Archive for February, 2015

Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. American Journal of Human Genetics (2010) 86: 832-838.

Sunday, February 1st, 2015

Pooled association tests for rare variants in exon-resequencing http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032073 Simulation shows advantage of mult. rarity thresholds

Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ,
Sunyaev SR. Pooled association tests for rare variants in
exon-resequencing studies. American Journal of Human Genetics (2010)
86: 832-838.

SUMMARY

Multiple studies indicate strong association between rare variants and
resulting phenotype. This paper describes a population-genetics
simulation framework to study the influence of variant allele
frequency on the corresponding phenotype. In a prior study, causal
relationship between variants and phenotype was resolved by performing
association test on set of variants having allele frequency below a
fixed threshold. However, here it is observed that simulation
frameworks based on a variable allele frequency threshold provide
higher accuracy in association test compared to the fixed allele
frequency model. In addition, inclusion of predicted functional
effects of variants (Polyphen-2 scores) increases the accuracy of the
variable frequency threshold model. Overall, this paper describes a novel methodology, which can be
used to explore the association between rare variants and various
diseases.

Will nanotechnology soon allow you to ‘swallow the doctor’? – CNN.com

Sunday, February 1st, 2015

http://www.cnn.com/2015/01/29/tech/mci-nanobots-eth/

Secret microbiome forensic study reveals #deflategate culprit | The Megabiome

Sunday, February 1st, 2015

http://megabiome.net/2015/01/secret-microbiome-forensic-study-reveals-deflategate-culprit/

My Childhood Memories Are Locked in a Yahoo Account

Sunday, February 1st, 2015

My Childhood Memories Are Locked in a Yahoo Account http://www.theatlantic.com/technology/archive/2014/06/i-asked-the-internet-to-guess-the-answers-to-my-security-questions/373223 Nice example illustrating difficult tradeoffs in #datasecurity

The Long Road to Maxwell’s Equations – IEEE Spectrum

Sunday, February 1st, 2015

The Long Road to #Maxwell’s Equations
http://spectrum.ieee.org/telecom/wireless/the-long-road-to-maxwells-equations Heaviside simplified the original 20 eqns. to the current 4 w. vector fields

Also, Hertz’s 2 “loop” experiments were key!

A great grave to visit.

QT:{{”

Should you wish to pay homage to the great physicist James Clerk Maxwell, you wouldn’t lack for locales in which to do it. There’s a memorial marker in London’s Westminster Abbey, not far from Isaac Newton’s grave. A magnificent statue was recently installed in Edinburgh, near his birthplace. Or you can pay your respects at his final resting place near Castle Douglas, in southwestern Scotland, a short distance from his beloved ancestral estate.

You could start the clock in 1800, when physicist Alessandro Volta reported the invention of a battery, which allowed experimenters to begin working with continuous direct current. Some 20 years later,Hans Christian Ørsted obtained the first evidence of a link between electricity and magnetism, by demonstrating that the needle of a compass would move when brought close to a current-carrying wire. Soon after, André-Marie Ampère showed that two parallel current-carrying wires could be made to exhibit a mutual attraction or repulsion depending on the relative direction of the currents. And by the early 1830s, Michael Faraday had shown that just as electricity could influence the behavior of a magnet, a magnet could affect electricity, when he showed that drawing a magnet through a loop of wire could generate current.

A major seed was planted by Faraday, who envisioned a mysterious, invisible “electrotonic state” surrounding the magnet—what we would today call a field. He posited that changes in this electrotonic state are what cause electromagnetic phenomena.

The net result of all of this complexity is that when Maxwell’s theory made its debut, almost nobody was paying attention.

But a few people were. And one of them was Oliver Heaviside. Once described by a friend as a “first rate oddity,” Heaviside, who was raised in extreme poverty and was partially deaf, never attended university.

Heaviside ended up reproducing a result that had already been published by another British physicist, John Henry Poynting. But he kept pushing further, and in the process of working through the complicated vector calculus, he happened upon a way to reformulate Maxwell’s score of equations into the four we use today.

Now confident that he was generating and detecting electromagnetic waves, Lodge planned to report his astounding results at a meeting of the British Association, right after he returned from a vacation in the Alps. But while reading a journal on the train out of Liverpool, he discovered he’d been scooped. In the July 1888 issue of Annalen der Physik, he found an article entitled “Über elektrodynamische Wellen im Luftraum und deren Reflexion” (“On electrodynamic waves in air and their reflection”) written by a little-known German researcher, Heinrich Hertz.

Hertz’s … noticed that something curious happened when he discharged a capacitor through a loop of wire. An identical loop a short distance away developed arcs across its unconnected terminals. Hertz recognized that the sparks in the unconnected loop were caused by the reception of electromagnetic waves that had been generated by the loop with the discharging capacitor.

Inspired, Hertz used sparks in such loops to detect unseen
radio-frequency waves. He went on to conduct experiments to verify that electromagnetic waves exhibit lightlike behaviors of reflection, refraction, diffraction, and polarization.
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How to Catch a Terrorist – The New Yorker

Sunday, February 1st, 2015

http://www.newyorker.com/magazine/2015/01/26/whole-haystack

Disambiguating Databases | January 2015 | Communications of the ACM

Sunday, February 1st, 2015

http://cacm.acm.org/magazines/2015/1/181618-disambiguating-databases/abstract

What the Web Said Yesterday – The New Yorker

Sunday, February 1st, 2015

http://www.newyorker.com/magazine/2015/01/26/cobweb