Answer is in your Heart

"I know you're searching for things, Lucas. And I hope with all my heart that you find the answers to your questions. But the answers that you're looking for are closer than you think. They're in your heart. And in the hearts of those who love you." -- One Tree Hill

Payment of Love

"Being a full-time mother is one of the highest salaried jobs in my field, since the payment is pure love." -- Mildred B. Vermont

Nature walk

"In every walk with nature one receives far more than he seeks." ~ John Muir

Informed consent: A broken contract

http://www.nature.com/news/informed-consent-a-broken-contract-1.10862?WT.ec_id=NEWS-20120626

Some customers were less than enthusiastic. Holly Dunsworth, for example, posted a comment two days later, asking: “When we agreed to the terms of service and then when some of us consented to participate in research, were we consenting to that research being used to patent genes? What's the language that covers that use of our data? I can't find it.”

The language is there, in both places. To be fair, the terms of service is a bear of a document — the kind one might quickly click past while installing software. But the consent form is compact and carefully worded, and approved by an independent review board to lay out clearly the risks and benefits of participating in research. “If 23andMe develops intellectual property and/or commercializes products or services, directly or indirectly, based on the results of this study, you will not receive any compensation,” the document reads.

It is not enough to strip out any information that would identify the donor, such as names and full health records, before the data are stored. In 2008, geneticists showed that they could easily identify individuals within pooled, anonymized data sets if they had a small amount of identified genetic information for reference (N. Homer et al. PLoS Genet 4, e1000167; 2008). And it may become possible to identify a person in a public database from other information collected during a study, such as data on ethnic background, location and medical factors unique to the study participants, or to predict a person's appearance from his or her DNA.

The opt-out model — which is used in only a few other places — troubles Misha Angrist, a genome policy analyst at Duke University, who says that it risks taking advantage of people when they are ill. “Even a routine visit to the clinic can be a vulnerable moment, and they're saying, 'Would you mind doing this for future generations, to help people just like you?'.”

Brain Banks for Autism Face Dearth

http://www.nytimes.com/2012/06/26/health/autism-research-hindered-by-scarcity-of-brain-samples.html?ref=science

Paramedics tried to revive the young woman, then rushed her to the hospital, and somewhere in that firestorm of activity and grief, the Trues, Jane and her husband, Jim, considered donation. “I thought of it as a gift, her brain,” she said. “To my mind, the idea that scientists would be learning from her for years to come — how can you put a price on that?”
      
The malfunction reduced by a third Harvard’s frozen autism collection, the world’s largest. A bank maintained by the University of Maryland has 52, and there are smaller collections elsewhere. Altogether there are precious few, given escalating research demands. The loss at the Harvard Brain Tissue Resource Center makes donations from parents like the Trues only more urgent.    

In an average year, the Maryland bank obtains four to eight viable donations, said Dr. Zielke. The Autism Speaks project has obtained an average of fewer than 10 new specimens a year, said Dr. Eric London, who founded the program and leads autism treatment research at the New York State Institute for Basic Research. “When we first stared doing this, we were very squeamish about it,” Dr. London said. “We didn’t want to scare parents away.”      

Regulatory variation tool performance evaluations

http://genepi_toolbox.i-med.ac.at/?page_id=1361
These issues do not allow a clear answer about the performance of each tool. We therefore report here a collection of articles, which have investigated this issue in different contexts. They provide data about the prediction quality, comparisons of different prediction tools, interesting peculiarities (such as different prediction performance for different variant types) or general discussions on this topic.

Performance of prediction tools for non-synonymous SNPs
Prediction tools for splicing regulation elements
Prediction of promoters, transcription factor binding sites and regulatory sites

Stronger than evil

"I believe that unarmed truth and unconditional love will have the final word in reality. That is why right, temporarily defeated, is stronger than evil triumphant." -- Martin Luther King Jr.

Wet iPod

http://www.iphonebuzz.com/iphoneipod-touch-have-water-seals-on-them-171643.php
http://iphone.appstorm.net/how-to/phone/how-to-save-a-wet-iphone-or-ipod-touch/
http://www.ehow.com/how_5129870_fix-washed-ipod.html
http://www.ehow.com/info_12201355_can-short-circuited-ipod-fixed.html
http://www.lovelyish.com/743098910/how-to-save-your-ipod-if-it-gets-wet-do-nothing/

Forgot your iPod in the washing machine? Dropped it in the pool, tub or toilet? Here's some things to try before throwing it out:

• Quickly pull it out from the water
• Don't turn it on (to avoid frying the circuits)
• Wipe off the liquids
• Don't heat it with a hair dryer
• Put the iPod inside a dry ziploc bag with rice grains (uncooked) (rice absorbs moisture) / silica packets
• Put the iPod in a warm dry place and leave it there for 1-2 days
• Charge it 
• Cross your fingers and turn it on.

