Allen Brain Atlas: Brain Explorer 2!

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As a fan of new gadgets and software, especially those related to the brain, I was quite stoked to see that the Allen Institute for Brain Science / Allen Brain Atlas (Seattle, WA) came out with a new version of their Brain Explorer, which is a program that you download and you have the brain at your fingertips!  It is, quite simply, amazing. (link is at bottom of post).

For those who don't know, Brain Explorer (BE) is a software used to visualize neuroanatomical locations in the brain.  It's better than a regular book atlas in that you can move the brain around to get a 3D view.

Now, Brain Explorer 1 is pretty cool.  I've used it before to demonstrate where the hippocampal formation is in a previous blog post (Ingredients of a Hippocampus, bottom two figures).  It nicely shows what structures you want it to show in relation to other structures, and, in the program, you can move the brain around on an X-Y-Z axis to get a real 3D view of it -- enough with the Styrofoam models!  This is really helpful to visualize and spatially pin-point unfamiliar neuroanatomical areas.

What's the upgrade to Brain Explorer 2? A big download of greatness! Read on for that & some pictures...

Cognits, Rhythms, & Memories

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Moving away from the hippocampus to straightup networks, the other theme of this blog, I'm deciding to do a post of a general overview on cortical networks and memory in general. After reading Olaf Sporn's Networks of the Brain, which I recommend, and re-reading a review article on memory and 'the cognit' (large neocortical networks supporting this function), I feel more confident in my ability to read, understand, and soundly comment on it.  I'm sure this is a highly incomplete story for anyone that wants to get technical.  For that, I recommend the book below.

Originally, I read Fuster's book (1) on the distributed networks (for a class in undergrad where it was assigned) and, since then, the general idea revolving around cognition and distributed processing has captured my attention.  Broadly, the 'cognit', as a term coined by JM Fuster, is a representation of some knowledge that is located in the neocortex: there is a hierarchical order to cognits and are neural networks that are widely distributed throughout the cortex.  Importantly, these cognits are highly interactive with each other.  Fuster is mainly concerned with the neocortex and, as such, does not talk much about subcortical areas but does not dispute that these areas are, too, wired  into the fabric (they have to be!).  Anyway, this idea builds on the a Hebbian synapse idea and cell assemblies (wiring of neurons 'together') but extends greatly upon it to include, most importantly, how cognition is generated.  It also extends on the fact that cognits can intertwine with other cognits and participate in several seemingly disparate processes.  The activation of this cognit that is serving a particular memory does indeed involve the original cortical areas (e.g. sensory) as well as far-reaching frontal areas. For me, the cognit and other distributed processing models make sense, especially in the light of "weighting" pathways depending on task/mental demands/properties and also makes perfect sense of how we can have knowledge constantly being integrated into memories and new associations that can activate memories.

One might not see how this is different from other distributed network or associative models of the brain, but the idea is not necessarily that it's radically different in terms of networks in the brain. Rather, it's a new way of thinking of how these networks act and how these networks give rise to cognition (memory; mind).  While the book of the cognit goes through attention, memory, perception, language, and intelligence, many cognitive functions, very broadly, can be distilled down into memory, whereby the absence of this faculty would render most other cognitive properties (but not all), well, useless.


(read on for: modules, networks, rhythms, & the cognit

The Public Understanding of Neuroscience: My Work

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While looking at my blog statistics, I realized that one of the more popular posts here is Neuroscience At All Levels.  This is likely because of its broad overview and accessibility to the public.  I am a fan of Neuroscience "outreach" and there have been some interesting posts on the matter of how scientists should be doing more of it. scicurious (part II), one of Nature's blogs, and there are others circulating.

The basic story from what I can see:  One side says that scientists should be telling the public about their research in an attempt to help them understand what's going on in their world!  The opposite side: we don't have time! (Please excuse the brevity and feel free to add more arguments in the comments.)  While I think both sides have valid points, I fall in the middle, luckily!  Yes, I am a graduate student and do research and my postings here have been going downhill lately, because I've been busy with research.  I also don't have the added enormous pressure, as of yet, to publish in order to save my career and do not have to worry about grant writing or giving talks at conferences.

