Smells like ice

I am reconsidering my last posting. While my attempted ode to the glories of fall was done in sincerity, it has now turned really cold (unpleasantly so). Early in the morning the wind searches you out, finds a vulnerable spot and tunnels in. Tiny little icicles form in your blood stream and melt slowly over the rest of the day.

[Note: Thanks to FG for the photo, it captures the feeling beautifully.]

In adventures in baking: I did make the quinoa-apple-banana-chocolate bread last night. It turned out so-so. It is a little dense. I brought it in to the office, where it is enjoying some popularity. I think it might be worth another try someday.

Smells like Fall

Our thermometers and the angle of the sun in the sky have dropped lately. We are wrapping ourselves in scarves again and sunlight now has a golden sheen. Long distance runners are running the last of the year’s marathons. But what a great time of the year to jog! Any excuse to be out, gulping down gallons of purified autumn air, smelling like apples and wet grass.

I was thinking the other day about E. M. Forster. He might not agree with me. Of autumn smells he said that they are “odours of decay,” “pathetic” because they remind one of spring. However Forster was a depressive English man living in a depressing gray climate who wrote books about idealistic English girls traveling to sun-drenched places to be forever changed by an unexpected incident (okay, ‘sun-drenched’ in A Passage to India and ‘sun-kissed’ for his books in Italy. It seems that Tuscan weather is occasionally punctuated by powerful thunderstorms which stir passions and alter destinies.) However in Central Europe autumn has felt like a release, in the same way the harvest is the fulfillment of the growing season.

In addition to wear scarves and going for autumnal runs, I’m going to start baking -- so take that Forster. Project for the week:

Quinoa, banana and apple bread from La Tartine Gourmande (http://www.latartinegourmande.com/2009/09/25/quinoa-banana-bread/). Wish me well, and stop by for a bite if you’re in town.

Hawking report

Stephen Hawking spoke at CERN this afternoon in a sold out show. At least . . . it would have been sold out if tickets were available and I suppose it is actually more of a ‘colloquium’ than a ‘show.’

Anticipating a large crowd, my colleague and I arrived at 1:45 p.m. for a 3:30 talk and the auditorium was already nearly filled. I’m pleased also to say that the crowd was almost exclusively the 35 and under crowd. Amid these physics-loving, hipster types, with artfully disheveled hair the atmosphere was truly pre-concert: a few cold beers and Wilco-oozing speakers would not have been amiss. Folks were making themselves comfortable, swapping jokes, stories and snacks. I saw one girl with a large bag of kettle corn and a couple of lads splitting a bucket of pretzels.

This none-the-less being CERN people observations were peppered with statistics.

Guy on his mobile, “Dude you better get here soon, I’d say the seats are 75% filled.” One guy to another guy, “If these were benches instead of seats, 50% more people could probably sit in here.”

In this spirit we waited, the air in the room growing more and more stuffy, until Hawking entered. The room hushed reverently and there was much camera clicking.

Seeing him speak in person was a worthwhile experience, even if I was pretty much lost after the third slide of his presentation. (If you’d like to venture in to this territory, you can see a video of the presentation here.)

If you want the punch line of the presentation, I’ll distill it down for you: Standard Field Theory and Quantum Gravity lead to the spontaneous formation of universes.

He will also be giving a less-technical talk at the University of Geneva in a week's time—I might try to catch that too.

Battle cries!

I went swimming this weekend in our happy little Lake Geneva (more properly Lac Leman). There is nothing so unusual about that.

I also became convinced—not just once, but twice—that jumping off a platform five meters above the water (a little more than 16 feet) would be a good idea. This is rather more unusual. It sure was fun, but I could not hurl myself from the platform without releasing a primal scream of fear the whole way down. This has got me thinking, what is the link between fear, screaming and courage?

A little superficial Googling has turned up nothing of interest so I’m only going on my own (largely anecdotal, highly scientific) knowledge. It seems to me that our shouts and cries are meant to be advertisements that we are not afraid. We are after all drawing attention to ourselves. Perhaps this is also meant to disorient and frighten an enemy? Think of the marauding Berserkers, fierce Norse warriors who frightened the entrails out of people with their fearsome battle cries.

I bet anything that our “battle cries” (as mine certainly was when I was leaping off the platform in to the lake—I screamed so loud I have a sore throat) are more often than not a kind of bluff, a behaviour to make us temporarily feel braver than we believe ourselves to be. Just what the mechanism is for this I have no idea, but I bet it is there. And, as it got me off the tower and in to the lake, I’m grateful for it!

Improving Alzheimer's research a million scans at a time

New item in this week's iSGTW ....

Improving Alzheimer's research a million scans at a time

As you read this, your brain is busily working. In a complex but unconscious process, it scans the pixels on your screen, analyzes the images and turns them into meaningful information.

This week, a similar work began, neuGRID, that might help keep our minds whirring wonderfully as we (alas) age.

