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Part of the book series: Springer Theses ((Springer Theses))

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Abstract

Reconstruction of the human connectome, as the set of structural and functional brain’s neuronal interconnections at different scales, is a fundamental issue in modern neuroscience. Adopting reduced and simplified models may represent an efficient strategy to overcome the complexity of the brain’s neural circuits. This manuscript reports on statistical algorithms designed to infer functional connectivity of in vitro neural networks chronically coupled to Micro Electrodes Arrays (MEAs). The developed collection includes algorithms designed to maximize computational accuracy (e.g., successfully reconstructing the inhibitory functional links) and efficiency. This PhD thesis comprises methods to compute the most significant functional connectivity graph, while extracting its topological properties based on graph theory.

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References

  1. Makarov VA, Panetsos F, de Feo O (2005) A method for determining neural connectivity and inferring the underlying network dynamics using extracellular spike recordings. J Neurosci Methods 144:265–279. https://doi.org/10.1016/j.jneumeth.2004.11.013

    Article  Google Scholar 

  2. Yuste R (2015) From the neuron doctrine to neural networks. Nat Rev Neurosci 16:487–497

    Article  Google Scholar 

  3. Sporns O, Tononi G, Edelman GM (2000) Connectivity and complexity: the relationship between neuroanatomy and brain dynamics. Neural Netw 13:909–922

    Article  Google Scholar 

  4. Sporns O (2011) The human connectome: a complex network. Ann N Y Acad Sci 1224:109–125. https://doi.org/10.1111/j.1749-6632.2010.05888.x

    Article  Google Scholar 

  5. Sporns O, Tononi G, Kotter R (2005) The human connectome: a structural description of the human brain. PLoS Comput Biol 1:e42. https://doi.org/10.1371/journal.pcbi.0010042

    Article  Google Scholar 

  6. Sporns O, Tononi G (2002) Classes of network connetivity and dynamics. Complexity 7:28–38

    Article  Google Scholar 

  7. Buchs P-A, Muller D (1996) Induction of long-term potentiation is associated with major ultrastructural changes of activated synapses. Proc Natl Acad Sci USA 93:8040–8045

    Article  Google Scholar 

  8. Poli D, Pastore VP, Massobrio P (2015) Functional connectivity in in vitro neuronal assemblies. Front Neural Cir 9:57. https://doi.org/10.3389/fncir.2015.00057

    Article  Google Scholar 

  9. Letourneau PC (1975) Possible roles of cell to substratum adhesion in neuronal morphogenesis. Dev Biol 44:77–91

    Article  Google Scholar 

  10. Potter SM, DeMarse TB (2001) A new approach to neural cell culture for long-term studies. J Neurosci Methods 110:17–24

    Article  Google Scholar 

  11. Berdondini L et al (2009) Active pixel sensor array for high spatio-temporal resolution electrophysiological recordings from single cell to large scale neuronal networks. Lab Chip 9:2644–2651

    Article  Google Scholar 

  12. Frey U, Egert U, Heer F, Hafizovic S, Hierlemann A (2009) Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices. Biosens Bioelectron 24:2191–2198. https://doi.org/10.1016/j.bios.2008.11.028

    Article  Google Scholar 

  13. Wagenaar DA, Madhavan R, Pine J, Potter SM (2005) Controlling bursting in cortical cultures with closed-loop multi-electrode stimulation. J Neurosci 25:680–688. https://doi.org/10.1523/JNEUROSCI.4209-04.2005

    Article  Google Scholar 

  14. Pancrazio JJ et al (2003) A portable microelectrode array recording system incorporating cultured neuronal networks for neurotoxin detection. Biosens Bioelectron 18:1339–1347

    Article  Google Scholar 

  15. Levy O, Ziv NE, Marom S (2012) Enhancement of neural representation capacity by modular architecture in networks of cortical neurons. Eur J Neurosci 35:1753–1760. https://doi.org/10.1111/j.1460-9568.2012.08094.x

    Article  Google Scholar 

  16. Massobrio P, de Arcangelis L, Pasquale V, Jensen HJ, Plenz D (2015) Criticality as a signature of healthy neural systems. Front Syst Neurosci 9:22. https://doi.org/10.3389/fnsys.2015.00022

    Article  Google Scholar 

  17. Maccione A et al (2012) Multiscale functional connectivity estimation on low-density neuronal cultures recorded by high-density CMOS micro electrode arrays. J Neurosci Methods 207:161–171. https://doi.org/10.1016/j.jneumeth.2012.04.002

    Article  Google Scholar 

  18. Garofalo M, Nieus T, Massobrio P, Martinoia S (2009) Evaluation of the performance of information theory-based methods and cross-correlation to estimate the functional connectivity in cortical networks. PLoS ONE 4:e6482. https://doi.org/10.1371/journal.pone.0006482

    Article  Google Scholar 

  19. Van Bussel F, Kriener B, Timme M (2011) Inferring synaptic connectivity from spatio-temporal spike patterns. Front Comput Neurosci 5:3. https://doi.org/10.3389/fncom.2011.00003

    Article  Google Scholar 

  20. Doiron B, Litwin-Kumar A, Rosenbaum R, Ocker GK, Josic K (2016) The mechanics of state-dependent neural correlations. Nat Neurosci 19:383–393. https://doi.org/10.1038/nn.4242

    Article  Google Scholar 

  21. Sporns O (2013) Structure and function of complex brain networks. Dialogues Clin Neurosci 15:247–262

    Article  Google Scholar 

  22. Eversmann B et al (2003) A 128 x 128 CMOS biosensor array for extracellular recording of neural activity. IEEE J Solid-State Circ 38:2306–2317

