The neuron classification problem

Bota, Mihail; Swanson, Larry W.

doi:10.1016/j.brainresrev.2007.05.005

Cited by 100 publications

(99 citation statements)

References 43 publications

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“…But it is designed to complement and extend the National Library of Medicine's Unified Medical Language System (58); Foundational Model of Anatomy (10, 59), a pioneering domain ontology representing a coherent body of explicit declarative knowledge about human anatomy applicable to other species; and Neuroscience Information Framework (60) with its NeuroLex. The FMC is fully compatible with BAMS (30, 31, 35), a neuroinformatics workbench to store, mine, and model structural connectivity information with five modules-parts, with divisions, regions, and tracts (5), cell types, including neurons and neuron parts (46), molecules (50), connections (53), and relations (30).…”

Section: Discussionmentioning

confidence: 99%

“…This problem is key for describing nervous system structural connectivity, and its solution is contentious. According to one approach (46) (47), combinatorial patterns make a vast number of gene expression neuron types possible, most with probable connectional heterogeneity. In fact, it has been suggested that there may be no strict correlation between gene expression patterns and classical neuronal functional subsystems (48).…”

Section: Neuron Typesmentioning

confidence: 99%

“…Neurons can be arranged in a seven-level taxonomic hierarchy with neuron as a cell type on top and neuron varieties on the bottom (figure 3 in ref. 46). …”

Section: Neuron Typesmentioning

confidence: 99%

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Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture

Swanson

Bota

2010

Proc. Natl. Acad. Sci. U.S.A.

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The nervous system is a biological computer integrating the body's reflex and voluntary environmental interactions (behavior) with a relatively constant internal state (homeostasis)-promoting survival of the individual and species. The wiring diagram of the nervous system's structural connectivity provides an obligatory foundational model for understanding functional localization at molecular, cellular, systems, and behavioral organization levels. This paper provides a high-level, downwardly extendible, conceptual framework-like a compass and map-for describing and exploring in neuroinformatics systems (such as our Brain Architecture Knowledge Management System) the structural architecture of the nervous system's basic wiring diagram. For this, the Foundational Model of Connectivity's universe of discourse is the structural architecture of nervous system connectivity in all animals at all resolutions, and the model includes two key elements-a set of basic principles and an internally consistent set of concepts (defined vocabulary of standard terms)-arranged in an explicitly defined schema (set of relationships between concepts) allowing automatic inferences. In addition, rules and procedures for creating and modifying the foundational model are considered. Controlled vocabularies with broad community support typically are managed by standing committees of experts that create and refine boundary conditions, and a set of rules that are available on the Web.There is no set of organs, in the formation of which, we find so perfect a gradation from the simple to the compound, as in the. . .nervous system; in fact, this system is established on a uniform plan in the whole animal scale." Friedrich Tiedemann (1).

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Section: Discussionmentioning

confidence: 99%

Section: Neuron Typesmentioning

confidence: 99%

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Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture

Swanson

Bota

2010

Proc. Natl. Acad. Sci. U.S.A.

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“…First, because of considerable complexity-for example, human isocortex on one side has 6-9 billion neurons (9-11) interconnected by orders-of-magnitude-more synapses-three hierarchical (nested) levels analysis are considered (12,13). A macroconnection between two gray-matter regions considered as black boxes is at the top of the hierarchy, a mesoconnection between two neuron types (14) within or between regions is nested within a macroconnection, and a microconnection between two individual neurons anywhere in the nervous system is nested within a mesoconnection. Second, small mammals, instead of humans, are analyzed.…”

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confidence: 99%

Architecture of the cerebral cortical association connectome underlying cognition

Bota

Sporns

Swanson

2015

Proc. Natl. Acad. Sci. U.S.A.