So, onward with the Outreach!  What I'm doing is trying to understand the relationship between the hippocampus, anxiety, and behavior.  My story follows...

A Thought on Cognition & Emotion

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I am in the midst of writing a longer, more substantial post, but, because I have not written a post in awhile, I thought it would be better to give a bit of a prelude to the upcoming post.  This short post is more about asking the fundamental question regarding those functions relating to 'cognition' and those of 'emotion'.  This post is really just something that has been spinning through my head for the past few months, inspired by an article I read questioning such a distinction and the nature of the two terms.  As such, I am very much eager to hear others' arguments and opinions on the subject.  As should be mentioned before long, I am primarily talking about rodents.

Do these functions matter, meaning can cognition and emotion ever be twisted apart; does this unraveling even matter, since they are so inter-connected and joined that maybe they are one entity; finally, maybe more importantly, are these terms neurally meaningless and just semantically-null labels we give functions because we can simply ask the questions and label the function?

While this cognition/emotion question is relevant to all psychological processes, it seems to be a particularly tricky problem in the hippocampus and especially with non-human animals.

(read more after the jump...) 

Rewind: The Path from Behaviorism to Mental Maps [update: other hpc functions added; video at bottom]

All students agree as to the facts. They disagree, however, on theory and explanation
 Tolman, 1948

Animals DO think!!
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Occasionally, I like to venture back to older papers and see what they found, how they interpreted it, and how the data would be interpreted today (okay, I just stumble upon them usually).  With the guise of a scientific model/framework of how a certain region of the brain works, some (much?) older data is disregarded, because it does not fit the mold of the current understanding.  This disregarded data may be legitimate and it may not be legitimately disregarded.  It may just be disregarded because of selective "cherry picking" of what fits the model (confirmation bias).  Some of the data are still relevant and maybe more so today, as it gives pause to the person and makes them question the model, if ever so briefly.

One extraordinary example of this comes from the field of adult neurogenesis.  It was discovered in the rat (and confirmed, re-confirmed a few years later) by Altman & Das (1965).  Post-natal neurogenesis was disregarded, because it did not 'fit' the current model of how the brain operates (e.g. brain only generates new neurons before or soon-after birth).  After 40 years, the phenomenon was re-examined, has subsequently been confirmed, and now has a large literature dedicated to it.  This example shows the importance of thinking about our current models of interpretation, always question them, and also raises our consciousness to the fact that scientific findings are not under a monolithic interpretation.  The hippocampus is thought largely today to be the neural equivalent of the 'cognitive map', which was formulated in experimental psychology by Tolman.

*note: I've decided to cover a wider spectrum of information here in order to thrust towards a larger point: Question.

read on for a brief history of behaviorism, latent learning, vicarious trial and error, Tolman and the cognitive map, and where we are today... and video!

Qualia & Behavior: A Rambling

Qualia: the property or characteristic experienced by a person.
By definition, qualia is personal
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This post was inspired by me watching rats in a behavioral task (testing for 9+ hours a day makes you think of some interesting things!) at lab.

As a kid, I remember asking my mom if she sees the same colors as I do (not in such a straight-forward manner).  I said something like, 'What if you grew up seeing my purple in grass, while I see it as being green, but that we all use the word "green" to describe the color of the grass?  You grew up figuring purple was the normal color of grass'.  To my enjoyment as a junior in college, I found out this was, in fact, an epistemological question and a question of great interest in some sectors of neuroscience!  And this is when my interest in 'qualia' really grew (though I find it completely intractable -- maybe due to my lack of imagination-- to research, I do enjoy reading about it and seeing if anyone can 'crack the code').  I started reading more John Searle books (here,  here, here), David Hume (here), Ian Ravenscroft (here), Bertrand Russell (here), and Benedictus de Spinoza (here; though, I must admit, I only made it half-way through - maybe I'll finish it some day).  John R. Searle and Bertrand Russell, and the bits of  Hume I've read have been of great inspiration to how I think --- if anyone can recommend some works of the like, let me know, especially those related to the topics that Searle discusses!  Not all of the books listed above relate to qualia, but all have a theme in common, which we can't see anything truly objectively, because, in order to do that, we need to go outside consciousness, no matter what the issue at hand is, and we are bound by, you guessed it, consciousness (even in our 'objective' measurements).

