Saturday, August 31, 2013

Test Knitting

The mitt pattern is being tested...

by a few seasoned knitters.

So far we've found a few errors and some improvements are being made.

Friday, August 30, 2013

A More Simple Time

During a recent visit to the Hancock Shaker Village I was reminded of how our lives were not so fast-paced.
The iconic round stone barn
A bucolic scene
A natural dye garden

Naturally dyed yarn

I hope you are enjoying Labor Day weekend!

Tuesday, August 27, 2013

August Update

Dear Oogy,
Would you believe that I am still watching my Craftsy class?  I have a block of free time on the horizon, so maybe I'll get it finished before August ends.  It's been very interesting so far, and I'm dreaming up all kinds of ways to use short rows.
Meanwhile, I have been knitting.
The prototype, knit in the round
I'm working out the details of a mitt pattern, which I plan to provide to the Camel Knitters so that we can make and sell them at our annual fundraiser.  I have often thought it would be fun to write a pattern, especially when a knit-as-you-go project turns out great.  It's not fun, I'm sorry to say, but I will be proud of the final product.  I hope my fellow Camels don't swear too much when they try to follow what I've written.  The mitts pictured above are knit in the round.  I have a separate set of instructions written for straight knitting.
Eeww, mitt guts.

My Triboro Tam is done.  It is reversible, and I find myself partial to the wrong side.

The wrong side

The right side
I have not forgotten about the reverse engineering project--I have made plans to acquire the necessary yarn in the very near future.
I hope your August has been relaxing and fun!

Sunday, August 18, 2013

(Semi) Weekly Brain Update: Navigation

This week’s task of deciphering the Journal of Neuroscience has felt much easier than the previous attempt.  There were two articles in the July 31, 2013 issue that leapt off the screen, into my download file.  They are both about memory, a topic I have been considering deeply as I read Suzanne Corkin’s book about H.M., Permanent Present Tense.  Incidentally, I love this book, and I plan to write to Dr. Corkin and thank her profusely for writing it.

The first article about memory is from Zhang and Little and their colleagues.  They examined cellular changes that correspond to memory formation in flies.  Yes, much of what we understand about genetic control of cell function comes from research on fruit flies.  Next time you swat one of those pests, remember to thank it first.  In this study the researchers measured the flies’ ability to remember that a particular odor was a signal for shock.  Then they measured the ability of a protein called Notch to cause accumulation of a protein called CREB, which gets manufactured in the cell and then moves into the cell’s nucleus, where it convinces specific genes to be transcribed.  These genes then produce even more proteins, which act to link cells together and promote their ability to communicate.  It is clearly established that long-term memory depends on physical changes in cells so that they establish connections with each other, but the mechanisms and signals inside the cell that initiate the new connections are still being worked out.  This research shows that the CREB production happens in a cycle, which the authors propose allows the circuit that was activated by the odor + shock situation to get re-stimulated every half hour or so, which strengthens the circuit and allows the fly to remember the next day that that particular odor is bad news. 
It’s always fun to try deciphering a fly article—fly researchers like to be creative with the names they give genes and proteins.  The article mentions Klingon (attaches neurons to glial cells).  You can learn anything on the Web, so I looked it up and found an alphabetical list including armadillo, bag pipe, big brain, blown fuse, and cappuccino (I stopped at C).  See The Interactive Fly for more!  More importantly, the mechanisms in fruit flies are remarkably similar to what is happening in our own cells, so this type of work has provided important information about human brain function.

