Michael Schirner
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View article: TVB C++: A Fast and Flexible Back‐End for The Virtual Brain
TVB C++: A Fast and Flexible Back‐End for The Virtual Brain Open
This study introduces TVB C++, a streamlined and fast C++ Back‐End for The Virtual Brain (TVB), a renowned platform and a benchmark tool for full‐brain simulation. TVB C++ is engineered with speed as a primary focus while retaining the fle…
View article: Biological Database Mining for LLM-Driven Alzheimer’s Disease Drug Repurposing
Biological Database Mining for LLM-Driven Alzheimer’s Disease Drug Repurposing Open
BACKGROUND This study presents a software pipeline that leverages LLMs to apply knowledge stored in natural language (such as in pharmacological texts) and ontologies in a transparent Drug Repurposing (DR) information structure. METHODS Al…
View article: Homeodynamic feedback inhibition control in whole-brain simulations
Homeodynamic feedback inhibition control in whole-brain simulations Open
Simulations of large-scale brain dynamics are often impacted by overexcitation resulting from heavy-tailed structural network distributions, leading to biologically implausible simulation results. We implement a homeodynamic plasticity mec…
View article: Multiscale detrended cross-correlation coefficient: estimating coupling in non-stationary neurophysiological signals
Multiscale detrended cross-correlation coefficient: estimating coupling in non-stationary neurophysiological signals Open
The brain consists of a vastly interconnected network of regions, the connectome. By estimating the statistical interdependence of neurophysiological time series, we can measure the functional connectivity (FC) of this connectome. Pearson’…
View article: A lesion‐aware automated processing framework for clinical stroke magnetic resonance imaging
A lesion‐aware automated processing framework for clinical stroke magnetic resonance imaging Open
Magnetic resonance imaging (MRI) and MRI based computational modelling studies provide insights into severity and recovery of ischemic stroke patients. The presence of brain lesions, however, can heavily distort and impair state‐of‐the‐art…
View article: TVB C++: A Fast and Flexible Back-End for The Virtual Brain
TVB C++: A Fast and Flexible Back-End for The Virtual Brain Open
This paper introduces TVB C++, a streamlined and fast C++ Back-End for The Virtual Brain (TVB), a renowned platform and a benchmark tool for full-brain simulation. TVB C++ is engineered with speed as a primary focus while retaining the fle…
View article: Human connectome topology directs cortical traveling waves and shapes frequency gradients
Human connectome topology directs cortical traveling waves and shapes frequency gradients Open
Traveling waves and neural oscillation frequency gradients are pervasive in the human cortex. While the direction of traveling waves has been linked to brain function and dysfunction, the factors that determine this direction remain elusiv…
View article: Connectomes, simultaneous EEG-fMRI resting-state data and brain simulation results from 50 healthy subjects
Connectomes, simultaneous EEG-fMRI resting-state data and brain simulation results from 50 healthy subjects Open
We present raw and processed multimodal empirical data as well as simulation results from a study with The Virtual Brain (TVB). Simultaneous electroencephalography (EEG) - functional magnetic resonance imaging (fMRI) resting-state data, di…
View article: Multiscale Detrended Cross-Correlation Coefficient: Estimating Coupling in Nonstationary Neurophysiological Signals
Multiscale Detrended Cross-Correlation Coefficient: Estimating Coupling in Nonstationary Neurophysiological Signals Open
The brain consists of a vastly interconnected network of regions, the connectome. By estimating the statistical interdependence of neurophysiological time series, we can measure the functional connectivity (FC) of this connectome. Pearson’…
View article: The past, present, and future of the brain imaging data structure (BIDS)
The past, present, and future of the brain imaging data structure (BIDS) Open
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown …
View article: The Past, Present, and Future of the Brain Imaging Data Structure (BIDS).