In Anxiety, the PFC-ventral Hippocampus-Amygdala Sync Up (extended version)

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Ever since the functional double dissociation (also here) between the dorsal (dHPC) and ventral hippocampus (vHPC), a lot of research after has focused mainly on the dHPC and spatial memory/processing; however, less research has been done on the ventral portion.  This region is known to be largely in charge of mediating anxiety-like behaviors.  Some interesting findings have been presented on the poster floor here at Society for Neuroscience (2011).  I had the pleasure to see a few posters that relate to anxiety and this brain region.  The emerging story is that the vHPC interacts closely with the prefrontal cortex to regulate anxiety behaviors through the oscillatory pattern known as the theta rhythm, whereby the amygdala also plays a crucial role, along with the VTA.  This synchronized rhythm between multiple brain areas is how these regions coordinate neural communication with each other.


read more for the poster info on the brain regions and diagrams I made - they're pretty professional!

SfN Recap day I/II & Video: Neural Connectivity

At SfN, I have never been so blown away by the amount of posters, at least of those that I saw, that are dedicated to how areas connect to each other.  For instance, I have been focused on fear and anxiety circuits as of late.  Maybe it is just that area, as we know it has a wide-ranging network of connections, but there seems to be an overwhelming number.  Many fMRI studies, too, are focusing on functional connectivity...  Not sure if it is like this in other areas of neuroscience at SfN '11.  Anyway, some really, really cool posters that I went to:


Changes in rhythmic activity in hippocampus and medial prefrontal cortex induced by benzodiazepine anxiolytics in mice
Zhang, le Novere, & Gross


Functional connectivity in descending hippocampal projections to cortex and septum during anxiety in mice (Wednesday)
Madronal, Silva, & Gross


Theta oscillations in the vHip-mPFC-BLA underlie discrimination between aversive and neutral stimuli
Likhtik, Topiwala, & Gordon

Single units in the medial prefrontal cortex with anxiety-related firing patterns are preferentially influenced by ventral hippocampal activity
Adhikar, Topiwala, & Gordon

Extinction switches hippocampal context signaling from danger to safety
Pardilla-Delgado, Sotres-Bayton, Sierra-Mercado, & Quirk

Prelimbic inactivation blocks avoidance without reducing freezing: Resolving the conflict
Bravo-Rivera, Martinez-Maria, Sotres-Bayton, & Quirk

read more for a quick discussion of connectivity and the video link

The Big Picture: Neuroscience At All Levels!

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This is a shorter, somewhat informative post really aimed towards people outside neuroscience (or students just beginning neuroscience) in order to let them know all the levels of analysis researchers take.

The story begins: 


Too often, science researchers forget the big picture.  They get involved and captivated by their little niche of research, which is a good thing, for the most part!  For example, those electrophysiologists and their networks, cognitive scientists and their 'bigger' questions, chemists and their molecules, etc.  I, too, am guilty, as I rarely venture outside the realm of what I am researching (though I try), let alone outside neuroscience or some aspects of psychology!

So, I wanted to bring it back to reality (for me, at least) and think of 'The Big Picture' and just appreciate the other areas of neuroscience for a bit that give rise to one of my favorite things to study.  For an example, why does behavior captivate me?  I first became interested in neuroscience and behavior upon recognizing the seamless integration of behaviors within the central and peripheral nervous system.  Such a simple task as stalking prey while simultaneously hunting with a pack of fellow attackers is almost mind-blowing when one cogitates the vast complexity of levels.

Stress: Receptors and Responses

Corticosterone, a stress hormone
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Why have we evolved to 'feel' stress? What are the implications of stress on the behavior of the animal?   Those are all relatively easy questions that we can probably give a cursory answer to at this time.  In every-day thinking, we evolved to have the ability to 'feel' stress to serve as a motivator, which plays out behaviorally in order to accomplish goals.  It is a motivator to write the next paper, reach the project's deadline, or, from a more evolutionary perspective, such things as go out and find food, find a mate, or build a shelter to stay safe.  These are the cursory answers.