    Article  Google Scholar 

  23. Maccione A et al (2009) A novel algorithm for precise identification of spikes in extracellularly recorded neuronal signals. J Neurosci Methods 177:241–249

    Article  Google Scholar 

  24. Ide AN, Andruska A, Boehler M, Wheeler BC, Brewer GJ (2010) Chronic network stimulation enhances evoked action potentials. J Neural Eng 7:016008. https://doi.org/10.1088/1741-2560/7/1/016008

    Article  Google Scholar 

  25. Egert U et al (2002) MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB. J Neurosci Methods 117:33–42

    Article  Google Scholar 

  26. Borghi T, Gusmeroli R, Spinelli AS, Baranauskas G (2007) A simple method for efficient spike detection in multiunit recordings. J Neurosci Methods 163:176–180

    Article  Google Scholar 

  27. Gerstein GL, Perkel DH (1969) Simultaneously recorded trains of action potentials: analysis and functional interpretation. Science 164:828–830

    Article  Google Scholar 

  28. Brown EN, Kass RE, Mitra PP (2004) Multiple neural spike train data analysis: state-of-the-art and future challenges. Nat Neurosci 7:456–461

    Article  Google Scholar 

  29. Friston KJ (2009) Modalities, modes and models in functional neuroimaging. Science 326:399–403. https://doi.org/10.1126/science.1174521

    Article  Google Scholar 

  30. Ventura V, Cai C, Kass RE (2005) Statistical assessment of time-varying dependency between two neurons. J Neurophysiol 94:2940

    Article  Google Scholar 

  31. Brosch M, Schreiner CE (1999) Correlations between neural discharges are related to receptive field properties in cat primary auditory cortex. Eur J Neurosci 11:3517–3530. https://doi.org/10.1046/j.1460-9568.1999.00770.x

    Article  Google Scholar 

  32. Salinas E, Sejnowski TJ (2001) Correlated neuronal activity and the flow of neural information. Nat Rev Neurosci 2:539–550

    Article  Google Scholar 

  33. Bedenbaugh P, Gerstein GL (1997) Multiunit normalized cross correlation differs from the average single-unit normalized correlation. Neural Comput 9:1265–1275

    Article  Google Scholar 

  34. Poli D, Pastore VP, Martinoia S, Massobrio P (2016) From functional to structural connectivity using partial correlation in neuronal assemblies. J Neural Eng 13:026023

    Article  Google Scholar 

  35. Eichler M, Dahlhaus R, Sandkuhler J (2003) Partial correlation analysis for the identification of synaptic connections. Biol Cybern 89:289–302

    Article  Google Scholar 

  36. Quiroga QR, Panzeri S (2009) Extracting information from neuronal populations: information theory and decoding approaches. Nat Rev Neurosci 10:173–185

    Article  Google Scholar 

  37. Nigam S et al (2016) Rich-club organization in effective connectivity among cortical neurons. J Neurosci 36:670–684. https://doi.org/10.1523/JNEUROSCI.2177-15.2016

    Article  Google Scholar 

  38. Friston KJ (2011) Functional and effective connectivity: a review. Brain Connectivity 1:13–36. https://doi.org/10.1089/brain.2011.0008

    Article  Google Scholar 

  39. Ito S et al (2011) Extending Transfer entropy improves identification of effective connectivity in a spiking cortical network model. PLoS ONE 6:e27431. https://doi.org/10.1371/journal.pone.0027431

    Article  Google Scholar 

  40. Freeman GM Jr, Krock RM, Aton SJ, Thaben P, Herzog ED (2013) GABA networks destabilize genetic oscillations in the circadian pacemaker. Neuron 78:799–806. https://doi.org/10.1016/j.neuron.2013.04.003

    Article  Google Scholar 

  41. Zaytsev YV, Morrison A, Deger M (2015) Reconstruction of recurrent synaptic connectivity of thousands of neurons from simulated spiking activity. J Comput Neurosci 39:77–103. https://doi.org/10.1007/s10827-015-0565-5

    Article  MathSciNet  MATH  Google Scholar 

  42. Abeles M (1991) Corticonics: neural circuits of the cerebral cortex. Cambridge University Press, Cambridge

    Book  Google Scholar 

  43. Aertsen A et al (1991) Neural interactions in the frontal cortex of a behaving monkey: signs of dependence on stimulus context and behavioral state. J Hirnforsch 32:735–743

    Google Scholar 

  44. Muller J et al (2015) High-resolution CMOS MEA platform to study neurons at subcellular, cellular, and network levels. Lab Chip 15:2767–2780. https://doi.org/10.1039/c5lc00133a

    Article  Google Scholar 

  45. Viswam V, Dragas J, Muller J, Hierlemann A In: IEEE international solid-state circuits conference. IEEE, pp 394–396

    Google Scholar 

  46. Pastore VP, Godjoski A, Martinoia S, Massobrio P (2017) SPICODYN: a toolbox for the analysis of neuronal network dynamics and connectivity from multi-site spike signal recordings. Neuroinformatics 1:15–30. https://doi.org/10.1007/s12021-017-9343-z

    Article  Google Scholar 

  47. Pastore VP, Poli D, Godjoski A, Martinoia S, Massobrio P (2016) ToolConnect: a functional connectivity toolbox for in vitro networks. Front Neuroinf https://doi.org/10.3389/fninf.2016.00013

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Pastore, V.P. (2021). Introduction. In: Estimating Functional Connectivity and Topology in Large-Scale Neuronal Assemblies. Springer Theses. Springer, Cham. https://doi.org/10.1007/978-3-030-59042-0_1

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  • DOI: https://doi.org/10.1007/978-3-030-59042-0_1

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