30 January 2006
From Shakespeare to Star Trek and beyond: a Medline search for literary and,other allusions in biomedical titles -- BMJ [clip]
BMJ. 2005 Dec 24;331(7531):1540-2.
>From Shakespeare to Star Trek and beyond: a Medline search for literary and other allusions in biomedical titles.
OBJECTIVES: To document biomedical paper titles containing literary and
other allusions. DESIGN: Retrospective survey. SETTING: Medline (1951 to
mid-2005) through Dialog Datastar. MAIN OUTCOME MEASURE: Allusions to
Shakespeare, Hans Christian Andersen, proverbs, the Bible, Lewis Carroll, and
movie titles, corrected and scaled for five year periods 1950-4 to 2000-4.
RESULTS: More than 1400 Shakespearean allusions exist, a third of them to
"What's in a name" and another third to Hamlet-mostly to "To be or not to be."
The trend of increasing use of allusive titles, identified from Shakespeare and
Andersen, is paralleled by allusions to Carroll and proverbs; the trend of
biblical allusions is also upward but is more erratic. Trends for newer
allusions are also upwards, including the previously surveyed "paradigm shift."
Allusive titles are likely to be to editorial or comment rather than to original
research. CONCLUSIONS: The similar trends are presumably a mark of a particular
learnt author behaviour. Newer allusions may be becoming more popular than older
ones. Allusive titles can be unhelpful to reviewers and researchers, and many
are now cliches. Whether they attract readers or citations is unknown, but
better ways of gaining attention exist.
Useful Bioinformatics Related Courses at Yale
MCDB 200a. Genetics. Stephen Dellaporta and staff. TTh 11:30-12:45
An introduction to classical, molecular and population genetics, of both prokaryotes and eukaryotes and their central importance in biological sciences. Emphasis on analytical approaches and techniques of genetics used to investigate mechanisms of heredity and variation. Topics include transmission genetics, cytogenetics, DNA structure and function, recombination, gene mutation, selection, and recombinant DNA technology.
Gene Mining Strikes Gold - eweek [clip]
Plackett-Burman designs [clip]
YALE is an environment for machine learning experiments and data mining. Experiments can be made up of a large number of arbitrarily nestable operators and their setup is described by XML files which can easily be created with a graphical user interface. Applications of YALE cover both research and real-world data mining tasks.
29 January 2006
The LOV Domain Family: Photoresponsive Signaling Modules Coupled to Diverse Output Domains
Random Subspace Method for Linear Classifiers [clip]
28 January 2006
Emergent behavior of growing knowledge about molecular interactions.
Cokol M, Iossifov I, Weinreb C, Rzhetsky A.
A billion nonredundant molecular interactions lie buried in the biomedical literature. A text-mining approach could help scientists better exploit this knowledge.
http://liveplasma.com + Like This? You'll Hate That. (Not All Web Recommendations Are Welcome.) -- NY Times [url]
Like This? You'll Hate That. (Not All Web Recommendations Are Welcome.)
By LAURIE J. FLYNN
Published: January 23, 2006
SAN FRANCISCO, Jan. 22 - On Amazon.com, a customer interested in buying the novel "The Life of Pi" is also shown "The Kite Runner" because other Amazon customers - presumably with similar tastes - also purchased that book. That's just one approach among many in the science of recommendation software.
24 January 2006
Demystifying the eBay Selling Experience -- NY Times [clip]
Demystifying the eBay Selling Experience
By ALINA TUGEND
Published: January 21, 2006
THE two collectible "Star Wars" light sabers - authentic sound effects! glowing
bright blue blade! - had been hanging around our garage for months. They were a
present from a well-meaning aunt to our 7-year-old son, who, unfortunately, had
outgrown his "Star Wars" phase a few years before.....Others, like iSold It -
the biggest eBay drop-off chain in the country, with about 500 branches - are individually owned franchises that complete the whole process internally. Typically, its commission is 30 percent of the first $500 and 20 percent of the remaining amount, which includes eBay listing fees.