While fruit flies have been invaluable tools for sleuthing out the cellular mechanisms of memory, brain imaging techniques have provided a window into the neural basis of memory in humans, even while they are learning.  Magnetic resonance imaging (MRI) provides very clear and precise pictures of areas of brain cells (gray matter), and a new form of MRI, called diffusion tensor imaging (DTI), allows one to see the connectivity (white matter) between these areas of cells.  Hofstetter and colleagues used DTI to examine a specific area after humans AND rats learned a new skill.  The humans played the video game The Need for Speed 16 times in 2 hours and had their brains scanned before and after playing.   The rats learned the location of a hidden platform in a pool of water over the course of one day, also being scanned before and after “playing”.  These time frames are considered very short in the realm of brain imaging studies that aim to show structural differences that arise from experience.  DTI measures diffusivity of water molecules in tissue.  In nervous system white matter, the water molecules typically align themselves along the length of the axon, which is the part of the cell that extends from one brain area to another.  A reduction in diffusivity is taken as a sign that the axons have increased their capacity to send information.  Hofstetter and colleagues showed that learning in both humans and rats was associated with decreased diffusivity in the fornix, a band of fibers that connects the hippocampus to other brain structures.  The researchers also demonstrated that the change in white matter was correlated with increased volume of the hippocampus gray matter. In addition, they examined in humans how much they learned about the race course, asking them to arrange scenes of the course in the order that they appear in the video.  The more they learned about the course, the less diffusivity they had in the fornix.

Oogy and I have designated August as the month that we each sign up for a Craftsy class, with the hope of learning something new.  She has decided on a class about shuttle tatting, while so far I have chosen a free mini class on short row techniques in knitting.  Her tatting class is about 245 minutes long, while my “mini” class is 135 minutes.   While we are learning how to tat and short row, perhaps the mean diffusivity of our fornix regions will decrease, indicating that the connections between the hippocampus and the memory regions that will eventually store our newfound knowledge have increased.  While it would be impossible to show it directly, we might also assume that our ability to form these new memories will be due to cyclical CREB production in these brain areas.    

Along with learning some new knitting skills, I also have exercised my hippocampus and fornix recently with a trip to New York City, with my buddy Selma Moss Ward.  We traversed much of Manhattan, beginning in the financial district, where Selma took this great shot of One World Trade Center, I think from Fulton Street.  We made our way uptown and found ourselves in a yarn store on the upper west side, The Yarn Company.  I found one of Amy’s designs especially appealing and procured it and a few skeins of Lorna’s Laces sock yarn in NYC-inspired color ways unique to this shop.  The design is for a hat in the tam o’shanter style called Triboro Tam.   I’m making mine in the suggested Buildings and Sky colorway, and if I like it enough, I’ll make another in Newsprint.
Lorna's Laces Sheperd Sock in "Buildings and Sky"

Same yarn in "Newsprint"
It’s only recently that my trips to NYC have taken me outside the general area between the train stations, so exploring the upper west side and downtown has been very interesting.  I’ve learned to navigate the grid of streets and avenues by foot and subway, and now I can even say I’ve ridden in a taxi.  Lots of CREB cycling through my hippocampus!         

Sunday, August 4, 2013

Weekly Brain Update: Deciding and Disseminating

Written early in the week of July 29…

In the July 24 issue of the Journal of Neuroscience I saw several articles that piqued my interest.  The first article, in fact, was a manifesto urging neuroscientists to be more active in communicating with the general public about work in this field.  While the primary goal in doing these posts has been to motivate myself to read the Journal every week, one byproduct of this is a public dissemination of information.  Hopefully it is acceptable to define “public” as the 5 or 6 of you who read this blog!
There were a number of articles that were focused on the generation of new neurons in the brain.  Many studies have demonstrated that learning is associated with an increase in the production of new neurons in the dentate gyrus of the hippocampus, one of two places in the adult brain where new neurons are made (see below for the other!).  This week’s study by Haditsch and colleagues showed that the increased production of new neurons caused by learning a new task was due to more precursor cells being generated, as opposed to the greater survival of already-formed new cells, which has been the predominant view of how this works.  Furthermore, they showed that the signal to increase the production of precursor cells was dependent on signals from the forebrain.  Another article about new cells was by Tailor and colleagues, who obtained hindbrain neuroepithelial stem cells from 5-7 week human embryos (a controversial source, for certain) and showed that the cells could be stimulated to multiply into functional neurons that would work as part of a circuit in the cerebellum. With so many neural diseases in which specific types of cells degenerate, cell replacement would be a valuable therapeutic tool.  It’s still science fiction now, but this type of research is making some progress.  Speaking of degenerative diseases, the third new-neuron article was about an animal model of Alzheimer’s Disease in which the authors, led by Cheng, examined the function of olfactory sensory neurons that had been temporarily infected with humanized mutated amyloid precursor protein, which is thought to be the main culprit in the formation of neural plaques.  Olfactory sensory neurons are the second type of neuron that gets regenerated throughout adulthood.  Every three weeks your olfactory sensory neurons are getting replaced by new ones, and so they have to constantly reestablish connections in the olfactory bulb and from there, to areas in the cortex.  It’s like a new circuit gets built continuously.  One of the earliest signs of Alzheimer’s is an altered sense of smell, so it might be possible to use this system as a diagnostic tool, but also as a model in animals for testing the effects of treatments that are meant to delay or prevent the disease.  Cheng and colleagues were able to show that if they decreased the expression of the mutant amyloid protein, the cells could reestablish their connections and the mouse could smell normally again.  Researchers usually use aged rodents in order to examine disease progression, but this olfactory system provides a faster alternative.
I have unwittingly challenged myself a bit too much with the article I chose for this week’s post.  I decided to read this particular article because the abstract seemed to be written in a new language, which looked to me like a combination of classic behavioral terms and computational neuroscience.  I felt fairly confident that with enough concentration and contemplation I would understand the research enough to relate it to knitting and describe it to you.  Well, we’ll see if I can make sense of it. 

