András Jakab

University of Zurich | UZH · University Children´s Hospital Zürich, Center for MR-Research

Our purpose was to evaluate the within-subject reproducibility of in utero diffusion tensor imaging (DTI) metrics and the visibility of major white matter structures. Images for 30 fetuses (20–33. postmenstrual weeks, normal neurodevelopment: 6 cases, cerebral pathology: 24 cases) were acquired on 1.5 T or 3.0 T MRI. DTI with 15 diffusion-weighting...

The aim of this work was to use probabilistic diffusion tractography to examine the organization of the human insular cortex based on the similarities of its remote projections. Forty right-handed healthy subjects (33.8 ± 12.7 years old) with no history of neurological injury were included in the study. After the spatial standardization of diffusio...

The functional connectivity architecture of the adult human brain enables complex cognitive processes, and exhibits a remarkably complex structure shared across individuals. We are only beginning to understand its heterogeneous structure, ranging from a strongly hierarchical organization in sensorimotor areas to widely distributed networks in areas...

Diffusion tensor imaging (DTI) and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establi...

Diffusion MRI (dMRI) of the developing brain can provide valuable insights into the white matter development. However, slice thickness in fetal dMRI is typically high (i.e., 3–5 mm) to freeze the in-plane motion, which reduces the sensitivity of the dMRI signal to the underlying anatomy. In this study, we aim at overcoming this problem by using aut...

Fetal brain magnetic resonance imaging serves as an emerging modality for prenatal counseling and diagnosis in disorders affecting the brain. Machine learning based segmentation plays an important role in the quantification of brain development. However, a limiting factor is the lack of sufficiently large, labeled training data. Our study explored...

Diffusion MRI (dMRI) of the developing brain can provide valuable insights into the white matter development. However, slice thickness in fetal dMRI is typically high (i.e., 3-5 mm) to freeze the in-plane motion, which reduces the sensitivity of the dMRI signal to the underlying anatomy. In this study, we aim at overcoming this problem by using aut...

Objective To compare the use of neonatal conventional brain magnetic resonance imaging (MRI) with that of clinical factors and socioeconomic status (SES) to predict long-term neurodevelopment in children with severe congenital heart disease (CHD). Study design In this prospective cohort study, perioperative MRIs were acquired in 57 term-born infan...

Background Altered neurometabolite ratios in neonates undergoing cardiac surgery for congenital heart defects (CHD) may serve as a biomarker for altered brain development and neurodevelopment (ND). Methods We analyzed single voxel 3T PRESS H ¹ -MRS data, acquired unilaterally in the left basal ganglia and white matter of 88 CHD neonates before and...

Deep learning models for medical image segmentation can fail unexpectedly and spectacularly for pathological cases and images acquired at different centers than training images, with labeling errors that violate expert knowledge. Such errors undermine the trustworthiness of deep learning models for medical image segmentation. Mechanisms for detecti...

Accurate characterization of in utero human brain maturation is critical as it involves complex and interconnected structural and functional processes that may influence health later in life. Magnetic resonance imaging is a powerful tool to investigate equivocal neurological patterns during fetal development. However, the number of acquisitions of...

Fetal brain diffusion magnetic resonance images (MRI) are often acquired with a lower through-plane than in-plane resolution. This anisotropy is often overcome by classical upsampling methods such as linear or cubic interpolation. In this work, we employ an unsupervised learning algorithm using an autoencoder neural network for single-image through...

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consumi...

Deep learning models for medical image segmentation can fail unexpectedly and spectacularly for pathological cases and for images acquired at different centers than those used for training, with labeling errors that violate expert knowledge about the anatomy and the intensity distribution of the regions to be segmented. Such errors undermine the tr...

Objectives: The significance of intraoperative cerebral desaturation (CD) measured by near-infrared spectroscopy (NIRS) to predict neurological outcome after congenital heart surgery is uncertain. The goal of this study was to compare brain structure changes and neurodevelopmental outcome in patients with severe congenital heart disease with and w...

Background: Neonates born with severe type of congenital heart defects (CHD) are at risk for neurodevelopmental (ND) impairment. Cerebral magnetic resonance imaging (MRI) studies revealed altered brain development. Little is known about perioperative metabolic changes in neonates undergoing open-heart surgery and the relationship between altered me...

Deep learning (DL) models have provided the state-of-the-art performance in a wide variety of medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors h...

Fetal brain diffusion magnetic resonance images are often acquired with a lower through-plane than in-plane resolution. This anisotropy is often overcome by classical upsampling methods such as linear or cubic interpolation. In this work, we employ an unsupervised learning algorithm using an autoencoder neural network to enhance the through-plane r...