Might work for other electronic devices too.

Linear regression in R

http://www.montefiore.ulg.ac.be/~kvansteen/GBIO0009-1/ac20092010/Class8/Using%20R%20for%20linear%20regression.pdf

http://www.montefiore.ulg.ac.be/~kvansteen/Teaching20082009.html

> conc
[1] 0 10 20 30 40 50
> signal
[1] 4 22 44 60 82

lm(Y ~ model)

> lm(signal ~ conc)
Call:
lm(formula = signal ~ conc)
Coefficients:
(Intercept)
3.60
conc
1.94

> lm.r = lm(signal ~ conc)

> summary(lm.r)
Call:
lm(formula = signal ~ conc)
Residuals:
1
2
3
4
5
0.4 -1.0 1.6 -1.8 0.8
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 3.60000 1.23288 2.92
0.0615 .
conc
1.94000 0.05033 38.54 3.84e-05 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 1.592 on 3 degrees of freedom
Multiple R-Squared: 0.998,
Adjusted R-squared: 0.9973
F-statistic: 1486 on 1 and 3 DF, p-value: 3.842e-05

Before accepting the result of a linear regression it is important to evaluate it suitability at
explaining the data. One of the many ways to do this is to visually examine the residuals.
If the model is appropriate, then the residual errors should be random and normally
distributed. In addition, removing one case should not significantly impact the model’s
suitability. R provides four graphical approaches for evaluating a model using the plot( )
command.

> layout(matrix(1:4,2,2))

> plot(lm.r)

# Suppose we wish to predict the signal for concentrations of 0.05, 0.15, 0.25, 0.35 and
0.45 along with the confidence interval for each

> newconc=c(5,15,25,35,45);newconc
[1] 5 15 25 35 45
> predict(lm.r,data.frame(conc = newconc), level = 0.9, interval = "confidence")

# add regression line to plots

> plot(conc, signal)
> abline(lm.r)

Pangolin

http://en.wikipedia.org/wiki/Pangolin

Not armadillo

Health information

http://www.hicareers.com/health_information_101/health_information_101.aspx

Health information professionals care for patients by caring for their medical data. They ensure that all of a patient’s health information is complete, accurate, and protected, yet readily available for healthcare providers when needed. There are three professional and academic areas of health information that you can learn about below: Health Information Management, Health Information Technology, and Health Informatics.


understand the workflow in any healthcare provider organization from large hospital systems to the private physician practice.

http://chcm.ubc.ca/


If You’re Not Keeping Score You’re Only Practicing
Evaluating a System-wide Lean Implementation
With Dr. Martin Puterman

http://chcm.ubc.ca/files/2012/03/Lean-Evaluation-CHCM-Mar-2012.pdf

Business analyst 101

http://www.bridging-the-gap.com/how-to-become-a-business-analyst-when-you-have-an-it-background/
http://businessanalystmentor.com/2009/06/12/becoming-a-business-analyst-assessing-your-competence-gap/
http://modernanalyst.com/Careers/InterviewQuestions/tabid/128/Default.aspx
http://harvard-business.alltop.com/
http://2wtx.com/business-analysis/books
https://www.e-junkie.com/ecom/gb.php?ii=276598&c=ib&aff=80220
Join International Institute of Business Analysis (IIBA) ($125 USD (includes account activation fee)) http://www10.iiba.org/source/iiba_signup/GTM_Tier_Display.cfm?Section=Sign_up
http://www.bridging-the-gap.com/leveraging-your-expertise-to-become-a-business-analyst/
http://www.bridging-the-gap.com/become-a-ba-8-5-business-analyst-job-search-mistakes/

by Adriana Beal

Business analysts solve problems for organizations

Having solid technical skills can be a great starting point for someone looking to develop a career in business analysis. In Why do we see technical skills in business analyst jobs? Laura lists a good reason why many BA jobs ask for technical skills: BAs with technical knowledge are more likely to ask the right questions about technical implementation.

