183 research outputs found
Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures
The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids
Equilibrium Properties of Temporally Asymmetric Hebbian Plasticity
A theory of temporally asymmetric Hebb (TAH) rules which depress or
potentiate synapses depending upon whether the postsynaptic cell fires before
or after the presynaptic one is presented. Using the Fokker-Planck formalism,
we show that the equilibrium synaptic distribution induced by such rules is
highly sensitive to the manner in which bounds on the allowed range of synaptic
values are imposed. In a biologically plausible multiplicative model, we find
that the synapses in asynchronous networks reach a distribution that is
invariant to the firing rates of either the pre- or post-synaptic cells. When
these cells are temporally correlated, the synaptic strength varies smoothly
with the degree and phase of synchrony between the cells.Comment: 3 figures, minor corrections of equations and tex
PULSED DOPPLER FROM THE SUPRASTERNAL NOTCH SYSTEMATICALLY UNDERESTIMATES MEAN BLOOD FLOW VELOCITY IN THE ASCENDING AORTA COMPARED TO PHASE CONTRAST MRI
Background
Continuous pulsed-wave Doppler readings of flow velocity in the ascending aorta from the suprasternal
position (sCD) are widely used in estimating stroke volume, particularly during physiological challenge
maneuvers such as head-up tilt testing. Stroke volume is derived from velocity time integrals and vessel
area. We compared the sCD against an established gold standard.
Methods
In 12 healthy women and men, we obtained 2D cross sectional, velocity encoded phase contrast MRI of
the ascending aorta (2DMRI) and sCD to measure mean blood flow velocity (Vmean) at the ascending
aorta. We compared sCD insonation depth to the distance between Doppler probe and sinotubular
junction measured by MRI. Within an aortic 4D-Flow dataset, allowing flow measurements in every
anatomical point along the ascending aorta, Vmean was determined at the sCD measurement point for
comparison.
Results
sCD significantly underestimated Vmean compared with 2DMRI at the sinotubular junction (Vmean
2DMRI – Vmean sCD = 24.42 cm/s ± 12.55 cm/s, p = <0.001). Moreover, sCD sampled flow velocities
21.8 mm ± 7mm (p = <0.001) or 26% off the sinotubular junction. Yet, depth and velocity differences
between sCD and 2DMRI were not correlated with each other (Pearson r = -0.147; p = 0.648). When we
applied 4DMRI to assess flow velocity at the sCD measurement site, the Vmean difference between
methodologies was reduced to 9.1 cm/s ± 12.38 cm/s (p = 0.035).
Conclusion
sCD profoundly underestimates Vmean in the ascending aorta compared to 4DMRI. The methodology
has important limitations in accessing the ideal position for aortic flow measurements and precise
information regarding the position of data acquisition for vessel area quantification cannot be
ascertained. Overall, sCD is of limited utility in measuring absolute stroke volum
An associative memory of Hodgkin-Huxley neuron networks with Willshaw-type synaptic couplings
An associative memory has been discussed of neural networks consisting of
spiking N (=100) Hodgkin-Huxley (HH) neurons with time-delayed couplings, which
memorize P patterns in their synaptic weights. In addition to excitatory
synapses whose strengths are modified after the Willshaw-type learning rule
with the 0/1 code for quiescent/active states, the network includes uniform
inhibitory synapses which are introduced to reduce cross-talk noises. Our
simulations of the HH neuron network for the noise-free state have shown to
yield a fairly good performance with the storage capacity of for the low neuron activity of . This
storage capacity of our temporal-code network is comparable to that of the
rate-code model with the Willshaw-type synapses. Our HH neuron network is
realized not to be vulnerable to the distribution of time delays in couplings.
The variability of interspace interval (ISI) of output spike trains in the
process of retrieving stored patterns is also discussed.Comment: 15 pages, 3 figures, changed Titl
Markov analysis of stochastic resonance in a periodically driven integrate-fire neuron
We model the dynamics of the leaky integrate-fire neuron under periodic
stimulation as a Markov process with respect to the stimulus phase. This avoids
the unrealistic assumption of a stimulus reset after each spike made in earlier
work and thus solves the long-standing reset problem. The neuron exhibits
stochastic resonance, both with respect to input noise intensity and stimulus
frequency. The latter resonance arises by matching the stimulus frequency to
the refractory time of the neuron. The Markov approach can be generalized to
other periodically driven stochastic processes containing a reset mechanism.Comment: 23 pages, 10 figure
Histological response to injected gluteraldehyde cross-linked bovine collagen based implant in a rat model
BACKGROUND: The aim of present study is to investigate the short and long term histopathological alterations caused by submucosal injection of gluteraldehyde cross-linked bovine collagen based on an experimental rat model. METHODS: Sixty Sprague-Dawley rats were assigned into two groups as group I and II each containing 30 rats. 0.1 ml of saline solution and 0.1 ml of gluteraldehyde cross-linked bovine collagen were injected into the submucosa of bladder of first (control) and second groups, respectively. Both group I and II were further subdivided into 3 other groups as Group IA, IB, IC and Group IIA, IIB, IIC according to the sacrification period. Group IA and IIA, IB and IIB, IC and IIC rats (10 rats for each group) were sacrificed 3, 6, and 12 months after surgical procedure, respectively. Two slides prepared from injection site of the bladder were evaluated completely for each rat by being unaware of the groups and at random by two independent senior pathologists to determine the fibroblast invasion, collagen formation, capillary ingrowth and inflammatory reaction. Additionally, randomized brain sections from each rat were also examined to detect migration of the injection material. The measurements were made using an ocular micrometer at ×10 magnification. The results were assessed using t-tests for paired and independent samples, with p < 0.05 considered to indicate significant differences; all values were presented as the mean (SD). RESULTS: Migration to the brain was not detected in any group. Significant histopathological changes in the gluteraldehyde cross-linked bovine collagen injected groups were fibroblast invasion in 93.3%, collagen formation in 73.3%, capillary ingrowth in 46.6%, inflamatory reaction in 20%. CONCLUSION: We emphasize that the usage of gluteraldehyde cross-linked bovine collagen in children appears to be safe for endoscopic treatment of vesicoureteral reflux
