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Modeling driver cells in developing neuronal networks [article]

Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Modol, Vitor Hugo Sousa, Paolo Bonifazi, Alessandro Torcini
2018 biorxiv/medrxiv   pre-print
We have developed a spiking network model capable to reproduce the experimental results, thus identifying two classes of driver cells: functional hubs and low functionally connected (LC) neurons.  ...  We show that in the model the presence of inhibitory neurons together with the assumption that younger cells are more excitable and less connected is crucial for the emergence of LC drivers.  ...  Secondly, we develop a network model able to fully reproduce the experimental observations.  ... 
doi:10.1101/260422 fatcat:sj2nfgbbw5eynefsokkb5cpbay

Modeling driver cells in developing neuronal networks

Stefano Luccioli, David Angulo-Garcia, Rosa Cossart, Arnaud Malvache, Laura Módol, Vitor Hugo Sousa, Paolo Bonifazi, Alessandro Torcini, Michele Giugliano
2018 PLoS Computational Biology  
We have developed a spiking network model capable to reproduce the experimental results, thus identifying two classes of driver cells: functional hubs and low functionally connected (LC) neurons.  ...  Secondly, we develop a network model able to fully reproduce the experimental observations.  ...  Driver cells in developing brain circuits LC drivers impact hub neurons. The SNS of LC1 drivers could induce, in 10 cases over 14 identified LC1 cells, a complete silencing in the network.  ... 
doi:10.1371/journal.pcbi.1006551 fatcat:nlms2zbta5bepftoojv4rv27uu

Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity

Felix Effenberger, Jürgen Jost, Anna Levina, Abigail Morrison
2015 PLoS Computational Biology  
Firing rates and mean outgoing weights of excitatory cells. Each dot represents one excitatory cell. Driver cells are shown in red, others in gray.  ...  Here we present an adaptive model of a balanced neuronal network that combines two different types of plasticity, STDP and synaptic scaling.  ...  those cells due to network activity [3] , a similar situation as observed for the driver neurons in our model.  ... 
doi:10.1371/journal.pcbi.1004420 pmid:26335425 pmcid:PMC4559467 fatcat:nihvf6llf5bupm5oljzyexkmmu

Control of Neuronal Network in Caenorhabditis elegans

Rahul Badhwar, Ganesh Bagler, Aamir Nazir
2015 PLoS ONE  
Identification of driver neurons and its characterization adds a new dimension in controllability of C. elegans neuronal network.  ...  We identified 'driver neurons' which can provide full control over the network.  ...  Number of driver neurons are higher in C. elegans neuronal connectivity network (16.5%) as compared with its degree distribution conserved (9.6%) and random network (0.3%) models.  ... 
doi:10.1371/journal.pone.0139204 pmid:26413834 pmcid:PMC4586142 fatcat:tq3tgmm6rjeyhk4tq4hyeb4c24

A Distinct Class of Slow ( 0.2-2 Hz) Intrinsically Bursting Layer 5 Pyramidal Neurons Determines UP/DOWN State Dynamics in the Neocortex

M. L. L rincz, D. Gunner, Y. Bao, W. M. Connelly, J. T. R. Isaac, S. W. Hughes, V. Crunelli
2015 Journal of Neuroscience  
This study, therefore, identifies an important role for cell-type-specific neuronal activity in driving neocortical UP states.  ...  neurons fires earlier during the onset of network oscillations compared with all other types of neurons recorded.  ...  Comparison of the development of UP states in "network driver" cells and conventional IB neurons following cholinergic receptor activation in vitro.  ... 
doi:10.1523/jneurosci.3603-14.2015 pmid:25855163 pmcid:PMC4388913 fatcat:tdymobgcevdkzedsbatl2q2mse

Molecular Networks and Key Regulators of the Dysregulated Neuronal System in Alzheimer's Disease [article]

