediterranean Diet: Can It Help Memory?

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Unless you’ve been living without print or electronic media for the past several years, you’ve heard of the Mediterranean Diet. It focuses on the use of olive oil for cooking and in salads, lots of fruits and vegetables, nuts, some cheese and yogurt, and plenty of fatty fish, with less red meat and butter.

Full disclosure: I pretty much grew up on this diet, but it wasn’t “Mediterranean” then. It was just how we ate, strongly influenced by my mother’s family – the Greek side – and especially her father. He caught his own salmon as often as possible, used olive oil by the gallon, and cracked nuts in the shell after dinner to eat with dried fruit. His family came from Crete, where the diet is said to have originated. He felt it was healthy to eat this way, but it was also his culture.

Fast forward to a few years in the past and the PREDIMED project, a huge multicenter trial that basically divides people into three groups: two groups counseled to follow the Med Diet supplemented with either olive oil or nuts (a combination of almonds, hazelnuts, and walnuts), and a control group advised to follow a general low-fat diet. The diet was so successful at reducing heart disease risk that it was stopped early so the control group could partake of the Med Diet benefits.

Beyond Healthy Hearts

The researchers also looked into the effects of the diet on memory. A just-published study, a subset of the PREDIMED trials, used the same diet but then tested global cognitive function, memory performance, and a composite of frontal functions, both at the beginning of the study and after the end of the 5-year period.

Here’s the boil-down: compared with the control group, those on the Med diet supplemented with extra-virgin olive oil performed better on both frontal and global composite scores, and subjects on the Med diet supplemented with nuts did better on memory composite tests.

What Do I Like About the PREDIMED Research?

The dietary intervention was simple and easy for anyone to implement. The extra-virgin olive oil subjects replaced about two tablespoons of butter and other oils for a similar amount of olive oil or an ounce of nuts. It’s about as easy as any dietary change is going to get. This study didn’t give specific calorie advice per se or put people on weight-loss diets. Even chocolate was allowed as long as it’s the dark stuff.

The Med Diet does get a thumbs up from the recent Dietary Guidelines Advisory Committee report. This group also endorsed the DASH diet – Dietary Approaches to Stop Hypertension – that centers on lots of fruits and vegetables and three servings a day of low-fat dairy (although you also get about four ounces of cheese a week). Dairy foods aren’t a huge part of the Med Diet, and the diet can be low in calcium and vitamin D. Culturally it wasn’t a part of my grandparents’ diets, but maybe it should have been – both had osteoporosis.

The “MediterDASHean Diet”

No connection to Kim here. This is my idea of combining the best of both diets. My grandparents might have done better with this diet – they both lived to an old age but had severe osteoporosis, one with hip fractures and all – because it combines the strengths of both endorsed diets. My grandfather would probably approve – he spent many years as a dairy farmer just south of San Francisco.

He wouldn’t approve of swapping out nuts for nut milk alternatives, though. An almond glass doesn’t actually contain many almonds. Crushed almonds, at an ounce a day, would be better.

As for olive oil, it could probably be replaced by canola oil, which is also loaded with monounsaturated fats — but the flavor isn’t there. Better to save it for foods and dishes where the olive oil flavors are less useful (this is just a personal opinion, so no emails on that, please).

Bottom line: this latest research underscores that there may be benefits beyond heart health of a diet that includes a modest amount of olive oil and/or nuts like almonds, hazelnuts, and walnuts on a daily basis. I can hear my grandparents yelling that they didn’t need researchers to tell them about how good it was.

The Insecurity And Narcissism Hiding In Facebook Posts

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Entertainment News: The Insecurity And Narcissism Hiding In Facebook Posts

The Insecurity And Narcissism Hiding In Facebook Posts

Trending News: How Your Facebook Posts Reveal Your Deepest Insecurities

Why Is This Important?

Because we live much of our lives on the internet.

Long Story Short

Research from Brunel University London reveals that your Facebook posts may have a dark side. After surveying over 500 users, the researchers found a high correlation between certain status updates and personality traits like narcissism.

Long Story

Facebook, for any stable-minded adult, is borderline unusable. The average person’s news feed is clogged with so much self-aggrandizing, “look at me” drivel that Facebook is constantly retooling their algorithm to create the slimmest chance that something – anything – of value will pop up in your news feed. As for why that is, researchers from Brunel University London found what many of us already suspected: People who post a lot of Facebook have a few screws loose.

