Independently Outgrowing Neurons and Geometry-Based Synapse Formation Produce Networks with Realistic Synaptic Connectivity
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{"title"=>"Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity", "type"=>"journal", "authors"=>[{"first_name"=>"Arjen", "last_name"=>"Van Ooyen", "scopus_author_id"=>"56207446800"}, {"first_name"=>"Andrew", "last_name"=>"Carnell", "scopus_author_id"=>"57173995000"}, {"first_name"=>"Sander", "last_name"=>"De Ridder", "scopus_author_id"=>"56600326300"}, {"first_name"=>"Bernadetta", "last_name"=>"Tarigan", "scopus_author_id"=>"25823367000"}, {"first_name"=>"Huibert D.", "last_name"=>"Mansvelder", "scopus_author_id"=>"6602241744"}, {"first_name"=>"Fetsje", "last_name"=>"Bijma", "scopus_author_id"=>"56114575700"}, {"first_name"=>"Mathisca", "last_name"=>"De Gunst", "scopus_author_id"=>"56036388600"}, {"first_name"=>"Jaap", "last_name"=>"Van Pelt", "scopus_author_id"=>"7005618394"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84898622034", "sgr"=>"84898622034", "pui"=>"372838555", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24454938", "doi"=>"10.1371/journal.pone.0085858"}, "id"=>"5d27614f-5f66-317a-8199-c2ddf06c7b53", "abstract"=>"Neuronal signal integration and information processing in cortical networks critically depend on the organization of synaptic connectivity. During development, neurons can form synaptic connections when their axonal and dendritic arborizations come within close proximity of each other. Although many signaling cues are thought to be involved in guiding neuronal extensions, the extent to which accidental appositions between axons and dendrites can already account for synaptic connectivity remains unclear. To investigate this, we generated a local network of cortical L2/3 neurons that grew out independently of each other and that were not guided by any extracellular cues. Synapses were formed when axonal and dendritic branches came by chance within a threshold distance of each other. Despite the absence of guidance cues, we found that the emerging synaptic connectivity showed a good agreement with available experimental data on spatial locations of synapses on dendrites and axons, number of synapses by which neurons are connected, connection probability between neurons, distance between connected neurons, and pattern of synaptic connectivity. The connectivity pattern had a small-world topology but was not scale free. Together, our results suggest that baseline synaptic connectivity in local cortical circuits may largely result from accidentally overlapping axonal and dendritic branches of independently outgrowing neurons.", "link"=>"http://www.mendeley.com/research/independently-outgrowing-neurons-geometrybased-synapse-formation-produce-networks-realistic-synaptic", "reader_count"=>42, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>11, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>1, "Mathematics"=>2, "Agricultural and Biological Sciences"=>18, "Medicine and Dentistry"=>2, "Arts and Humanities"=>1, "Neuroscience"=>6, "Physics and Astronomy"=>5, "Psychology"=>2, "Computer Science"=>2, "Decision Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>6}, "Decision Sciences"=>{"Decision Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Psychology"=>{"Psychology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>18}, "Computer Science"=>{"Computer Science"=>2}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Greece"=>1, "France"=>2, "Belarus"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1349108"], "description"=>"<p><b>a</b>, The different segments and nodes that can be distinguished and the labeling of segments based on centrifugal order. The centrifugal order of a segment is the number of branch points along the path from the root to the terminal tip of the segment. Terminal tip is equivalent to growth cone. <b>b</b>, Labeling of segments based on degree. The degree of a segment is the number of terminal tips in the (sub) tree carried by the segment.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "neuritic", "trees", "illustrating"], "article_id"=>902406, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_neuritic_trees_illustrating_tree_terminology_/902406", "title"=>"Schematic neuritic trees illustrating tree terminology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349109"], "description"=>"<p><b>A</b>, Synapse formation in NETMORPH. The shortest distance between an axonal (A) and a dendritic (D) branch is defined as the orthogonal distance between a pair of crossing axonal and dendritic line pieces. If this shortest distance is smaller than a given threshold value, the orthogonal line (purple) marks the location of a synapse. <b>B</b>, Different ways to express synapse location. <b>a</b>, Two connected cells showing axons (green), dendrites (red), somata (purple) and synapses (yellow circles). <b>b</b>, Postsynaptic path distance (blue line). <b>c</b>, Postsynaptic Euclidean distance. <b>d</b>, Presynaptic path distance. <b>e</b>, Presynaptic Euclidean distance. <b>C</b>, Determining the mean shortest path length and clustering coefficient of an undirected graph consisting of four nodes and four edges. The numbers are the path lengths between the nodes. The mean shortest path length of the graph is the average of these numbers, 1.3333. The clustering coefficients of nodes A, B, C and D are 0, 2/6, 2/2, and 2/2, respectively. The clustering coefficient of the graph is the average of these numbers, 0.5833.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "measures", "characterizing", "synapse"], "article_id"=>902407, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synapse_formation_and_illustration_of_measures_characterizing_synapse_location_and_connectivity_/902407", "title"=>"Synapse formation and illustration of measures characterizing synapse location and connectivity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349110"], "description"=>"<p>Axons are shown in green, and dendrites are depicted in red. The neurons were grown with outgrowth parameters (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085858#pone-0085858-t001\" target=\"_blank\">Table 1</a>) optimized on the dataset of L2/3 pyramidal cells from NeuroMorpho.org.