Minghui Wang, Aiqun Li, Michiko Sekiya, Noam D Beckmann, Xiuming Quan, Nadine Schrode, Michael B. Fernando, Alex Yu, Li Zhu, Jiqing Cao, Liwei Lyu, Emrin Horgusluoglu (+27 others)
2019 bioRxiv   pre-print
manipulation of human induced pluripotent stem cell derived neurons and RNAi-based knockdown in transgenic Drosophila models.  ...  by LOAD and the resulting network models provide a blueprint for developing next generation therapeutics against LOAD.  ...  We anticipate generating region-specific singlecell multi-Omics data of LOAD and developing cell type-specific network models will offer invaluable in-depth understanding of the cellular complexity and  ... 
doi:10.1101/788323 fatcat:dbdtio7a2zd5rhhkoduc4z3k4q

Tonic-Clonic Transitions in Computer Simulation

William W. Lytton, Ahmet Omurtag
2007 Journal of clinical neurophysiology  
Network simulations can help identify underlying mechanisms of epileptic activity that are hard to isolate in biologic preparations.  ...  Intrinsic neuronal excitability is not always a predictor of network epileptiform activity but may paradoxically produce antiepileptic effects, depending on the settings of other parameters.  ...  Network A (NetA) had 10 drivers, 1,000 expressors, and 40 inhibitory cells. Network B (NetB) had 1,000 drivers, 2,000 expressors, and 500 inhibitory cells.  ... 
doi:10.1097/wnp.0b013e3180336fc0 pmid:17414973 pmcid:PMC2633473 fatcat:gspv5dw5jfbmpeqq4owvhcjg2i

Evolving toward a human-cell based and multiscale approach to drug discovery for CNS disorders

Eric E. Schadt, Sean Buchanan, Kristen J. Brennand, Kalpana M. Merchant
2014 Frontiers in Pharmacology  
Keywords: stem cell-based screening, systems biology and network biology, drug discovery screening, complex disease mechanism, high throughput biology Frontiers in Pharmacology | Experimental Pharmacology  ...  and exemplify the impact of, a multiscale biology approach that can integrate panomic, clinical, imaging, and literature data in order to construct predictive disease network models that can (i) elucidate  ...  ACKNOWLEDGMENTS The Schadt Laboratory is supported in part by NIH grants R01 MH097276 (NIMH) and RO1 AG046170 (NIA) Kristen J. Brennand is a New York Stem Cell Robertson Investigator.  ... 
doi:10.3389/fphar.2014.00252 pmid:25520658 pmcid:PMC4251289 fatcat:ta7horidwbd5vfrnlhy4ldg6c4

Reconfiguration of the Pontomedullary Respiratory Network: A Computational Modeling Study With Coordinated In Vivo Experiments

I. A. Rybak, R. O'Connor, A. Ross, N. A. Shevtsova, S. C. Nuding, L. S. Segers, R. Shannon, T. E. Dick, W. L. Dunin-Barkowski, J. M. Orem, I. C. Solomon, K. F. Morris (+1 others)
2008 Journal of Neurophysiology  
We developed a network model with PRG-VRC connectivity inferred from coordinated in vivo experiments.  ...  Neurons were modeled in the "integrate-and-fire" style; some neurons had pacemaker properties derived from the model of Breen et al.  ...  APPENDIX A FIG. 3 . 3 . 4) was developed using the initial model as a basis but incorporated new in vivo data presented in the A: schematic of network module illustrating inactivation of the I-Driver population  ... 
doi:10.1152/jn.90416.2008 pmid:18650310 pmcid:PMC2576193 fatcat:nsqsilaztbeyjg7u3qln6cgcae

Coregulation of Ion Channel Conductances Preserves Output in a Computational Model of a Crustacean Cardiac Motor Neuron

J. M. Ball, C. C. Franklin, A.-E. Tobin, D. J. Schulz, S. S. Nair
2010 Journal of Neuroscience  
We then developed a methodology of sampling a multidimensional parameter space to select an appropriate model set for meaningful comparison with variations in correlations seen in biological datasets.  ...  To determine whether balances of intrinsic currents potentially resulting from such correlations preserve certain electrical cell outputs, we developed a nominal biophysical model of the crustacean cardiac  ...  Conclusions Biophysical models of neurons and neuronal networks developed using biological data typically capture nominal behavior.  ... 
doi:10.1523/jneurosci.6435-09.2010 pmid:20573909 pmcid:PMC4473856 fatcat:52tonmsz7rguxcvhfro3fgtghe

