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references.bib
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@{biblatex-control,
}
@article{Song2005,
author = {Song, Sen and Sj{\"o}str{\"o}m, Per Jesper and
Reigl, Markus and Nelson, Sacha and
Chklovskii, Dmitri B},
journal = {PLoS Biol},
month = mar,
number = {3},
pages = {e68},
title = {Highly {{Nonrandom Features}} of {{Synaptic
Connectivity}} in {{Local Cortical Circuits}}},
volume = {3},
year = {2005},
abstract = {A dataset of hundreds of recordings in which four
neurons were simultaneously monitored reveals
clustered connectivity patterns among cortical
neurons.},
doi = {10.1371/journal.pbio.0030068},
}
@article{Perin2011,
author = {Perin, Rodrigo and Berger, Thomas K. and
Markram, Henry},
journal = {Proceedings of the National Academy of Sciences},
month = mar,
number = {13},
pages = {5419--5424},
title = {A Synaptic Organizing Principle for Cortical Neuronal
Groups},
volume = {108},
year = {2011},
abstract = {Neuronal circuitry is often considered a clean slate
that can be dynamically and arbitrarily molded by
experience. However, when we investigated synaptic
connectivity in groups of pyramidal neurons in the
neocortex, we found that both connectivity and
synaptic weights were surprisingly predictable.
Synaptic weights follow very closely the number of
connections in a group of neurons, saturating after
only 20\% of possible connections are formed between
neurons in a group. When we examined the network
topology of connectivity between neurons, we found
that the neurons cluster into small world networks
that are not scale-free, with less than 2 degrees of
separation. We found a simple clustering rule where
connectivity is directly proportional to the number
of common neighbors, which accounts for these small
world networks and accurately predicts the connection
probability between any two neurons. This pyramidal
neuron network clusters into multiple groups of a few
dozen neurons each. The neurons composing each group
are surprisingly distributed, typically more than 100
$\mu$m apart, allowing for multiple groups to be
interlaced in the same space. In summary, we
discovered a synaptic organizing principle that
groups neurons in a manner that is common across
animals and hence, independent of individual
experiences. We speculate that these elementary
neuronal groups are prescribed Lego-like building
blocks of perception and that acquired memory relies
more on combining these elementary assemblies into
higher-order constructs.},
doi = {10.1073/pnas.1016051108},
issn = {0027-8424, 1091-6490},
language = {en},
}
@article{Markram1997,
author = {Markram, Henry and L{\"u}bke, Joachim and
Frotscher, Michael and Roth, Arnd and Sakmann, Bert},
journal = {The Journal of Physiology},
month = apr,
number = {Pt 2},
pages = {409--440},
title = {Physiology and Anatomy of Synaptic Connections
between Thick Tufted Pyramidal Neurones in the
Developing Rat Neocortex.},
volume = {500},
year = {1997},
abstract = {1. Dual voltage recordings were made from pairs of
adjacent, synaptically connected thick tufted layer 5
pyramidal neurones in brain slices of young rat
(14-16 days) somatosensory cortex to examine the
physiological properties of unitary EPSPs. Pre- and
postsynaptic neurones were filled with biocytin and
examined in the light and electron microscope to
quantify the morphology of axonal and dendritic
arbors and the number and location of synaptic
contacts on the target neurone. 2. In 138 synaptic
connections between pairs of pyramidal neurones 96
(70\%) were unidirectional and 42 (30\%) were
bidirectional. The probability of finding a synaptic
connection in dual recordings was 0.1. Unitary EPSPs
evoked by a single presynaptic action potential (AP)
had a mean peak amplitude ranging from 0.15 to 5.5 mV
in different connections with a mean of 1.3 +/- 1.1
mV, a latency of 1.7 +/- 0.9 ms, a 20-80\% rise time
of 2.9 +/- 2.3 ms and a decay time constant of 40 +/-
18 ms at 32-24 degrees C and -60 +/- 2 mV membrane
potential. 3. Peak amplitudes of unitary EPSPs
fluctuated randomly from trial to trial. The
coefficient of variation (c.v.) of the unitary EPSP
amplitudes ranged from 0.13 to 2.8 in different
synaptic connections (mean, 0.52; median, 0.41). The
percentage of failures of single APs to evoke a
unitary EPSP ranged from 0 to 73\% (mean, 14\%;
median, 7\%). Both c.v. and percentage of failures
decreased with increasing mean EPSP amplitude. 4.
