Biology subjects

Jacobs, R. E.

Publications and source records attributed to Jacobs, R. E..

4 recordsLinked to original sources

bioRxiv2026

Quality Assurance Strategies for Brain State Characterization by MEMRI

BackgroundManganese-enhanced magnetic resonance imaging (MEMRI) is a powerful approach for mapping brain-wide neural activity and axonal projections in vivo. Yet standardized computational frameworks for voxel-wise and atlas-based characterization of brain states across large experimental cohorts remain limited. New methodHere, we present methodological advances for preprocessing and statistical analysis of MEMRI datasets to support scalable, reproducible cohort-level analyses. Quality assurance metrics were developed to evaluate images, cohort-level anatomical alignment, and intensity normalization. Using simulated data, we optimized smoothing, effect-size, and cluster-size thresholds to balance sensitivity and specificity in voxel-wise statistical mapping. We developed InVivoSegment software to apply to our new InVivo Atlas for segmentation of MEMRI data and interpretation of brain-wide activity. ResultsQuality assurance analyses established benchmarks for Mn(II)-induced signal- and contrast-to-noise evaluation, precise cohort-level alignment at 100 m isotropic resolution, and robust intensity normalization. Balanced accuracy and Youdens J statistics were calculated from simulated true positive and noise-only intensities, which defined optimal parameters for smoothing kernel, cluster-size and effect-size thresholds during voxel-wise mapping. Segmentation of simulated data demonstrated reliable transformation of voxel-wise results into regional summaries and identified secondary thresholds that minimize noise-driven artifacts. Comparison with existing methodsApproach to optimize correction parameters for statistical mapping using simulated images improves voxel- and segment-wise sensitivity compared to FDR/FWE-based correction procedures. ConclusionsThese methodological advances enable scalable, reproducible, brain-wide quantification of longitudinal changes in MEMRI studies, strengthen mechanistic investigation of brain-state dynamics relevant to human health, and provide broadly applicable tools for neuroimaging analyses beyond MEMRI applications. HighlightsO_LIQuantitative assurance of image quality complements visual assessment for cohort-level batch processing. C_LIO_LIOptimization of parameters using simulated noise-only images with and without investigator-embedded signal for voxel-wise mapping. C_LIO_LIA new software, "InVivoSegment" together with a labeled atlas, automates reliable user-friendly segmentation of voxel-wise data. C_LIO_LIMethodological advances in MEMRI data processing and computational analyses support scalable voxel- and segment-wise quantification of brain-wide neural activity. C_LI

neuroscience↗

bioRxiv2023

Reconfiguration of Brain-Wide Neural Activity After Early Life Adversity

Early life adversity (ELA) predisposes individuals to physical and mental disorders lifelong. How ELA affects brain functions, leading to these vulnerabilities, is a mystery. To understand ELAs impacts, investigations into neural activity affected by ELA must go beyond localized areas toward simultaneous recordings from multiple widely distributed regions over time. Such studies will expose relative activity between regions and discover shifts in regional activity in response to different experiences. Here, we performed longitudinal manganese-enhanced magnetic resonance imaging (MEMRI) to measure degrees of brain-wide neural activity in ELA-exposed mice across a series of experiences in adulthood. To ascertain whether ELA resulted in atypical brain activity, results were compared to those of the standard mouse (Std). MEMRI captured activity in the freely moving home cage condition, and short- and long-term after exposure to TMT, a naturalistic predator threat. Images were normalized and aligned then analyzed with statistical mapping and automated segmentation. We found that neural activity in the home cage was greater in ELA compared to Std in multiple striatal-pallidal and hypothalamic regions. Upon acute threat, neural activity in Std increased in these regions to become more similar to that in ELA, while new hyperactive responses in ELA emerged in the midbrain and hindbrain. Nine days after acute threat, heightened neural activity in ELA persisted within locus coeruleus and increased within posterior amygdala, ventral hippocampus, and dorsomedial and ventromedial hypothalamus. These results reveal functional imbalances that arise between multiple brain-systems after ELA, which are dependent upon context and cumulative experiences into adulthood. Significance StatementEarly life adversity (ELA) is a crucial determinant of adult health. Yet the neurobiological basis for this remains elusive. Localized brain regions display atypical neural activity in rodents who experienced ELA, but how this contributes to overall brain state dynamics has been unknown. Here, we used longitudinal manganese-enhanced MRI to detect brain-wide activities altered by ELA in the adult across a series of conditions: freely moving, experiencing threat or its aftermath. Computational analyses revealed that ELA produced widespread dynamic reconfiguration of brain-wide neural activity in response to threat, shown here for the first time. Dynamic brain state remodeling after ELA provides critical insights into human mental health vulnerabilities associated with adverse childhood experiences (ACEs), and suggests plausible targets for intervention.