“It might come as little surprise that Facebook status updates reflect people’s personality traits. However, it is important to understand why people write about certain topics on Facebook because their updates may be differentially rewarded with ‘likes’ and comments,” said psychology lecturer Dr Tara Marshall.

The researchers analyzed data from 555 Facebook users who voluntarily completed a survey concerning the “big five” personality traits – extroversion, neuroticism, openness, agreeableness and conscientiousness. Also included in the survey were narcissism and self-esteem. Not surprisingly, the data showed a high correlation between Facebook posts and those last two traits.

They found that people who post more updates about their romantic partners tended to exhibit lower self-esteem, while people who post often about their achievements are narcissists looking for attention and validation. The same is true for people who post their diet and workout routines, proving once and for all that CrossFitters are the worst.

This may come as news of the “no shit” variety for a lot of us, but not necessarily. It’s normal, when seeing that girl from high school post about her “bae” or the formerly fat classmate post their WOD, to assume “oh, she’s just happy”/ ”he’s just showing off.” But it may not be so benign – the research indicates that rather than meaningless self-expression, these sorts of posts are direct indicators of someone’s personality. That’s a much scarier thought.

Society isn’t crumbling; the internet just showcases how fragile it’s always been.

Own The Conversation

Ask The Big Question: Is it dangerous for people to rely on likes and comments to bolster their self-esteem and narcissism?

Disrupt Your Feed: I’d offer commentary on this but I’m afraid of what such a status update might say about me.

Drop This Fact: Facebook’s messenger app pinpoints the latitude and longitude coordinates of message locations to more than 5 decimal places of precision.

A Biology as Holistic as Life.

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Systems Biology Is No Longer a Fringe Discipline. It’s Getting to the Heart of Disease Processes

  • The “systems” in systems biology become apparent only when the whole is contemplated, not the parts—or even the sum of the parts. Mere accumulation cannot account for life’s complexity.

    Rather, this complexity is emergent. It is more than the sum of the parts. It is the result of collective behaviors that cannot be reduced to the individual behaviors of simple components.

    By modeling the interactions of biological components across multiple scales—from tiny feedback loops to far-flung networks—systems biology can depict complex and dynamic living systems more accurately than the traditional reductionist approach. Systems biology has been applied not only in bacteria and yeast, but also in plants and animals. In the past decade, systems biology has advanced so much that it has accomplished a shift: It is no longer a fringe discipline. It is now a mainstream science.

    This transformation was much in evidence at a recent meeting, Systems Biology: Networks. Here, under the auspices of the Cold Spring Harbor Laboratory (CSHL), researchers discussed developments in this rapidly evolving field including novel approaches to understand gene regulatory networks, signal coordination, and the metabolome by integrating technology, computation, and critical human insights.

  • Gene Regulatory Networks

    Plants have much to teach about biology and life. After all, Austrian biologist and monk Gregor Mendel provided the first clues to genetic inheritance and the nature of genes by meticulously crossbreeding pea plants. Further, American cytogeneticist Barbara McClintock received the Nobel Prize for work that revealed genetic transposition in maize.

    Researchers are still utilizing plants to decipher gene regulatory networks. For example, Siobhan M. Brady, Ph.D., an associate professor at the University of California, Davis, utilizes the plant modelArabidopsis thaliana.

    “A plant cell’s shape and function are largely determined by its cell walls. The primary wall surrounds the plasma membrane, and the secondary wall (such as those found in xylem) functions in water transport and protection against pathogens,” said Dr. Brady at the CSHL event. “It is also provides dietary fiber for humans, raw material for paper, and components for biofuel production.”

    “Despite its importance, we know very little about precise regulatory mechanisms in time and space that give rise to the secondary cell wall’s three main components—cellulose, lignin, and hemicelluloses,” Dr. Brady admitted. Of the three main cell wall components, lignin is the most problematic. It impedes the extraction of cellulose and hemicelluloses for biofuel production.

    The production of different cell wall components could be subject to manipulation. Already, ideas for how such manipulation could be accomplished are emerging from Dr. Brady’s group, which seeks to map the gene regulatory networks responsible for the biosynthesis of these components.

