30 December 2006

Tennis Venues

Crosstown Tennis, 14 W. 31st St., New York
East River Tennis Club, 44-02 Vernon Blvd., Long Island City
Eastside Tennis Club, 220 E. 76th St., New York
Forest Hills Tennis Stadium, 69th Ave. And Burns Rd, Forest Hills
Hrc Tennis, South St., Piers 13 And 14, New York
Midtown Tennis Club, 341 Eighth Ave., New York
New York Health And Racquet Club - Village Tennis Courts, 110 University Place, New York
Prospect Park Tennis Center, 305 Coney Island Ave., Brooklyn
Randall's Island Indoor Tennis, Randall's Island Tennis Field House, New York
Tennis Club Grand Central, 15 Vanderbilt Ave., New York
Tower Tennis Courts, 1725 York Ave., New York
U.S.T.A. National Tennis Center, Flushing Meadows-Corona Park, Flushing
Van Cortlandt Park - Stadium Tennis Courts, W. 241st St. And Broadway, Bronx

29 December 2006

Lucrative store locations pinpointed by new model -- New Scientist

Interesting "geo" (realestate) mining

Lucrative store locations pinpointed by new model
07 October 2006
>From New Scientist Print Edition.
The old mantra about the three most important factors for a shop's success - location, location and location - has been borne out by a new mathematical model. It could help retailers pinpoint lucrative sites for their stores....

28 December 2006

A Letter in response to "Cyber-Neologoliferation" -- NY Times

Here's the letter I wrote in response to this article (which was never published):
I was struck by the recent article on the development of the third edition of the Oxford English Dictionary. I was impressed by the degree to which the curators of this dictionary are embracing modern, computerized search in addition to manual annotation. The parallels between making a lexicon of all the English words and the way scientists are annotating the genes in many genomes being sequenced are quite striking. In both cases, people are looking for where it (word or gene) first appeared and how it's varied in usage across many different contexts. One crucial difference, however, is in the gene annotation business, researchers are very interested in how often a gene is duplicated or how common it is. I feel that people should probably do the same in relation to the OED, tabulating words by their frequency of usage. In a rough fashion, this can simply be done by looking at some statistics, such as the number of "Google hits" for a given term.

Published: November 5, 2006
When I got to John Simpson and his band of lexicographers in Oxford earlier this
fall, they were working on the P's. Pletzel, plish, pod person, point-and-shoot,
polyamorous — these words were all new, one way or another. They had been
plowing through the P's for two years but were almost done (except that they'll
never be done), and the Q's will be "just a twinkle of an eye," Simpson said. He
prizes patience and the long view. A pale, soft-spoken man of middle height and
profound intellect, he is chief editor of the Oxford English Dictionary and sees
himself as a steward of tradition dating back a century and a half....

ooo[clip]ooo ooo[general]ooo ooo[L2E]ooo

26 December 2006

Oenology: Red wine procyanidins and vascular health -- Nature

Looks like I should shift from California Reds to those from département of Gers in the Midi-Pyrenees in southwest France and those from Nuoro province, Sardinia.

Nature 444, 566 (30 November 2006) | doi:10.1038/444566a; Received 29 August 2006; Accepted 9 November 2006; Published online 29 November 2006
Oenology: Red wine procyanidins and vascular health
R. Corder1, W. Mullen2, N. Q. Khan1, S. C. Marks2, E. G. Wood1, M. J. Carrier1 and A. Crozier1
Regular, moderate consumption of red wine is linked to a reduced risk of coronary heart disease and to lower overall mortality1, but the relative contribution of wine's alcohol and polyphenol components to these effects is unclear2. Here we identify procyanidins as the principal vasoactive polyphenols in red wine and show that they are present at higher concentrations in wines from areas of southwestern France and Sardinia, where traditional production methods ensure that these compounds are efficiently extracted during vinification. These regions also happen to be associated with increased longevity in the population....We used the 1999 census data to identify unusual patterns of ageing in France (see supplementary information) and found that there are relatively more men aged 75 or over in the département of Gers in the Midi-Pyrenees in southwest France.Wines from Nuoro and the Gers area have 2–4-fold more biological activity and OPC content than other wines (Fig. 1c, d). This difference remains (P < 0.001) when OPC measurements are extended to a wider selection of wines from the Gers area (2.9 0.1 mM, n = 58), from France (1.8 0.1 mM, n = 61) and from other parts of the world (1.5 0.04 mM, n = 227)....