The biggest obstacle for IT professionals interested in developing a BA career is the lack of well-developed business skills. One might argue that “soft skills” (the ability to communicate with clarity, precision and eloquence, work well with other people building effective contacts and relationships across and outside the organization, and so on) are more important for a BA than being business-savvy. However, in my experience, software engineers who are passioned about business analysis already value and develop their soft skills, so it’s typically not the main competence gap they face when they try to switch to a BA position.

Understanding things like revenue streams and profit centers, on the other hand, may require a mode of thinking that is relatively unfamiliar to many technical people. Often, IT professionals are more skilled at writing elegant code, and producing software rich and features and functions, than at helping stakeholders determine the right set of project requirements capable of balancing the needs of the company, the market, and the users.

http://www.bridging-the-gap.com/help-a-ba-can-i-make-the-transition-from-sales-to-business-analysis/
Most of my roles have been fairly technical. So I’ll let the readers here chime in with some ideas for you there.

• technical writing
• interviewing stakeholders
• between business and development
• product and stakeholder knowledge
• know the products

• Industry experience
• Functional / domain experience
• Application expertise
• Organization expertise
• "We all have something unique to offer. What’s your point of differentiation?" http://www.bridging-the-gap.com/how-industry-expertise-can-impact-your-business-analyst-job-search/
• Most BAs do not qualify for the vast majority of BA jobs. 
• Business analysts exist to support organizations.

Within your career history lie valuable experiences and transferable skills. Are you emphasizing your most relevant qualifications? Have you fully mined your past to demonstrate your potential to succeed in the future? Does your resume communicate how perfectly well-qualified you are for the positions to which you apply?


Your resume can indirectly sell the following message: “I’m a great business analyst and I just applied for the perfect position. You should contact me because I can help you solve this problem you are having.” That’s positioning.

1) listening 2) asking right questions at right time 3) documenting the outcomes 4) identifying the challenges 5) reporting them to the proper channel at proper time 6) identifying opportunities and resources to make them successful and recommending them to management.

Books:

• The Software Requirements Memory Jogger (Goal Q P C Inc)
• The Memory Jogger II (Goal Q P C Inc)
• Blueprint for success as a New Business Analyst
• How to Start a Business Analyst Career: A guidebook to help you explore the business analyst profession and find entry-level business analyst jobs

Turning point: Jim Hoch

http://www.nature.com/naturejobs/science/articles/10.1038/nj7402-283a?WT.ec_id=NATUREjobs-20120621

Molecular biologist describes how he has held onto a grant for more than 30 years.

In April, Jim Hoch, a molecular biologist at the Scripps Research Institute in San Diego, California, celebrated the ninth renewal of the grant supporting his study of bacterial signalling proteins. Here, he reflects on how his efforts to unravel sporulation led to a three-decade US National Institutes of Health (NIH) grant — one of the longest-running at Scripps.

How have NIH requirements changed?

Proposals used to be more than 20 pages long, and the study sections that review grants lasted for three days. Now, proposals are 12 pages, study sections last one day and half of the applications, the less-impressive ones, are not even discussed. There is a lesson here. Applications of 12 pages need to be clear and concise to make them understandable outside the field. Most importantly, they need to be exciting to read. A proposal needs to have clearly articulated goals that transmit your excitement.

Infinite perception

"If the doors of perception were cleansed everything would appear to man as it is, infinite." -- William Blake

Canadian Society of Microbiologists (CSM)

http://www.csm-scm.org/english/wn_meetings.asp

Surrender

"If you surrender completely to the moments as they pass, you live more richly those moments." -- Anne Morrow Lindbergh

Terra Nova Rural Park, Richmond, bc

Terra Nova Rural Park, Richmond, bc

http://www.richmond.ca/parksrec/ptc/trails/exploring/terranova.htm

Human genetics: Fruits of exome sequencing for autism

http://www.nature.com/nrg/journal/v13/n6/full/nrg3248.html?WT.ec_id=NRG-201206

A role for de novo mutations in ASD has been suggested by previous studies of copy number variation and smaller-scale exome sequencing studies. In the recent studies, Iossifov et al. sequenced 343 family 'quads' (the parents of a single child on the autism spectrum and its unaffected sibling), and Sanders et al. also included 200 quads in the 238 families they sequenced. O'Roak et al. selected 189 trios (a child with ASD and its parents), and Neale et al. also sequenced 175 trios. Although the details differ among the four studies, the findings reveal several shared patterns and interesting leads.