    Such work, Dr. Brady indicated, requires a systems biology approach, the better to distill the large amount of data generated into organizing principles. She went on to describe her group’s particular systems biology approach: a combination of high-spatial-resolution gene expression data and a review of the literature on xylem cell specification.

    “Instead of following single genes, we looked at the function of hundreds of transcription factors and enzymes in the regulatory network of xylem,” explained Dr. Brady. “We were able to derive hundreds of novel regulators and gain considerable insight into xylem developmental regulation.

    “We found that under specific stress conditions, such as iron deprivation and salt stress, we could enhance production of individual components. This is important because it shows that regulation of these enzymes can be uncoupled and allows us to potentially manipulate the system to enhance production of biofuels.”

    Dr. Brady is also examining this network in sorghum: “We’d like to understand how gene regulation networks are wired in the secondary walls of other species. Ultimately, we may be able to find existing plants that won’t require engineering to build better biofuels.”

  • Integrating Signaling Networks

    Click Image To Enlarge +
    Scientists at Harvard Medical School are studying galactose metabolism by growing natural yeast isolates in mixtures of glucose and galactose. Strain BC187 has been engineered to constitutively express mTagBFP2 (blue cells), whereas strain YJM978 constitutively expresses mCherry (red cells). Both strains also express GAL1pr-YFP as a transcriptional reporter in the galactose-utilization (GAL) pathway (green overlay). Expression of this pathway can vary widely across genetically identical cells, as well as between different strain backgrounds. Here, turquoise (blue + green) and yellow (red + green) correspond to BC187 and YJM978 cells that have high GAL expression, whereas blue and red cells have low GAL expression. [Jue Wang, Renan Escalante-Chong]

    Understanding the sophisticated communication networks in cells requires an in-depth knowledge of how cells integrate signals, noted Michael Springer, Ph.D., an assistant professor of systems biology at Harvard Medical School. Dr. Springer, who focuses on signaling network interactions, is studying the induction of galactose metabolic genes when budding yeast are grown in mixtures of glucose and galactose.

    “This is a classical, well-studied system that one might think would yield no new insights, but this is precisely the perfect system for the type of research we do,” said Dr. Springer. “We use a combination of quantitative high-throughput assays with modern genetic approaches such as xQTL (a web platform that maps quantitative trait loci) and systematic deletion collections to analyze natural variants and mutant strains.

    “Basically, we threw the kitchen sink at the problem: microscopy, flow cytometry, mass spectrometry—whatever we thought would help us answer our questions. Working on a system that is so well understood makes it possible for us to make sense of our results.”

    According to Dr. Springer, there were many studies that looked at glucose repression of galactose genes, but none in quite the way they did: “Our strategies, combined with some simple models and quantitative approaches, are what led to our novel insights. Our key published result is that yeast respond to the ratio of glucose and galactose. This ratio sensing occurs upstream of the canonical signaling pathway, likely at the transporters, which are typically thought of as passive players in the response.”

    But there are also some remaining challenges that Dr. Springer’s laboratory must still address: “I think this is a perfect system to start to hack away at the relationship between genotype and phenotype. There are many perspectives and angles to this that I think will keep us and others busy for a while. We are currently attacking the problem with a number of techniques. Over the next couple of years, I hope to be able to bridge these typically orthogonally used approaches. We hope this bridging will have a broad impact beyond just our knowledge of carbohydrate metabolism in yeast.”

    • Jason Papin, Ph.D., an associate professor of biomedical engineering at the University of Virginia, is studying how to integrate high-throughput data into predictive, computational models for the interrogation of metabolic and regulatory networks. He is particularly interested in networks that relate to pathogens and human disease.

      His lab recently compared the metabolic and virulence capabilities of two multidrug-resistant bacteria,Burkholderia cenocepacia and Burkholderia multivorans.Burkholderia are Gram-negative bacilli whose members run the gamut from potential bioterror agents to nonpathogenic species of interest in agricultural biotechnology.

      “Multidrug-resistant pathogens are an enormous health concern as they can cause chronic infection in a variety of patients,” noted Dr. Papin, “and yet there are only limited sources for treatment. We studied two bacterial species that account for the majority of B. cepaciacomplex (BCC) infection in cystic fibrosis patients and other immunocompromised individuals.

      “Although similar in their genetic compositions, they have important differences in pathogenesis. The predictive power of computational modeling and systems analysis provides a way to reconstruct the biochemical networks for hundreds to thousands of metabolites involved in virulence and other biological activities of pathogens such as these.”

