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  • Neuroinformatics
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  • National Science Foundation
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Duncan B, Leitch; Diana K, Sarko; Kenneth C, Catania;

    AbstractWe investigated the relationship between body size, brain size and fibers in selected cranial nerves in shrews and moles. Species include tiny masked shrews (S. cinereus) weighing only a few grams and much larger mole species weighing up to 90 grams. It also includes closely related species with very different sensory specializations – such as the star-nosed mole and the common, eastern mole. We found that moles and shrews have tiny optic nerves with fiber counts not correlated with body or brain size. Auditory nerves were similarly small but increased in fiber number with increasing brain and body size. Trigeminal nerve number was by far the largest and also increased with increasing brain and body size. The star-nosed mole was an outlier, with more than twice the number of trigeminal nerve fibers than any other species. Despite this hypertrophied cranial nerve, star-nosed mole brains were not larger than predicted from body size, suggesting that magnification of their somatosensory systems does not result in greater overall CNS size.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Article . 2014
    Data sources: PubMed Central
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    Scientific Reports
    Article . 2014 . Peer-reviewed
    License: CC BY
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    Scientific Reports
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Europe PubMed Central
      Article . 2014
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      Scientific Reports
      Article . 2014 . Peer-reviewed
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      Scientific Reports
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    Authors: Saket Navlakha; Alison L Barth; Ziv Bar-Joseph;

    Robust, efficient, and low-cost networks are advantageous in both biological and engineered systems. During neural network development in the brain, synapses are massively over-produced and then pruned-back over time. This strategy is not commonly used when designing engineered networks, since adding connections that will soon be removed is considered wasteful. Here, we show that for large distributed routing networks, network function is markedly enhanced by hyper-connectivity followed by aggressive pruning and that the global rate of pruning, a developmental parameter not previously studied by experimentalists, plays a critical role in optimizing network structure. We first used high-throughput image analysis techniques to quantify the rate of pruning in the mammalian neocortex across a broad developmental time window and found that the rate is decreasing over time. Based on these results, we analyzed a model of computational routing networks and show using both theoretical analysis and simulations that decreasing rates lead to more robust and efficient networks compared to other rates. We also present an application of this strategy to improve the distributed design of airline networks. Thus, inspiration from neural network formation suggests effective ways to design distributed networks across several domains. Author Summary During development of neural circuits in the brain, synapses are massively over-produced and then pruned-back over time. This is a fundamental process that occurs in many brain regions and organisms, yet, despite decades of study of this process, the rate of synapse elimination, and how such rates affect the function and structure of networks, has not been studied. We performed large-scale brain imaging experiments to quantify synapse elimination rates in the developing mouse cortex and found that the rate is decreasing over time (i.e. aggressive elimination occurs early, followed by a longer phase of slow elimination). We show that such rates optimize the efficiency and robustness of distributed routing networks under several models. We also present an application of this strategy to improve the design of airline networks.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Europe PubMed Central
    Article . 2015
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    PLoS Computational Biology
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    PLoS Computational Biology
    Article . 2015 . Peer-reviewed
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      Europe PubMed Central
      Article . 2015
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      Article . 2015 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jennifer Langel; Tomoko Ikeno; Lily Yan; Antonio A. Nunez; +1 Authors

    Light influences the daily patterning of activity by both synchronizing internal clocks to environmental light-dark cycles and acutely modulating arousal states, a process known as masking. Masking responses are completely reversed in diurnal and nocturnal species. In nocturnal rodents, masking is mediated through a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) whose projections are similar in diurnal and nocturnal rodents. This raises the possibility that differences in responsivity to signals that these cells release might underlie chronotype differences in masking. We explored one aspect of this hypothesis by examining the distribution of excitatory and inhibitory neuronal populations in many ipRGC target areas of a diurnal species (Nile grass rat) and a nocturnal one (Norway rat). We discovered that while many of these regions were very similar in these two species, there were striking differences in the ventral lateral geniculate nucleus (vLGN; higher density of glutamate cells in Norway rats) and in the lateral habenula (LHb; GABAeric cells present in grass rats, but not Norway rats). These patterns raise the possibility that the vLGN and LHb contribute to differences in masking and/or circadian regulation of diurnal and nocturnal species.