Each of the studies identified de novo mutations that are predicted to disrupt gene function in some of the affected children: the total haul is 127 gene-disrupting mutations. Although only a proportion of these would be expected to be causal — Iossifov et al. estimate 65 of them — it is particularly noteworthy that six genes were found to have a gene-disrupting de novo mutation in more than one individual with ASD, and many others genes are 'hit' by missense mutations more than once. These will be important leads for follow-up work.

Iossifov, I. et al. De novo gene disruptions in children on the autistic spectrum. Neuron 74, 285–299 (2012)

PhenOMIM: an OMIM-based secondary database purported for phenotypic comparison.

http://www.ncbi.nlm.nih.gov/pubmed/22255115

Phenotypic comparison may provide crucial information for obtaining insights into molecular interactions underlying various diseases. However, few attempts have been made to systematically analyze the phenotypes of hereditary disorders, mainly owing to the poor quality of text descriptions and lack of a unified system of descriptors. Here we present a secondary database, PHENOMIM, for translating the phenotypic data obtained from the Online Mendelian Inheritance in Man (OMIM) database into a structured form. Moreover, a web interface has also been developed for visualizing the data and related information from the OMIM and PhenOMIM databases. The data is freely available online for reviewing and commenting purposes and can be found at http://faculty.neu.edu.cn/bmie/han/PhenOMIM/.

Fast Access to Records Helps Fight Epidemics

http://www.nytimes.com/2012/06/19/health/states-using-electronic-medical-records-to-track-epidemics.html?ref=science

More than one-third of the nation’s 5,000 acute care hospitals now use electronic medical records, and the share of primary care doctors using them has doubled to 40 percent in the last two years, said Dr. Farzad Mostashari, the Obama administration’s national coordinator for health information technology.

The technology’s spread is helping “officials faced with events of public health significance to know sooner, act faster and manage better,” said Dr. Seth Foldy, a senior adviser to the Centers for Disease Control and Prevention.

In February, public health officials in Michigan noted an increase in electronic reports from clinical laboratories indicating E. coli cases in several counties. Eleven patients were identified, including six who were hospitalized.        

Tending the Body’s Microbial Garden

http://www.nytimes.com/2012/06/19/science/studies-of-human-microbiome-yield-new-insights.html?ref=science

 The scientists reared mice that lacked any microbiome. In their guts and lungs, the germ-free mice developed abnormally high levels of immune cells called invariant natural killer T cells. Normally, these cells trigger a swift response from the immune system against viruses and other pathogens. In Dr. Blumberg’s microbe-free mice, however, they caused harmful inflammation. As adults, the mice were more likely to suffer from asthma and inflammatory bowel disease.

This experiment parallels studies of children in recent years. Children who take high levels of antibiotics may be at greater risk of developing allergies and asthma later on, many researchers have suggested.        

‘Ome,’ the Sound of the Scientific Universe Expanding

http://www.nytimes.com/2012/05/04/science/it-started-with-genome-omes-proliferate-in-science.html

The word “genome” was first used in 1920, by Hans Winkler, a German scientist, to mean all the material on the chromosomes in a sperm or egg, but did not become really popular until the end of the last century, when genome mapping began. Various experts had differing ideas on where the suffix came from, but it seems to be one that was made up. In any case, it clearly meant the totality of something. Dr. Lederberg, who coined a few scientific terms himself, contributed “microbiome” — all the microbes that live in and on humans — to the growing trend.        

The Predictive Capacity of Personal Genome Sequencing

New DNA sequencing methods will soon make it possible to identify all germline variants in any individual at a reasonable cost. However, the ability of whole-genome sequencing to predict predisposition to common diseases in the general population is unknown. To estimate this predictive capacity, we use the concept of a “genometype”. A specific genometype represents the genomes in the population conferring a specific level of genetic risk for a specified disease. Using this concept, we estimated the capacity of whole-genome sequencing to identify individuals at clinically significant risk for 24 different diseases. Our estimates were derived from the analysis of large numbers of monozygotic twin pairs; twins of a pair share the same genometype and therefore identical genetic risk factors. Our analyses indicate that: (i) for 23 of the 24 diseases, the majority of individuals will receive negative test results, (ii) these negative test results will, in general, not be very informative, as the risk of developing 19 of the 24 diseases in those who test negative will still be, at minimum, 50 - 80% of that in the general population, and (iii) on the positive side, in the best-case scenario more than 90% of tested individuals might be alerted to a clinically significant predisposition to at least one disease. These results have important implications for the valuation of genetic testing by industry, health insurance companies, public policy makers and consumers.                    

http://stm.sciencemag.org/content/early/2012/04/02/scitranslmed.3003380

Neuroscience: The mind reader

http://www.nature.com/news/neuroscience-the-mind-reader-1.10816?WT.ec_id=NEWS-20120619

Adrian Owen has found a way to use brain scans to communicate with people previously written off as unreachable. Now, he is fighting to take his methods to the clinic.

