This document provides a summary of recent advances in neuroscience, including new techniques such as optogenetics, which uses light to control neural activity, expansion microscopy to view fine neural structures, and CLARITY to render tissues transparent. It discusses efforts to map structural and functional brain networks, characterize different cell types, and model the worm Caenorhabditis elegans nervous system. The document also covers decoding neural representations, reconstructing images from brain activity, and applications like brain-to-brain communication and potential for lie detection with fMRI.

1. From Brains to BRAINS:
Neuroscience at the Cutting Edge
John Borghi, PhD
@JohnBorghi
@BoldSignalsPod

2. Open
Connectome
Project

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Superfluous Neuroscience

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6. Noble, K. G., Houston, S. M., Brito, N. H., Bartsch, H., Kan, E., Kuperman, J. M., ... & Sowell, E. R. (2015). Family income, parental education and brain
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8. Adapted From: Brodmann K (1909). Vergleichende Lokalisationslehre der Grosshirnrinde.

11. Lafer-Sousa, R., Hermann, K.L., & Conway, B.R. (2015). Striking individual differences in color perception uncovered by ‘the dress’ photograph. Current Biology.

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Transsynaptic Tracing

14. Chen, F., Tillberg, P. W., & Boyden, E. S. (2015). Expansion microscopy. Science, 347(6221), 543-548
Expansion Microscopy

15. Chung, K., Wallace, J., Kim, S. Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., ... & Deisseroth, K. (2013). Structural and molecular interrogation of
intact biological systems. Nature, 497(7449), 332-337.
CLARITY

16. Chung, K., Wallace, J., Kim, S. Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., ... & Deisseroth, K. (2013). Structural and molecular interrogation of
intact biological systems. Nature, 497(7449), 332-337.
CLARITY

17. Lichtman, J. W., Livet, J., & Sanes, J. R. (2008). A technicolour approach to the connectome. Nature Reviews Neuroscience, 9(6), 417-422.
Golgi Stain
Brainbow

18. Chung, K., Wallace, J., Kim, S. Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., ... & Deisseroth, K. (2013). Structural and molecular interrogation of
intact biological systems. Nature, 497(7449), 332-337.

19. Allen Cell Types Database

20. Optogenetic actuators
(e.g. channelrhodopsin)
Optogenetic sensors
(e.g. Clomeleon, Mermaid)
Genetic Construct
inserted into virus
Virus is injected
into animal
Laser light is used to
Control activity of infected
neurons
Activity of infected
neurons is measured via
optic sensor
Optogenetics

21. Baratta, M. V., Nakamura, S., Dobelis, P., Pomrenze, M. B., Dolzani, S. D., & Cooper, D. C. (2012). Optogenetic control of genetically-targeted pyramidal
neuron activity in prefrontal cortex. arXiv preprint arXiv:1204.0710.

22. Ramirez, S., Liu, X., Lin, P. A., Suh, J., Pignatelli, M., Redondo, R. L., ... & Tonegawa, S. (2013). Creating a false memory in the
hippocampus. Science,341(6144), 387-391.
Image: Evan Wondolowski of Collective Next

23. Tanaka, K. Z., Pevzner, A., Hamidi, A. B., Nakazawa, Y., Graham, J., & Wiltgen, B. J. (2014). Cortical Representations Are Reinstated by the Hippocampus
during Memory Retrieval. Neuron, 84(2), 347-354.

24. Grosenick, L., Marshel, J. H., & Deisseroth, K. (2015). Closed-Loop and Activity-Guided Optogenetic Control. Neuron, 86(1), 106-139.
“Closed Loop” Optogenetics

25. Transcranial Direct
Current Stimulation
foc.us tDCS v2
Ghostbusters (1984)

26. Grau, C., Ginhoux, R., Riera, A., Nguyen, T. L., Chauvat, H., Berg, M., ... & Ruffini, G. (2014). Conscious brain-to-brain communication in humans using non-
invasive technologies. PloS one, 9(8), e105225.
Brain-to-Brain Communication

27. Park, H. J., & Friston, K. (2013). Structural and functional brain networks: from connections to cognition. Science, 342(6158), 1238411.