August 4, after trying all week to digest the article by Liljeholm and colleagues

Liljeholm and colleagues, from the Computational and Neural Systems Program at California Institute of Technology, examined choice behaviors in humans while they were being scanned for activity in specific brain regions.  There’s been a lot of research looking at choice behavior in humans, some of which has been described here in previous posts, but this study was unique in that they tested the degree to which people perceived differences in how likely it was that their choice would yield an appealing outcome.  Of course, they used food as the goal.  A person would have to choose between a banana and Milano cookies, but would need to depend on previous experience to know how likely would their choice actually yield the desired outcome.  If all was equal, you and I would choose the Milanos, but if the chance of actually getting the Milanos was very small, we might instead decide to have the banana, if it was more likely that our choice would be rewarded.  They had a long list of tasty treats in the experiment, including Godiva dark chocolate bars and peanut M&Ms.  

The authors were interested in determining what brain area was necessary to make the comparison of possible outcomes, with the idea that every decision we make is a complex computation of the expected immediate and long-term impacts of the decision, as well as how the situation affects the outcome of our actions.  They called this a “cognitive map” of goal-directed behavior.  In the choice above, it’s not just about how much tastier Milanos are compared to the banana, but when, where and under what conditions the decision is being made.  If it’s 7 a.m. and I’m well-rested and staring at a picture on the refrigerator of me at the age of 24, I will probably choose the banana.  However, I am more likely to choose the Milanos under any other circumstance.

Honestly, I understood very little about how the authors manipulated the cognitive maps of their participants, but I can tell you that they demonstrated that the anterior portion of the supramarginal gyrus of the inferior lobule of the parietal cortex is the hot spot for comparison of potential outcomes of a behavior.  I can also say that they confirmed the role of the medial prefrontal cortex in computing the expected value of the items (Milanos are far superior to bananas, everyone knows).  Their article deserves a much better description than that, but it’s going to take more time and additional background reading to make that possible. 

Here’s how I believe this relates to knitting:
Developing a pattern for mitts

The fair isle sweater is resting in the Pretend Yarn Store

The Albers Pullover (from Interweave Knits summer 2013) 10 rows from being done.
How do I decide which project to work on, the mitts, the fair isle sweater, or the Albers Pullover?  Based only on the appeal of the project, I would choose the fair isle sweater.  However, the cognitive map of my goal directed behavior is more complex than that.  It includes considerations such as: "there are only 10 rows left on the Albers Pullover" and "I need to write the pattern for the mitts in time to test it before the Camel Knitters need to use it" and "the weather is too warm to wear the Albers Pullover, even though it is meant to be a summer sweater" and "I have done enough of the fair isle sweater to know that the pattern is working".  This kept the inferior lobule of my parietal cortex busy and I'll let you know what that activity yielded in the next post.