Adrian Owen still gets animated when he talks about patient 23. The patient was only 24 years old when his life was devastated by a car accident. Alive but unresponsive, he had been languishing in what neurologists refer to as a vegetative state for five years, when Owen, a neuro-scientist then at the University of Cambridge, UK, and his colleagues at the University of Liège in Belgium, put him into a functional magnetic resonance imaging (fMRI) machine and started asking him questions.

Affinity in a Moment

"It is wrong to think that love comes from long companionship and persevering courtship. Love is the offspring of spiritual affinity and unless that affinity is created in a moment, it will not be created for years or even generations." -- Kahlil Gibran

Blend as defense

"Some spiders change colors to blend into their environment. It's a defense mechanism." -- Spiderman

Lost and replaced

"Lost wealth may be replaced by industry, lost knowledge by study, lost health by temperance or medicine, but lost time is gone forever." --Samuel Smiles

Virtuous

"The most virtuous are those who content themselves with being virtuous without seeking to appear so." -- Plato

Ubuntu 12 - Where is the print screen dialogue?

http://askubuntu.com/questions/118573/where-is-the-print-screen-dialogue

If you use "Gnome classic"

sudo apt-get install gnome-panel
sudo apt-get install gnome-install

when you hit "Print screen", the screen flashes but no dialog. That's because the pictures are automatically saved in the "/home/user/Pictures" directory.

Hint: You can hold Shift+Ctrl+Print screen to save a region of interest.

Faster Firefox

http://www.hongkiat.com/blog/how-to-reduce-firefox-memory-consumption/
http://kb.mozillazine.org/Memory_Leak

about:config

browser.sessionhistory.max_entries  10
config.trim_on_minimize true
browser.sessionhistory.max_total_viewers 6000
browser.cache.memory.capacity 8000
browser.cache.memory.enable true

Or install and use the Opera browser

Bacteria and germs

http://latino.foxnews.com/latino/health/2012/06/14/germs-are-necessary-to-keep-humans-healthy/

And like environmental ecosystems, your microbial makeup varies widely by body part. Your skin could be like a rainforest, your intestines teeming with different species like an ocean.

Staphylococcus aureus harmlessly in their noses or on their skin but can infect others.

First, the researchers had to collect tissue samples from more than a dozen body sites — the mouth, nose, different spots of skin, the vagina in women, and from feces. Then they teased apart the bacterial DNA from the human DNA, and started analyzing organisms with some daunting names: Lactobacillus crispatus, Streptococcus mitis, Corynebacterium accolens.

Another surprise: There isn't one core set of bacteria that perform those functions. A wide variety can do the same jobs, the researchers found.

Consider the intestinal superbug named C. difficile that people all too often catch while they're in the hospital, and that sometimes kills.

Microbiology: Learning about who we are

Microbial inhabitants outnumber our body's own cells by about ten to one. These residents have become the subject of intensive research, which is beginning to elucidate their roles in health and disease. 

http://www.nature.com/nature/journal/v486/n7402/full/486194a.html

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium

http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html

Human gut microbiome viewed across age and geography
http://www.nature.com/nature/journal/v486/n7402/full/nature11053.html
Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. 

Erowid.org - Documenting the Complex Relationship Between Human & Psychoactives

Erowid.org

Mendeley is a free reference manager and academic social network

It’s time to change the way we do research.