22 January 2006
The Battle of the Sexes
Harry Ostrer, MD
Recent research suggests that women are more complex than men because men have only 45 chromosomes while women have 46.
"M.B.A. COM; Studying With Stanford-Columbia-Chicago*
April 25, 2004, Sunday
By SCOTT JASCHIK (NYT); Education Life Supplement
Late Edition - Final, Section 4A, Page 33, Column 3, 1008 words
DISPLAYING FIRST 50 OF 1008 WORDS -Last fall, I decided I should learn a little theory-of-business-strategy for a venture I was about to undertake, so I fired off e-mail inquiries to e-Cornell, Cardean University and the University of Phoenix. The first thing I noticed was the eagerness to sign me up for just one master's..."
21 January 2006
Masters of the Semantic Web -- Bio-IT world [clip]
Masters of the Semantic Web
By Salvatore Salamone
Oct 17, 2005
“I see a huge amount of energy from people in the life sciences getting excited about the Semantic Web and what it can do to solve the big IT problems... But also the people involved in the Semantic Web pushing it along are also very excited about getting involved in the life sciences — it’s one of those areas that affect humankind, finding drugs, curing AIDS and cancer, etc. There seems to be a huge energy, and lots of practical technical reasons why this area is crying out to be one of the flagship areas that the Semantic Web really takes off...” — Sir Tim Berners-Lee, Bio•IT World Conference+Expo, May 2005
20 January 2006
Coding a Bridge Across the Data Divide -- The Scientist [clip]
by Jane Salodof MacNeil
Coding a Bridge Across the Data Divide
Email: Jane Salodof MacNeil
The Scientist 2004, 18(24):25 -- Published 20 December 2004
If you want to know how biology will be practiced in the coming decades,
check out a recent National Academy of Sciences colloquium on frontiers
in bioinformatics. Assembling data is no longer the biggest challenge,
says meeting cochair Russ B. Altman, citing sophisticated presentations
on pseudogenes, RNA splicing, and molecular evolution. Instead, the
major hurdle these days is one of data integration....
Bioinformatics on the Brink -- The Scientist [clip]
Bioinformatics on the Brink
Email: Kate Fodor - email@example.com
The Scientist 2004, 18(24):34
Published 20 December 2004
When a working map of the human genome was announced in June 2000, it was immediately clear that it would open new avenues of study and transform the life sciences, both in academia and in industry. One of the many new opportunities was in bioinformatics: the use of computers to rapidly scan databases, analyze sequence data, and help predict protein structure based on DNA sequence. Companies and universities would be eager to purchase bioinformatics tools to help them manage the massive amounts of genomics and proteomics data they would be generating.
That has, indeed, turned out to be true. But for a number of reasons, the market opportunity for bioinformatics tools hasn't been as expansive as was thought, and many companies have suffered as a result.....
Despite the struggles that bioinformatics companies are experiencing, heavyweight, diversified IT companies such as IBM and Sun Microsystems show no signs of shying away from partnerships with the smaller companies or giving up on the bioinformatics market. "All the large IT vendors are getting very involved in life science," Zimmerman says. The big companies don't actually develop bioinformatics software, but they see opportunity in partnering with the software developers by providing hardware, service, and support for bioinformatics tools, and selling the complete package to firms involved in drug discovery.
War of the Worlds [clip]
18 January 2006
New Improved Brooklyn -- New York Magazine [clip]
New Improved Brooklyn
By Alexandra Lange
A glittering skyline, waterfront condos, new jobs, Frank Gehry buildings galore:
Brooklyn is on the verge of a makeover even more extreme than you thought,
re-creating itself in Manhattan’s image. What’s wrong with this picture?
Nailing Your New York Number -- New York Magazine [clip]
Nailing Your New York Number
Here’s what it will take for you to stop working and never run out of money. A formula for the good life.