neuroscience↗

bioRxiv2020

A model of traumatic brain injury using human iPSC-derived cortical brain organoids

Traumatic brain injury confers a significant and growing public health burden and represents a major environmental risk factor for dementia. Previous efforts to model traumatic brain injury and elucidate pathologic mechanisms have been hindered by complex interactions between multiple cell types, biophysical, and degenerative properties of the human brain. Here, we use high-intensity focused ultrasound to induce mechanical injury in 3D human pluripotent stem cell-derived cortical organoids to mimic traumatic brain injury in vitro. Our results show that mechanically injured organoids recapitulate key hallmarks of traumatic brain injury, phosphorylation of tau and TDP-43, neurodegeneration, and transcriptional programs indicative of energy deficits. We present high-intensity focused ultrasound as a novel, reproducible model of traumatic brain injury in cortical organoids with potential for scalable and temporally-defined mechanistic studies.

neuroscience↗

bioRxiv2020

Evolution of brain-wide activity in the awake behaving mouse after acute fear by longitudinal manganese-enhanced MRI

Life threatening fear after a single exposure evolves in a subset of vulnerable individuals to anxiety, which may persist for their lifetime. Yet neither the whole brains response to innate acute fear nor how brain activity evolves over time is known. Sustained neuronal activity may be a factor in the development of anxiety. We couple two experimental protocols to obtain a fear response leading to anxiety. Predator stress (PS) is a naturalistic approach that induces fear in rodents; and the serotonin transporter knockout (SERT-KO) mouse responds to PS with sustained defensive behavior. Behavior was monitored before, during and at short and long times after PS in WT and SERT-KO mice. Both genotypes responded to PS with defensive behavior, and SERT-KO retained defensive behavior for 23 days, while wild type (WT) mice return to baseline exploratory behavior by 9 days. Thus, differences in neural activity between WT and SERT-KO at 9 days after PS will identify neural correlates of persistent defensive behavior. We used longitudinal manganese-enhanced magnetic resonance imaging (MEMRI) to identify brain-wide neural activity between behavioral sessions. Mn2+ accumulation in active neurons occurs in awake behaving mice and is retrospectively imaged. To confirm expected effects of PS, behavior was monitored throughout. Following the same two cohorts of mice, WT and SERT-KO, longitudinally allowed unbiased quantitative comparisons of brain-wide activity by statistical parametric mapping (SPM). During natural behavior in WT, only low levels of activity-induced Mn2+-accumulation were detected, while much more accumulation appeared immediately after PS in both WT and SERT-KO, and evolved at 9 days to a new activity pattern at p<0.0001, uncorr., T=5.4. Patterns of accumulation differed between genotypes, with more regions of the brain and larger volumes within regions involved in SERT-KO than WT. A new computational segmentation analysis, using our InVivo Atlas based on a manganese-enhanced MR image of a living mouse, revealed dynamic changes in the volume of significantly enhanced voxels within each segment that differed between genotypes across 45 of 87 segmented regions. At Day 9 after PS, the striatum and ventral pallidum were active in both genotypes but more so in the anxious SERT-KO. SERT-KO also displayed sustained or increased volume of Mn2+ accumulation between Post-Fear and Day 9 in eight segments where activity was decreased or silenced in WT. Staining of the same mice fixed at the conclusion of imaging sessions for c-fos, a marker of neural activity, confirmed that MEMRI detected active neurons. Intensity measurements in 12 regions of interest (ROIs) supported the SPM results. Between group comparisons by SPM and of ROI measurements identified specific regions differing between time points and genotypes Thus we report brain-wide activity in response to a single exposure of acute fear, and, for the first time, its evolution to new activity patterns over time in individuals vulnerable to anxiety. Our results demonstrate the power of longitudinal MEMRI to discover how brain-wide activity evolves during recovery or persistence of fear responses leading to anxiety.

physiology↗