American Culture’s French Connection -- NY Times

Why isn't there an AmericanCulture.org? The answer from France.

American Culture's French Connection
Published: December 26, 2006
In "Culture in America," Frédéric Martel challenges the view that (French) culture financed by the government is good and that (American) culture shaped by market forces is bad.... Reviewing the book in Le Monde, Michel Guerrin and Emmanuel de Roux also said its strength lay in its emphasis on investigation over opinion. And another article in Le Monde took the American cultural statistics collected by Mr. Martel and compared them with similar figures for France. Its unexpected conclusion was that measured per capita the cultural infrastructures in the two countries were roughly similar... The first half of "Culture in America" — the title echoes Tocqueville's own "Democracy in America" — is built around a question that puzzles some French: Why doesn't the United States have a Culture Ministry?...He seemed to be looking forward to a fight. "That's why my book is about France," he said, "while being about America."

Route to LGA over Queensboro

over queensboro bridge
* Northern Ave
* 51 St.
* 32 Ave.
* somehow get to 25 Ave.
* enter highway near 60T

"Everything before the but is a lie" -- anonymous quote

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts -- PNAS

Interesting analysis of some yeast pseudogenes. However, omits reference to Harrison et al. (2002) JMB.

Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14144-9. Epub 2004 Sep 20.
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts.

25 December 2006

Literature mining for the biologist: from information retrieval to biological discovery -- Nat. Rev. Genetics

Good review... but doesn't mention pubnet!

Nat Rev Genet. 2006 Feb;7(2):119-29. 
Literature mining for the biologist: from information retrieval to biological discovery.Jensen LJ, Saric J, Bork P.

Co-evolution of transcriptional and post-translational cell-cycle regulation -- Nature

Regulatory network evolution

Co-evolution of transcriptional and post-translational cell-cycle regulation
Nature. 2006 Oct 5;443(7111):594-7. Epub 2006 Sep 27.


some bio textmining

Richard K. Belew
"Literature and its referents: Analyzing PubMed citations across PFAM", Richard K. Belew, Robert Finn, Alex Bateman, Poster at ISMB02

Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics -- J Mol. Biol.

Datamining the struc. genomics pipeline

Good Fats, Bad Fats, and Trans Fats -- sciencefriday.com

For the podcast listener: Thought this was a particularly good one. Nice discussion of different types of fats: good (monounsaturated and polyunsaturated, particularly from plants) and bad (saturated, trans-, from partially hydrogenated vegetable oil)

Restrictions on Trans Fats - SciFri Podcast - 2006110324
Good Fats, Bad Fats, and Trans Fats
A sizzling steak with a pat of butter on top. Tuna, trout, or herring. A pile of crispy french fries. A flaky biscuit or delicate pie crust. Sure, all have some fat in them - but which fats are good, which are bad, and which are somewhere in between?...

from http://en.wikipedia.org/wiki/Trans_fat
Trans fatty acids (commonly termed trans fats) are a type of unsaturated fat (and may be monounsaturated or polyunsaturated)...
Chemically, trans fats are made of the same building blocks as non-trans fats, but have a different shape. In trans fat molecules, the double bonds between carbon atoms (characteristic of all unsaturated fats) are in the trans rather than the cis configuration, resulting in a straighter, rather than a kinked shape. As a result, trans fats are less fluid and have a higher melting point than the equivalent cis fats.

Slow Is Beautiful -- NY Times

Turtles! living up to 250 years on a very sparse diet.

Slow Is Beautiful
Published: December 12, 2006
This was no euphemistic brushoff, no reptilian version of ''Sorry, I'll be busy that night washing my hair.'' Paddling around in a tropically appointed pool at the National Aquarium in Baltimore, the husky female Gibba turtle from South America made all too palpable her disdain for the petite male Gibba that pursued her....''The tale of the tortoise and the hare is the turtle's life story,'' said Mr. Cover, who calls himself a card-carrying member of the ''turtle nerds'' club. ''Slow and steady wins the race.'' With its miserly metabolism and tranquil temperament, its capacity to forgo food and drink for months at a time, its redwood burl of a body shield, so well engineered it can withstand the impact of a stampeding wildebeest, the turtle is one of the longest-lived creatures Earth has known. Individual turtles can survive for centuries, bearing silent witness to epic swaths of human swagger. Last March, a giant tortoise named Adwaita said to be as old as 250 years died in a Calcutta zoo, having been taken to India by British sailors, records suggest, during the reign of King George II....