But, if one takes a closer look from a psychological and/or neuroscientific viewpoint, and truly investigates these questions, the answer is complex and remains, for the most part, unanswered.  Right now, if you're coming from a science background, stop reading and just take a second to think about (A) how percepts from the world (the sensory information) inform our mind to let us know this sensorial information is a stressor, (B) the regions of the brain involved in this activation once it is or before it is 'realized', (C) our physiological and behavioral reactions to stress, and (D) how our mind and thoughts inform our future analysis of the percepts.  Just some interesting questions to think about.

Here, I will give brief descriptions of stress at the molecular and cellular level, and I will also describe two popular behavioral tasks used in rodent research to try and quantify/observe the responses after experiencing a stressful event.

after the jump, HPA axis, receptors, behavioral responses involved in the stress response...

Face Processing: Connecting the Nodes Across the Brain

Since I have rather tended to focus on the hippocampus, I’ve decided to diverge a bit into the neural connectivity of face processing* -- after all, this blog is mainly about neural connectivity, not only within a region but between multiple regions, as well.

Angry face of a female intending to seriously
hurt or scare someone/thing. Blue points represent
fixations from a person looking at the picture
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Faces convey a wealth of information, including physical characteristics, gender, emotional state, trustworthiness, beauty, and intentions (especially through eye-gaze direction).  How do we glean all this information from a subtle glance at a face, though?  In order to understand this, we need to start out with a basic model of face processing and how our brain recognizes a face.  Yet, this question is not so simple to answer, as you will soon see with regards to the fusiform face area!  

Other than the fusiform area, the rest of the post will be dedicated to the connectivity between interacting brain areas involved in face processing.

First, I will discuss general visual processing.

Second, how does visual processing of faces differ in fusiform face area?

Third, there is a face network -- feedforward connectivity.

Fourth, feedback connectivity with the help from an example: Emotions.

read more for description of the whole-brain connectivity of face processing and a video...

Ingredients of a Hippocampus: Connectivity

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What is needed in the recipe?
intra-, inter-, extra-, and mysterious-hippocampal connectivity
Serving Size: 1 hemisphere

While being one of the most extensively studied structures amongst the subcortical and cortical tissues, the hippocampus has shown itself to have quite complex connectivity and still remains an enigmatic structure, both in terms of functional, local, and regional connectivity.  While great strides have been made through anatomical, electrophysiological, and image-based tracing, the hippocampal formation leaves much to be desired.

With the advent of the 'human connectome project' and the 'rodent connectome project' (see references), mapping brain circuitry has never been visualized easier or more beautifully.

Of interest to me, of course, is the hippocampal local and regional connectivity.  For an extensive, interactive version of the connections, check out here (right click 'Interactive Diagram PDF' and 'Save As')  From here, my references to any hippocampal connections will be in regards to the rodent, as many connections mentioned are shared within the human brain.

Read more for connectivity of entorhinal cortex to hippocampus and beyond!

Flashbulb Memories: Real or Rehearsed?

http://www.spring.org.uk/images/flashbulb.jpg

I have put off working on my new post relating to hippocampal connectivity to write this.  It just occurred to me that tomorrow is 9/11 and would make for a nice post on memory.  I tried to get this out before 9/11, but I failed by about 1.5 hours.  When I realized this at around 8:30 or 9 PM, I naturally started thinking about flashbulb memories, and then it led to writing a post on them.  Hopefully it's somewhat informative.

Flashbulb memories are those that contain vivid details, more so than regular memories, and they are also accompanied by an enhanced confidence in reporting these details.  Flashbulb memories are reported to 'occur' after striking events that are highly dramatic, either for good or bad.  Most individuals can recall with enhanced detail where they were/time they heard about it/specific location when you heard it/what you were wearing/etc. (although, not flawlessly!).  These are often reported after large stories, like presidential assassinations, 9/11, or the space shuttle Challenger explosion.

after the jump, are emotional memories different from flashbulb memories or other episodic memories?  Also, a video clip on flashbulb memories of 9/11.

Social Anxiety: What Do They Think of Me*?

Here's a bone for you more psychology-based people.

Is Social Anxiety Disorder just "shyness"?  Well, yes and no, but, more importantly, no.