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    Brain Research
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Brain Research
    Article . 2018 . Peer-reviewed
    License: Elsevier TDM
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      Brain Research
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Brain Research
      Article . 2018 . Peer-reviewed
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    Authors: Ban, Yue; Smith, Benjamin E.; Markham, Michael R.;

    The bioelectrical properties and resulting metabolic demands of electrogenic cells are determined by their morphology and the subcellular localization of ion channels. The electric organ cells (electrocytes) of the electric fish Eigenmannia virescens generate action potentials (APs) with Na+currents >10 μA and repolarize the AP with Na+-activated K+(KNa) channels. To better understand the role of morphology and ion channel localization in determining the metabolic cost of electrocyte APs, we used two-photon three-dimensional imaging to determine the fine cellular morphology and immunohistochemistry to localize the electrocytes' ion channels, ionotropic receptors, and Na+-K+-ATPases. We found that electrocytes are highly polarized cells ∼1.5 mm in anterior-posterior length and ∼0.6 mm in diameter, containing ∼30,000 nuclei along the cell periphery. The cell's innervated posterior region is deeply invaginated and vascularized with complex ultrastructural features, whereas the anterior region is relatively smooth. Cholinergic receptors and Na+channels are restricted to the innervated posterior region, whereas inward rectifier K+channels and the KNachannels that terminate the electrocyte AP are localized to the anterior region, separated by >1 mm from the only sources of Na+influx. In other systems, submicrometer spatial coupling of Na+and KNachannels is necessary for KNachannel activation. However, our computational simulations showed that KNachannels at a great distance from Na+influx can still terminate the AP, suggesting that KNachannels can be activated by distant sources of Na+influx and overturning a long-standing assumption that AP-generating ion channels are restricted to the electrocyte's posterior face.

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    Europe PubMed Central
    Other literature type . 2015
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    Journal of Neurophysiology
    Article . 2015 . Peer-reviewed
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      Europe PubMed Central
      Other literature type . 2015
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      Article . 2015 . Peer-reviewed
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    Authors: Getz, W.M.; Brückner, D.; Smith, K.B.;

    International audience

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    Other literature type . Article . 1989
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      Hyper Article en Ligne; Hal-Diderot
      Other literature type . Article . 1989
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      Apidologie
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      Apidologie
      Article . 1989 . Peer-reviewed
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    Authors: Sit, Kevin K.; Goard, Michael J.;

    Perception of visual motion is important for a range of ethological behaviors in mammals. In primates, specific visual cortical regions are specialized for processing of coherent visual motion. However, whether mouse visual cortex has a similar organization remains unclear, despite powerful genetic tools available for measuring population neural activity. Here, we use widefield and 2-photon calcium imaging of transgenic mice to measure mesoscale and cellular responses to coherent motion. Imaging of primary visual cortex (V1) and higher visual areas (HVAs) during presentation of natural movies and random dot kinematograms (RDKs) reveals varied responsiveness to coherent motion, with stronger responses in dorsal stream areas compared to ventral stream areas. Moreover, there is considerable anisotropy within visual areas, such that neurons representing the lower visual field are more responsive to coherent motion. These results indicate that processing of visual motion in mouse cortex is distributed heterogeneously both across and within visual areas. Processing of coherent motion has been extensively studied in the primate visual system, but has not been well characterized in mice. Here, the authors use widefield calcium imaging to reveal that coherent motion responses are organized anisotropically both across and within visual areas in mice.

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    bioRxiv
    Preprint . 2019
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    Europe PubMed Central
    Article . 2020 . Peer-reviewed
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    Nature Communications
    Article . Preprint
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    Nature Communications
    Article . 2020
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    Nature Communications
    Article . 2020 . Peer-reviewed
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    Nature Communications
    Article . 2020
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      Nature Communications
      Article . 2020
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    Authors: W. Jeffrey Johnston; David J. Freedman;

    A pedestrian crossing a street during rush hour often looks and listens for potential danger. When they hear several different horns, they localize the cars that are honking and decide whether or not they need to modify their motor plan. How does the pedestrian use this auditory information to pick out the corresponding cars in visual space? The integration of distributed representations like these is called the assignment problem, and it must be solved to integrate distinct representations across but also within sensory modalities. Here, we identify and analyze a solution to the assignment problem: the representation of one or more common stimulus features in pairs of relevant brain regions—for example, estimates of the spatial position of cars are represented in both the visual and auditory systems. We characterize how the reliability of this solution depends on different features of the stimulus set (e.g., the size of the set and the complexity of the stimuli) and the details of the split representations (e.g., the precision of each stimulus representation and the amount of overlapping information). Next, we implement this solution in a biologically plausible receptive field code and show how constraints on the number of neurons and spikes used by the code force the brain to navigate a tradeoff between local and catastrophic errors. We show that, when many spikes and neurons are available, representing stimuli from a single sensory modality can be done more reliably across multiple brain regions, despite the risk of assignment errors. Finally, we show that a feedforward neural network can learn the optimal solution to the assignment problem, even when it receives inputs in two distinct representational formats. We also discuss relevant results on assignment errors from the human working memory literature and show that several key predictions of our theory already have support.