The Man on the Table Devised the Surgery -- NY Times

Thought this was a great medical, human interest story....

The Man on the Table Devised the Surgery
Published: December 25, 2006
Dr. Michael DeBakey, one of the first surgeons to perform a coronary bypass operation, is its oldest survivor


Interesting niche data mining for sports.

Discounting NBA tickets like airline seats
An entrepreneur helps pro sports teams fill stadiums more efficiently, using new technology that tracks ticket sales.
FORTUNE Small Business Magazine
By Maggie Overfelt, FSB Magazine
December 11 2006: 10:06 AM EST
(FSB Magazine) -- As the NBA season gets underway, experts predict a tough slog for the Boston Celtics. Last year's team finished with 33 wins and 49 losses, and the roster this season is filled with younger players and few big names. The bottom line? Senior management has to rely on something else to help attract fans: StratBridge, a 15-person firm based in Cambridge, Mass.....

NIH in the Post-Doubling Era: Realities and Strategies -- Science magazine

Thought this was an interesting article on where NIH is going for the year.

Elias A. Zerhouni

Some notes from Data Mining 2006 (cs545)

Data mining lecture slides for courses based on reference text books

Ian Witten and Eibe Frank:

Margaret Dunham:

Pang-Ning Tan, Michael Steinbach, and Vipin Kumar:

Jiawei Han and Micheline Kamber:


Markov Blankets

Market Blankets (MB) are a promising, relatively new, set of datamining techniques for handling feature selection and related issues on Bayesian networks. Learn about MBs, read about different algorithms for implementing them , try them out for some typical problems (especially ones with many features), and write a short review paper.


Those Inflatable Santas: Eyepoppers to Eyesores -- NY Times

Seems to be an expensive new fad

Those Inflatable Santas: Eyepoppers to Eyesores
Published: December 22, 2006
Whatever else Christmas in America means, it now also includes inflatable outdoor decorations.... But the inflatables have brought the notion of Christmas self-expression to another plane. Now, the Macy's Thanksgiving Day Parade, that televised triumphal march that inaugurates the season, can live on in miniature for weeks at a time, swaying and bobble-heading across the front lawn of anyone willing to pay the electric bill — maybe a thousand dollars if you keep them inflated all the time, less if you leave the skins of your Christmas characters sprawled on the ground most of the day, their crumpled faces staring blankly at the sky or the sod, depending....The inflatables sell off the shelf for $69 to $300, and Gemmy Industries Corporation of Coppell, Tex., which claims to produce the majority of the large figures sighted this year on lawns, porches, terraces and roofs from Long Island to Los Angeles, is not shy about the product's corner-cutting appeal.

Dosage sensitivity and the evolution of gene families in yeast -- Nature

Interesting in relation to copy number. (Also, other papers by Hurst.)

Nature. 2003 Jul 10;424(6945):194-7.Click here to read  Links
Dosage sensitivity and the evolution of gene families in yeast.
Papp B,Pal C, Hurst LD.

Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations -- J Comput Biol.

structure and covariation angle looks interesting

J Comput Biol. 2006 May;13(4):929-45.
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations.
Gunewardena S, Jeavons P, Zhang Z.

24 December 2006

A particular only bacterial fold

A particular only bacterial fold -- beta-lactamases and D-Ala carboxypeptidases.
These enzymes perform functions associated with the unique structure of the bacterial cell wall (i.e. antibiotic resistance and cleavage of D-Ala peptides).

23 December 2006

A Scientist's Nightmare: Software Problem Leads to Five Retractions -- Science

Computer bugs mess up membrane protein structures... Could this have been seen ahead of time? (Also note use of Google scholar by Science to find citations.)

Until recently, Geoffrey Chang's career was on a trajectory most young scientists only dream about. ...His lab generated a stream of high-profile papers detailing the molecular structures of important proteins embedded in cell membranes....Then the dream turned into a nightmare. In September, Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang's group had described in a 2001 Science paper. When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure. Unfortunately, his group had used the program to analyze data for other proteins. As a result, on page 1875, Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures....Chang's MsbA structure was the first molecular portrait of an entire ABC transporter, and many researchers saw it as a major contribution toward figuring out how these crucial proteins do their jobs. That paper alone has been cited by 364 publications, according to Google Scholar.