This massive scanning project will feed 6,300 magnetic resonance (MR) scans from more than 700 patients — a bit less than 200 images per patient, making for an impressive total of 1,260,000 images — through an automated series of calculations. This “pipeline” will analyze the cortical thickness of the brain (a measurement aligned with brain health) and its deterioration over time. The images are from the Alzheimer’s Disease Neuroimaging Initiative in the US, the largest public database of MR scans of patients with Alzheimer’s Disease and a lesser condition termed Mild Cognitive Impairment.

Feeding this entire database through these steps will allow neurological researchers to compare questions across populations, such as: What areas of the of the brain degenerate first? How relevant and accurate are the algorithms we use to model this disease? What morphological changes are disease markers? What drugs might halt or slow this disease?

Alzheimer’s is the second most feared disease associated with aging, following cancer, according to the Alzheimer Society of Canada. Patients with early symptoms have trouble remembering recent events, solving simple math problems, and remembering names of people and places. As the brain degenerates, patients in advanced stages of the disease lose mental and physical functions and need 24-hour care. Doctors do not know what causes Alzheimer’s. Although it affects about half of all people aged 85 and older, it is not considered part of the normal aging process.

neuGRID, a project funded by the European Commission, is analyzing the Alzheimer’s Disease Neuroimaging Initiative data set, squeezing the equivalent of five years of processing time on a single desktop into two weeks, to lay the foundation for much of their work in the future. This project is building a grid to support neuroscience research and hopes to become the flagship e-infrastructure for the community.

“Tweny years ago when I started in this field,” says Giovanni Frisoni, neuGRID partner and doctor who splits his time between reserach and patient care, “Alzheimer’s was equated with aging and regarded as a hopeless disease. Now we are starting to have the first medical treatments. This is an extremely exciting time to be in Alzheimer’s research.”

Application screenshot, showing the output of the CIVET pipeline - Human Cerebral Cortex. Darker areas indicate cortical thinning. Image courtesy neuGRID

Pooled resources

“This community has great computing needs,” says David Manset of Maat G, neuGRID services area leader. “These needs involve large data storage, fast access and massive processing for developing and testing new markers of disease — which grid technology can significantly help to address.”

The ability to evaluate disease markers — indicators of disease progression — will allow companies evaluate new drugs for treatment, speeding up the availability of new treatments to patients.

Computing clusters at three hospitals currently form the nodes of neuGRID’s infrastructure: Fatebenefratelli in Brescia, Italy, Karolinska Institutet in Stockholm, Sweden, and VU University Medical Center in Amsterdam, The Netherlands. Combined, their resources equal about 500 processing cores and 12 terabytes of storage capacity. Early next year, as the project moves into production, neuGRID hopes to access far more resources by joining with the Enabling Grids for E-sciencE “Biomed VO,” or biomedical virtual organization.

“I hope that in a few years we’ll be able to treat Alzheimer’s patients like we can treat hypertension patients,” says Frisoni. “With the correct drugs and care they can be essentially asymptomatic — showing no evidence of the disease.”

For many patients and their families, this would be a dream.

neuGRID will be showcasing this technology at EGEE’09. Don’t miss their live demo on Tuesday, 22 September at 4:30pm. They will demonstrate the real-time functionality of the infrastructure including data acquisition, algorithm execution and the advanced visualization output, accessible from an off-site desktop.

—Danielle Venton, EGEE. neuGRID will use the CIVET pipeline, developed at McGill University, Canada by Yasser Ad-Dab'bagh, et al. Learn more at neuGRID

Hiking: good for the body, more importantly good for the soul

Nicholas Kristof of the New York Times has been writing some good stuff lately of the joys of hiking, including a "how-to guide." My recent trip to the Alps reminded me of the pleasures of this simple, honest pursuit. If done right, you are left humbled, exhausted and inspired.

Here is a teaser from his piece "How to Recharge Your Soul":
"In short: Go take a hike! Backpacking is the cheapest of vacations, and it links you intimately and directly to the world around you. It reminds us that we are just a part of the natural order, not lord of it, and that humble acknowledgment is the first step to improve our stewardship.

Backpacking means you take on your shoulders everything you need to hike and camp. The key is to carry very little, say 10 pounds not including food and water. I frequently see tortured backpackers stumbling along as they lug gargantuan packs that dangle frying pans; in their torment, they gaze enviously at my small pack and mistake me for a day-hiker."

Read the full column.

What lies beneath . . .

Submerged beneath the waves lies a large part of human history.

For our ancestors, the ancient coastlines were attractive places to settle and experiment with what became the foundations of civilization. As the major glaciers melted between sixteen and six thousand years ago, these sites — where people first began to make fishing equipment, build boats and create permanent settlements — became engulfed by the rising seas.

But rather than destroying these ancient landscapes, the rising sea level instead preserved many of them, and with them many details in the story of our past.

“We have a lot to learn by looking under-water. There are many sites to discover and examine, and preservation is in fact often better than on land,” says Geoff Bailey, at the Department of Archaeology, University of York, UK. “There are large gaps in our general knowledge of early history.”

Read the full story in iSGTW.