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    PLoS Computational Biology
    Article . 2023 . Peer-reviewed
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      PLoS Computational Biology
      Article . 2023 . Peer-reviewed
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    Authors: Timothy A, Allen; Nandakumar S, Narayanan; Dianna B, Kholodar-Smith; Yanjun, Zhao; +2 Authors

    Abstract Muscimol is a GABA A -agonist that causes rapid and reversible suppression of neurophysiological activity. Interpretations of the effects of muscimol infusions into the brain have been limited because of uncertainty about spread of the drug around the injection site. To solve this problem, the present study explored the use of a fluorophore-conjugated muscimol molecule (FCM). Whole-cell recordings from horizontal brain slices demonstrated that bath-applied FCM acts like muscimol in reversibly suppressing excitatory synaptic transmission. Two types of in vivo experiments demonstrated that the behavioral effects of FCM infusion are similar to the behavioral effects of muscimol infusion. FCM infusion into the rat amygdala before fear conditioning impaired both cued and contextual freezing, which were tested 24 or 48 h later. Normal fear conditioning occurred when these same rats were subsequently given phosphate-buffered saline infusions. FCM infusion into the dorsomedial prefrontal cortex impaired accuracy during a delayed-response task. Histological analysis showed that the region of fluorescence was restricted to 0.5–1 mm from the injection site. Myelinated fiber tracts acted as diffusional barriers, thereby shaping the overall spread of fluorescence. The results suggest that FCM is indeed useful for exploring the function of small brain regions.

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    Europe PubMed Central
    Other literature type . 2008
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Journal of Neuroscience Methods
    Article . 2008 . Peer-reviewed
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      Other literature type . 2008
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Journal of Neuroscience Methods
      Article . 2008 . Peer-reviewed
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    Authors: Franklin, J; Andrade, R; Daniels, ML; Fairbairn, P; +19 Authors

    AbstractAimSeasonally dry tropical forest (SDTF) of the Caribbean Islands (primarily West Indies) is floristically distinct from Neotropical SDTF in Central and South America. We evaluate whether tree species composition was associated with climatic gradients or geographical distance. Turnover (dissimilarity) in species composition of different islands or among more distant sites would suggest communities structured by speciation and dispersal limitations. A nested pattern would be consistent with a steep resource gradient. Correlation of species composition with climatic variation would suggest communities structured by broad‐scale environmental filtering.LocationThe West Indies (The Bahamas, Cuba, Hispaniola, Jamaica, Puerto Rico, US Virgin Islands, Guadeloupe, Martinique, St. Lucia), Providencia (Colombia), south Florida (USA) and Florida Keys (USA).TaxonSeed plants—woody taxa (primarily trees).MethodsWe compiled 572 plots from 23 surveys conducted between 1969 and 2016. Hierarchical clustering of species in plots, and indicator species analysis for the resulting groups of sites, identified geographical patterns of turnover in species composition. Nonparametric analysis of variance, applied to principal components of bioclimatic variables, determined the degree of covariation in climate with location. Nestedness versus turnover in species composition was evaluated using beta diversity partitioning. Generalized dissimilarity modelling partitioned the effect of climate versus geographical distance on species composition.ResultsDespite a set of commonly occurring species, SDTF tree community composition was distinct among islands and was characterized by spatial turnover on climatic gradients that covaried with geographical gradients. Greater Antillean islands were characterized by endemic indicator species. Northern subtropical areas supported distinct, rather than nested, SDTF communities in spite of low levels of endemism.Main conclusionsThe SDTF species composition was correlated with climatic variation. SDTF on large Greater Antillean islands (Hispaniola, Jamaica and Cuba) was characterized by endemic species, consistent with their geological history and the biogeography of plant lineages. These results suggest that both environmental filtering and speciation shape Caribbean SDTF tree communities.