Challenges of understanding brain function by selective modulation of neuronal subpopulations

Arvind Kumar, Ioannis Vlachos, Ad Aertsen, Clemens Boucsein
2013 Trends in Neurosciences  
We demonstrate limits of the selective modulation approach and argue that, even though highly successful in some instances, the approach fails in networks with complex connectivity.  ...  Neuronal networks confront researchers with an overwhelming complexity of interactions between their elements.  ...  activity in feedforward networks is not influenced by the type of neuron model, and feedforward networks with integrate-and-fire neurons [38, 39] behave similarly to those with detailed neuron models  ... 
doi:10.1016/j.tins.2013.06.005 pmid:23876423 fatcat:4mjh3mx2rnfsjolkh6xn6lpzwm

WONOEP appraisal: Molecular and cellular imaging in epilepsy

Kyle P. Lillis, Chris Dulla, Atul Maheshwari, Douglas Coulter, Istvan Mody, Uwe Heinemann, Moritz Armbruster, Jokūbas Žiburkus
2015 Epilepsia  
of epilepsy, which in turn may inform and improve development of next generation anti-epileptic and anti-epileptogenic drugs.  ...  Furthermore, easily accessible genetic technologies for targeting expression of fluorescent protein-based indicators make it possible to study, in animal models of epilepsy, epileptogenic changes to neural  ...  in the driver mouse.  ... 
doi:10.1111/epi.12939 pmid:25779014 pmcid:PMC4397142 fatcat:rds6l2t6k5h7ngw35mfwheqxea

Six Networks on a Universal Neuromorphic Computing Substrate

Thomas Pfeil, Andreas Grübl, Sebastian Jeltsch, Eric Müller, Paul Müller, Mihai A. Petrovici, Michael Schmuker, Daniel Brüderle, Johannes Schemmel, Karlheinz Meier
2013 Frontiers in Neuroscience  
In this study, we present a highly configurable neuromorphic computing substrate and use it for emulating several types of neural networks.  ...  Its configurability allows the realization of almost arbitrary network topologies and the use of widely varied neuronal and synaptic parameters.  ...  network (Thomas Pfeil); cortical attractor model (Mihai A.  ... 
doi:10.3389/fnins.2013.00011 pmid:23423583 pmcid:PMC3575075 fatcat:yqkre36bzfce5eettvxhu3pytm

Realizing biological spiking network models in a configurable wafer-scale hardware system

Johannes Fieres, Johannes Schemmel, Karlheinz Meier
2008 2008 IEEE International Joint Conference on Neural Networks (IEEE World Congress on Computational Intelligence)  
Model parameters other than the net topology (e.g., electrical neuron and synapse parameters) are not covered here. The hardware architecture is reviewed in section II.  ...  This paper focuses on the usability of the system by demonstrating that biologically relevant network models can in fact be mapped to this system.  ...  Checkerboard cells mark groups of 16x8 neurons hosted by the same network chip. Neurons sending signals to at least one neuron on the center network chip are marked black.  ... 
doi:10.1109/ijcnn.2008.4633916 dblp:conf/ijcnn/FieresSM08 fatcat:5uenkstvvfhh5hxexjvin7xkkm

Epigenetic pathways and glioblastoma treatment

Jennifer Clarke, Clara Penas, Chiara Pastori, Ricardo J Komotar, Amade Bregy, Ashish H Shah, Claes Wahlestedt, Nagi G Ayad
2013 Epigenetics  
Verma and colleagues demonstrated that neurons de-differentiate and become tumor-initiating cells in mouse models of glioma (ref. 5; Fig. 1 ).  ...  in GBM. 13 In simple terms, a driver event is usually defined as one that occurs early in tumorigenesis and occurs in pathways considered critical to the development of any of the hallmarks of cancer  ... 
doi:10.4161/epi.25440 pmid:23807265 pmcid:PMC3883781 fatcat:xhtaxw3kgrd6vl4uglfa54b26a
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