By Lee Eisenberg
How large a nest egg do you need to fund a secure, satisfied post-career life in New York and be confident that your assets will outlast your pulse? What is your New York Number? It’s an annoying question, fraught with the things you don’t want to think about: destitution, deterioration, death. It’s therefore a question that’s usually asked at night, almost always silently. How you frame the question depends on your age and temperament......
Lowering Expectations at Science's Frontier -- nytimes.com [clip]
Lowering Expectations at Science's Frontier
Jeon Kyung Woo/Newsis via Reuters
By NICHOLAS WADE
Published: January 15, 2006
THERE is considerable disorder in heaven when stem-cell scientists are chided by the Roman Catholic Church for the folly of pursuing "miracle cures." But such are the paradoxes generated by the implosion of a South Korean researcher's widely believed claims to have created human embryonic stem cells from patients.....The contrast between the fallibility of Dr. Hwang's claims and the general solidity of scientific knowledge arises from the existence of two kinds of science - a distinction that is often blurred when new advances are reported first by scientific journals and then by the news media. There is textbook science and frontier science, and the two types carry quite different expiration dates.
Textbook science is material that has stood the test of time and can be largely relied upon. It may include findings made just a few years ago, but which have been reasonably well confirmed by other laboratories. Science from the frontiers of knowledge, on the other hand, is wild, untamed and often either wrong or irrelevant to future research. A few years after they are published, most scientific papers are never cited again. Scientific journals try to impose order on the turbulent flow of new claims by having expert reviewers assess their merit. But even at the best journals, reviewers provide only a rough screen. Many papers slip through that later turn out to be innocently wrong. A few, like Dr. Hwang's, are found to be fraudulent....
Mashups mix data into global service -- Nature [clip]
Nature 439, 6-7 (5 January 2006) | doi:10.1038/439006a
Mashups mix data into global service
Is this the future for scientific analysis?
Will 2006 be the year of the mashup? Originally used to describe the mixing together of musical tracks, the term now refers to websites that weave data from different sources into a new service. They are becoming increasingly popular, especially for plotting data on maps, covering anything from cafés offering wireless Internet access to traffic conditions. And advocates say they could fundamentally change many areas of science — if researchers can be persuaded to share their data.....
Nature 439, 19-20 (5 January 2006) doi:10.1038/439019a
A robust approach
The functional overlap between different components protects biological systems.
BOOK REVIEWED - Robustness and Evolvability in Living Systems
by Andreas Wagner
When sitting on an aeroplane, we obviously hope that it won't crash. A tacit assumption behind this wish is that our biological system isn't about to crash either. It so happens that these systems share several features. Both have specific parts that serve certain functions. The plane was designed by engineers, who were in turn designed by evolution through natural selection. Both systems seem robust and yet fragile, but how can we reconcile these two seemingly opposing features? One answer is that they are robust and fragile to different perturbations, being particularly robust to perturbations that are common in their 'niche'. Another answer is that robustness can be in a trade-off with other features, such as price and reproduction rate...
17 January 2006
Alone in the Dark -- New Yorker [clip]
ALONE IN THE DARK
Kim Jong Il plays a canny game with South Korea and the U.S.
by PHILIP GOUREVITCH
Issue of 2003-09-08
In 1866, the S.S. General Sherman, an ironclad schooner recommissioned for use in the China trade after service for the Union as a blockade runner in the Civil War, came sailing across the Yellow Sea and entered the mouth of the Taedong River on the west coast of the Korean peninsula. What the ship’s commander, a Captain Preston, was after—trade or spying or pillage, or all three—remains a matter of speculation. Korea, a feudal kingdom ruled according to a strictly paternalistic Confucian code, was notoriously hostile to foreigners, and with reason......