A impressionists view of Connecticut

"Road to the Land of Nod" 1910 by Frederick Childe Hassam
was painted in the Weir farm in CT
The image -- http://mylifestream.net/photostream/2006/12/c-hassam-road-to-land-of-nod-20dec06.html]

http://metnet.vrac.iastate.edu/browser -- pubmed assistant

Perhaps worth a download...


17 December 2006

Some random but interesting quotes and tidbits

Some random but interesting quotes and tidbits I've been accumulating.... might find them interesting.

"This will be a better world when the power of love replaces the love of power."

"Ontology = Specification of a conceptualization"

"REST = random episodic silent thought"

"The 'four M's', measurement, mining, modeling and manipulation" -- D Lauffenburger.

"When easter is: 1st Sunday after 1st full moon after Vernal equinox"
(difficult to place because involves joining solar & lunar calendars)

"The more choices we are presented with, the more likely it is we'll become a "maximizer" and cease being a "sufficer", (to use the terminology psychologist Barry Schwartz uses in The Paradox of Choice), meaning we're more likely to be unsatisfied with anything less than perfection. "
(from http://www.popmatters.com/pm/columns/article/6668/freedom-from-choice)

13 December 2006

12 December 2006

‘Sonic Hedgehog’ Sounded Funny, at First -- NY Times

Interesting article on gene names in the same spirit as "What's in a name?"

'Sonic Hedgehog' Sounded Funny, at First
Published: November 12, 2006
"Lunatic fringe," "head case" and "one-eyed pinhead" might sound like insults from the schoolyard or talk radio. But these are actually examples of the kind of oddball names that scientists give to genes they discover....

Listing of Statistical Software, besides R

Made up this listing of Statistical Software, besides R -- thought it might be useful

Splus -- http://www.mathsoft.com/webstore
SAS -- http://www.sas.com/software/products.html
statview -- www.statview.com (mac only?)
statistica ??
sigma plot -- www.spss.com
sigma stat --
SPSS -- www.spss.com
MatLab statistics -- http://www.mathworks.com/
NAG excel add ins -- http://www.nag.com/
atlantis -- http://sigmasoftc.com/atlantis/
Good listing of software at


Perhaps (!) a promising biotech startup, as featured in the 16 Nov. WSJ


11 December 2006

The Artist and the Mathematician -- Science Friday

"Chris" lives!

Science Friday > Archives > 2006 > November > November 17, 2006, Hour Two:
The Family that Couldn't Sleep / The Artist and the Mathematician
Starting in the 1930s, Nicolas Bourbaki published dozens of papers, becoming a famous mathematician. There was just one problem: he didn't exist. Join Ira in this hour on Science Friday for a conversation with Amir Aczel about the genius mathematician who never existed.

KT event

According to Wikipedia, mice and men diverged 75 million years ago and then we had the major KT event 10 million years later.


Cycling Around NYC

Top of Manhattan

Route on Google maps

Summary Data
Total Time (h:m:s) 3:41:08 10:46 pace
Moving Time (h:m:s) 2:33:33 7:28 pace
Distance (mi ) 20.53
Moving Speed (mph) 8.0 avg. 24.5 max.
Elevation Gain (ft) +7,875 / -8,006

Avg. Heart Rate 74 bpm Zone 0.8

Temperature (°F) 50.4°F avg. 51.8°F high
Wind Speed ( mph) S 3.7 avg. S 5.8 max.

Central Park to Prospect Park

Route on Google maps
http://www.onnyturf.com/subway and http://monkeyhomes.com/map/nycsubway.php have matching subway maps giving connections back.

Summary Data
Total Time (h:m:s) 5:09:31 11:24 pace
Moving Time (h:m:s) 4:02:56 8:57 pace
Distance (mi ) 27.14
Moving Speed (mph) 6.7 avg. 49.2 max.
Elevation Gain (ft) +2,803 / -2,833

Avg. Heart Rate 84 bpm Zone 0.9

Temperature (°F) 63°F avg. 64.4°F high
Wind Speed ( mph) SSE 6.2 avg. SSE 8.1 max.

