finished frontal cortex section -- need to fill in lots of details in motor thalamus on that page, but motor is mostly done now.

Author: rcoreilly

citedrefs.json

@@ -0,0 +1,10 @@
++++
+Categories = ["Rubicon", "Neuroscience"]
+bibfile = "ccnlab.json"
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+
+The **amygdala** is the central hub for [[emotion]].
+
+<!--- TODO: McGarryCarter17 PL <-> BLA -->
+
+

content/amygdala.md

@@ -54,6 +54,8 @@ We can infer from this evolutionary trajectory that the goal-driven PFC areas do
 
 [[#figure_pfc-fun]] provides an elaborated version of the primate PFC, assigning more fine-grained functional labels based on the connectivity with subcortical areas described by [[@^OngurPrice00]]. These subcortical areas, which have relatively well-defined and circumscribed neural response properties that are under strong evolutionary control, can then anchor the learning in these corresponding PFC areas to represent the relevant information needed for control over survival relevant factors, as discussed in [[emotion]].
 
+<!--- TODO: AnastasiadesCarter21 and PL, ORBm, ILA, ACA = AMS; McGarryCarter17 PL <-> BLA CheriyanKaushikFerreiraEtAl16 -- BLA <-> IL; PL -> fear acquisition; IL = extinction; IL is more L5 based and projects to central amygdala.  -->
+
 ### Neural coding data
 
 There is a wealth of neural recording data across multiple species that is generally consistent with the above functional anatomy of ventral and medial PFC areas. However, much of the data in animals is from individual neuron recordings, which inevitably shows that neurons across all of these different PFC areas exhibit some sensitivity to the functional variables that are ascribed to specific areas in the above framework (e.g., [[@KennerleyBehrensWallis11]] and references therein).
@@ -102,7 +104,7 @@ Recent experimental data has provided strong support for this gating-like influe
 
 Further refinement of the organization of the deep layer 5 PT neurons is provided by [[@^EconomoViswanathanTasicEtAl18]], who found evidence for two distinct types of these neurons as shown in [[#figure_economo-18]]. The PT-upper neurons are the ones involved in the thalamocortical loops shown in [[#figure_alm-thal-loop]], while the PT-lower neurons project down to brainstem motor areas such as the medulla oblongata.
 
-The presence of these two neuron types provides a mechanism for distinguishing between preparatory motor planning versus actual motor execution, to prevent premature execution during the planning stage. However, [[@^EconomoViswanathanTasicEtAl18]] found that there was not a simple clean dissociation between these two neural populations, with both types of neurons exhibiting activity during delay and response phases. Nevertheless, there was an increased likelihood of PT-lower neurons firing immediately prior and during the response, while PT-upper neurons were more likely to exhibit sustained firing during the preparatory delay period. Thus, as discussed in [[distributed representations]] and shown in [[#figure_hunt-rsa]], population-level patterns shaped by learning are always the most relevant for driving behavior.
+The presence of these two neuron types provides a mechanism for distinguishing between preparatory motor planning versus actual motor execution, to prevent premature execution during the planning stage ([[@ChurchlandShenoy24]]). However, [[@^EconomoViswanathanTasicEtAl18]] found that there was not a simple clean dissociation between these two neural populations, with both types of neurons exhibiting activity during delay and response phases. Nevertheless, there was an increased likelihood of PT-lower neurons firing immediately prior and during the response, while PT-upper neurons were more likely to exhibit sustained firing during the preparatory delay period. Thus, as discussed in [[distributed representations]] and shown in [[#figure_hunt-rsa]], population-level patterns shaped by learning are always the most relevant for driving behavior.
 
 Consistent with the properties of these thalamocortical loops and the earlier computational models, multiple studies have shown that the thalamus indeed plays a critical role in shaping the dynamics of PFC activity in a task-relevant context ([[@StokesBest90]]; [[@GilmartinBalderstonHelmstetter14]]; [[@GuoLiHuberEtAl14]]; [[@BolkanStujenskeParnaudeauEtAl17]]; [[@SchmittWimmerNakajimaEtAl17]]; [[@RikhyeGilraHalassa18]]; [[@DacreColliganClarkeEtAl21]]; [[@InagakiChenRidderEtAl22]];  [[@WilhelmSychFominsEtAl23]]). 
 

content/media/fig_motor_hill_muscle.png

@@ -176,6 +176,8 @@
 
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@@ -278,6 +280,8 @@
 
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+
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+<p id="IsaMarquez-LegorretaGrillnerEtAl21">Isa, T., Marquez-Legorreta, E., Grillner, S., & Scott, E.K. (2021). The tectum/superior colliculus as the vertebrate solution for spatial sensory integration and action. <i>Current Biology, 31</i>, R741-R762. <a href="https://www.sciencedirect.com/science/article/pii/S0960982221004796">https://www.sciencedirect.com/science/article/pii/S0960982221004796</a><a href="http://doi.org/10.1016/j.cub.2021.04.001"> http://doi.org/10.1016/j.cub.2021.04.001</a></p>
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content/motor.md

@@ -3,7 +3,7 @@ Categories = ["Neuroscience", "Cognition"]
 bibfile = "ccnlab.json"
 +++
 
-The **superior colliculus** (SC) is the [[evolution]]ary expansion of the **tectum** in mammals, and can be thought of as the subcortical, evolutionarily primary version of the [[neocortex]], by integrating various sensory inputs to drive more complex motor behavior. Whereas the neocortex is much more strongly shaped by [[synaptic plasticity]] (learning), the SC is more strongly shaped by evolution and is thought to be a major locus of innate behavior. Whereas the SC is primarily driven by visual input (i.e., the _optic tectum_ in non-mammalian species), the the **inferior colliculus** (IC) is primarily driven by auditory input (i.e., the _auditory tectum_). The two are densely interconnected and the same overall principles apply to both structures.
+The **superior colliculus** (SC) is the [[evolution]]ary expansion of the **tectum** in mammals, and can be thought of as the subcortical, evolutionarily primary version of the [[neocortex]], by integrating various sensory inputs to drive more complex motor behavior ([[@IsaMarquez-LegorretaGrillnerEtAl21]]). Whereas the neocortex is much more strongly shaped by [[synaptic plasticity]] (learning), the SC is more strongly shaped by evolution and is thought to be a major locus of innate behavior. Whereas the SC is primarily driven by visual input (i.e., the _optic tectum_ in non-mammalian species), the the **inferior colliculus** (IC) is primarily driven by auditory input (i.e., the _auditory tectum_). The two are densely interconnected and the same overall principles apply to both structures.
 
 The SC has massive interconnectivity with every other major network in the brain [[@BenavidezBienkowskiZhuEtAl21]], including the [[neocortex]], [[basal ganglia]], [[cerebellum]] and the [[motor]] brainstem and spinal cord. It sends sensory signals to the [[amygdala]] and [[acetylcholine]] (ACh) areas that then drive neuromodulation of the entire brain, consistent with the [[Rubicon]] model.