      Dr. Papin and colleagues utilized a variety of prediction/assessment tools to carry out the genome-wide reconstruction. These tools included flux balance analysis and the Model SEED, an online resource for the generation, optimization, curation, and analysis of genome-scale metabolic models.

      “These models integrate annotated genome data and provide a framework for investigating the metabolic architecture of pathogens,” explained Dr. Papin. “The method accounts for all metabolic enzymes within a given cellular network, mapping the annotated genome to the proteome and associated chemical transformations in a mathematically driven comparative process.”

      However, it’s not as simple as just pushing a button and then getting a cup of coffee. The analysis also requires human input. “I’d say 90% of the content of a network reconstruction requires 10% of the effort and time, but that last 10% of the content of the network reconstruction requires 90% of the overall effort and time,” advised Dr. Papin. “You can’t automate everything as it is still important for the scientist to carefully evaluate the currently available, and sometimes conflicting, data and literature.”

      Overall, Dr. Papin’s team demonstrated by computational modeling that B. cenocepacia can produce a wider variety of virulence factors than B. multivorans and can utilize clinically relevant substrates more effectively while doing so.

      “This supported the clinical observations that B. cenocepacia is more virulent,” remarked Dr. Papin. “Considering the large genomes and their ability for metabolic adaptation as a key factor in their pathogenesis, such reconstructions have wide-ranging implications for employing a systems biologyapproach for comparing the metabolic profiles of many other harmful pathogens as well as for developing new treatment strategies.”

    • Stratifying Tumor Mutations

      Cancers are complex (driven by a variety of genes), but also wildly heterogeneous, said Trey Ideker, Ph.D., a professor of genetics at the University of California, San Diego. “Gene combinations can vary greatly among patients,” he added. “Groups such as The Cancer Genome Atlas and the International Cancer Genome Consortium focus on systematically profiling tumors utilizing multiple levels of genome-scale data such as mRNA and microRNA expression profiles, DNA copy number and methylation signatures, and DNA sequences.”

      Dr. Ideker and colleagues recently introduced a new way to analyze these complexities. With their approach, they hope to accomplish one of the fundamental goals of cancer informatics, the stratification of tumors into clinically and biologically relevant subtypes by comparing their molecular profiles.

      “Although a promising new source of data to do this is the somatic mutation profile, which uses high-throughput sequencing of a patient’s tumor, this has proved challenging,” noted Dr. Ideker. “Fewer than 100 mutated bases can be found in most patient exomes and they are remarkably heterogeneous with often no more than a single mutation shared between clinically identical patients.”

      The answer, he said, may lie in looking more broadly at combined data: “Cancer is not only a disease of single genes, but rather combinations of genes acting in molecular networks such as in cell proliferation and apoptosis. This suggests that cancers may share networks affected by these mutations.”

      Although such cancer pathway maps are still being developed, researchers can access much relevant information from public databases of human protein-protein, functional, and pathway interactions. “By integrating these network databases with tumor molecular profiles, the molecular pathways of cancer are beginning to emerge,” Dr. Ideker indicated. “For example, we developed a network-based stratification method for integrating somatic tumor genomes with gene networks. This creates a stratification of various cancers into subtypes derived from clustering together patients who have mutations in similar network regions.”

      In a proof-of-principal study, Dr. Ideker’s team used ovarian, lung, and uterine cancer cohorts from The Cancer Genome Atlas. The study identified network regions in each subtype that helped predict clinical outcomes such as patient survival time and development of drug resistance.

      “We continue to improve upon the network-based stratification model,” Dr. Ideker asserted. “Although we demonstrated the utility of gene-gene interactions, other networks may be valuable to analyze such as those involved in signaling, metabolism, and transcription. We’ve only just begun to fully exploit the capabilities of using systems biology to stratify cancer subtypes.”

    • Mapping the Interactome

      The genomic revolution is poised within our lifetime for an explosion that will provide a complete description of virtually all human genomic variations whether deleterious, advantageous, or neutral, suggested Marc Vidal, Ph.D., director of the Center for Cancer Systems Biology, Dana-Farber Cancer Institute. However, genomic sequencing alone cannot provide answers to fundamental questions relating to genotype-phenotype relationships. To “connect the dots,” proponents of the genomic revolution will have to decipher the complex cellular interactions of genes and their gene products. That is, they will have to explicate interactome networks.