Up West Side to NJ

Route on Google maps

Summary Data
Total Time (h:m:s) 3:12:13 16:19 pace
Moving Time (h:m:s) 1:38:16 8:20 pace
Distance (mi ) 11.78
Moving Speed (mph) 7.2 avg. 17.6 max.
Elevation Gain (ft) +4,407 / -4,375

Avg. Heart Rate 83 bpm Zone 0.9

Temperature (°F) 45.8°F avg. 46.4°F high
Wind Speed ( mph) N 1.9 avg. N 5.8 max.

10 December 2006

Metcalfe's Law is Wrong -- IEEE Spectrum

Thought this social networking analogy gave some nice intuition about the power-law network structures.

Metcalfe's Law is Wrong
By Bob Briscoe, Andrew Odlyzko, and Benjamin Tilly
Communications networks increase in value as they add members—but by how much? The devil is in the details

Of all the popular ideas of the Internet boom, one of the most dangerously influential was Metcalfe's Law. Simply put, it says that the value of a communications network is proportional to the square of the number of its users....The foundation of his eponymous law is the observation that in a communications network with n members, each can make (n–1) connections with other participants. If all those connections are equally valuable—and this is the big "if" as far as we are concerned—the total value of the network is proportional to n(n–1), that is, roughly, n^2.... We propose, instead, that the value of a network of size n  grows in proportion to n log(n)....To understand how Zipf's Law leads to our n log(n) law, consider the relative value of a network near and dear to you—the members of your e-mail list. Obeying, as they usually do, Zipf's Law, the members of such networks can be ranked in the same sort of way that Zipf ranked words—by the number of e-mail messages that are in your in-box. Each person's e-mails will contribute 1/k to the total "value" of your in-box, where k is the person's rank. The person ranked No. 1 in volume of correspondence with you thus has a value arbitrarily set to 1/1, or 1. (This person corresponds to the word "the" in the linguistic example.) The person ranked No. 2 will be assumed to contribute half as much, or 1/2. And the person ranked kth will, by Zipf's Law, add about 1/k to the total value you assign to this network of correspondents. That total value to you will be the sum of the decreasing 1/k values of all the other members of the network. So if your network has n members, this value will be proportional to 1 + 1/2 + 1/3 +… + 1/(n–1), which approaches log(n). More precisely, it will almost equal the sum of log(n) plus a constant value. Of course, there are n-1 other members who derive similar value from the network, so the value to all n of you increases as n log(n). Zipf's Law can also describe in quantitative terms a currently popular thesis called The Long Tail.....

To Probe Further
David P. Reed argues for his law in "The Sneaky Exponential" on his Web site at http://www.reed.com/Papers/GFN/reedslaw.html.
Several additional quantitative arguments are made for the n log(n) value for Metcalfe's Law on the authors' Web sites at http://www.cs.ucl.ac.uk/staff/B.Briscoe and http://www.dtc.umn.edu/~odlyzko.
Chris Anderson's article "The Long Tail" was featured in the October 2004 issue of Wired. Anderson now has an entire Web site devoted to the topic at http://www.thelongtail.com.
An article in the December 2003 issue of IEEE Spectrum, "5 Commandments," which can be found at http://www.spectrum.ieee.org/dec03/5com, discusses Moore's and Metcalfe's laws, as well as three others: Rock's Law ("the cost of semiconductor tools doubles every four years"); Machrone's Law ("the PC you want to buy will always be $5000"); and Wirth's Law ("software is slowing faster than hardware is accelerating").

03 December 2006

cycling fast loops in Central Park

4 fast (for me) loops in Central Park. Some stats and images below.

route on Google Maps
Total Time (h:m:s) 2:08:16 5:08 pace
Moving Time (h:m:s) 1:55:04 4:36 pace
Distance (mi ) 24.96
Moving Speed (mph) 13.0 avg. 30.9 max.
Avg. Heart Rate 133 bpm
Temperature (°F) 53.6°F avg. 53.6°F high
Wind Speed ( mph) WNW 8.0 avg. WNW 12.6 max.

Cycling Around New Haven

Route on Google Maps [static cached image]
Elevation Profile

Total Time (h:m:s)7:36:5110:54 pace
Moving Time (h:m:s)4:52:576:59 pace
Distance (mi )41.91
Moving Speed (mph)8.6 avg.20.0 max.
Elevation Gain (ft) +3,583 / -3,586

Avg. Heart Rate88 bpm Zone 1.0

Temperature (°F)48°F avg.57.2°F high
Wind Speed ( mph)SSE 5.1 avg.SSE 8.1 max.