Intrinsic Stability of Temporally Shifted Spike-Timing Dependent Plasticity
Spike-timing dependent plasticity (STDP), a widespread synaptic modification mechanism, is sensitive to correlations between presynaptic spike trains and it generates competition among synapses. However, STDP has an inherent instability because strong synapses are more likely to be strengthened than weak ones, causing them to grow in strength until some biophysical limit is reached. Through simulations and analytic calculations, we show that a small temporal shift in the STDP window that causes synchronous, or nearly synchronous, pre- and postsynaptic action potentials to induce long-term depression can stabilize synaptic strengths. Shifted STDP also stabilizes the postsynaptic firing rate and can implement both Hebbian and anti-Hebbian forms of competitive synaptic plasticity. Interestingly, the overall level of inhibition determines whether plasticity is Hebbian or anti-Hebbian. Even a random symmetric jitter of a few milliseconds in the STDP window can stabilize synaptic strengths while retaining these features. The same results hold for a shifted version of the more recent “triplet” model of STDP. Our results indicate that the detailed shape of the STDP window function near the transition from depression to potentiation is of the utmost importance in determining the consequences of STDP, suggesting that this region warrants further experimental study
Dynamics of Action Potential Initiation in the GABAergic Thalamic Reticular Nucleus In Vivo
Understanding the neural mechanisms of action potential generation is critical to establish the way neural circuits generate and coordinate activity. Accordingly, we investigated the dynamics of action potential initiation in the GABAergic thalamic reticular nucleus (TRN) using in vivo intracellular recordings in cats in order to preserve anatomically-intact axo-dendritic distributions and naturally-occurring spatiotemporal patterns of synaptic activity in this structure that regulates the thalamic relay to neocortex. We found a wide operational range of voltage thresholds for action potentials, mostly due to intrinsic voltage-gated conductances and not synaptic activity driven by network oscillations. Varying levels of synchronous synaptic inputs produced fast rates of membrane potential depolarization preceding the action potential onset that were associated with lower thresholds and increased excitability, consistent with TRN neurons performing as coincidence detectors. On the other hand the presence of action potentials preceding any given spike was associated with more depolarized thresholds. The phase-plane trajectory of the action potential showed somato-dendritic propagation, but no obvious axon initial segment component, prominent in other neuronal classes and allegedly responsible for the high onset speed. Overall, our results suggest that TRN neurons could flexibly integrate synaptic inputs to discharge action potentials over wide voltage ranges, and perform as coincidence detectors and temporal integrators, supported by a dynamic action potential threshold
Formation of feedforward networks and frequency synchrony by spike-timing-dependent plasticity
Spike-timing-dependent plasticity (STDP) with asymmetric learning windows is
commonly found in the brain and useful for a variety of spike-based
computations such as input filtering and associative memory. A natural
consequence of STDP is establishment of causality in the sense that a neuron
learns to fire with a lag after specific presynaptic neurons have fired. The
effect of STDP on synchrony is elusive because spike synchrony implies unitary
spike events of different neurons rather than a causal delayed relationship
between neurons. We explore how synchrony can be facilitated by STDP in
oscillator networks with a pacemaker. We show that STDP with asymmetric
learning windows leads to self-organization of feedforward networks starting
from the pacemaker. As a result, STDP drastically facilitates frequency
synchrony. Even though differences in spike times are lessened as a result of
synaptic plasticity, the finite time lag remains so that perfect spike
synchrony is not realized. In contrast to traditional mechanisms of large-scale
synchrony based on mutual interaction of coupled neurons, the route to
synchrony discovered here is enslavement of downstream neurons by upstream
ones. Facilitation of such feedforward synchrony does not occur for STDP with
symmetric learning windows.Comment: 9 figure
The spike-timing-dependent learning rule to encode spatiotemporal patterns in a network of spiking neurons
We study associative memory neural networks based on the Hodgkin-Huxley type
of spiking neurons. We introduce the spike-timing-dependent learning rule, in
which the time window with the negative part as well as the positive part is
used to describe the biologically plausible synaptic plasticity. The learning
rule is applied to encode a number of periodical spatiotemporal patterns, which
are successfully reproduced in the periodical firing pattern of spiking neurons
in the process of memory retrieval. The global inhibition is incorporated into
the model so as to induce the gamma oscillation. The occurrence of gamma
oscillation turns out to give appropriate spike timings for memory retrieval of
discrete type of spatiotemporal pattern. The theoretical analysis to elucidate
the stationary properties of perfect retrieval state is conducted in the limit
of an infinite number of neurons and shows the good agreement with the result
of numerical simulations. The result of this analysis indicates that the
presence of the negative and positive parts in the form of the time window
contributes to reduce the size of crosstalk term, implying that the time window
with the negative and positive parts is suitable to encode a number of
spatiotemporal patterns. We draw some phase diagrams, in which we find various
types of phase transitions with change of the intensity of global inhibition.Comment: Accepted for publication in Physical Review
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