      Dr. Vidal and colleagues recently charted the proteomics of the human interactome network. Using a variety of systems biology tools, they generated a comprehensive binary protein-protein interaction map. They also plumbed the functional depths of thousands of proteins, as shown for candidates identified in genomic cancer screening studies. The investigators found specific interconnectivities between known and candidate cancer gene products.

      “We created a new dataset experimentally of 14,000 interactions and compared it to existing literature datasets totaling 11,000 interactions,” said Dr. Vidal. “The main message is that at this point we have mapped more interactions than the whole community combined, and our dataset is much less systematically biased.”

      As systems biology continues to make strides in technology, modeling, and deciphering complex biological interactions, immediate benefits include identifying disease-related mechanisms and biomarkers, and revealing novel drug targets.

Magic mushrooms ‘less harmful than thought’ and should be reclassified, says leading psychiatrist – disinformation

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Magic mushrooms ‘less harmful than thought’ and should be reclassified, says leading psychiatrist

RuthArt (CC BY 2.0)

 

Psychedelic drugs including LSD and magic mushrooms are much less harmful than has been claimed, and should be reclassified to make it easier for scientists to research their potential benefits, a leading psychiatrist has said.

Promising medical research into psychedelics ground to a halt as long ago as 1967, when they were made illegal amid widespread concern about their psychological and social harms.

However, writing in the BMJ, psychiatrist Dr James Rucker, said that no evidence had ever shown the drugs to be habit-forming. There is also little evidence of harm when used in controlled settings, and a wealth of studies indicating that they have uses in the treatment of common psychiatric disorders, he said.

Researchers are beginning to look again at how LSD and psilocybin – the active compound in magic mushrooms – might be of benefit in the treatment of addiction, for obsessive compulsive disorder and even, according to one small Swiss study, to alleviate the symptoms of anxiety in terminally ill patients.

However, larger trials are “almost impossible”, Dr Rucker argues, because of the “practical, financial, and bureaucratic obstacles” imposed by the drugs’ legal status.

 

The Effect of OSA on Work Disability and Work-Related Injuries

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OSA is a common yet underdiagnosed respiratory disorder characterized by recurrent upper airway obstruction during sleep. OSA results in sleep fragmentation and repetitive hypoxemia and is associated with a variety of adverse consequences including excessive daytime sleepiness, reduced quality of life, cardiovascular disease, decreased learning skills, and neurocognitive impairment. Neurocognitive impairments that have been linked to poor sleep include memory deficits, decreased learning skills, inability to concentrate, and decreased alertness. Furthermore, the societal and economic costs of OSA are substantial; for example, patients with OSA have a significantly greater risk of motor vehicle crashes, consume more health-care resources, and have associated annual costs in the billions of dollars per year. It is increasingly recognized that OSA may also have substantial economic consequences. Specifically, there is accumulating evidence implicating OSA as an important contributor to work disability (including absenteeism, presenteeism) and work-related injuries. This review summarizes the current state of knowledge in these two areas.

Big Sequencing Beclouds Big Data

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  • According to Illumina, next-generation sequencing data volume has doubled every year since 2007, representing over a 1,000-fold increase in the amount of data that needs to be processed. Add in proteomics, metabolomics, medical records, and other information, and it is obvious that Big Data is growing at an explosive rate.

    But without the proper computational and informaticstools more data won’t necessarily amount to more, or better, information. Ongoing governmental initiatives and commercial advances are shaping the way the scientific community addresses this challenge. Bioinformatics leaders recently convened at CHI’s Bioinformatics for Big Data, Converting Data into Information and Knowledge conference to discuss progress in the field.

    The National Center for Multiscale Modeling of Biological Systems (MMBioS)—a collaborative effort between the University of Pittsburgh, Carnegie Mellon University, the Pittsburgh Supercomputing Center, and the Salk Institute for Biological Studies—was established in 2012, in the first round of Biomedical Technology Research Resources (BTRRs). Today, 35 NIH-funded BTRRs create and apply unique technology and methods in their respective fields while facilitating the research of NIH-funded laboratories.

    The MMBioS Resource focuses on neurobiological as well as immunological applications. To gain deeper mechanistic understandings, MMBioS develops multiscale simulations to bridge molecular events and disease and organ functions. In particular, MMBioS sustains technology development projects in molecular modeling, cell modeling, and image processing.