Magnetic resonance imaging (MRI) has become an essential diagnostic modality for congenital disorders of the central nervous system. Recent advancements have transformed foetal MRI into a clinically feasible tool, and in an effort to find predictors of clinical outcomes in spinal dysraphism, foetal MRI began to unveil its potential. The purpose of...

The quantitative assessment of the developing human brain in utero is crucial to fully understand neurodevelopment. Thus, automated multi-tissue fetal brain segmentation algorithms are being developed, which in turn require annotated data to be trained. However, the available annotated fetal brain datasets are limited in number and heterogeneity, h...

Diffusion Magnetic Resonance Imaging (dMRI) has become widely used to study in vivo white matter tissue properties non-invasively. However, fetal dMRI is greatly limited in Signal-to-Noise ratio and spatial resolution. Due to the uncontrollable fetal motion, echo planar imaging acquisitions often result in highly degraded images, hence the ability...

Accurate characterization of in utero human brain maturation is critical as it involves complex and interconnected structural and functional processes that may influence health later in life. Magnetic resonance imaging is a powerful tool to investigate equivocal neurological patterns during fetal development. However, the number of acquisitions of...

Diffusion Magnetic Resonance Imaging (dMRI) has become widely used to study in vivo white matter tissue properties non-invasively. However, fetal dMRI is greatly limited in Signal-to-Noise ratio and spatial resolution. Due to the uncontrollable fetal motion, echo planar imaging acquisitions often result in highly degraded images, hence the ability...

Funding Acknowledgements Type of funding sources: None. Purpose We sought to retrospectively evaluate the feasibility of identifying the fetal cardiac and thoracic vascular structures with non-gated dynamic balanced steady-state free precession MRI sequences. Methods We retrospectively assessed the visibility of cardiovascular anatomy in 66 fetus...

It is critical to quantitatively analyse the developing human fetal brain in order to fully understand neurodevelopment in both normal fetuses and those with congenital disorders. To facilitate this analysis, automatic multi-tissue fetal brain segmentation algorithms are needed, which in turn requires open datasets of segmented fetal brains. Here w...

The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions (MICCAI) society. Since its inception, BraTS has been focusing on being a common benchmarking venue...

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often...

There is emerging evidence for delayed brain development in neonates with congenital heart disease. We hypothesize that the perioperative development of the structural brain connectome is a proxy to such delays. Therefore, we set out to quantify the alterations and longitudinal pre- to postoperative changes in the connectome in congenital heart dis...

It is critical to quantitatively analyse the developing human fetal brain in order to fully understand neurodevelopment in both normal fetuses and those with congenital disorders. To facilitate this analysis, automatic multi-tissue fetal brain segmentation algorithms are needed, which in turn requires open databases of segmented fetal brains. Here...

Introduction The thalamus is a key hub for regulating cortical connectivity. Dysmaturation of thalamocortical networks that accompany white matter injury has been hypothesized as neuroanatomical correlate of late life neurocognitive impairment following preterm birth. Our objective was to find a link between thalamocortical connectivity measures at...

Segmentation of the developing fetal brain is an important step in quantitative analyses. However, manual segmentation is a very time-consuming task which is prone to error and must be completed by highly specialized individuals. Super-resolution reconstruction of fetal MRI has become standard for processing such data as it improves image quality a...

There is emerging evidence for delayed brain development in neonates with congenital heart disease (CHD). We hypothesize that the perioperative development of the structural brain connectome is a proxy to such delays. Therefore, we set out to quantify the alterations and longitudinal pre- to postoperative changes in the connectome in CHD neonates a...

Segmentation of the developing fetal brain is an important step in quantitative analyses. However, manual segmentation is a very time-consuming task which is prone to error and must be completed by highly specialized indi-viduals. Super-resolution reconstruction of fetal MRI has become standard for processing such data as it improves image quality...

Cardiosphere-derived cells (CDC) are progenitor cells derived from heart tissue and have shown promising results in preclinical models. APOSEC, the secretome of irradiated peripheral blood mononuclear cells, has decreased infarct size in acute and chronic experimental myocardial infarction. We enhanced the effect of CDCs with APOSEC preconditioning...

Inhibition abilities are often impaired in children born very preterm. In typically-developing individuals, inhibition has been associated with structural brain connectivity (SC). As SC is frequently altered following preterm birth, this study investigated whether aberrant SC underlies inhibition deficits in school-aged children born very preterm....