Postsynaptic glutamate receptors which mediate
unitary EPSPs at -60 mV were predominantly of the
L-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate
(AMPA) receptor type. Receptors of the N-methyl-D-aspartate (NMDA) type
contributed only a small fraction ($<$ 20\%) to the voltage-time integral of
the unitary EPSP at -60 mV, but their contribution increased at more positive
membrane potentials. 5. Branching patterns of dendrites and axon collaterals
of forty-five synaptically connected neurones, when examined in the light
microscope, indicated that the axonal and dendritic anatomy of both
projecting and target neurones and of uni- and bidirectionally connected
neurones was uniform. 6. The number of potential synaptic contacts formed by
a presynaptic neurone on a target neurone varied between four and eight
(mean, 5.5 +/- 1.1 contacts; n = 19 connections). Synaptic contacts were
preferentially located on basal dendrites (63\%, 82 +/- 35 microns from the
soma, n = 67) and apical oblique dendrites (27\%, 145 +/- 59 microns, n =
29), and 35\% of all contacts were located on tertiary basal dendritic
branches. The mean geometric distances (from the soma) of the contacts of a
connection varied between 80 and 585 microns (mean, 147 microns; median, 105
microns). The correlation between EPSP amplitude and the number of
morphologically determined synaptic contacts or the mean geometric distances
from the soma was only weak (correlation coefficients were 0.2 and 0.26,
respectively). 7. Compartmental models constructed from camera lucida
drawings of eight target neurones showed that synaptic contacts were located
at mean electrotonic distances between 0.07 and 0.33 from the soma (mean,
0.13). Simulations of unitary EPSPs, assuming quantal conductance changes
with fast rise time and short duration, indicated that amplitudes of quantal
EPSPs at the soma were attenuated, on average, to $<$ 10\% of dendritic EPSPs
and varied in amplitude up to 10-fold depending on the dendritic location of
synaptic contacts. The inferred quantal peak conductance increase varied
between 1.5 and 5.5 nS (mean, 3 nS). 8. The combined physiological and
morphological measurements in conjunction with EPSP simulations indicated
that the 20-fold range in efficacy of the synaptic connections between thick
tufted pyramidal neurones, which have their synaptic contacts preferentially
located on basal and apical oblique dendrites, was due to differences in
transmitter release probability of the projecting neurones and, to a lesser
extent, to differenc},
issn = {0022-3751},
}
@article{Lefort2009,
author = {Lefort, Sandrine and Tomm, Christian and
Floyd Sarria, J. -C. and Petersen, Carl C. H.},
journal = {Neuron},
month = jan,
number = {2},
pages = {301--316},
title = {The {{Excitatory Neuronal Network}} of the {{C2
Barrel Column}} in {{Mouse Primary Somatosensory
Cortex}}},
volume = {61},
year = {2009},
abstract = {Summary Local microcircuits within neocortical
columns form key determinants of sensory processing.
Here, we investigate the excitatory synaptic neuronal
network of an anatomically defined cortical column,
the C2 barrel column of mouse primary somatosensory
cortex. This cortical column is known to process
tactile information related to the C2 whisker.