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

• Automatically generate bibliographies
• Collaborate easily with other researchers online
• Easily import papers from other research software
• Find relevant papers based on what you’re reading
• Access your papers from anywhere online
• Read papers on the go, with our new iPhone app

http://www.mendeley.com/

Backup with rsync and cron

crontab -e




# m h  dom mon dow   command

12 3 * * * /usr/bin/rsync -ar --exclude-from="/home/user/.rsync-exclude" --delete --delete-excluded /home/user/. myserver:~/.workstation/




copies local files to remote myserver 

Ubuntu 12 old feel with Gnome

http://debianhelp.wordpress.com/2012/03/09/to-do-list-after-installing-ubuntu-12-04-lts-aka-precise-pangolin/

sudo apt-get install gnome-session-fallback
sudo apt-get install indicator-applet-appmenu
sudo apt-get install gnome-tweak-tool

Then log out and select “GNOME Classic” at the LightDM login screen. You
 need to click on the the little-gear-looking-icon next to where you 
type your password to change your session to Ubuntu Classic “Fallback” 
session. 

Dental science: Oral observatory

http://www.nature.com/naturejobs/science/articles/10.1038/nj7401-147a?WT.ec_id=NATUREjobs-20120607
Studying the mouth, including the diagnostic potential of saliva, is offering opportunities to explore overall health.
In 2010, Michael Lau received an e-mail from a recruiter seeking candidates for a position at the University of California, Los Angeles (UCLA). Would he be interested, the recruiter asked, in applying for a postdoc related to salivary diagnostics? Lau, who was finishing his biochemistry and molecular biology PhD at the University of California, Riverside, and considering his career options, was intrigued and surprised. “I had no idea that you could actually detect systemic diseases, and oral diseases, using saliva,” says Lau.

The opening was in the laboratory of David Wong, associate dean of research at the UCLA School of Dentistry. Wong's group had found in saliva potential biomarkers for oral cancer and the autoimmune disease Sjögren's syndrome, and was searching for others. With his interest piqued, and keen on the potential for practical diagnostic use, Lau successfully applied for the post.

http://dx.doi.org/10.1371/journal.pone.0033037

The National Institute of Dental and Craniofacial Research (NIDCR) in Bethesda, Maryland, invested US$65.6 million into salivary diagnostics research between 2002 and 2011, and the human salivary proteome — an inventory of proteins secreted by salivary glands — was published in 2008 (P. Denny et al. J. Proteome Res. 7, 1994–2006; 2008).

Daniel Malamud says now is the perfect time to become a oral-diagnostics researcher.

Turning point: Rachel O'Reilly

http://www.nature.com/naturejobs/science/articles/10.1038/nj7401-149a?WT.ec_id=NATUREjobs-20120607

You spent some time working alone before collaborating with other researchers. Why?

You have to be able to develop the technology and the methods yourself first, so that you can then go on to make a contribution as a collaborator. That is probably harder for younger people. You can get approached to collaborate while you are still developing ideas and methods, and then end up unable to produce what you need for the collaboration to work. I held off for a few years to actually make sure I could say, 'Yes, we can make that; yes, we can do that'.

What has been your most difficult challenge?

Having grants and papers rejected are probably the things I've found hardest. You have to be able to accept failure. I still feel that when I am talking about my research ideas I am baring part of my soul. It is a very personal thing. I have learned to realize that a rejection may be the result of not communicating my ideas effectively, and not because I am a failure. I try to use negative criticism as constructively as possible.

Postgraduate options: Academia misses the mark

http://www.nature.com/naturejobs/science/articles/10.1038/nj7399-535a?WT.ec_id=NATUREjobs-20120607

Many faculty members still don't realize that only a tiny fraction of US postgraduates land a tenure-track academic research position, says Patrick Brandt, director of science, training and diversity at the University of North Carolina in Chapel Hill. Brandt, a former biochemist, has also initiated several career-advice programmes, including one in which former researchers talk about their non-academic careers. “We are ethically bound to provide broad-spectrum career guidance to rising biomedical scientists,” he says.

Soh says that those who are in a position to influence students are showing subtle, but encouraging, signs of a shift away from the pro-academia bias. “It's not a tidal wave,” she says. “But more questions are being asked and there is more momentum building.”

