linkstream2 microblog

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. “}}

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.
“}}

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

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

[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.
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A man who recorded every detail of his life for 5 yrs
http://qz.com/519298/the-story-of-a-man-who-recorded-every-detail-of-his-life-for-five-years/ Interesting combo of hi-tech camera & low-tech written logbook

QT:{{”
“For example, the camera captured a meeting with a colleague in the office corridor, but that didn’t make it in to the log book. Or the log book captured a 30-minute task completed on the computer, but the camera missed that.

The result, as he had suspected, was that the combination was helping him capture more of his day. The log book allowed for reflection and the narrative camera added texture to the reflection.

The power of introspection

There is some scientific evidence of the benefits of Villarroel’s practice. “The experience is consistent with mindfulness practices, which have been shown to have great benefits,” Ronald Riggio, a psychologist at Claremont McKenna College, told Quartz. “The perception of time, however, is subjective.””
“}}

Alphabet passes Apple market cap http://www.cnbc.com/2016/02/01/google-passes-apple-as-most-valuable-company.html 4 largest now in tech ($GOOG $547B, $AAPL 529, $MSFT 425, $FB 326) w/ big oil at #5
QT:{{"
Shares of Alphabet opened nearly 3 percent higher Tuesday, pushing the
technology giant’s market capitalization past Apple to become the
world’s most valuable public company.

Alphabet has a market cap of $547.1 billion, higher than Apple’s
$529.3 billion as of 9:45 a.m. ET.

Apple’s massive market cap is still trailed by Microsoft ($425.7
billion),Facebook ($326.2 billion) and Exxon Mobil ($310.1 billion) to
round out the list of the world’s five biggest companies.
"}}

Dara sharing http://www.nejm.org/doi/full/10.1056/NEJMe1516564 Deems #datascientists as “research parasites,” using another’s data for their own ends via @dspakowicz

QT:{{”
“A second concern held by some is that a new class of research person will emerge — people who had nothing to do with the design and execution of the study but use another group’s data for their own ends, possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what the original investigators had posited. There is concern among some front-line researchers that the system will be taken over by what some researchers have characterized as “research parasites.””
“}}

The Life & Death of an $AMZN Warehouse Temp
http://highline.huffingtonpost.com/articles/en/life-and-death-amazon-temp/ Monitoring every move for max efficiency. Assembly Line of the future?

QT:{{”
“In the years since Amazon became the symbol of the online retail economy, horror stories have periodically emerged about the conditions at its warehouses—workers faced with near-impossible targets, people dropping on the job from heat or extreme fatigue. This isn’t one of those stories. Jobs at Amazon are physically demanding and the expectations can be high, but the company’s fulfillment centers are not sweatshops. In late September, I visited the Chester warehouse for an hour-long guided tour. Employees were working at a speed that seemed brisk yet reasonable. There were no idle moments, but no signs of exhaustion, either.

At the same time, we are living in an era of maximum productivity. It has never been easier for employers to track the performance of workers and discard those who don’t meet their needs. This applies to employees at every level, from warehouse grunts to white-collar workers like those at Amazon headquarters who were recently the subject of a much-discussed New York Times piece about the company’s brutally competitive corporate culture. The difference is that people like Jeff don’t have the option of moving to Google, Microsoft or a tech startup eager to poach managers and engineers with Amazon on their resume.

When it comes to low-wage positions, companies like Amazon are now able to precisely calibrate the size of its workforce to meet consumer demand, week by week or even day by day. Amazon, for instance, says it has 90,000 full-time U.S. employees at its fulfillment and sorting centers—but it plans to bring on an estimated 100,000 seasonal workers to help handle this year’s peak. Many of these seasonal hires come through Integrity Staffing Solutions, a Delaware-based temp firm. The company’s website recently listed 22 corporate offices throughout the country, 15 of which were recruiting offices for Amazon fulfillment centers, including the one in Chester.”
“}}

Glycan Notation Standardized http://cen.acs.org/articles/94/i1/Glycan-Notation-Standardized-Last.html Merging 2 systems: essentials (sugars) & Oxford (bonds/angles). A prereq. for glycomics

QT:{{"Carbohydrate chemists and glycobiologists have now agreed on an expanded and standardized symbol nomenclature based primarily on the Essentials notation (Glycobiology 2015, DOI:10.1093/glycob/cwv091). The agreement “is a major step, as without a common vocabulary and language the glycosciences cannot advance as genomics and proteomics have,” says carbohydrate chemist Peter H. Seeberger of the Max Planck Institute of Colloids & Interfaces. For nonglycan experts, here we explain the two notation systems. ▪
…
The newly standardized Essentials system permits an optional mixed form of notation in which the Oxford system’s angles and dashed and solid bonds are used but its sugar symbols are not.
"}}