Through multiple simultaneous whole-cell recordings,
we quantify connectivity maps between individual
excitatory neurons located across all cortical layers
of the C2 barrel column. Synaptic connectivity
depended strongly upon somatic laminar location of
both presynaptic and postsynaptic neurons, providing
definitive evidence for layer-specific signaling
pathways. The strongest excitatory influence upon the
cortical column was provided by presynaptic layer 4
neurons. In all layers we found rare large-amplitude
synaptic connections, which are likely to contribute
strongly to reliable information processing. Our data
set provides the first functional description of the
excitatory synaptic wiring diagram of a
physiologically relevant and anatomically
well-defined cortical column at single-cell
resolution.},
doi = {10.1016/j.neuron.2008.12.020},
issn = {0896-6273},
}
@article{Bourjaily2011,
author = {Bourjaily, Mark A. and Miller, Paul},
journal = {Frontiers in Computational Neuroscience},
pages = {37},
title = {Excitatory, Inhibitory, and Structural Plasticity
Produce Correlated Connectivity in Random Networks
Trained to Solve Paired-Stimulus Tasks},
volume = {5},
year = {2011},
abstract = {The pattern of connections among cortical excitatory
cells with overlapping arbors is non-random. In
particular, correlations among connections produce
clustering \textendash{} cells in cliques connect to
each other with high probability, but with lower
probability to cells in other spatially intertwined
cliques. In this study, we model initially randomly
connected sparse recurrent networks of spiking
neurons with random, overlapping inputs, to
investigate what functional and structural synaptic
plasticity mechanisms sculpt network connections into
the patterns measured in vitro. Our Hebbian
implementation of structural plasticity causes a
removal of connections between uncorrelated
excitatory cells, followed by their random
replacement. To model a biconditional discrimination
task, we stimulate the network via pairs (A + B, C +
D, A + D, and C + B) of four inputs (A, B, C, and D).
We find networks that produce neurons most responsive
to specific paired inputs \textendash{} a building
block of computation and essential role for cortex
\textendash{} contain the excessive clustering of
excitatory synaptic connections observed in cortical
slices. The same networks produce the best
performance in a behavioral readout of the networks'
ability to complete the task. A plasticity mechanism
operating on inhibitory connections, long-term
potentiation of inhibition, when combined with
structural plasticity, indirectly enhances clustering
of excitatory cells via excitatory connections. A
rate-dependent (triplet) form of
spike-timing-dependent plasticity (STDP) between
excitatory cells is less effective and basic STDP is
detrimental. Clustering also arises in networks
stimulated with single stimuli and in networks
undergoing raised levels of spontaneous activity when
structural plasticity is combined with functional
plasticity. In conclusion, spatially intertwined
clusters or cliques of connected excitatory cells can
arise via a Hebbian form of structural plasticity
operating in initially randomly connected networks.},
doi = {10.3389/fncom.2011.00037},
}
@article{Gilbert1959,
author = {Gilbert, E. N.},
journal = {The Annals of Mathematical Statistics},
month = dec,
note = {Mathematical Reviews number (MathSciNet) MR108839,
Zentralblatt MATH identifier0168.40801},
number = {4},
pages = {1141--1144},
title = {Random {{Graphs}}},
volume = {30},
year = {1959},
abstract = {Project Euclid - mathematics and statistics online},
doi = {10.1214/aoms/1177706098},
issn = {0003-4851, 2168-8990},
language = {EN},
}
@article{Erdos1959,
author = {Erd{\H o}s, P. and R{\'e}nyi, A.},
journal = {Publicationes Mathematicae (Debrecen)},
pages = {290--297},
title = {On Random Graphs, {{I}}},
volume = {6},
year = {1959},
}
@article{Jensen1906,
author = {Jensen, J. L. W. V.},
journal = {Acta Mathematica},
month = dec,
number = {1},
pages = {175--193},
title = {{Sur les fonctions convexes et les in{\'e}galit{\'e}s
entre les valeurs moyennes}},
volume = {30},
year = {1906},
doi = {10.1007/BF02418571},
issn = {0001-5962, 1871-2509},
language = {fr},
}
@book{Cover2006,
address = {Hoboken, N.J},
author = {Cover, Thomas M. and Thomas, Joy A.},
edition = {2 edition},
month = jul,
publisher = {{Wiley-Interscience}},
title = {Elements of {{Information Theory}} 2nd {{Edition}}},
year = {2006},
abstract = {The latest edition of this classic is updated with
new problem sets and material The Second Edition of
this fundamental textbook maintains the book's
tradition of clear, thought-provoking instruction.
Readers are provided once again with an instructive
mix of mathematics, physics, statistics, and
information theory. All the essential topics in
information theory are covered in detail, including
entropy, data compression, channel capacity, rate
distortion, network information theory, and
hypothesis testing. The authors provide readers with
a solid understanding of the underlying theory and
applications. Problem sets and a telegraphic summary
at the end of each chapter further assist readers.