The thalamus is a key hub for regulating cortical connectivity. Dysmaturation of thalamocortical networks that accompany white matter injury have been hypothesized as neuroanatomical correlate of late life neurocognitive impairment following preterm birth. Our objective was to find a link between thalamocortical connectivity measures at term equiva...

Cognitive and neurobehavioral problems are among the most severe adverse outcomes in very preterm infants. Such neurodevelopmental impairments may be mitigated through nonpharmacological interventions such as creative music therapy (CMT), an interactive, resource- and needs-oriented approach that provides individual social contact and musical stimu...

Open spina bifida (SB) is one of the most common congenital defects and can lead to impaired brain development. Emerging fetal surgery methods have shown considerable success in the treatment of patients with this severe anomaly. Afterwards, alterations in the brain development of these fetuses have been observed. Currently no longitudinal studies...

Open spina bifida (SB) is one of the most common congenital defects and can lead to impaired brain development. Emerging fetal surgery methods have shown considerable success in the treatment of patients with this severe anomaly. Afterwards, alterations in the brain development of these fetuses have been observed. Currently no longitudinal studies...

Open spina bifida (SB) is one of the most common congenital defects and can lead to impaired brain development. Emerging fetal surgery methods have shown considerable success in the treatment of patients with this severe anomaly. Afterwards, alterations in the brain development of these fetuses have been observed. Currently no longitudinal studies...

Developmental pathoconnectomics is an emerging field that aims to unravel the events leading to and outcome from disrupted brain connectivity development. Advanced magnetic resonance imaging (MRI) technology enables the portrayal of human brain connectivity before birth and has the potential to offer novel insights into normal and pathological huma...

Background The disturbance of cardiac energy substrate metabolism has a decisive role in the pathogenesis of adverse cardiac remodeling and heart failure. Under normoxic conditions, the free fatty acid metabolism is the predominant pathway by providing the highest energy per substrate molecule. Severe myocardial hypoxia leads to a switch from beta-...

Children with congenital heart disease (CHD) remain at risk for neurodevelopmental impairment despite improved perioperative care. Our prospective cohort study aimed to determine the relationship between perioperative brain volumes and neurodevelopmental outcome in neonates with severe CHD. Pre- and postoperative cerebral MRI was acquired in term b...

Aims: The clinical application of doxorubicin is severely compromised by its cardiotoxic effects, which limit the therapeutic index and the cumulative dose. Liposomal encapsulation of doxorubicin (Myocet®) provides a certain protective effect against cardiotoxicity by reducing myocardial drug accumulation. We aimed to evaluate transcriptomic respo...

We investigated the antiarrhythmic effects of ischemic preconditioning (IPC) and postconditioning (PostC) by intracardiac electrocardiogram (ECG) and measured circulating microRNAs (miRs) that are related to cardiac conduction. Domestic pigs underwent 90-min. percutaneous occlusion of the mid left anterior coronary artery, followed by reperfusion....

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions...

Congenital heart defects are the most common congenital anomalies, accounting for a third of all congenital anomaly cases. While surgical correction dramatically improved survival rates, the lag behind normal neurodevelopment appears to persist. Deficits in higher cognitive functions are particularly common, including developmental delay in communi...

Periventricular white matter injury is common in very preterm infants and it is associated with long term neurodevelopmental impairments. While evidence supports the protective effects of erythropoetin (EPO) in preventing injury, we currently lack the complete understanding of how EPO affects the emergence and maturation of anatomical brain connect...

Region of interest abbreviations and locations.

Diffusion tensor tractography script used in the manuscript.

Diffusion tensor image processing script used in the manuscript.

Neonatal fractional anisotropy (FA) template used in the manuscript.

Our research [Team Name: URAN] of 'Neuromorphic Neural Network for Multimodal Brain Tumor Segmentation and Survival analysis' demonstrates its performance on 'Overall Survival Prediction', without any prior training using multi-modal MRI Image segmentation by medical doctors (though provided by BraTS 2018 challenge data). Two segmentation categorie...

Periventricular white matter injury is common in very preterm infants and it is associated with long term neurodevelopmental impairments. While evidence supports the protective effects of erythropoetin (EPO) in preventing injury, we currently lack the complete understanding of how EPO affects the emergence and maturation of anatomical brain connect...

Children with congenital heart disease (CHD) remain at risk for neurodevelopmental impairment despite improved peri- and intraoperative care. Our prospective cohort study aimed to determine the relationship between perioperative brain volumes and neurodevelopmental outcome in neonates with severe CHD. Pre- and postoperative cerebral MRI was acquire...