Abstract:
:Encoding brain regions and their connections as a network of nodes and edges captures many of the possible paths along which information can be transmitted as humans process and perform complex behaviors. Because cognitive processes involve large, distributed networks of brain areas, principled examinations of multi-node routes within larger connection patterns can offer fundamental insights into the complexities of brain function. Here, we investigate both densely connected groups of nodes that could perform local computations as well as larger patterns of interactions that would allow for parallel processing. Finding such structures necessitates that we move from considering exclusively pairwise interactions to capturing higher order relations, concepts naturally expressed in the language of algebraic topology. These tools can be used to study mesoscale network structures that arise from the arrangement of densely connected substructures called cliques in otherwise sparsely connected brain networks. We detect cliques (all-to-all connected sets of brain regions) in the average structural connectomes of 8 healthy adults scanned in triplicate and discover the presence of more large cliques than expected in null networks constructed via wiring minimization, providing architecture through which brain network can perform rapid, local processing. We then locate topological cavities of different dimensions, around which information may flow in either diverging or converging patterns. These cavities exist consistently across subjects, differ from those observed in null model networks, and - importantly - link regions of early and late evolutionary origin in long loops, underscoring their unique role in controlling brain function. These results offer a first demonstration that techniques from algebraic topology offer a novel perspective on structural connectomics, highlighting loop-like paths as crucial features in the human brain's structural architecture.
journal_name
J Comput Neuroscijournal_title
Journal of computational neuroscienceauthors
Sizemore AE,Giusti C,Kahn A,Vettel JM,Betzel RF,Bassett DSdoi
10.1007/s10827-017-0672-6subject
Has Abstractpub_date
2018-02-01 00:00:00pages
115-145issue
1eissn
0929-5313issn
1573-6873pii
10.1007/s10827-017-0672-6journal_volume
44pub_type
杂志文章abstract::A critical component of any statistical modeling procedure is the ability to assess the goodness-of-fit between a model and observed data. For spike train models of individual neurons, many goodness-of-fit measures rely on the time-rescaling theorem and assess model quality using rescaled spike times. Recently, there ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-018-0698-4
更新日期:2018-10-01 00:00:00
abstract::We develop a new computationally efficient approach for the analysis of complex large-scale neurobiological networks. Its key element is the use of a new phenomenological model of a neuron capable of replicating important spike pattern characteristics and designed in the form of a system of difference equations (a map...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/B:JCNS.0000037683.55688.7e
更新日期:2004-09-01 00:00:00
abstract::Gamma oscillations can synchronize with near zero phase lag over multiple cortical regions and between hemispheres, and between two distal sites in hippocampal slices. How synchronization can take place over long distances in a stable manner is considered an open question. The phase resetting curve (PRC) keeps track o...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-011-0315-2
更新日期:2011-10-01 00:00:00
abstract::The voltage-gated currents in the fly lobula plate tangential cells were examined using the switched electrode voltage clamp technique. In CH cells, two currents were identified (Figs. 1, 2): a slow calcium inward current and a delayed rectifying, noninactivating potassium outward current. HS and VS cells appear to po...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008804117334
更新日期:1997-11-01 00:00:00
abstract::The resistive or non-resistive nature of the extracellular space in the brain is still debated, and is an important issue for correctly modeling extracellular potentials. Here, we first show theoretically that if the medium is resistive, the frequency scaling should be the same for electroencephalogram (EEG) and magne...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-010-0252-5
更新日期:2010-06-17 00:00:00
abstract::Avian brain area HVC is known to be important for the production of birdsong. In zebra finches, each RA-projecting neuron in HVC emits a single burst of spikes during a song motif. The population of neurons is activated in a precisely timed, stereotyped sequence. We propose a model of these burst sequences that relies...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-007-0032-z
更新日期:2007-12-01 00:00:00