    These technology efforts are guided by biomedical projects that MMBioS conducts with research groups across the country. These projects focus on glutamate transport, synaptic signaling, dopamine transporter function, T-cell signaling, and neural circuits. Besides these driving biomedical projects, MMBioS engages in a large number of collaborations with experimental and computational research groups. In addition, information and technology is disseminated to the larger scientific community through MMBioS’ website, training workshops, and tutorials.

    “This phenomenal type of joint effort is extremely useful,” said Ivet Bahar, Ph.D., distinguished professor and John K Vries chair, department of computational and systems biology, School of Medicine, University of Pittsburgh. “The problems we are dealing with are much more complicated than an individual laboratory can handle. Our role is to build the technology, which we devise in response to existing research needs and challenges.

    “The computations we develop are very fast, efficient, and inexpensive so in silico experiments can minimize the wet lab benchtop effort. Computations serve two important roles: they help interpret experimental data in the framework of well-defined quantitative models and methods, and they help build new hypotheses, which are then tested experimentally.”

    Pittsburgh also has a new BD2K (Big Data to Knowledge) Center of Excellence. This BD2K project, called the Center for Causal Modeling and Discovery, is a collaboration between the University of Pittsburgh, Carnegie Mellon University, the Pittsburgh Supercomputing Center, and Yale University.

    The project’s diverse participants include Carnegie Mellon’s philosophy department. Causality and logic models used for a variety of applications will be further expanded to biomedical Big Data to gain insight into mechanisms of function and to understand relationships important for therapy, especially personalized medicine. A short course for teaching causal modeling techniques is currently being organized.

  • Large Systems Perspectives

    Simple solutions do not solve problems in complex systems. At IPQ Analytics, disease-agnostic models take a large-system perspective and span the entire patient experience, from conditions preceding illness onset to symptom display, diagnosis, treatment decision, physician compliance, patient adherence, and outcome.

    Because the basic disease process remains the same, many elements are present in all diseases. Specific risk factors, however, may be weighted differently, and new elements may be added to customize and extend the general model. For example, in a rare pediatric disease, the model was extended to look at pregnancy history and in utero exposures, factors that are also relevant in breast cancer.

    “We need to consider the complete system and think about the real-world problem before we can ask the right questions,” insisted Michael Liebman, Ph.D., managing director of IPQ Analytics. “Transitioning data to information to knowledge to clinical utility is difficult. We try to identify how large the gap is, what crucial issues need to be addressed, and what questions need to be answered.

    “If the patient is at the top of a pyramid and you work to fill in only the pieces necessary to answer critical questions, then the pyramid remains stable. If you build from the bottom up, as each new technology develops a block, something will always be missing to complete the base, making the pyramid unstable.”

    Some data may be expensive and hard to collect. Modeling enables evaluation of the impact of missing information, and it allows identification and prioritization of what the model needs to make it more precise in its predictions.

    In the modeling of breast cancer risk, the personalized history of the patient, which may contain information such as changes in weight over the patient’s lifetime and time of menarche, will be scrutinized. The modeling will do so while recognizing breast cancer fundamentals, such as the concept that the breast undergoes developmental change throughout a woman’s lifetime, and the concept that hormonal changes, which produce long-term effects, are influenced by body fat and other factors.

    These changes need to be appreciated if modeling it to capture the understanding that risk is not uniform over a woman’s lifetime but varies from stage to stage of personal development. More in-depth analysis of specific regulatory pathways and molecular processes at each stage of development may point to sources of risk and help identify better biomarkers and ways to manage or prevent the disease.

    • Making Data Accessible

      Basic clinical and outcomes research data must be accessible, ideally not just to investigators within an institution, but also across institutions, which may include pharmaceutical companies. Such accessibility is the aim of SPIRIT (Software Platform for Integrated Research Information and Transformation), an integrated research information platform. SPIRIT is designed to enable the integration of in-house, open source, and commercial off-the-shelf applications for the City of Hope (COH).

      “We wanted to develop the platform not just to integrate the data and serve the operational needs, but also as a springboard to put together proof of concepts and new applications, such as machine learning and biomedical natural language processing pipelines, which allow us to analyze data and provide results much faster,” discussed Ajay Shah, Ph.D., director of research informatics and systems, COH National Medical Center.