Overview:

Anxiety is a good thing.  It allows us to adapt to our environment and modify behaviors appropriately.  It motivates us to accomplish tasks and also increases our cognitive skills, such as enhancing memory of certain things and focusing our attention.  It is only when anxiety becomes inappropriate (or hyperactivity of this state) that this becomes termed a disorder.  The effects of anxiety disorders can be quite pervasive, interfere with several aspects of life, and often can become crippling to the sufferer.  My previous posts on the septo-hippocampal system are very relevant to this post. 

Anxiety disorders are not on a single "anxiety axis" but are multi-dimensional in nature (figure below).  Anxiety, in a broad sense, is an exaggeration of uncertainty within the world.  You can't just have "normal anxiety" or "irregular anxiety" (this may be the case within a specific class of the disorder, but on the whole, there are several different classes -- I hope you get my point).

(after the jump is a short clip describing social anxiety)

From Cognition to Behavior: The Intermediate Zone

How are our cognitive processes integrated together to produce a seemingly flawless behavior/motor output? 


In short, the ‘Perception-Action Cycle,’ proposed by Joaquin M. Fuster (Fuster, 1990), who I had the distinct pleasure of conversing with at SfN, tries to link the two distinct neural processes into a coherent sum via what he terms a ‘cognit’ (resembles a cell assembly but is distinctly dedicated to cortical linking).


This perception-action cycle focuses on just the question posed here.  




Continue reading for more detailed analysis and pictures.

Behavioral Inhibition System - What it means

Chorpita et al. (1998)

I've recently summarized the role of the septo-hippocampal system of Gray & McNaughton's (2000) theory (see here).  After thinking about "why" I like the theory, I decided to write another post, not just on G & M theory, but also on the state of neuroscience in general.


One thing that strikes me as odd is that a lot of people tend to only focus on a certain brain area or set of local connections in review articles or just chit-chat with a colleague... which is fine and may be the point of the review/conversation!

The story of Gray and McNaughton (2000), as because there has been some recent posts on the subject, goes beyond this and (tries) to explain a wide range of observed phenomena, ranging from anxiety, fear, OCD, depression, memory (amnesia comes to mind in addition to spatial fields, which they do not deny), etc, and set all these into a hierarchical system. 

Septo-Hippocampal System - Gray & McNaughton

A comment awhile ago asked me to summarize the entire theory of the septo-hippocampal system by Gray & McNaughton (2000) in five sentences...  now, you would need to read the entire book (below) to appreciate the depth and girth of this elegant, thorough, and simple theory, but I gave it a shot:

1) The septo-hippocampal system detects conflict between two or more competing goals that are both highly activated (these goals can take many forms, e.g. escaping, food, threat, etc..), which ultimately leads to an approach-approach, approach-avoid, avoid-avoid behavior, depending on a number of factors.

2) There is a distinct difference between fear (immediate threat, mainly controlled by amygdala with other areas) and anxiety (threat is possible but not here at present (uncertainty), mainly controlled, according to this theory, by the septo-hippocampal system, with of course its surrounding circuit connections with other areas, such as amygdala (so fear/anxiety overlap largely but they are distinct negative affective emotions) 


3) Anxiety is mainly produced by the competition between two goals, ideas, etc, which is controlled/viewed by the septo-hippocampus, and this region tries to disambiguate this confusion/competition by largely inhibition or certain behaviors.

The start.

I've always wanted to create a neuroscience blog that focuses around what I think of a particular study, theory, or what is going on with a certain phenomenon.  After writing a post on Google+ and just writing for my own sake, I thought I would try a somewhat formal platform and see where it goes.  It can't hurt, right?

Hopefully, after some time, I'll have a better design up and possibly a non-blogspot.com URL.

I hope the general theme of this blog will be more geared towards the hippocampus and surrounding cortical regions that work together with it (hence the title, 'Neural Connections').  However, I know that sometimes it might get diverted into general neuroscience, philosophy of the mind, etc., which is fine (and fun).

I hope this is a resources for professionals and individuals with an interest in the sciences, and especially neuroscience and/or psychology.  I also hope to garner a sort of science community where thoughts/ideas/facts can be shared on a local forum.  I think science should be more community based, and, because of this, I think some interesting ideas can emerge from this experiment.