The historical notes that follow each chapter recap
the main points. The Second Edition features: *
Chapters reorganized to improve teaching * 200 new
problems * New material on source coding, portfolio
theory, and feedback capacity * Updated references
Now current and enhanced, the Second Edition of
Elements of Information Theory remains the ideal
textbook for upper-level undergraduate and graduate
courses in electrical engineering, statistics, and
telecommunications. An Instructor's Manual presenting
detailed solutions to all the problems in the book is
available from the Wiley editorial department.},
isbn = {978-0-471-24195-9},
language = {English},
}
@article{Thomson2002,
author = {Thomson, Alex M. and West, David C. and Wang, Yun and
Bannister, A. Peter},
journal = {Cerebral Cortex},
month = jan,
number = {9},
pages = {936--953},
title = {Synaptic {{Connections}} and {{Small Circuits
Involving Excitatory}} and {{Inhibitory Neurons}} in
{{Layers}} 2\textendash{}5 of {{Adult Rat}} and {{Cat
Neocortex}}: {{Triple Intracellular Recordings}} and
{{Biocytin Labelling In Vitro}}},
volume = {12},
year = {2002},
abstract = {Dual and triple intracellular recordings with
biocytin labelling in slices of adult neocortex
explored small circuits of synaptically connected
neurons. 679 paired recordings in rat and 319 in cat
yielded 135 and 42 excitatory postsynaptic potentials
(EPSPs) and 37 and 26 inhibitory postsynaptic
potentials (IPSPs), respectively. Patterns of
connectivity and synaptic properties were similar in
the two species, although differences of scale and in
the range of morphologies were observed. Excitatory
`forward' projections from layer 4 to 3, like those
from layer 3 to 5, targeted pyramidal cells and a
small proportion of interneurons, while excitatory
`back' projections from layer 3 to 4 selected
interneurons, including parvalbumin immuno-positive
basket cells. Layer 4 interneurons that inhibited
layer 3 pyramidal cells included both basket cells
and dendrite-targeting cells. Large interneurons,
resembling cells previously described as large basket
cells, in layers 4 and 3 (cat), with long myelinated
horizontal axon collaterals received frequent
excitatory inputs from both layers. A very high rate
of connectivity was observed between pairs of
interneurons, often with quite different
morphologies, and the resultant IPSPs, like the EPSPs
recorded in interneurons, were brief compared with
those recorded in pyramidal and spiny stellate
cells.},
doi = {10.1093/cercor/12.9.936},
issn = {1047-3211, 1460-2199},
language = {en},
}
@article{Lee2016a,
author = {Lee, Wei-Chung Allen and Bonin, Vincent and
Reed, Michael and Graham, Brett J. and Hood, Greg and
Glattfelder, Katie and Reid, R. Clay},
journal = {Nature},
month = mar,
title = {Anatomy and Function of an Excitatory Network in the
Visual Cortex},
year = {2016},
doi = {10.1038/nature17192},
issn = {0028-0836, 1476-4687},
}
@book{Hogg1978,
address = {New York},
author = {Hogg, Robert V. and Craig, Allen T.},
edition = {4th ed},
publisher = {{Macmillan}},
title = {Introduction to Mathematical Statistics},
year = {1978},
isbn = {978-0-02-355710-1},
}
@article{Ko2011,
author = {Ko, Ho and Hofer, Sonja B. and Pichler, Bruno and
Buchanan, Katherine A. and
Sj{\"o}str{\"o}m, P. Jesper and
Mrsic-Flogel, Thomas D.},
journal = {Nature},
month = may,
number = {7345},
pages = {87--91},
title = {Functional Specificity of Local Synaptic Connections
in Neocortical Networks},
volume = {473},
year = {2011},
abstract = {Neuronal connectivity is fundamental to information
processing in the brain. Therefore, understanding the
mechanisms of sensory processing requires uncovering
how connection patterns between neurons relate to
their function. On a coarse scale, long-range
projections can preferentially link cortical regions
with similar responses to sensory stimuli. But on the
local scale, where dendrites and axons overlap
substantially, the functional specificity of
connections remains unknown. Here we determine
synaptic connectivity between nearby layer 2/3
pyramidal neurons in vitro, the response properties
of which were first characterized in mouse visual
cortex in vivo. We found that connection probability
was related to the similarity of visually driven
neuronal activity. Neurons with the same preference
for oriented stimuli connected at twice the rate of
neurons with orthogonal orientation preferences.
