DOI: 10.5061/dryad.zw3r228d2
title: Harvard Ascending Arousal Network Atlas – Version 2.0

description: The ascending arousal network (AAN) is a subcortical neural network that
 is critical to consciousness. AAN neurons connect the brainstem to the
 thalamus, hypothalamus, basal forebrain and cortex, activating
 cortically-based awareness networks. The reticular core of the AAN was
 first described by Moruzzi and Magoun in 1949, who coined the classical
 term "ascending reticular activating system" (Electroencephalogr
 Clin Neurophysiol 1949;1:455-73). Here, we use the term AAN because many
 brainstem nuclei that contribute to arousal are located outside of the
 pontine and midbrain reticular core (e.g., locus coeruleus, parabrachial
 complex, etc.), and because we believe that the word "network"
 appropriately connotes the physiological mechanisms by which multiple
 modular circuits interrelate to enable the emergent property of arousal,
 and hence consciousness. To date, the majority of studies investigating
 AAN connectivity have utilized animal models. As a result, current
 knowledge about the structural and functional connectivity of the human
 AAN is limited and largely based upon extrapolations from animal data. We
 created this AAN atlas to facilitate research into the structural and
 functional connectivity of the human AAN. The study of AAN
 "connectomics" has the potential to increase knowledge about
 arousal physiology in the human brain, as well as arousal pathology in
 neurological diseases, such as coma and other disorders of consciousness.
 In addition, the study of AAN connectomics may advance knowledge about
 reciprocal connectivity between this subcortical arousal network and
 cortically based awareness networks, such as the default mode network. In
 2012, we released the Harvard AAN Atlas Version 1.0. The atlas was
 generated using several sources of data: 1) histologic data from a
 dissected ex vivo human brainstem/diencephalon specimen (Edlow et
 al. JNEN 2012; https://pubmed.ncbi.nlm.nih.gov/22592840/); 2) correlative
 diffusion data from the same specimen (scanned prior to serial sectioning
 and staining); and 3) cross-reference to the Paxinos human brainstem atlas
 (Paxinos G, Xu-Feng H, Sengul G, Watson C. Organization of Brainstem
 Nuclei, in The Human Nervous System, 3rd ed. Mai JK and Paxinos G eds.
 Amsterdam: Elsevier, 2011). Additional details about the development of
 Version 1.0 are provided at
 https://www.nmr.mgh.harvard.edu/resources/aan-atlas. Here, we release
 Version 2.0 of the atlas, which incorporates updates to AAN node
 neuroanatomy and nomenclature. Neuroanatomic updates are based on new
 immunostaining data from human brainstem specimens, which can be found
 at https://histopath.nmr.mgh.harvard.edu. Nomenclature updates
 are to ensure consistency with the Paxinos 2011 Atlas (Paxinos G, Xu-Feng
 H, Sengul G, Watson C. Organization of Brainstem Nuclei, in The Human
 Nervous System, 3rd ed. Mai JK and Paxinos G eds. Amsterdam: Elsevier,
 2011).   The updates in Version 2.0 are: 1) Updates to Node
 Nomenclature mRt: cuneiform/subcuneiform nucleus (CSC) --&gt;
 mesencephalic reticular formation (mRt) PTg: pedunculopontine nucleus
 (PPN) --&gt; pedunculotegmental nucleus (PTg) 2) Updates to Node
 Neuroanatomy mRt: In Version 1.0, the CSC was localized to the rostral
 midbrain, based on Moruzzi and Magoun’s seminal study in which stimulation
 of the rostral midbrain tegmentum led to arousal and cortical activation
 in lightly anesthetized cats.  In Version 2.0, we renamed this
 node mRt and changed its anatomic boundaries such that it now extends
 throughout the entire rostro-caudal axis of the midbrain tegmentum,
 consistent with the Paxinos Atlas.  Specifically, our mRt node
 now contains all of the following subnuclei described by Paxinos 2011:
 CnF, isRt, PrCnF, mRt, CeMe, and p1Rt. VTA: The VTA node in Version 2.0
 has two major differences compared to the VTA ROI used in Version 1.0: 1)
 its lateral extent and 2) its rostral extent.  In Version 1.0, we
 did not include the lateral wing-like extensions of the parabrachial
 pigmented nucleus of the VTA (PBP), as shown in Paxinos, because this
 subregion is difficult to differentiate from the nearby substantia
 nigra.  However, with our new tyrosine hydroxylase
 immunostaining, and with reference to the Paxinos atlas, we were able to
 make this distinction between PBP and SN in Version 2.0. With respect to
 the rostral extent of the VTA node, in Version 1.0 we based the
 neuroanatomic borders of the VTA on hematoxylin-and-eosin-stained sections
 from human brainstem specimens, which revealed the highest density of
 catecholamine neurons, as demonstrated by the presence of neuromelanin, in
 the caudal midbrain.  However, we recognize that VTA neurons have
 been identified in the rostral mesencephalon by other laboratories using a
 variety of staining techniques, such as tyrosine hydroxylase.
  Thus, we performed new tyrosine hydroxylase stains on midbrain
 sections from human brainstem specimens.  These stains revealed a
 distribution of VTA neurons that was consistent with that described in
 prior studies by Oades, Halliday, Pearson, and colleagues. 
 Therefore, we extended the VTA node in Version 2.0 such that it runs
 throughout the entire rostro-caudal axis of the midbrain.  We do
 not include the rostral linear nucleus as part of the VTA, although some
 dopaminergic cells may reside in this region, because this nucleus is
 primarily serotonergic. Finally, we edited the midline portion of the VTA
 node, based on the observation that VTA neurons in the midline of the
 midbrain were only seen at the level of the red nucleus, not at the level
 of the superior cerebellar peduncle.  This immunostaining
 observation is consistent with the VTA anatomic borders in the Paxinos
 atlas along the rostro-caudal axis of the midbrain.  Thus, we
 removed the midline VTA voxels at the level of the superior cerebellar
 peduncle in Version 2.0. In summary, the VTA node in Version 2.0 contains
 the following nuclear subregions described by Paxinos: parainterfascicular
 nucleus (PIF); paranigral nucleus of ventral tegmental area (PN); ventral
 tegmental area (VTA); ventral tegmental area, rostral part (VTAR); and
 parabrachial pigmented nucleus of the VTA (PBP).   PTg: Deleted
 one voxel in the PTg at MNI axial level z53 and reassigned this voxel to
 the VTA, based on tyrosine hydroxylase staining data and based on the
 anatomic boundaries in the Paxinos atlas. LDTg: Whereas LDTg was not
 included in Version 1.0, we have added LDTg to Version 2.0.