Vahid Rahmati

Vahid Rahmati
Universitätsklinikum Jena · Klinik für Neurologie

Doctor

About

30
Publications
3,316
Reads
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108
Citations
Citations since 2016
27 Research Items
107 Citations
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20162017201820192020202120220510152025

Publications

Publications (30)
Article
Full-text available
Calcium imaging has been used as a promising technique to monitor the dynamic activity of neuronal populations. However, the calcium trace is temporally smeared which restricts the extraction of quantities of interest such as spike trains of individual neurons. To address this issue, spike reconstruction algorithms have been introduced. One limitat...
Article
Full-text available
During neocortical development, network activity undergoes a dramatic transition from largely synchronized, so-called cluster activity, to a relatively sparse pattern around the time of eye-opening in rodents. Biophysical mechanisms underlying this sparsification phenomenon remain poorly understood. Here, we present a dynamic systems modeling study...
Article
Full-text available
Synchronized activity is a universal characteristic of immature neural circuits that is essential for their developmental refinement and strongly depends on GABAergic neurotransmission. A major subpopula-tion of GABA-releasing interneurons (INs) expresses somatostatin (SOM) and proved critical for rhythm generation in adulthood. Here, we report a m...
Article
Full-text available
Ataxia Telangiectasia and Rad3-related (ATR) protein, as a key DNA damage response (DDR) regulator, plays an essential function in response to replication stress and controls cell viability. Hypomorphic mutations of ATR cause the human ATR-Seckel syndrome, characterized by microcephaly and intellectual disability, which however suggests a yet unkno...
Article
Significance Neuronal circuits develop in an activity-dependent manner. In vitro data suggest that the intracellular accumulation of chloride—a universal characteristic of immature nerve cells—drives network maturation through a depolarizing action of the neurotransmitter GABA. We here demonstrate that deletion of the chloride cotransporter NKCC1 f...
Preprint
Full-text available
Tactile sensation and vision are often both utilized for the exploration of objects that are within reach though it is not known whether or how these two distinct sensory systems might combine such information. Here in mice we find that stimulation of the contralateral whisker array suppresses visually evoked activity in a subarea of primary visual...
Preprint
Full-text available
Specific autoantibodies against the NMDA-receptor (NMDAR) GluN1 subunit cause severe and debilitating NMDAR-encephalitis. Autoantibodies induce prototypic disease symptoms resembling schizophrenia, including psychosis and cognitive dysfunction. Using a mouse passive transfer model applying human monoclonal anti-GluN1-autoantibodies, we observed CA1...
Preprint
Full-text available
Spontaneous correlated activity is a universal hallmark of immature neural circuits. However, the cellular dynamics and intrinsic mechanisms underlying neuronal synchrony in the intact developing brain are largely unknown. Here, we use two-photon Ca ²⁺ imaging to comprehensively map the developmental trajectories of spontaneous network activity in...
Preprint
NKCC1 is the primary transporter mediating chloride uptake in immature principal neurons, but its role in the development of in vivo network dynamics and cognitive abilities remains unknown. Here, we address the function of NKCC1 in developing mice using electrophysiological, optical and behavioral approaches. We report that NKCC1 deletion from tel...
Article
The role of synchronous firing in sensory coding and cognition remains controversial. While studies, focusing on its mechanistic consequences in attentional tasks, suggest that synchronization dynamically boosts sensory processing, others failed to find significant synchronization levels in such tasks. We attempt to understand both lines of evidenc...
Thesis
Full-text available
Calcium imaging has emerged as a promising technique to indirectly measure the neural activity of populations of neurons, thereby enabling the functional analysis of these assemblies. This technique has been used to study the neural mechanisms and phenomena under a wide range of experimental and behavioral conditions. These include, as a point of i...
Preprint
The role of synchronous firing in sensory coding and cognition remains controversial. While studies, focusing on its mechanistic consequences in attentional tasks, suggest that synchronization dynamically boosts sensory processing, others failed to find significant synchronization in such tasks. We attempt to understand both lines of evidence withi...
Data