Meet our 15 finalists and Science in Action winner.

http://www.google.com/events/sciencefair/projects/gsf83.html
Global Neural Network Cloud Service for Breast Cancer

Nine Google Science Fair Projects That Could Change the World
http://www.pcmag.com/slideshow/story/264613/nine-google-science-fair-projects-that-could-change-the-worl/1

Communication Between the Synapse and the Nucleus in Neuronal Development, Plasticity, and Disease

http://www.ncbi.nlm.nih.gov/pubmed/18616423

Communication Between the Synapse and the Nucleus in Neuronal Development, Plasticity, and Disease

Sonia Cohen1,2 and Michael E. Greenberg1,*

ABSTRACT

Sensory experience is critical for the proper development and plasticity of the brain throughout life. Successful adaptation to the environment is necessary for the survival of an organism, and this process requires the translation of specific sensory stimuli into changes in the structure and function of relevant neural circuits. Sensory-evoked activity drives synaptic input onto neurons within these behavioral circuits, initiating membrane depolarization and calcium influx into the cytoplasm. Calcium signaling triggers the molecular mechanisms underlying neuronal adaptation, including the activity-dependent transcriptional programs that drive the synthesis of the effector molecules required for long-term changes in neuronal function. Insight into the signaling pathways between the synapse and the nucleus that translate specific stimuli into altered patterns of connectivity within a circuit provides clues as to how activity-dependent programs of gene expression are coordinated and how disruptions in this process may contribute to disorders of cognitive function.

Caging and uncaging of biological signalling molecules

http://www.prairie-technologies.com/resources/techniques/photochemistry.html

Photolabile “caged” compounds are biological signaling inactive molecules with a photoactivatable group. When these compounds absorb photon(s), the caged group can be cleaved and the active biological signaling molecule is released at the site of action. The photochemical reaction can be very fast, with release of the active species often complete within less than a millisecond.

Caged substances range from ions, second messengers and amino acids to fluorescent dyes. A wide range of bioactive molecules such as second messengers or neurotransmitters are now available with conjugated caging groups. These caging groups render the molecule inert until the cage is opened by photolysis. Using this technique it is possible to precisely control in space and time the application of an experimentally applied signal molecule. This technique is providing new avenues of understanding into neurological disorders and drug delivery methods.

uncage = release

http://www.ncbi.nlm.nih.gov/pubmed/16278654

Shiretoko National Park

http://en.wikipedia.org/wiki/Shiretoko_National_Park
Shiretoko National Park (知床国立公園 Shiretoko Kokuritsu Kōen^?) covers most of the Shiretoko Peninsula at the northeastern tip of the island of Hokkaidō, Japan. The word "Shiretoko" is derived form an Ainu word "sir etok", meaning "end of the Earth".

One of the most remote regions in all of Japan, much of the peninsula is only accessible on foot or by boat. The park is best known as the home of Japan's largest brown bear population and for offering views of the disputed Kunashiri Island, claimed by Japan. The park has a hot springs waterfall called Kamuiwakka Falls (カムイワッカの滝 Kamuiwakka-no-taki^?). Kamui wakka means "water of the gods" in Ainu.

Subventricular zone - site of neurogenesis

http://en.wikipedia.org/wiki/Subventricular_zone

The SVZ is a known site of neurogenesis and self-renewing neurons in the adult brain,^[7] serving as such given the interacting cell types and extracellular molecules promoting such cellular proliferation. Along with the subgranular zone of dentate gyrus, the subventricular zone serves as a source of neural stem cells in the process of adult neurogenesis. It harbors the largest population of proliferating cells in the adult brain of rodents, monkeys and humans.^[8] In 2010, it was shown that the balance between neural stem cells (NSCs) and neural progenitor cells (NPCs) is maintained by an interaction between the epidermal growth factor receptor signaling pathway and the Notch signaling pathway.^[9]

While it has yet to have been studied in-depth in the human brain, the SVZ function in the rodent brain has been, to a certain extent, examined and defined for its abilities. With such research, it has been found that the dual-functioning astrocyte is the dominant cell in the rodent SVZ; this astrocyte acts as not only a neuronal stem cell, but also as a supporting cell that promotes neurogenesis through interaction with other cells.^[4] This function is also induced by microglia and endothelial cells that interact cooperatively with neuronal stem cells to promote neurogenesis in vitro, as well as extracellular matrix components such as teneascin-C (helps define boundaries for interaction) and Lewis X (binds growth and signaling factors to neural precursors).^[10] The human SVZ is different, however, from the rodent SVZ in two distinct ways; the first is that the astrocytes of humans are not in close juxtaposition to the ependymal layer, rather separated by a layer lacking cell bodies; the second is that the human SVZ lacks chains of migrating neuroblasts seen in rodent SVZ, in turn providing for a lesser number of neuronal cells in the human than the rodent.^[2] For this reason, while rodent SVZ proves as a valuable source of information regarding the SVZ and its structure-to-function relationship, the human model will prove significantly different.