28. Szigeti, B., Gleeson, P., Vella, M., Khayrulin, S., Palyanov, A., Hokanson, J., ... & Larson, S. (2014). OpenWorm: an open-science approach to modeling
Caenorhabditis elegans. Frontiers in computational neuroscience, 8.
OpenWorm

29. Varshney, L. R., Chen, B. L., Paniagua, E., Hall, D. H., & Chklovskii, D. B. (2011). Structural properties of the Caenorhabditis elegans neuronal network. PLoS
computational biology, 7(2), e1001066.
Robot Worms

30. Oh, S. W., Harris, J. A., Ng, L., Winslow, B., Cain, N., Mihalas, S., ... & Zeng, H. (2014). A mesoscale connectome of the mouse brain.
Nature, 508(7495), 207-214.

31. EyeWire

32. The Human Brain Project

33. The Human Connectome
Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C. J., Wedeen, V. J., & Sporns, O. (2008). Mapping the structural core of human cerebral
cortex.PLoS biology, 6(7), e159.

34. Irimia, A., Chambers, M. C., Torgerson, C. M., & Van Horn, J. D. (2012). Circular representation of human cortical networks for subject and population-level
connectomic visualization. Neuroimage, 60(2), 1340-1351.

35. Fornito, A., Zalesky, A., & Breakspear, M. (2015). The connectomics of brain disorders. Nature Reviews Neuroscience, 16(3), 159-172.
The Human Connectome

36. Fox, C. J., Iaria, G., & Barton, J. J. (2009). Defining the face processing network: optimization of the functional localizer in fMRI. Human brain mapping,30(5),
1637-1651.
The Face Processing Network

37. Glahn, D. C., Winkler, A. M., Kochunov, P., Almasy, L., Duggirala, R., Carless, M. A., ... & Blangero, J. (2010). Genetic control over the resting
brain.Proceedings of the National Academy of Sciences, 107(3), 1223-1228.
The Default Mode Network

38. Brain Training Games
Kesler, S. R., Sheau, K., Koovakkattu, D., & Reiss, A. L. (2011). Changes in
frontal-parietal activation and math skills performance following adaptive
number sense training: Preliminary results from a pilot
study.Neuropsychological rehabilitation, 21(4), 433-454.
Owen, A. M., Hampshire, A., Grahn, J. A., Stenton, R., Dajani, S., Burns, A. S., ... &
Ballard, C. G. (2010). Putting brain training to the test. Nature,465(7299), 775-778.

39. Jones-Hagata, L. B., Ortega, B. N., Zaiko, Y. V., Roach, E. L., Korgaonkar, M. S., Grieve, S. M., ...
& Etkin, A. (2015). Identification of a Common Neurobiological Substrate for Mental Illness.
JAMA Psychiatry
Shackman, A. J., Salomons, T. V., Slagter, H. A., Fox, A. S., Winter, J. J., & Davidson, R. J.
(2011). The integration of negative affect, pain and cognitive control in the cingulate cortex.
Nature Reviews Neuroscience, 12(3), 154-167.

40. Kaplan, J. T., Man, K., & Greening, S. G. (2015). Multivariate cross-classification: applying machine learning techniques to characterize abstraction in neural
representations. Frontiers in human neuroscience, 9.
Multi-Voxel Patten Analysis

41. Woo, C. W., Koban, L., Kross, E., Lindquist, M. A., Banich, M. T., Ruzic, L., ... & Wager, T. D.
(2014). Separate neural representations for physical pain and social rejection. Nature
communications, 5.
Eisenberger, N. I., Lieberman, M. D., & Williams, K. D. (2003). Does rejection hurt? An fMRI study
of social exclusion. Science, 302(5643), 290-292.
Multi-Voxel
Patten Analysis

42. Schoenmakers, S., Barth, M., Heskes, T., & van Gerven, M. (2013). Linear reconstruction of perceived images from human brain activity. NeuroImage, 83, 951-
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Neural Decoding with MVPA

43. Cowen, A. S., Chun, M. M., & Kuhl, B. A. (2014). Neural portraits of perception: reconstructing face images from evoked brain
activity. Neuroimage, 94, 12-22.

44. fMRI and Lie Detection?
Langleben, D. D., Loughead, J. W., Bilker, W. B., Ruparel, K., Childress, A. R., Busch, S. I., & Gur, R. C. (2005). Telling truth from lie in individual subjects with
fast event‐related fMRI. Human brain mapping, 26(4), 262-272.

45. Sentiment Analysis by Emotient

46. Clarity by Neurokky
Neuroscience Fiction

47. Thanks!
John Borghi, PhD
John.Borghi@Gmail.com
@JohnBorghi
Bold Signals Podcast
BoldSignalsi@Gmail.com
@BoldSignalsPod