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Cognition presumably emerges from neural activity in the network of association connections between cortical regions that is modulated by inputs from sensory and state systems and directs voluntary behavior by outputs to the motor system. To reveal global architectural features of the cortical association connectome, network analysis was performed on >16,000 reports of histologically defined axonal connections between cortical regions in rat. The network analysis reveals an organization into four asymmetrically interconnected modules involving the entire cortex in a topographic and topologic core-shell arrangement. There is also a topographically continuous U-shaped band of cortical areas that are highly connected with each other as well as with the rest of the cortex extending through all four modules, with the temporal pole of this band (entorhinal area) having the most cortical association connections of all. These results provide a starting point for compiling a mammalian nervous system connectome that could ultimately reveal novel correlations between genome-wide association studies and connectome-wide association studies, leading to new insights into the cellular architecture supporting cognition.T he cerebral cortex is the core of the brain's cognitive system (1, 2). Emerging evidence suggests that misdirected and/or dysfunctional cortical connections established during neurodevelopment, or degenerative events later in life, are fundamental to cognitive alterations associated with brain disorders like Alzheimer's disease, autism spectrum disorder, and schizophrenia (3). Presumably, an understanding of biological mechanisms underlying cognition and the control of voluntary behavior rests at least partly on the structure-function wiring diagram of the cortex. Design principles of this neural circuitry are based on a network of interactions between distributed nervous system regions, and on the underlying function of their constituent neuron populations, and individual neurons.Unfortunately, a global structure-function wiring diagram of the cortex has not yet been elaborated (4). A necessary, but not sufficient, prerequisite for establishing this basic plan is a comprehensive structural model of cortical connectivity (5-7). Such a "roadmap" could then be used as a database scaffolding for molecular, cellular, physiological, behavioral, and cognitive data and for modeling (8)-analogous to a Google Maps for the brain. The research strategy described here provides the starting point for such a model, as well as a framework, benchmark, and infrastructure for developing a global account of nervous system structural network organization as a whole.The conceptual framework underlying our strategy to analyze global nervous system connection architecture is twofold. First, because of considerable complexity-for example, human isocortex on one side has 6-9 billion neurons (9-11) interconnected by orders-of-magnitude-more synapses-three hierarchical (nested) levels analysis are considered (12, 13). A macroconnection be...

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“…Moreover, there exist an increasing amount of meta-studies of connectomes of many other organisms from Caenorhabditis elegans (Towlson et al 2013) up to primates (Kötter 2004;Stephan et al 2001a;Passingham et al 2002). The unique feature of the rat project within neuroVIISAS is (1) the preservation of hierarchical terminologies in the form of an advanced neuroontology (Bota and Swanson 2007a), (2) the explicit collation of ipsi-and contralateral connections, (3) the extraction of collateral projections, (4) transneuronal and transsynaptic connectivity, (5) the multimodal integration of digital atlases, (6) and the integration of populationbased simulations using NEST (Gewaltig and Diesmann 2007). Moreover, the rat connectome project encompasses about 90 % of the available tract-tracing literature of the rat nervous system indexed in PubMed (http://www.ncbi.…”

Section: Rat Connectome Studiesmentioning

confidence: 99%

The connectome of the basal ganglia

et al. 2014

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The basal ganglia of the laboratory rat consist of a few core regions that are specifically interconnected by efferents and afferents of the central nervous system. In nearly 800 reports of tract-tracing investigations the connectivity of the basal ganglia is documented. The readout of connectivity data and the collation of all the connections of these reports in a database allows to generate a connectome. The collation, curation and analysis of such a huge amount of connectivity data is a great challenge and has not been performed before (Bohland et al. PloS One 4:e7200, 2009) in large connectomics projects based on meta-analysis of tract-tracing studies. Here, the basal ganglia connectome of the rat has been generated and analyzed using the consistent cross-platform and generic framework neuroVIISAS. Several advances of this connectome meta-study have been made: the collation of laterality data, the network-analysis of connectivity strengths and the assignment of regions to a hierarchically organized terminology. The basal ganglia connectome offers differences in contralateral connectivity of motoric regions in contrast to other regions. A modularity analysis of the weighted and directed connectome produced a specific grouping of regions. This result indicates a correlation of structural and functional subsystems. As a new finding, significant reciprocal connections of specific network motifs in this connectome were detected. All three principal basal ganglia pathways (direct, indirect, hyperdirect) could be determined in the connectome. By identifying these pathways it was found that there exist many further equivalent pathways possessing the same length and mean connectivity weight as the principal pathways. Based on the connectome data it is unknown why an excitation pattern may prefer principal rather than other equivalent pathways. In addition to these new findings the local graph-theoretical features of regions of the connectome have been determined. By performing graph theoretical analyses it turns out that beside the caudate putamen further regions like the mesencephalic reticular formation, amygdaloid complex and ventral tegmental area are important nodes in the basal ganglia connectome. The connectome data of this meta-study of tract-tracing reports of the basal ganglia are available for further network studies, the integration into neocortical connectomes and further extensive investigations of the basal ganglia dynamics in population simulations.

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The neuron classification problem

Cited by 100 publications

References 43 publications

Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture

Foundational model of structural connectivity in the nervous system with a schema for wiring diagrams, connectome, and basic plan architecture

Architecture of the cerebral cortical association connectome underlying cognition

The connectome of the basal ganglia

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