G. Allan Johnson
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View article: 3D microscopic whole brain neurodegenerative MRI
3D microscopic whole brain neurodegenerative MRI Open
3D microscopic whole brain neurodegenerative MRI This article by G. Allan Johnson, Ph.D., focuses on advanced MRI techniques for studying neurodegenerative diseases, exploring the challenges of screening therapies for conditions like Alzhe…
View article: Directed connectomes across species reveal conserved and divergent pathways of neural signaling
Directed connectomes across species reveal conserved and divergent pathways of neural signaling Open
Understanding how brain networks support cognition requires knowing not only which regions are connected but the direction in which neuronal signals propagate. However, directed connectivity cannot be measured non-invasively in primates or…
View article: A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans
A hierarchical framework for cortical and subcortical gray-matter parcellation across rodents, primates, and humans Open
Translational neuroscience requires consistent anatomical frameworks to compare brain organization across species despite differences in size and specialization. Existing atlases are species-specific, limiting cross-species analyses. Here …
View article: Is All the Information in the Price? LLM Embeddings versus the EMH in Stock Clustering
Is All the Information in the Price? LLM Embeddings versus the EMH in Stock Clustering Open
This paper investigates whether artificial intelligence can enhance stock clustering compared to traditional methods. We consider this in the context of the semi-strong Efficient Markets Hypothesis (EMH), which posits that prices fully ref…
View article: The Duke Mouse Brain Atlas: MRI and light sheet microscopy stereotaxic atlas of the mouse brain
The Duke Mouse Brain Atlas: MRI and light sheet microscopy stereotaxic atlas of the mouse brain Open
Atlases of the brain are critical resources that make it possible to share data in a common reference frame. Unexpectedly, there is no three-dimensional (3D) stereotaxic atlas of the mouse brain that provides whole brain coverage at macro …
View article: Considerations and recommendations from the <scp>ISMRM</scp> diffusion study group for preclinical diffusion <scp>MRI</scp> : Part 2—Ex vivo imaging: Added value and acquisition
Considerations and recommendations from the <span>ISMRM</span> diffusion study group for preclinical diffusion <span>MRI</span> : Part 2—Ex vivo imaging: Added value and acquisition Open
The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non‐invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI h…
View article: Considerations and recommendations from the <scp>ISMRM</scp> diffusion study group for preclinical diffusion <scp>MRI</scp> : Part 1: In vivo small‐animal imaging
Considerations and recommendations from the <span>ISMRM</span> diffusion study group for preclinical diffusion <span>MRI</span> : Part 1: In vivo small‐animal imaging Open
Small‐animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition,…
View article: Considerations and recommendations from the <scp>ISMRM</scp> Diffusion Study Group for preclinical diffusion <scp>MRI</scp> : Part 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography
Considerations and recommendations from the <span>ISMRM</span> Diffusion Study Group for preclinical diffusion <span>MRI</span> : Part 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography Open
Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non‐invasive characterization of tissu…
View article: Global dissection of the impact of Alzheimer’s disease on brain architecture and behavior: High resolution MRH resolves robust regional effects
Global dissection of the impact of Alzheimer’s disease on brain architecture and behavior: High resolution MRH resolves robust regional effects Open
Alzheimer’s disease (AD) affects brain regions with remarkable heterogeneity, but the precise impact of this disease on hundreds of small cortical, subcortical, and brainstem regions remains poorly defined. Here, as a prelude to testing pr…
View article: Multiscale comparative connectomics
Multiscale comparative connectomics Open
The connectome, a map of the structural and/or functional connections in the brain, provides a complex representation of the neurobiological phenotypes on which it supervenes. This information-rich data modality has the potential to transf…
View article: Brain Iron Accumulation in Neurodegenerative Disorders: Does Air Pollution Play a Role?