      Yet much medical data are free-text notes that are challenging to extract and put into a coded searchable database. To address free-text notes, COH combined open-source packages into a platform for biomedical natural language processing. To facilitate the standardization of biomedical and clinical data, COH’s SPIRIT platform leverages the Unified Medical Language System (UMLS), a set of files and software that brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems.
      COH also uses i2b2 (Informatics for Integrating Biology and the Bedside), which was funded by the NIH and developed by the nonprofit organization Partners Healthcare to provide a platform for integrating data across biomedical domains. At COH, i2b2 is used primarily for cohort identification and the determination of biospecimen availability for clinical trials, and it is integrated with the clinical trial management system, cancer registry, biospecimen database, and other data sources via the enterprise data warehouse.
      SPIRIT remains a work in progress. Technical challenges include codification of data, keeping the primary system updated, reconciling differences in ontologies, and such. IP challenges and goal-alignment efforts must also be dealt with, even while a data-sharing culture is inculcated.
      The enormous power of Big Data is exemplified by several initiatives, such as the Shared Health Research Information Network (SHRINE), which enables data integration from various institutions via i2b2, and the Oncology Research Information Exchange Network (ORIEN), which is an evolving partnership between North American premier cancer institutes to leverage multiple data sources and match patients to targeted treatments.

    • Processing Data Faster

      Click Image To Enlarge +
      The Cray Urika-XA analytics server represents the convergence of supercomputers and analytics. Containing over 1,500 cores, the Urika-XA transitions a data center from batch-mode processing to low-latency fast analytics.

      Scientific innovation is progressing at a faster pace than most organizations’ ability to refresh their IT infrastructure; big data requires compute density. For example, usage and technical innovation are driving down sequencing costs, which continues to fuel the informatics demand for higher throughput and accuracy.

      The Cray Urika-XA analytics server contains 48 nodes, over 1,500 cores with 6 TB of RAM, a 38 TB solid-state drive, and a 120 TB POSIX-compliant parallel file system. The small-footprint server is preconfigured and delivered with Hadoop and Spark, is optimized for use at high density, and offers a lower total cost of ownership for a normal data center life cycle of three to five years.

      Because the server has over 1,500 cores, it can run more than 1,500 compute events simultaneously, two to three times the density of other platforms.

      “What makes Urika so cool is the compute density. This convergence of supercomputers and analytics allows scaling from proof of concept to production in the same environment,” stated David Anstey, global head of life sciences at Cray. “You can get more done faster. Think about the possibilities if there were no constraints. What would the impact be if you could ask tougher, more probing questions in an iterative way?”

      A combination of technology and people’s ability to leverage that technology effectively, Anstey insisted, will determine how fast precision medicine evolves.

      The Urika-XA can transition a data center from batch-mode processing to low-latency fast analytics. End users can run their own jobs while the software handles the workflow, simplifying the scientific analysis.

      A large cancer group’s analysis of over 30,000 samples, where the goal was to look at the effect of genetic mutation on gene expression, previously took 6 minutes per sample to complete, almost 3,600 hours for the panel. Rerunning this analysis on Spark using Urika-XA decreased the analysis time to 20 minutes, demonstrating the effectiveness of using in-memory analytics across a significant amount of compute.

      The storage capacity of the Urika-XA platform can allow data to be augmented with additional information, such as metabolic and lifestyle histories, and then reanalyzed without data movement, minimizing expense.

Slimy but nutritious: why we need to eat more seaweed

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Seaweed is cheap, plentiful and food for you – but will we ever learn to love it?
Seaweed is cheap and very nutritious

Seaweed is cheap and very nutritious

‘Try this one, it tastes just like truffle,” says Dan, pulling his hand out of the sea, dousing some purplish-brown weed in fresh water and handing it to me. I nibble a corner, and as the flavour bursts in my mouth, I eat a whole frond of the pepper dulse, amazed by how much taste has been released.

Next up is sea lettuce – that bright green, almost transparent seaweed you see around Britain’s shoreline. It tastes fresh and, you guessed it, just like a type of lettuce.

With these flavours, it’s no wonder this superfood is taking the culinary world by storm. James Martin has been cooking with it on Saturday Kitchen, last weekend Radio 4 devoted an entire episode of The Food Programme to it, sea spaghetti is now available in Tesco and chefs all over the world are cooking with it.

