linkstream2 microblog

QT:{{”
“Bill Hart-Davidson, MSU’s associate dean for graduate education, suggests that the likely answer is “text-mining,” the use of computer programs to analyze large collections of documents to generate data. When I called Hart-Davidson, I suggested that the East Lansing Sci-Hub scraper might be someone from his own research team. But he laughed and said that he had no idea who it was. But he understands why the scraper goes to Sci-Hub even though MSU subscribes to the downloaded ” “}}

Who’s downloading pirated papers? Everyone
http://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone freely available data on @scihub usage
http://datadryad.org/resource/doi:10.5061/dryad.q447c

AstraZeneca…proj. to seq. 2M
http://www.nature.com/news/astrazeneca-launches-project-to-sequence-2-million-genomes-1.19797 Ironic @JCVenter Qt: Think carefully before you just dump your genome on the Internet

For complete irony, compare this qt w/ commentary on @JCVenter’s original personal
sequencehttp://www.WashingtonPost.com/wp-dyn/content/article/2007/09/06/AR2007090602362.htmlhttps://twitter.com/markgerstein/status/726064243695583232

QT:{{”
“Human Longevity’s databases are kept locked behind layers of security. “If I were advising a younger Craig Venter, I’d say, ‘Think carefully before you just dump your genome on the Internet’,” Venter says. “The levels of prediction are getting much more interesting.” “}}

QT:{{”
“I have a recurring nightmare. It is years into the future. All the wonderful everyday objects we once treasured have disappeared, gobbled up by an unstoppable interface: a slim slab of black glass. Books, calculators, clocks, compasses, maps, musical instruments, pencils, and paintbrushes, all are gone. The artifacts, tools, toys, and appliances we love and rely on today have converged into this slice of shiny glass, its face filled with tiny, inscrutable icons that now define and control our lives. … In my nightmare, the cold, black slab has re-architected everything — our living and working spaces, our schools, airports, even bars and restaurants. We interact with screens 90 percent of our waking hours. The result is a colder, more isolated, less humane world. Perhaps it is more efficient, but we are less happy.”
“}}

http://www.businessinsider.com/enchanted-objects-by-david-rose-2014-8

In #Scrap…Market, Buyers Have to Tell Darth From Vader
http://www.wsj.com/articles/in-scrap-metal-market-buyers-have-to-tell-darth-from-vader-1459263473 Elmo for intact electric motors & Shelmo for shredded ones

QT:{{”

““I like a little double entendre,” says Mr. Goodman, recalling how he made up “Elmo” so that U.S. traders could sell recycled electric motors to China, and “Shelmo” for shredded electric motors. “You should have heard the chuckles when I proposed that.”

The result reads like absurdist poetry but helps buyers distinguish Cocoa (shredded wire containing at least 99% copper but no more than 0.25% tin) from Cobra (shredded wire with minimum 97% copper and not more than 0.5% aluminum). Zorba is a mix of eight metals.”

“}}

An…Attempt to Save the Reefs & Forests
http://NewYorker.com/magazine/2016/04/18/a-radical-attempt-to-save-the-reefs-and-forests Engineering the #chestnut tree to express OxO, a defense against its blight

QT:{{”

“Powell attended graduate school in the nineteen-eighties, around the same time as Gates, and, like her, he was fascinated by molecular biology. When he got a job at the forestry school, in 1990, he started thinking about how new molecular techniques could be used to help the chestnut. Powell had studied how the fungus attacked the tree, and he knew that its key weapon was oxalic acid. (Many foods contain oxalic acid—it’s what gives spinach its bitter taste—but in high doses it’s also fatal to humans.) One day, he was leafing through abstracts of recent scientific papers when a finding popped out at him. Someone had inserted into a tomato plant a gene that produces oxalate oxidase, or OxO, an enzyme that breaks down oxalic acid.

“I thought, Wow, that would disarm the fungus,” he recalled.

Years of experimentation ensued. The gene can be found in many grain crops; Powell and his research team chose a version from wheat. First they inserted the wheat gene into poplar trees, because poplars are easy to work with. Then they had to figure out how to work with chestnut tissue, because no one had really done that before. Meanwhile, the gene couldn’t just be inserted on its own; it needed a “promoter,” which is a sort of genetic on-off switch. The first promoter Powell tried didn’t work. The trees—really tiny
seedlings—didn’t produce enough OxO to fight off the fungus. “They just died more slowly,” Powell told me. The second promoter was also a dud. Finally, after two and a half decades, Powell succeeded in getting all the pieces in place. The result is a chestnut that is blight-resistant and—except for the presence of one wheat gene and one so-called “marker gene”—identical to the original Castanea dentata.”