Neurons responding similarly to naturalistic stimuli
formed connections at much higher rates than those
with uncorrelated responses. Bidirectional synaptic
connections were found more frequently between
neuronal pairs with strongly correlated visual
responses. Our results reveal the degree of
functional specificity of local synaptic connections
in the visual cortex, and point to the existence of
fine-scale subnetworks dedicated to processing
related sensory information.},
doi = {10.1038/nature09880},
issn = {0028-0836},
language = {en},
}
@article{Stepanyants2004,
author = {Stepanyants, Armen and Tam{\'a}s, G{\'a}bor and
Chklovskii, Dmitri B.},
journal = {Neuron},
month = jul,
number = {2},
pages = {251--259},
title = {Class-{{Specific Features}} of {{Neuronal Wiring}}},
volume = {43},
year = {2004},
abstract = {Brain function relies on specificity of synaptic
connectivity patterns among different classes of
neurons. Yet, the substrates of specificity in
complex neuropil remain largely unknown. We search
for imprints of specificity in the layout of axonal
and dendritic arbors from the rat neocortex. An
analysis of 3D reconstructions of pairs consisting of
pyramidal cells (PCs) and GABAergic interneurons
(GIs) revealed that the layout of GI axons is
specific. This specificity is manifested in a
relatively high tortuosity, small branch length of
these axons, and correlations of their trajectories
with the positions of postsynaptic neuron dendrites.
Axons of PCs show no such specificity, usually taking
a relatively straight course through neuropil.
However, wiring patterns among PCs hold a large
potential for circuit remodeling and specificity
through growth and retraction of dendritic spines.
Our results define distinct class-specific rules in
establishing synaptic connectivity, which could be
crucial in formulating a canonical cortical circuit.},
doi = {10.1016/j.neuron.2004.06.013},
issn = {0896-6273},
language = {English},
}
@article{Kalisman2005,
author = {Kalisman, Nir and Silberberg, Gilad and
Markram, Henry},
journal = {Proceedings of the National Academy of Sciences of
the United States of America},
month = jan,
number = {3},
pages = {880--885},
title = {The Neocortical Microcircuit as a Tabula Rasa},
volume = {102},
year = {2005},
abstract = {The neocortex has a high capacity for plasticity. To
understand the full scope of this capacity, it is
essential to know how neurons choose particular
partners to form synaptic connections. By using
multineuron whole-cell recordings and confocal
microscopy we found that axons of layer V neocortical
pyramidal neurons do not preferentially project
toward the dendrites of particular neighboring
pyramidal neurons; instead, axons promiscuously touch
all neighboring dendrites without any bias.
Functional synaptic coupling of a small fraction of
these neurons is, however, correlated with the
existence of synaptic boutons at existing touch
sites. These data provide the first direct
experimental evidence for a tabula rasa-like
structural matrix between neocortical pyramidal
neurons and suggests that pre- and postsynaptic
interactions shape the conversion between touches and
synapses to form specific functional microcircuits.
These data also indicate that the local neocortical
microcircuit has the potential to be differently
rewired without the need for remodeling axonal or
dendritic arbors.},
doi = {10.1073/pnas.0407088102},
issn = {0027-8424, 1091-6490},
language = {en},
}
@article{Clopath2010,
author = {Clopath, Claudia and B{\"u}sing, Lars and
Vasilaki, Eleni and Gerstner, Wulfram},
journal = {Nature Neuroscience},
month = mar,
number = {3},
pages = {344--352},
title = {Connectivity Reflects Coding: A Model of
Voltage-Based {{STDP}} with Homeostasis},
volume = {13},
year = {2010},
abstract = {Electrophysiological connectivity patterns in cortex
often have a few strong connections, which are
sometimes bidirectional, among a lot of weak
connections. To explain these connectivity patterns,
we created a model of spike
timing\textendash{}dependent plasticity (STDP) in
which synaptic changes depend on presynaptic spike
arrival and the postsynaptic membrane potential,
filtered with two different time constants. Our model
describes several nonlinear effects that are observed
in STDP experiments, as well as the voltage
dependence of plasticity. We found that, in a
simulated recurrent network of spiking neurons, our
plasticity rule led not only to development of
localized receptive fields but also to connectivity
patterns that reflect the neural code. For temporal
coding procedures with spatio-temporal input
correlations, strong connections were predominantly
unidirectional, whereas they were bidirectional under
rate-coded input with spatial correlations only.