Today, I am paddling in a kayak in Studland Bay in Dorset. My guide Dan Scott is founder-owner of Fore/Adventure, a company offering coastal experiences from wild swimming to paddle-boarding and kayaking, coasteering, bushcraft and forage feasts.

I have been fascinated by our shoreline and sea life ever since I was a child, when holidays were spent happily poking around the rugged Cornish coast. The joy of finding crabs, shrimps and small fish in rock pools has never left me, so when I found seaweeds on the menu at the recently opened Pig on the Beach in Studland, I wanted to go out foraging for myself.


Pooling resources: Abi Butcher and Dan Scott scour the Dorset shoreline for seaweed (JAY WILLIAMS)

Dan is a keen seaweed forager, and regularly supplies the Pig with his watery finds. The night before our trip I feasted on oysters with sea lettuce-infused mayonnaise and grilled hake on a bed of seaweed.

We head out at low spring tide, the perfect time to forage the coastline because the water is at its lowest. “You can forage all year round, but spring onwards is the best time because seaweeds are at their most nutritious and the plants on the foreshore – rock samphire, nettles, alexanders, sea purslane – are all starting to come through,” explains Dan, as he casts a fishing line from his kayak to “troll” for sea bass. He has also put down a small net to catch shoreline crabs.

“They’re soft and make excellent stocks and soups,” says Dan. “People are scared of crabs, but they’re not poisonous — you just cook them up and blend them, or push them through a sieve.”

Learning how to deal with foraged goods is key to making the most of our coastline, which I soon learn is brimming with produce.

“There are around 700 species of seaweed on British shores but only around 20 or so are good to eat,” Dan explains. “There are a few poisonous ones but they are very rare and further out to sea. They’re not like mushrooms where you can do yourself a nasty if you mis-identify.”

Seaweed is packed with minerals and trace elements, vitamins, antioxidants, amino acids and protein. The reality is that we consume it in such small quantities that the only mineral we realistically benefit from is iodine – critical for maintaining a healthy thyroid. One gram of brown seaweed contains roughly five to 50 times the recommended daily intake (though red and green seaweeds provide less), so the only danger is overdose if you eat buckets of the stuff.


Fresh sea bass- the perfect accompaniment to some foraged seaweed (JAY WILLIAMS)

After the truffle and lettuce, we stop at a small outcrop of rocks covered in an olive-green seaweed called Fucus serratus, commonly known as “toothed wrack” or “serrated wrack”. Dan grabs a fistful and cuts off the top two-thirds.

“You must cut, not pull the seaweed from its roots because by leaving them intact you allow the plant to regenerate,” he explains. “This is a must with any form of foraging — we need to be mindful of our relationship with the land and sea, and conserve what we have.”

Dan carries a bottle of fresh water with him to wash the seaweed before I taste it. Some can be eaten raw, others are best cooked first, but it’s important to wash off the salt water — and any bacteria too.

Dan doesn’t hand me this one to eat though. Cooking with seaweed is not just about eating it, some types are best used as a flavouring, cooking on or making into a stock. Irish moss is a natural gelatin and bladderwrack – one of the most common seaweeds we see on UK shores – is a superb moisturiser.

“Seaweed is great dried and then used later as a garnish or sprinkled over potatoes, but be careful how you do it,” Dan advises. “Do it on a radiator or dry in an oven at about 50C [125F] with the door open, being careful not to burn it.”

We paddle to the beach and scout around for razor clam holes, which you see in scores at low tide, sprinkling salt down them and watching the clams pop up. There’s an abundance of shellfish around the bay: whelks, winkles, cockles, mussels and slipper limpets. Vegetation on the sea shore is just as tasty, too. We harvest sea beets that taste like spinach, as well as three-cornered garlic and alexander.

We take our finds back to the Pig, where chef Andy Wright rubs his hands with glee. “It’s quite a challenge cooking with seaweed and that’s the most motivating thing – that you’re making something out of this slimy, salty sea vegetable,” he says. “There’s such an abundance on our coastline, so many flavours.”

I’m sold. Not only is this food free, but it’s healthy, natural and wild and a joy to go out and find. After my morning in Studland I resolve to be far more adventurous in the kitchen and count my lucky stars that I now live by the coast.