abstract::One of the most common examples of audiovisual speech integration is the McGurk effect. As an example, an auditory syllable /ba/ recorded over incongruent lip movements that produce "ga" typically causes listeners to hear "da". This report hypothesizes reasons why certain clinical and listeners who are hard of hearing...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-016-0610-z
更新日期:2016-10-01 00:00:00
abstract::Stellate cells in the cat antero-ventral cochlear nucleus (AVCN) maintain a robust rate-place representation of vowel spectra over a wide range of stimulus levels. This rate-place representation resembles that of low threshold, high spontaneous rate (SR) auditory nerve fibers (ANFs) at low stimulus levels, and that of...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章,评审
doi:10.1007/BF00961733
更新日期:1994-08-01 00:00:00
abstract::The primary goal of this study was to construct a simulation model of a biofeedback brain-computer interface (BCI) system to analyze the effect of biofeedback training on BCI users. A mathematical model of a man-machine visual-biofeedback BCI system was constructed to simulate a subject using a BCI system to control c...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-009-0148-4
更新日期:2009-12-01 00:00:00
abstract::The existence of electrical communication among pyramidal cells (PCs) in the adult cortex has been debated by neuroscientists for several decades. Gap junctions (GJs) among cortical interneurons have been well documented experimentally and their functional roles have been proposed by both computational neuroscientists...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-020-00762-5
更新日期:2020-11-01 00:00:00
abstract::The kinematics of the hand and fingers were studied during various keystrokes in typing. These movements were defined by 17 degrees of freedom of motion, and methods were developed to identify simplifying strategies in the execution of the task. Most of the analysis was restricted to the 11 degrees of freedom of the f...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008812426305
更新日期:1997-01-01 00:00:00
abstract::Implementation of double cable models to simulate the behavior of myelinated peripheral nerve fibers requires defining a segmentation of the internode between successive nodes of Ranvier. The number of internodal segments is a model parameter that is not well agreed on, with values in the literature ranging from 1 to ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-014-0503-y
更新日期:2014-10-01 00:00:00
abstract::The phase relationship between the activity of hippocampal place cells and the hippocampal theta rhythm systematically processes as the animal runs through the region in an environment called the place field of the cell. We present a minimal biophysical model of the phase precession of place cells in region CA3 of the...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008976210366
更新日期:2000-07-01 00:00:00
abstract::A Web-based simulation system of the spinal cord circuitry responsible for muscle control is described. The simulator employs two-compartment motoneuron models for S, FR and FF types, with synaptic inputs acting through conductance variations. Four motoneuron pools with their associated interneurons are represented in...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-008-0092-8
更新日期:2008-12-01 00:00:00
abstract::We investigated the effect of mean firing on the information rate of a spiking motion-sensitive neuron in the fly (H1-cell). In the control condition, the cell was stimulated repeatedly by identical zero-symmetrical white-noise motion. The mean firing rate was manipulated by adding a constant velocity offset either in...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1011225232120
更新日期:2001-03-01 00:00:00
abstract::The effect of a non-symmetric waveform on nerve conduction block induced by high-frequency biphasic stimulation is investigated using a lumped circuit model of the unmyelinated axon based on Hodgkin-Huxley equations. The simulation results reveal that the block threshold monotonically increases with the stimulation fr...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-014-0510-z
更新日期:2014-10-01 00:00:00
abstract::In this paper, we systematically investigate both the synfire propagation and firing rate propagation in feedforward neuronal network coupled in an all-to-all fashion. In contrast to most earlier work, where only reliable synaptic connections are considered, we mainly examine the effects of unreliable synapses on both...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-010-0279-7
更新日期:2011-06-01 00:00:00
abstract::Retinal ganglion cells (RGCs) display differences in their morphology and intrinsic electrophysiology. The goal of this study is to characterize the ionic currents that explain the behavior of ON and OFF RGCs and to explore if all morphological types of RGCs exhibit the phenomena described in electrophysiological data...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-013-0463-7
更新日期:2014-04-01 00:00:00