The Past, Present, and Future of the Brain Imaging Data Structure (BIDS). Open
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown …
View article: Topical Delivery of Tofacitinib in Dermatology: The Promise of a Novel Therapeutic Class Using Biodegradable Dendritic Polyglycerol Sulfates
Topical Delivery of Tofacitinib in Dermatology: The Promise of a Novel Therapeutic Class Using Biodegradable Dendritic Polyglycerol Sulfates Open
Inflammatory skin diseases, such as psoriasis, atopic dermatitis, and alopecia areata, occur when the regulatory tolerance of the innate immune system is disrupted, resulting in the activation of the Janus kinase-signal transducer and acti…
View article: SciOps: Achieving Productivity and Reliability in Data-Intensive Research
SciOps: Achieving Productivity and Reliability in Data-Intensive Research Open
Scientists are increasingly leveraging advances in instruments, automation, and collaborative tools to scale up their experiments and research goals, leading to new bursts of discovery. Various scientific disciplines, including neuroscienc…
View article: Lesion aware automated processing pipeline for multimodal neuroimaging stroke data and The Virtual Brain (TVB)
Lesion aware automated processing pipeline for multimodal neuroimaging stroke data and The Virtual Brain (TVB) Open
Background Processing stroke magnetic resonance imaging (MRI) brain data can be susceptible to lesion-based abnormalities. In this study we developed and validated the Lesion Aware automated Processing Pipeline (LeAPP) that incorporates mi…
View article: Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias
Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias Open
Introduction Neural circuit alterations lay at the core of brain physiopathology, and yet are hard to unveil in living subjects. The Virtual Brain (TVB) modeling, by exploiting structural and functional magnetic resonance imaging (MRI), yi…
View article: Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias
Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias Open
Neural circuit alterations, although laying at the core of brain physiopathology, are usually hard to unveil in living subjects. Virtual brain modelling (TVB), by leveraging structural and functional MRI to simulate brain dynamics, can yie…
View article: Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias
Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias Open
Neural circuit alterations, although laying at the core of brain physiopathology, are usually hard to unveil in living subjects. Virtual brain modelling (TVB), by leveraging structural and functional MRI to simulate brain dynamics, can yie…
View article: Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias
Virtual brain simulations reveal network-specific parameters in neurodegenerative dementias Open
Introduction Neural circuit alterations lay at the core of brain physiopathology, and yet are hard to unveil in living subjects. Virtual brain modelling (TVB), by exploiting structural and functional MRI, yields mesoscopic parameters of co…
View article: Dendritic polyglycerolsulfate-SS-poly(ester amide) micelles for the systemic delivery of docetaxel: pushing the limits of stability through the insertion of π–π interactions
Dendritic polyglycerolsulfate-SS-poly(ester amide) micelles for the systemic delivery of docetaxel: pushing the limits of stability through the insertion of π–π interactions Open
Highly stable micelles are facilitated by π–π interactions in an amphiphilic block copolymer system consisting of dPGS-SS-POxPPh-Py, where each building block contributes a particular ability.
View article: Pre- and post-surgery brain tumor multimodal magnetic resonance imaging data optimized for large scale computational modelling
Pre- and post-surgery brain tumor multimodal magnetic resonance imaging data optimized for large scale computational modelling Open
We present a dataset of magnetic resonance imaging (MRI) data (T1, diffusion, BOLD) acquired in 25 brain tumor patients before the tumor resection surgery, and six months after the surgery, together with the tumor masks, and in 11 controls…
View article: Chemical Approaches to Synthetic Drug Delivery Systems for Systemic Applications
Chemical Approaches to Synthetic Drug Delivery Systems for Systemic Applications Open
Poor water solubility and low bioavailability of active pharmaceutical ingredients (APIs) are major causes of friction in the pharmaceutical industry and represent a formidable hurdle for pharmaceutical drug development. Drug delivery rema…
View article: Personalized Connectome-Based Modeling in Patients with Semi-Acute Phase TBI: Relationship to Acute Neuroimaging and 6 Month Follow-Up
Personalized Connectome-Based Modeling in Patients with Semi-Acute Phase TBI: Relationship to Acute Neuroimaging and 6 Month Follow-Up Open
Following traumatic brain injury (TBI), cognitive impairments manifest through interactions between microscopic and macroscopic changes. On the microscale, a neurometabolic cascade alters neurotransmission, while on the macroscale diffuse …
View article: Integrating EEG–fMRI Through Brain Simulation
Integrating EEG–fMRI Through Brain Simulation Open
EEG and fMRI are thought to measure partly distinct, partly overlapping, and certainly incomplete aspects of neuronal activity. Brain network models (BNMs) are used to simulate neuronal activity, like the dynamics of postsynaptic potential…
View article: A DEEP LEARNING APPROACH TO ESTIMATING INITIAL CONDITIONS OF BRAIN NETWORK MODELS IN REFERENCE TO MEASURED FMRI DATA
A DEEP LEARNING APPROACH TO ESTIMATING INITIAL CONDITIONS OF BRAIN NETWORK MODELS IN REFERENCE TO MEASURED FMRI DATA Open
1. Abstract Brain Network Models (BNMs) are a family of dynamical systems that simulate whole brain activity using neural mass models to represent local activity in different brain regions that influence each other via a global structural …
View article: Brain Modelling as a Service: The Virtual Brain on EBRAINS
Brain Modelling as a Service: The Virtual Brain on EBRAINS Open
The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including t…