Monday, June 28, 2010

Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues.

"These data demonstrate consistent tissue specific methylation for certain CpG islands, with clear differences between white and grey matter of the brain."

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Childhood Adversity, Brain-Derived Neurotrophic Factor val/met and Serotonin Transporter Promoter Polymorphism in Adolescent Depression

NO Interaction Between Childhood Adversity, Brain-Derived Neurotrophic Factor val/met and Serotonin Transporter Promoter Polymorphism on Depression: The TRAILS Study

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Friday, June 25, 2010

Jaco Pastorius, Portrait of Tracy. 2:36 with scrolling score.

PLoS one: Plasma Protein Biomarkers for Depression and Schizophrenia by Multi Analyte Profiling of Case-Control Collections

"Plasma samples from 245 depressed patients, 229 schizophrenic patients and 254 controls were submitted to multi analyte profiling allowing the evaluation of up to 79 proteins, including a series of cytokines, chemokines and neurotrophins previously suggested to be involved in the pathophysiology of depression and schizophrenia."

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Wednesday, June 23, 2010

Learning about neuGRID

neuGRID is a user-friendly grid-based e-Infrastructure which enables the neuroscience community to collect and archive large amounts of imaging data and to access resources for computationally intensive data analyses.

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Nat Nanotech: Carbon nanotube eletrodes

High-power lithium batteries from functionalized carbon-nanotube electrodes

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Sunday, June 20, 2010

Active DNA demethylation in human postmitotic cells correlates with activating histone modifications, but not transcription levels

"Using a global, comparative CpG methylation profiling approach we identified many novel examples of active DNA demethylation and characterised accompanying transcriptional and epigenetic events at these sites during monocytic differentiation. We show that active DNA demethylation is not restricted to proximal promoters and that the time-course of demethylation varies for individual CpGs."

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Thursday, June 10, 2010

Canada, Check Your Privacy Settings [notes] #ncwk

Canada, Check Your Privacy Settings
Ann Cavoukian IPC
Ronald Deibert
Mod Jesse Hirsh

Ann Cavoukian
Need to get rid of zero sum game notion: functionality verus privacy is a bad news game.
Privacy relates to personally identifiable identifiers (PII) name address, social insrance number
Open access – re public information, non-PII.
Fundamental essence is that user controls PII. User in control. For non-PII, there should be little if any control.
State censorship the antithesis of privacy.
Human condition thrives on freedom.
Informational Self-Determination. Individual determines the fate of their information. Germany a world leader.
Privacy does not equal security.
Can have strong security without privacy.
You must have both.
Privacy is the first to go out the window e.g. 9/11.
We need to change the paradigm.
Need to prevent harms. Must prevent data breaches.
Change paradigm from zero-sum to positive sum, win-win.
Privacy must be embedded into the design of a system.
Add-on does not work as well as intrinsic methods.
End-to-end lifecycle protection – data destruction.
Respect for individuals.

Tracking Ghostnet
Shadows in the Cloud

Victims of cyber espionage dozens of governments media, UN, Deloitte, Associated Press
Advanced social engineering using email – Well written, real details malicious attachments /payload
One of the computers compromised was an antivirus service in Taiwan.

Indian govt compromised – 700 documents recovered that had been stolen. e.g. Armed Forces. Defense contract information.

Ghostnet and Shadows a disturbing arms race in cyberspace.
Disturbing geopolitical competition. Domain that is carved up, colonized and militarized.

  1. Global Treaty of Cyberspace needed. Because the web is a valuable commons.

  2. Global Monitoring and Early Warning System International Information sharing Mechanisms.

  3. Support Cyberspace Openness

European Privacy leadership and FTC and FCC leaders are embracing privacy by design.
Younger generations value privacy as much as older.
R. Deibert discusses ethical and legal framework of University and Canada. Citizenlab workers risk being declared spies by other countries.
Anything you put out, be mindful -- it could end up anywhere, without control.
Cloud computing/social network data does exist on real servers which may exist in jurisdictions where privacy legislation is different than here.
Many parts of the world there is no oversight, e.g. anonymous web surfing service hands over data to a research lab's request.
Smartgrid – will have privacy-by-design embedded in its development.

R. Deibert laments metamorphsois of word hacking. Hacking was originally about tinkering, not lawlessness. #hacktivism Now we have a litigious culture of fear. e.g. Don't open this digital lock, have a lawyer with you when you read your EULA.