15 January 2006
March of the Penguins [clip]
yalealumnimagazine.com : Yale's $8 billion man [clip]
Yale's $8 billion man
by Marc Gunther '73
Last spring, Yale president Richard C. Levin '74PhD held a cocktail reception for David F. Swensen '80PhD, who was celebrating his 20th year as Yale's chief investment officer. Inside the president's official residence, posters and news clippings mounted on easels tracked the growth of Yale's endowment from $1.3 billion to $14 billion under Swensen's stewardship. The display culminated in a bar chart titled "Value of Key Contributors to Yale University."...Towering above them was a bar bearing Swensen's name and an astonishing number: $7.8 billion....
Where America is most vulnerable and how the nation can better manage the risks ahead.
Dr. Irwin E. Redlener is in Baton Rouge, La., setting up mobile medical units. He has been in Louisiana and Mississippi for many long days helping people deal with the horror of Hurricane Katrina, and his voice is full of anger and despair. 'The country is really just not prepared for a major catastrophic event,' says the director of the National Center for Disaster Preparedness at Columbia University's Mailman School of Public Health. 'Whatever it is -- the Big One in San Francisco, a terrorist attack -- it doesn't matter. The unfortunate truth is our ability to imagine and plan for catastrophic disasters is woefully inadequate.....
Questions for Allegra Goodman -- nytimes.com [clip]
I think she's married to another classmate, David Karger.
Questions for Allegra Goodman
Interview by DEBORAH SOLOMON
Your new novel "Intuition" revolves around a scandal in which a research biologist in Cambridge, Mass., deliberately falsifies his data in order to get credit for a cancer breakthrough. Is it based on a true story?...
No. I had the idea of writing about a couple. One of them suspects the other one is cheating. But not cheating in the usual way. I've always found tales of adultery rather dull...
Galileos Daughter [clip]
Galileos Daughter by Dava Sobel
14 January 2006
nytimes.com: When the Market Values Hope Over Experience by a Factor
When the Market Values Hope Over Experience by a Factor of 18
By FLOYD NORRIS
Published: January 14, 2006
THREE companies with household names are worth about the same amount now - at least in the opinion of investors. Google, I.B.M. and Berkshire Hathaway all have market capitalizations in the vicinity of $135 billion...
Disclosure Won't Tame C.E.O. Pay
By JOSEPH NOCERA
Published: January 14, 2006
THIS Tuesday, the Securities and Exchange Commission plans to unveil its first overhaul of executive compensation disclosure rules in 14 years. The new rules, which were leaked to the news media this week, are intended to give investors a fuller picture of the staggering amounts of money going to America's chief executives and other top corporate officers.
13 January 2006
12 January 2006
Genetics: Copy correction and concerted evolution in the conservation of yeast genes [clip]
Genetics. 2005 Aug;170(4):1501-13. Epub 2005 May 23.
Copy correction and concerted evolution in the conservation of yeast genes.
Pyne S, Skiena S, Futcher B.
The yeast Saccharomyces cerevisiae and other members of the genus Saccharomyces are descendants of an ancient whole-genome duplication event. Although most of the duplicate genes have since been deleted, many remain, and so there are many pairs of related genes. We have found that poorly expressed genes diverge rapidly from their paralog, while highly expressed genes diverge little, if at all. This lack of divergence of highly expressed paralogous gene pairs seems to involve gene correction: one member of the pair "corrects" the sequence of its twin, and so the gene pair evolves as a unit. This correction presumably involves gene conversion and could occur via a reverse-transcribed cDNA intermediate. Such correction events may also occur in other organisms. These results support the idea that copies of poorly expressed genes are preserved when they diverge to take on new functions, while copies of highly expressed genes are preserved when they are needed to provide additional gene product for the original function.
Reviews on Systems Biology and Molecular Networks [clip]
* Some Yale reviews on data integration and molecular networks
* Reviews by Kitano on systems biology
Computational systems biology
Nature 420, 206-210 (14 November 2002)
Systems biology: a brief overview.
Science. 2002 Mar 1;295(5560):1662-4.
