Posts Tagged ‘quote’

Runs in the Family – The New Yorker

April 11, 2016

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 » American Scientist

March 27, 2016

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.” “}}

SF424 (R&R) Application and Electronic Submission Information for NIH

March 26, 2016

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

SF424 (R&R) Application and Electronic Submission Information for NIH

March 19, 2016

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 Nightmare – The New York Times

February 29, 2016

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 “}}

PLOS Genetics: A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

February 27, 2016

Model-Based Approach to Inferring…#Cancer Mutation Signatures http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005657 Assuming independence betw 3 NTs, 11 v 95 parameters

QT:{{”
The first contribution of this paper is to suggest a more parsimonious approach to modelling mutation signatures, with the benefit of producing both more stable estimates and more easily interpretable signatures. In brief, we substantially reduce the number of parameters per signature by breaking each mutation pattern into “features”, and assuming independence across mutation features. For example, consider the case where a mutation pattern is defined by the substitution and its two flanking bases. We break this into three features
(substitution, 3′ base, 5′ base), and characterize each mutation signature by a probability distribution for each feature (which, by our independence assumption, are multiplied together to define a distribution on mutation patterns). Since the number of possible values for each feature is 6, 4, and 4 respectively this requires 5 + 3 + 3 = 11 parameters instead of 96 − 1 = 95 parameters. Furthermore, extending this model to account for ±n neighboring bases requires only 5 + 6nparameters instead of 6 × 42n − 1. For example, considering ±2 positions requires 17 parameters instead of 1,535. Finally,
incorporating transcription strand as an additional feature adds just one parameter, instead of doubling the number of parameters. “}}

NOT-OD-16-011: Implementing Rigor and Transparency in NIH & AHRQ Research Grant Applications

February 14, 2016

New grant format w/ prelim. results under significance v. approach as nowhttp://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-011.html @NIH notice is cryptic. People’s thoughts?

+
need to use strength & weakness for each citation.

see also:
http://www.grantcentral.com/wp-content/uploads/2015/12/Supplement-Changes-in-Approach-Subsection.pdf http://grants.nih.gov/grants/forms_updates_faq.htm#2426
http://grants.nih.gov/grants/funding/424/index.htm

QT:{{”
One of the changes to this Chapter pertains to the format for the Approach subsection, which is reproduced, above. “Justification and Feasibility” and its two subdivisions have been lined out because, with the new approach that we recommend, they are no longer part of the Approach subsection. (We have moved them to the Significance subsection, Chapter 9). Without those components, the formatting for each aim “collapses” to include the Introductory Paragraph, Research Design, Expected Outcomes and Potential Problems & Alternative Strategies.
“}}

&

QT:{{”
Updates to Research Strategy Guidance
By November 25, 2015 application guide instructions will be updated to include the following additional guidance for the Significance and Approach sections of the Research Strategy, in addition to the existing instructions.
Significance
Describe the scientific premise for the proposed project, including consideration of the strengths and weaknesses of published research or preliminary data crucial to the support of your application. Approach
Describe the experimental design and methods proposed and how they will achieve robust and unbiased results.
“}}

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

February 12, 2016

Reprogramming…#epigenome & transcriptome in…muscle after training http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622000/ Delta(Me) from #exercise in 1 leg v. other

QT:{{”
Exercise has long been known to have an effect on health, lowering the incidence of cardiovascular disease, obesity, and type 2 diabetes. Recently, it has been found that exercise can have a direct effect on DNA methylation and gene expression. A group of 23 subjects exercised one leg but not the other for 45 minutes four times a week for three months. At the end of this period, the methylation and gene expression patterns were different in the exercised leg relative to the one that did not exercise, indicating a direct effect of exercise on
epigenetics.
“}}

Quote from:

https://books.google.com/books?id=qotyCwAAQBAJ&pg=PA91&lpg=PA91&dq=Exercise+has+long+been+known+to+have+an+effect+on+health,+lowering+the+incidence+of+cardiovascular+disease,+obesity,+and+type+2+diabetes.+Recently,+it+has+been+found+that+exercise+can+have+a+direct+effect+on+DNA+methylation+and+gene+expression.+A+group+of+23+subjects+exercised+one+leg+but+not+the+other+for+45+minutes+four+times+a+week+for+three+months.+At+the+end+of+this+period,+the+methylation+and+gene+expression+patterns+were+different+in+the+exercised+leg+relative+to+the+one+that+did+not+exercise,+indicating+a+direct+effect+of+exercise+on+epigenetics.&source=bl&ots=paSuwD6wvw&sig=gwFDNYvSMRlkFouTcaoyf9q3c20&hl=en&sa=X&ved=0ahUKEwjZzv7imu3KAhXK5SYKHaP6DdEQ6AEIHjAA#v=onepage&q=Exercise%20has%20long%20been%20known%20to%20have%20an%20effect%20on%20health%2C%20lowering%20the%20incidence%20of%20cardiovascular%20disease%2C%20obesity%2C%20and%20type%202%20diabetes.%20Recently%2C%20it%20has%20been%20found%20that%20exercise%20can%20have%20a%20direct%20effect%20on%20DNA%20methylation%20and%20gene%20expression.%20A%20group%20of%2023%20subjects%20exercised%20one%20leg%20but%20not%20the%20other%20for%2045%20minutes%20four%20times%20a%20week%20for%20three%20months.%20At%20the%20end%20of%20this%20period%2C%20the%20methylation%20and%20gene%20expression%20patterns%20were%20different%20in%20the%20exercised%20leg%20relative%20to%20the%20one%20that%20did%20not%20exercise%2C%20indicating%20a%20direct%20effect%20of%20exercise%20on%20epigenetics.&f=false

NIH precision vs personalized medicine

February 12, 2016

QT:{{”
There is a lot of overlap between the terms “precision medicine” and “personalized medicine.” According to the National Research Council, “personalized medicine” is an older term with a meaning similar to “precision medicine.” However, there was concern that the word “personalized” could be misinterpreted to imply that treatments and preventions are being developed uniquely for each individual; in precision medicine, the focus is on identifying which approaches will be effective for which patients based on genetic, environmental, and lifestyle factors. The Council therefore preferred the term “precision medicine” to “personalized medicine.”
“}}

http://ghr.nlm.nih.gov/handbook/precisionmedicine/precisionvspersonalized

New York Is Going to Turn Off Niagara Falls. Here’s How | WIRED

February 10, 2016

[Turning] Off Niagara Falls
http://www.wired.com/2016/01/new-york-is-going-to-turn-off-niagara-falls-heres-how When they “dry up, the effect will be equiv of looking
under your sofa for the 1st time”

QT:{{”
When the falls dry up, the effect will be the equivalent of looking under your sofa for the first time in decades. When crews shut down the falls in 1969, they found two bodies and millions of coins, most of which were removed. (As were the human remains, of course.) But in the last 50 years, tourism at Niagara has grown wildly. The
possibilities are endless—more coins, yes, but also lost cell phones,cameras, baby strollers, errant drones, and whatever else could be thrown or dropped by careless, thoughtless, or mischievous visitors. There is, of course, the possibility of human remains being discovered again—though there are no individuals known to have jumped or fallen in who haven’t been recovered.
“}}