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    Apollo
    Article . 2018
    License: CC BY NC ND
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    Apollo
    Other literature type . 2018
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    Journal of Biogeography
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    Journal of Biogeography
    Article . 2018 . Peer-reviewed
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      Journal of Biogeography
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      Journal of Biogeography
      Article . 2018 . Peer-reviewed
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    Authors: Nanda, Payal; Morris, Allyn; Kelemen, Jessica; Yang, Jane; +1 Authors

    To characterize the rat as a potential model of frontal-parietal auditory processing during sustained attention, target detection, and response inhibition, we recorded field potentials (FPs) at multiple sites in medial-dorsal frontal and posterior parietal cortex simultaneously while rats performed an equiprobable auditory go/no-go discrimination task. Event-related potentials (ERPs) were calculated by averaging tone-triggered FPs across hit, miss, false alarm (FA), and correct rejection (CR) trials separately for each recording session, and five peak amplitudes (termed N1, P2, N2, P3E, and P3L) were extracted from the individual-session ERPs. Comparing peak amplitudes across different trials types indicated a statistically significant amplification of the P2 peak on hit trials that accompanies detection of the target tone prior to the behavioral go response. This result appears analogous to human ERP phenomena during auditory target discrimination. Conversely, the rat P3 responses were not associated with target detection as in the human ERP literature. Likewise, we did not observe the “no-go N2” or “no-go P3” responses reported in the human literature in association with response inhibition, which might reflect differences in task context or a difference in auditory processing between rats and humans. We also present analyses of stimulus-induced spectral power and interarea coherence to characterize oscillatory synchronization which may contribute to ERPs, and discuss possible error-related processing at the N2, P3E, and P3L peaks. Visual Abstract

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    Europe PubMed Central
    Article . 2020
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Duncan B, Leitch; Diana K, Sarko; Kenneth C, Catania;

    AbstractWe investigated the relationship between body size, brain size and fibers in selected cranial nerves in shrews and moles. Species include tiny masked shrews (S. cinereus) weighing only a few grams and much larger mole species weighing up to 90 grams. It also includes closely related species with very different sensory specializations – such as the star-nosed mole and the common, eastern mole. We found that moles and shrews have tiny optic nerves with fiber counts not correlated with body or brain size. Auditory nerves were similarly small but increased in fiber number with increasing brain and body size. Trigeminal nerve number was by far the largest and also increased with increasing brain and body size. The star-nosed mole was an outlier, with more than twice the number of trigeminal nerve fibers than any other species. Despite this hypertrophied cranial nerve, star-nosed mole brains were not larger than predicted from body size, suggesting that magnification of their somatosensory systems does not result in greater overall CNS size.

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    Europe PubMed Central
    Article . 2014
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    Scientific Reports
    Article . 2014 . Peer-reviewed
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    Authors: Saket Navlakha; Alison L Barth; Ziv Bar-Joseph;

    Robust, efficient, and low-cost networks are advantageous in both biological and engineered systems. During neural network development in the brain, synapses are massively over-produced and then pruned-back over time. This strategy is not commonly used when designing engineered networks, since adding connections that will soon be removed is considered wasteful. Here, we show that for large distributed routing networks, network function is markedly enhanced by hyper-connectivity followed by aggressive pruning and that the global rate of pruning, a developmental parameter not previously studied by experimentalists, plays a critical role in optimizing network structure. We first used high-throughput image analysis techniques to quantify the rate of pruning in the mammalian neocortex across a broad developmental time window and found that the rate is decreasing over time. Based on these results, we analyzed a model of computational routing networks and show using both theoretical analysis and simulations that decreasing rates lead to more robust and efficient networks compared to other rates. We also present an application of this strategy to improve the distributed design of airline networks. Thus, inspiration from neural network formation suggests effective ways to design distributed networks across several domains. Author Summary During development of neural circuits in the brain, synapses are massively over-produced and then pruned-back over time. This is a fundamental process that occurs in many brain regions and organisms, yet, despite decades of study of this process, the rate of synapse elimination, and how such rates affect the function and structure of networks, has not been studied. We performed large-scale brain imaging experiments to quantify synapse elimination rates in the developing mouse cortex and found that the rate is decreasing over time (i.e. aggressive elimination occurs early, followed by a longer phase of slow elimination). We show that such rates optimize the efficiency and robustness of distributed routing networks under several models. We also present an application of this strategy to improve the design of airline networks.

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