Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation

The characteristic endogenous circadian rhythm of plasma glucocorticoid concentrations is made up from an underlying ultradian pulsatile secretory pattern. Recent evidence has indicated that this ultradian cortisol pulsatility is crucial for normal emotional response in man. In this study, we investigate the anatomical transcriptional and...

Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells...

Potential associations between immune signaling genes, deactivated microglia, and oligodendrocytes and cortical gray matter loss in patients with long-term remitted Cushing's disease

Introduction: Cushing's disease (CD) is a rare and severe endocrine disease characterized by hypercortisolemia. Previous studies have found structural brain alterations in remitted CD patients compared to healthy controls, specifically in the anterior cingulate cortex (ACC). However, potential mechanisms through which these persistent...

Transcriptomic Signatures Associated With Regional Cortical Thickness Changes in Parkinson’s Disease

Cortical atrophy is a common manifestation in Parkinson’s disease (PD), particularly in advanced stages of the disease. To elucidate the molecular underpinnings of cortical thickness changes in PD, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and patterns of cortical thickness...

Molecular characterization of the stress network in individuals at risk for schizophrenia

The biological mechanisms underlying inter-individual differences in human stress reactivity remain poorly understood. We aimed to identify the molecular underpinning of aberrant neural stress sensitivity in individuals at risk for schizophrenia. Linking mRNA expression data from the Allen Human Brain Atlas to task-based fMRI revealed 201...

Stochastic neighbor embedding as a tool for visualizing the encoding capability of magnetic resonance fingerprinting dictionaries

Objective: To visualize the encoding capability of magnetic resonance fingerprinting (MRF) dictionaries. Materials and methods: High-dimensional MRF dictionaries were simulated and embedded into a lower-dimensional space using t-distributed stochastic neighbor embedding (t-SNE). The embeddings were visualized via colors as a surrogate for...

Iron loading is a prominent feature of activated microglia in Alzheimer’s disease patients

Brain iron accumulation has been found to accelerate disease progression in amyloid-β(Aβ) positive Alzheimer patients, though the mechanism is still unknown. Microglia have been identified as key players in the disease pathogenesis, and are highly reactive cells responding to aberrations such as increased iron levels. Therefore, using...

Cingulate networks associated with gray matter loss in Parkinson's disease show high expression of cholinergic genes in the healthy brain

Structural covariance networks are able to identify functionally organized brain regions by gray matter volume covariance across a population. We examined the transcriptomic signature of such anatomical networks in the healthy brain using postmortem microarray data from the Allen Human Brain Atlas. A previous study revealed that a posterior...

Histogram-based standardization of intravascular optical coherence tomography images acquired from different imaging systems

Purpose: Intravascular optical coherence tomography (OCT) is widely used for analysis of the coronary artery disease. Its high spatial resolution allows for visualization of arterial tissue components in detail. There are different OCT systems on the market, each of which produces data characterized by its own intensity range and distribution...

Inter-station Intensity Standardization for Whole-Body MR Data

Purpose To develop and validate a method for performing inter-station intensity standardization in multispectral whole-body MR data. Methods Different approaches for mapping the intensity of each acquired image stack into the reference intensity space were developed and validated. The registration strategies included: “direct” registration to...

Automated Ischemic Lesion Segmentation in MRI Mouse Brain Data after Transient Middle Cerebral Artery Occlusion

Magnetic resonance imaging (MRI) has become increasingly important in ischemic stroke experiments in mice, especially because it enables longitudinal studies. Still, quantitative analysis of MRI data remains challenging mainly because segmentation of mouse brain lesions in MRI data heavily relies on time-consuming manual tracing and...

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease

Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and...

Computer-aided evaluation of inflammatory changes over time on MRI of the spine in patients with suspected axial spondyloarthritis: A feasibility study

Background: Evaluating inflammatory changes over time on MR images of the spine in patients with suspected axial Spondyloarthritis (axSpA) can be a labor-intensive task, requiring readers to manually search for and perceptually align a set of vertebrae between two scans. The purpose of this study was to assess the feasibility of computer...

MRI Mouse Brain Data of Ischemic Lesion after Transient Middle Cerebral Artery Occlusion

In this data report we make available to the community a highly variable longitudinal MRI mouse brain data set of ischemic lesion after transient middle cerebral artery occlusion (tMCAo). Together with the provided semi-automated and automated segmentations, these data can be used to further improve the method proposed by Mulder et al. (2017)...

Interactive local super-resolution reconstruction of whole-body MRI mouse data: A pilot study with applications to bone and kidney metastases

In small animal imaging studies, when the locations of the micro-structures of interest are unknown a priori, there is a simultaneous need for full-body coverage and high resolution. In MRI, additional requirements to image contrast and acquisition time will often make it impossible to acquire such images directly. Recently, a resolution...

Super-resolution reconstruction of late gadolinium enhanced MRI from multiple views

Oral presentation.