abstract::We developed a physiologically plausible model of the first steps of spatial visual information processing in the fovea of the human retina. With the predictions of this model we could support the hypothesis that, for moderate contracts (< or = 40%), hyperacuity is mediated by the magnocellular (MC-) pathway. Despite ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/BF00158338
更新日期:1996-03-01 00:00:00
abstract::Replicability and reproducibility of computational models has been somewhat understudied by "the replication movement." In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and m...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-018-0702-z
更新日期:2018-12-01 00:00:00
abstract::Firing-rate models provide a practical tool for studying signal processing in the early visual system, permitting more thorough mathematical analysis than spike-based models. We show here that essential response properties of relay cells in the lateral geniculate nucleus (LGN) can be captured by surprisingly simple fi...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-013-0456-6
更新日期:2013-12-01 00:00:00
abstract::When two-frame apparent motion stimuli are presented with an appropriate inter-stimulus interval (ISI), motion is perceived in the direction opposite to the actual image shift. Herein, we measured a simple eye movement, ocular following responses (OFRs), in macaque monkeys to examine the ISI reversal effect on oculomo...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-020-00756-3
更新日期:2020-07-17 00:00:00
abstract::The lack of a deeper understanding of how olfactory sensory neurons (OSNs) encode odors has hindered the progress in understanding the olfactory signal processing in higher brain centers. Here we employ methods of system identification to investigate the encoding of time-varying odor stimuli and their representation f...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-010-0265-0
更新日期:2011-02-01 00:00:00
abstract::We consider whole-cell voltage-clamp data of isolated currents characterized by the Hodgkin-Huxley paradigm. We examine the errors associated with the typical parameter estimation method for these data and show them to be unsatisfactorally large especially if the time constants of activation and inactivation are not s...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008880518515
更新日期:1999-03-01 00:00:00
abstract::The active dendritic conductances shape the input-output properties of many principal neurons in different brain regions, and the various ways in which they regulate neuronal excitability need to be investigated to better understand their functional consequences. Using a realistic model of a hippocampal CA1 pyramidal ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/b:jcns.0000004837.81595.b0
更新日期:2004-01-01 00:00:00
abstract::We construct a neuronal network to model the logic of associative conditioning as revealed in experimental results using the terrestrial mollusk Limax maximus. We show, in particular, how blocking to a previously conditioned stimulus in the presence of the unconditional stimulus, can emerge as a dynamical property of ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-006-8097-7
更新日期:2006-12-01 00:00:00
abstract::Following a flashed stimulus, I show that a simple neurophysiological mechanism in the primary visual system can generate orientation selectivity based on the first incoming spikes. A biological model of the lateral geniculate nucleus generates an asynchronous wave of spikes, with the most strongly activated neurons f...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1027420012134
更新日期:2003-11-01 00:00:00
abstract::The implications for motor learning of the model developed in the previous article are analyzed using idealized Pavlovian eyelid conditioning trials, a simple example of cerebellar motor learning. Results suggest that changes in gr-->Pkj synapses produced by a training trial disrupt equilibrium and lead to subsequent ...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1023/a:1008830427738
更新日期:1998-03-01 00:00:00
abstract::Nonlinear dynamics provides a complementary framework to control theory for the quantitative analysis of the oculomotor control system. This paper presents a number of findings relating to the aetiology and mechanics of the pathological ocular oscillation jerk congenital nystagmus (jerk CN). A range of time series ana...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-006-7816-4
更新日期:2006-10-01 00:00:00
abstract::In the mammalian retina, complementary ON and OFF visual streams are formed at the bipolar cell dendrites, then carried to amacrine and ganglion cells via nonlinear excitatory synapses from bipolar cells. Bipolar, amacrine and ganglion cells also receive a nonlinear inhibitory input from amacrine cells. The most commo...
journal_title:Journal of computational neuroscience
pub_type: 杂志文章
doi:10.1007/s10827-009-0170-6
更新日期:2009-12-01 00:00:00