The matlab code of this method is available here: https://github.com/VahidRahmati/UFARSA The main features of the method are as follow: 1) Automatic handling of different shapes of fluorescence transients 2) Reconstructing spike times and spike-counts from a fluoresce trace of 1,000,000 frames in less than 2 seconds. 3) Robust against noise 4) It...
Method
Full-text available
In Rahmati et al. (2018, Journal of Neurophysiology), we proposed a novel, heuristic model-free-type method which enables an ultra-fast, accurate, near-automatic reconstruction of spiking activities from noisy calcium imaging data. It also effectively corrects for several types of artifacts as typically observed in in-vitro and in-vivo data. We cal...
Data
Fig S6 of paper "Developmental Emergence of Sparse Coding: A Dynamic Systems Approach". The same format is used as in Fig. 1b. (b) The same format is used as in Fig. 4b. Cluster activities before (solid lines) and after (dashed lines) blocking the GABAergic receptors. This blockage led to a decrease in cluster activity size and prolonged cluster ac...
Data
Fig S7 of paper "Developmental Emergence of Sparse Coding: A Dynamic Systems Approach". (a) The effect of different E and I synaptic time constants τ_E and I τ_I on the size (first row) and duration (second row) of cluster activity, at P3 and P10. Note the change in the effect of larger α >1 (the elements below the dashed black line; α =τ_I/τ_E ) a...
Data
Fig S5 of paper "Developmental Emergence of Sparse Coding: A Dynamic Systems Approach". Postnatal changes in robustness of cluster activities against interfering inputs. (a) The effect of perturbing a cluster activity on its dynamics, during development. Following the first cluster activity (black line) elicited by a perturbation input applied to...
Data
Fig S1 of paper "Developmental Emergence of Sparse Coding: A Dynamic Systems Approach". The variability in spatiotemporal characteristics of postnatal spontaneous cluster activities. (a) The effect of synaptic recovery from a depressing state (lower panel) on size of cluster activities (upper panel) at P3. Following the first cluster activity (bla...
Data
Fig S2 of paper "Developmental Emergence of Sparse Coding: A Dynamic Systems Approach". Activity properties of developing networks in response to long-lasting inputs. (a) The same plots as in Fig 3a; the quasi Er- and Ir-nullclines were plotted in the absence of external input. (b) The emergence of stimulus-evoked attractors in developing networks...
Method
Full-text available
In (Rahmati et al. 2016), we proposed a new method for calcium imaging analysis based on the biophysical models of spiking neurons and Bayesian inference; we called our method CaBBI. This method has been implemented as Matlab code in the VBA toolbox (http://mbb-team.github.io/VBA-toolbox/), and is now publicly available as a part of this toolbox (h...
Data
Model specifications and parameters. (DOCX)
Data
Additional illustrative results of the proposed approach for in vitro fluorescence traces with slowly rising transients. The same format is used as in Fig 9. This figure shows the inferred membrane potentials (posterior means) when using the FHN and QGIF models for two representative in vitro fluorescence traces with slowly rising transients evoked...
Conference Paper
We are interested in understanding the neural correlates of attentional processes using first principles. Here we apply a recently developed first principles approach that uses transmitted information in bits per joule to quantify the energy efficiency of information transmission for an inter-spike-interval (ISI) code that can be modulated by means...
Conference Paper
Full-text available
Calcium imaging techniques have been used to monitor the dynamic activity of both individual neurons and assemblies of neurons. With these techniques the accurate reconstruction of action potentials (APs) from fluorescence signals is restricted because of noise, the low temporal resolution of these signals, as well as by an indirect nonlinear relat...
Article
Full-text available
We are interested in understanding the neural correlates of attentional processes using first principles. Here we apply a recently developed first principles approach that uses transmitted information in bits per joule to quantify the energy efficiency of information transmission for an inter-spike-interval (ISI) code that can be modulated by means...

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Projects

Projects (3)
Project
This project aims at addressing how antibodies disturb brain function in autoimmune encephalitis, by investigating the induced changes in proteomic, synaptic, single-cell, an neural network levels... to-be-completed
Project
We propose a new set of methods to infer neuronal dynamics and reconstruct spiking activities from calcium imaging data.
Project
Using experimental data together with computational/mathematical modelling and analysis, we aim at understanding how neural networks activity and sensory processing are refined during postnatal developmental period, both in-vitro and in-vivo.