* Reviews by Vidal on systems biology and data integration
Ge H, Walhout AJ, Vidal M.
Integrating 'omic' information: a bridge between genomics and systems biology.
Trends Genet. 2003 Oct;19(10):551-60. Review.
A Biological Atlas of Functional Maps
Cell. 2001 Feb 9;104(3):333-9.
09 January 2006
times.com: The Prodigy Puzzle [clip]
The Prodigy Puzzle
November 20, 2005, Sunday
By ANN HULBERT (NYT); Magazine
'So you're the geniuses,'' Senator Carl Levin said, looking pleased as he peered over his glasses. He was addressing the flaxen-haired Heidi Kaloustian, a 17-year-old freshman at the University of Michigan, and John Zhou, a superfriendly 17-year-old senior at Detroit Country Day School, unusual visitors to Room 269 of the Russell Office Building on Capitol Hill. Michigan had distinguished itself, Levin had been informed: the state boasted two Davidson Fellows, and he had clearly been told these teenagers came trailing brainy superlatives. ''Genius loves company,'' announced the September press release about the students who had won scholarships awarded annually since 2001 by the Davidson Institute for Talent Development, a foundation that supports ''profoundly intelligent'' youths, a more recent term for off-the-charts children. ''Seventeen prodigies,'' the press release went on, were ''to be honored at the Library of Congress for contributions to society'' in the fields of science, math, technology, music and literature....
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06 January 2006
Some groups interested in Computational Geometry in Relation to Proteins
Stanfordhttp://csb.stanford.edu (M Levitt)
http://papers.gersteinlab.org/papers/subject/volumes ... and, in particular,
05 January 2006
04 January 2006
stuff at live.com
Check out some of the views of Manhattan
at local.live.com -- e.g.
(click on the bird's eye icon!)
NYTimes: Credit Cards With Rewards Are Worth a Look [clip]
By DAMON DARLIN
Published: December 31, 2005
If it seems like you are getting a lot of credit card solicitations, you are. Credit card companies sent out about six billion letters in the last year. But if you opened any, you may have noticed a dwindling number of zero-percent balance-transfer offers and more pitches for cash-back reward cards. Half of them are for reward cards....TAG[General]ooo TAG[clip]ooo
03 January 2006
WSJ: Computer Makers Cater to Big Business, Slight the Rest of Us
December 29, 2005
Computer Makers Cater to Big Business, Slight the Rest of Us
By WALTER S. MOSSBERG
If you went to work this morning and sat down at your desk in front of a personal computer, your experience probably took one of two routes.
Lots of you found yourself logging in, probably multiple times, using passwords you could barely remember because you are forced to change them so often. Then, you entered a world of computing where much of the power and variety of the technology was closed off to you in the name of security or conformity by an information-technology department in your large corporation or organization. Various Web sites were off-limits, as were tools like instant messaging, even though they might have legitimate business purposes.....
TIG: Microeconomic principles explain an optimal genome size in bacteria [clip]
Trends Genet. 2005 Jan;21(1):21-5.
Microeconomic principles explain an optimal genome size in bacteria.
Ranea JA, Grant A, Thornton JM, Orengo CA
Bacteria can clearly enhance their survival by expanding their genetic
repertoire. However, the tight packing of the bacterial genome and the fact that
the most evolved species do not necessarily have the biggest genomes suggest
there are other evolutionary factors limiting their genome expansion. To clarify
these restrictions on size, we studied those protein families contributing most
significantly to bacterial-genome complexity. We found that all bacteria apply
the same basic and ancestral 'molecular technology' to optimize their
reproductive efficiency. The same microeconomics principles that define the
optimum size in a factory can also explain the existence of a statistical
optimum in bacterial genome size. This optimum is reached when the bacterial
genome obtains the maximum metabolic complexity (revenue )
for minimal regulatory genes (logistic cost).
More sopranos locations in NJ
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