Brain Iron Accumulation in Neurodegenerative Disorders: Does Air Pollution Play a Role? Open
Background Both excess brain Fe and air pollution (AP) exposures are associated with increased risk for multiple neurodegenerative disorders. Fe is a redox-active metal that is abundant in AP from traffic and industrial sources and in U.S.…
View article: Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 -- Ex vivo imaging: data processing, comparisons with microscopy, and tractography
Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 -- Ex vivo imaging: data processing, comparisons with microscopy, and tractography Open
Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissu…
View article: Transcriptome analysis identifies an ASD-Like phenotype in oligodendrocytes and microglia from C58/J amygdala that is dependent on sex and sociability
Transcriptome analysis identifies an ASD-Like phenotype in oligodendrocytes and microglia from C58/J amygdala that is dependent on sex and sociability Open
Background Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive…
View article: MR histology reveals tissue features beneath heterogeneous MRI signal in genetically engineered mouse models of sarcoma
MR histology reveals tissue features beneath heterogeneous MRI signal in genetically engineered mouse models of sarcoma Open
Purpose To identify significant relationships between quantitative cytometric tissue features and quantitative MR (qMRI) intratumorally in preclinical undifferentiated pleomorphic sarcomas (UPS). Materials and methods In a prospective stud…
View article: An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain
An Open Resource: MR and light sheet microscopy stereotaxic atlas of the mouse brain Open
We have combined MR histology and light sheet microscopy (LSM) of five postmortem C57BL/6J mouse brains in a stereotaxic space based on micro-CT yielding a multimodal 3D atlas with the highest spatial and contrast resolution yet reported. …
View article: Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability
Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability Open
Background Autism Spectrum Disorder (ASD) is a group of neurodevelopmental disorders with higher incidence in males and is characterized by atypical verbal/nonverbal communication, restricted interests that can be accompanied by repetitive…
View article: A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology
A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology Open
Information on regional variation in cell numbers and densities in the CNS provides critical insight into structure, function, and the progression of CNS diseases. However, variability can be real or a consequence of methods that do not ac…
View article: A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology
A rapid workflow for neuron counting in combined light sheet microscopy and magnetic resonance histology Open
Information on regional variation in cell numbers and densities in the CNS provides critical insight into structure, function, and the progression of CNS diseases. However, variability can be real or can be a consequence of methods that do…
View article: Merged magnetic resonance and light sheet microscopy of the whole mouse brain
Merged magnetic resonance and light sheet microscopy of the whole mouse brain Open
We have developed workflows to align 3D magnetic resonance histology (MRH) of the mouse brain with light sheet microscopy (LSM) and 3D delineations of the same specimen. We start with MRH of the brain in the skull with gradient echo and di…
View article: Restoring morphology of light sheet microscopy data based on magnetic resonance histology
Restoring morphology of light sheet microscopy data based on magnetic resonance histology Open
The combination of cellular-resolution whole brain light sheet microscopy (LSM) images with an annotated atlas enables quantitation of cellular features in specific brain regions. However, most existing methods register LSM data with exist…
View article: Volumetric analysis of the aging auditory pathway using high resolution magnetic resonance histology
Volumetric analysis of the aging auditory pathway using high resolution magnetic resonance histology Open
Numerous shown consequences of age-related hearing loss have been unveiled; however, the relationship of the cortical and subcortical structures of the auditory pathway with aging is not well known. Investigations into neural structure ana…
View article: Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice
Prenatal heroin exposure alters brain morphology and connectivity in adolescent mice Open
The United States is experiencing a dramatic increase in maternal opioid misuse and, consequently, the number of individuals exposed to opioids in utero. Prenatal opioid exposure has both acute and long‐lasting effects on health and wellbe…
View article: Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and acquisition
Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and acquisition Open
The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has sev…
View article: Considerations and Recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging
Considerations and Recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging Open
Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition,…
View article: Measuring Nonapoptotic Caspase Activity with a Transgenic Reporter in Mice
Measuring Nonapoptotic Caspase Activity with a Transgenic Reporter in Mice Open
The protease caspase-3 is a key mediator of apoptotic programmed cell death. But weak or transient caspase activity can contribute to neuronal differentiation, axonal pathfinding, and synaptic long-term depression. Despite the importance o…