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "netmorph-generated", "pyramidal"], "article_id"=>902408, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_NETMORPH_generated_L2_3_pyramidal_neurons_/902408", "title"=>"Examples of NETMORPH-generated L2/3 pyramidal neurons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349111"], "description"=>"<p><b>A</b>, Basal dendrites. <b>B</b>, Apical tuft. The NETMORPH-generated neurons are shown by solid lines, and the L2/3 pyramidal neurons from the NeuroMorpho.org database are shown by grey bars. For the basal dendrites, the n-values of degree and total tree length refer to the total number of dendritic trees. For the apical tufts, the n-values of degree and total tree length refer to the total number of apical dendrites (equal to the number of neurons used). For both the basal dendrites and the apical tufts, the n-values of centrifugal order refer to the total number of segments (intermediate and terminal), the n-values of intermediate segment length refer to the total number of intermediate segments, and the n-values of terminal segment length and path length refer to the total number of terminal segments.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "dendritic", "netmorph-generated", "empirical", "pyramidal"], "article_id"=>902409, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributions_of_dendritic_shape_characteristics_of_NETMORPH_generated_and_empirical_L2_3_pyramidal_cells_/902409", "title"=>"Distributions of dendritic shape characteristics of NETMORPH-generated and empirical L2/3 pyramidal cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349112"], "description"=>"<p><b>A</b>, Path distance to postsynaptic soma. <b>B</b>, Path distance to presynaptic soma. <b>C</b>, Euclidean distance to postsynaptic soma. <b>D</b>, Euclidean distance to presynaptic soma.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "euclidean", "distances", "post-", "presynaptic"], "article_id"=>902410, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_path_and_Euclidean_distances_of_synapses_to_their_post_and_presynaptic_somata_/902410", "title"=>"Distribution of path and Euclidean distances of synapses to their post- and presynaptic somata.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349113"], "description"=>"<p><b>A</b>, 4 µm. <b>B,</b> 6 µm. <b>C,</b> 8 µm. <b>D,</b> 10 µm.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "distributions", "distances"], "article_id"=>902411, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_distributions_of_number_of_synapses_per_connection_connection_strength_for_different_threshold_distances_for_the_formation_of_synapses_/902411", "title"=>"Frequency distributions of number of synapses per connection (connection strength) for different threshold distances for the formation of synapses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349115"], "description"=>"<p>Note that the minimum intersoma distance with which the network was created was 20 µm.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "probability", "neurons", "euclidean"], "article_id"=>902413, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Connection_probability_between_neurons_as_a_function_of_Euclidean_distance_between_their_somata_/902413", "title"=>"Connection probability between neurons as a function of Euclidean distance between their somata.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349126"], "description"=>"<p><b>A</b>, Connections via basal dendrites. <b>B</b>, Connections via apical dendrites. Note that the minimum intersoma distance with which the network was created was 20 µm.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "intersoma", "euclidean", "distances", "connected"], "article_id"=>902414, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_distribution_of_intersoma_Euclidean_distances_between_connected_neurons_/902414", "title"=>"Frequency distribution of intersoma Euclidean distances between connected neurons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349127"], "description"=>"<p><b>A</b>, In-degree for connections via apical dendrite. <b>B</b>, In-degree for connections via basal dendrite. <b>C</b>, Out-degree for connections via apical dendrite. <b>D</b>, Out-degree for connections via basal dendrite. <b>E</b>, Degree for connections via apical dendrite. <b>F</b>, Degree for connections via basal dendrite.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "distributions", "out-degree"], "article_id"=>902415, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_distributions_of_in_degree_out_degree_and_degree_of_neurons_/902415", "title"=>"Frequency distributions of in-degree, out-degree and degree of neurons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349129"], "description"=>"<p>Optimized values of the neurite outgrowth parameters in NETMORPH.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "neurite", "outgrowth"], "article_id"=>902417, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimized_values_of_the_neurite_outgrowth_parameters_in_NETMORPH_/902417", "title"=>"Optimized values of the neurite outgrowth parameters in NETMORPH.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-16 03:05:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349130"], "description"=>"<p>The n-values of degree and total tree length refer to the total number of axons (equal to the number of neurons used). The n-values of centrifugal order refer to the total number of segments (intermediate and terminal), the n-values of intermediate segment length refer to the total number of intermediate segments, and the n-values of terminal segment length and path length refer to the total number of terminal segments.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Neurological system", "synapses", "Computational biology", "computational neuroscience", "neuroscience", "Single neuron function", "neuroanatomy", "Connectomics", "neurophysiology", "netmorph-generated", "neurons", "pyramidal"], "article_id"=>902418, "categories"=>["Biological Sciences"], "users"=>["Arjen van Ooyen", "Andrew Carnell", "Sander de Ridder", "Bernadetta Tarigan", "Huibert D. Mansvelder", "Fetsje Bijma", "Mathisca de Gunst", "Jaap van Pelt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085858.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Axonal_shape_characteristics_of_NETMORPH_generated_neurons_and_L2_3_pyramidal_neurons_from_the_NeuroMorpho_org_database_/902418", "title"=>"Axonal shape characteristics of NETMORPH-generated neurons and L2/3 pyramidal neurons from the NeuroMorpho.org database.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-16 03:05:03"}

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Relative Metric

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