Thus, variable connectivity patterns in the brain
could reflect different coding principles across
brain areas; moreover, our simulations suggested that
plasticity is fast.},
doi = {10.1038/nn.2479},
issn = {1097-6256},
language = {en},
}
@article{Miner2016,
author = {Miner, Daniel and Triesch, Jochen},
editor = {Sporns, Olaf},
journal = {PLOS Computational Biology},
month = feb,
number = {2},
pages = {e1004759},
title = {Plasticity-{{Driven Self}}-{{Organization}} under
{{Topological Constraints Accounts}} for
{{Non}}-Random {{Features}} of {{Cortical Synaptic
Wiring}}},
volume = {12},
year = {2016},
doi = {10.1371/journal.pcbi.1004759},
issn = {1553-7358},
language = {en},
}
@article{Hopfield1982,
author = {Hopfield, J J},
journal = {Proceedings of the National Academy of Sciences of
the United States of America},
month = apr,
number = {8},
pages = {2554--2558},
title = {Neural Networks and Physical Systems with Emergent
Collective Computational Abilities.},
volume = {79},
year = {1982},
abstract = {Computational properties of use of biological
organisms or to the construction of computers can
emerge as collective properties of systems having a
large number of simple equivalent components (or
neurons). The physical meaning of content-addressable
memory is described by an appropriate phase space
flow of the state of a system. A model of such a
system is given, based on aspects of neurobiology but
readily adapted to integrated circuits. The
collective properties of this model produce a
content-addressable memory which correctly yields an
entire memory from any subpart of sufficient size.
The algorithm for the time evolution of the state of
the system is based on asynchronous parallel
processing. Additional emergent collective properties
include some capacity for generalization, familiarity
recognition, categorization, error correction, and
time sequence retention. The collective properties
are only weakly sensitive to details of the modeling
or the failure of individual devices.},
issn = {0027-8424},
}
@book{Abeles1982,
address = {Berlin, Heidelberg},
author = {Abeles, Moshe},
note = {OCLC: 858930943},
publisher = {{Springer Berlin Heidelberg}},
title = {Local {{Cortical Circuits}} an {{Electrophysiological
Study}}},
year = {1982},
isbn = {978-3-642-81708-3 978-3-642-81710-6},
language = {English},
}
@article{Diesmann1999,
author = {Diesmann, Markus and Gewaltig, Marc-Oliver and
Aertsen, Ad},
journal = {Nature},
month = dec,
number = {6761},
pages = {529--533},
title = {Stable Propagation of Synchronous Spiking in Cortical
Neural Networks},
volume = {402},
year = {1999},
abstract = {The classical view of neural coding has emphasized
the importance of information carried by the rate at
which neurons discharge action potentials. More
recent proposals that information may be carried by
precise spike timing have been challenged by the
assumption that these neurons operate in a noisy
fashion\textemdash{}presumably reflecting
fluctuations in synaptic input\textemdash{}and, thus,
incapable of transmitting signals with millisecond
fidelity. Here we show that precisely synchronized
action potentials can propagate within a model of
cortical network activity that recapitulates many of
the features of biological systems. An attractor,
yielding a stable spiking precision in the
(sub)millisecond range, governs the dynamics of
synchronization. Our results indicate that a
combinatorial neural code, based on rapid
associations of groups of neurons co-ordinating their
activity at the single spike level, is possible
within a cortical-like network.},
doi = {10.1038/990101},
issn = {0028-0836},
language = {en},
}