Question re emerging models of Electronic Health Records. Cavoukian Answer – Ontario is tied for last, at the bottom, with Nunavut, for EHR use. Cavoukian wants EHRs with privacy, the positive sum game. Says this as a patient who has had procedures. Cavoukian contacted Telus re HealthSpace, wanted to test it.

Q: The power government and capital have in benefiting from a lack of privacy.
A. Cavoukian and others influenced Google to make default gmail account secure.
Biometric encryption – there is no representation of your actual biometric – in Netherlands and Israel.

Cavoukian to @cavoukian: “Have the guts to put your own name on it . . . Appalling.”

The Future of the Web and the World [notes] #ncwk

The Future of the Web and the World

Gerri Sinclair

Lucy Bernholz

John Thackara

Mod Jesse Brown

Gerri Sinclair on the Future, trends.

Moore's Law + Network effect > change amplified


  1. Recombinant innovation – knowledge recombined, mashed up

  2. Beyond eLearning – lectures and slides uploaded, Open University. New models of collaboration – wikis. e.g.

  3. Demise of the professional - growth of the professional amateur

  4. Openness ubiquitious - Open Source; Open Data

  5. Mathematician as rockstar breakthrough in mathematics, data deluge; consumer as data.

  6. Transparency vs. privacy. Loss of privacy, but new accountability. Wikileaks- US Army. Classified data leaked in searchable format.

  7. Threats/ benefits of the cloud. Gmail, Facebook,

  8. Big Brother is watching you. Japan/Korea. Wireless sensors+robotics

  9. Evolution of the Web - 3d immersification

  10. Gameification of media – Education, Health, Fitness. Digital media becoming fundamental currency of eduction. Game engines, tourism, health, environment.

  11. Reality continuum – hybrid reality (SMS/homework); AR; continuous partial attention; Book Exodus to the Virtual World

  12. Online Demographics. Silent Gen. /Boomers/Gen X/ Gen Y/ Gen V (Avatars- relationships will be primarily digital). Penguin Club. Cartoon Doll Emporium.

  13. Multiple identities – Who am I?

Lucy Bernholz:

Technology having effects on how people do good.

Most ideas from her talk found in paper – Disrupting Philanthropy.

Data will be platform for change.

e.g. Action supporting Haiti earthquake relief by cell phone or computer. #crisiscamp

> went global – Ottawa London Bogata; no institutional support. Peoplefinder app for tagged photos of missing relatives. Creole > English tweet translator.

“Data is anything that can be digitized.”

Grandma biggest fan of iPad.

Phone gives proximity to data and expertise, gives value to organizations.

Fundamental upset to the role of the institution.

Governance is a problem for groups like Crisis Commons. Not an official nonprofit.

Laws will need to change.

A revolution in where social goods come from and how they change.

New roles for public, private, independent sector.

“We have a very new meaning of place.”

New defintions of scale – can be small and global at the same time.

John Thackara:

I don't want to be led by technology. It's a means for us to do things.

What needs to be fixed and how do we do it?

Doomsday economy: Actions described as positive for economy, direct consequences for

biosphere. Pretty serious.

Alternative solidarity economy: In some places, people are reorganizing their daily lives for reduced impact on environment.

The hours spent looking after others are ways of creating social good, just not yet described yet as economic activity. A very European point of view. More people have access to mobile phones than clean water in the world. Depraved: replacing care by people with care by machines.

You can't grow food with an iPhone.

You shouldn't look after an elderly person with an iPhone.

Brown/Bernholz interlude: OLPC > tablets, netbooks, drove price of tech down. >> micropayments to Africa – you control over investment vs. loan, set your own interest rate.

Panel – a sharing economy will be a huge part of sustainability

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Wednesday, June 9, 2010

The collapse of gene complement following whole genome duplication

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

Hackenberg et al. show that their clustering method, CpGcluster, is better at detecting short, often differentially methylated CpG islands
than sliding-window methods.
"The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by CpGcluster."

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Monday, June 7, 2010

Learning about tools that use gene #ontology for analysis of gene expression and #microarray data #GO

Big bundle of tools here, many web-based.
Make sure to read the disclaimer at the top of the page:

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Cell Research: SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm and epistasis in bipolar disorder

Hu et al.

SHEsisEpi, a GPU-enhanced genome-wide SNP-SNP interaction scanning algorithm, efficiently reveals the risk of genetic epistasis in bipolar disorder.

Hu and colleagues developed a method for analyzing epistasis in a GWAS of complex traits, and exclude the contamination of marginal effects caused by single-locus association. They analyzed the Wellcome Trust Case Control Consortium's (WTCCC) bipolar disorder GWAS data.

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