“}}

Runs in the Family
http://www.newyorker.com/magazine/2016/03/28/the-genetics-of-schizophrenia Overview of recent results that #SCZ is due to synaptic overpruning from excessive C4 activity

QT:{{”
A magnificently simple theory began to convulse out of the results. Perhaps C4A, like the other immunological factors that Stevens had identified in synapse pruning, marks neuronal synapses destined to be eliminated during normal brain development. During the maturation of the brain, microglia recognize these factors as tags and engulf the tagged synapses. Variations in the C4A gene cause different amounts of the C4A protein to be expressed in the human brain. The overabundance of C4A protein in some people contributes to an excessively exuberant pruning of synapses—thereby decreasing the number of synapses in the brain, which would explain the well-established fact that
schizophrenic patients tended to have fewer neuronal connections. That the symptoms of schizophrenia break loose during the second and third decades of life makes sense, in retrospect: adolescence and early adulthood are periods when synaptic pruning reaches a climax in the regions of the brain that govern planning and thinking.
“}}

The Most Powerful Movements in #Biology
http://www.americanscientist.org/issues/id.16405,y.2015,no.5,content.true,page.1,css.print/issue.aspx How nature uses the latched bow-&-arrow construct in many contexts

QT:{{”
Just like the bow and arrow example, mantis shrimp raptorial appendages contain a spring and a latch to generate extreme power amplification. Their mechanism for power amplification is just a tweak to the standard antagonistic muscle contractions that characterize most animals’ motor systems. Just like the extensor and flexor muscle pairs that extend and flex our limbs, mantis shrimp raptorial appendages use extensor muscles to swing out their hammer and flexor muscles to fold appendage segments toward the body during normal, daily activities. However, when they need to do a high-powered blow, they contract the flexor and extensor muscles simultaneously (similar to the antagonistic leg muscle contractions that we do prior to a jump). When they co-contract these muscles, the large, bulky extensor muscles compress an elastic system and tiny flexor muscles pull latch-like mineralizations of their apodemes (tendons) over a small lump inside the appendage, thus providing effective mechanical advantage over the high forces of the large extensor muscles. The result is no movement at all! The system is primed to strike as soon as the flexor muscles relax, release the latches, and permit the stored elastic energy to release over an extremely short time period to push the hammer forward with extreme power output.

“To varying degrees, this is the trick that all high-power systems use: They temporally and spatially separate slow loading and energy storage from the rapid release of energy that confers power
amplification. Trap-jaw ants release tiny latches that block their preloaded mandibles (watch a video on Patek’s research on trap-jaw ants). Two droplets slowly grow until the point at which they fuse over exceedingly short time scales to yield the power to launch a fungal ballistospore. The jellyfish’s stinger waits within a slowly pressurizing cell; a trigger hair dramatically releases the stored pressure and ejects the stinger toward its target. Thus, whether a muscle-based movement or a fluid-driven motion, the underlying mechanisms of ultrafast systems are all about power amplification.” “}}

Yet more thoughts on squeezing in stuff:

Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing:
– 12 pt spacing exactly & 0 before & after + 4 pt before major heads (except for in-line figures, then automatic ‘single spacing’) such as INNOVATION

– no widow/orphan control

– no spaces before paragraphs, just indents

– bullet (*) lists (eg for people)

Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) ****

Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. ****

Titles: Cambria 12 pt looks nice, but flexible.

References: NIH Style EndNote. [1]

QT:{{”
NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}

QT:{{”

11. Descriptive Title of Applicant’s Project

Enter a brief descriptive title of the project. This field is required.

A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.

A “revision” application must have the same title as the currently funded grant.

NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).

“}}

The above is OLD. Now you can go above 81 characters.

QT:{{”
Font

Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}

Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.

QT:{{”
Paper Size and Page Margins

Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.

….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}

http://grants.nih.gov/grants/funding/424

More thoughts on this. One person’s condensed summary of this for Word:

QT:{{
Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing: 12 pt exactly (except for in-line figures, then automatic ‘single spacing’)
Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) **** Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. **** Titles: Cambria 12 pt looks nice, but flexible.
References: NIH Style EndNote. [1]

NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}

QT:{{”

11. Descriptive Title of Applicant’s Project

Enter a brief descriptive title of the project. This field is required.

A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.

A “revision” application must have the same title as the currently funded grant.

NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).

“}}

The above is OLD. Now you can go above 81 characters.

QT:{{”
Font

Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}

Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.

QT:{{”
Paper Size and Page Margins

Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.

….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}

http://grants.nih.gov/grants/funding/424

The Lawyer Who Became DuPont’s Worst
Nightmarehttp://NYTIMES.com/2016/01/10/magazine/the-lawyer-who-became-duponts-worst-nightmare.html Scary account of the risks from unregulated flurochemicals incl #PFOA
QT:{{”
Last May, 200 scientists from a variety of disciplines signed the Madrid Statement, which expresses concern about the production of all fluorochemicals, or PFASs, including those that have replaced PFOA. P “}}