Biology subjects

Strahle, J. M.

Publications and source records attributed to Strahle, J. M..

5 recordsLinked to original sources

bioRxiv2026

Automated Ventricle Assessment via Three-dimensional Anatomical Reconstruction (AVA-TAR): a computational toolkit for autonomous lateral ventricle assessment in preclinical hydrocephalus models

IntroductionCurrent workflows for studying hydrocephalus in rodent models rely on manual segmentation or qualitative assessment of ventricular size on small animal magnetic resonance imaging, which are both inefficient and prone to variability. Atlas-based methods enable more streamlined segmentation, but their analysis is limited to morphologically normal samples. ObjectiveThis study aimed to develop and internally validate a deep learning model that performs automated segmentation of lateral ventricles in rodent brain MRIs, allowing for 3D ventricle reconstruction, morphological analysis, and ventriculomegaly detection. MethodsFour U-Net++ neural networks, each with different encoder backbones, were trained using 307 rodent brain MRIs (262 rats, 45 mice), each with manually segmented lateral ventricles serving as the ground truth. Model performance was evaluated using the Dice coefficient, intersection over union (IoU), and Hausdorff index. The most optimal model was evaluated further for its ability to quantify ventricle volume, convexity, surface area, and symmetry. ResultsThe U-Net++ model with an EfficientNet-B1 encoder achieved high accuracy (Dice: 0.823 {+/-} 0.136; IoU: 0.721 {+/-} 0.85). Further assessment of its morphological predictions found strong correlations with manual measurements of ventricular morphology, with Pearson and interclass correlation coefficients exceeding 0.96 across all metrics. The full validated pipeline was packaged into a publicly available application, hosted at https://ava-tar.org. ConclusionThis study introduces a deep learning tool for automated segmentation and morphological analysis of lateral ventricles in rodent MRIs. The tools efficiency and accuracy in quantifying ventricle morphology offers significant utility in preclinical hydrocephalus research with potential future application in the clinical setting.

neuroscience↗

bioRxiv2026

Simultaneous Real-time Imaging of Neurofluid and Neurovascular Dynamics Using Ultrafast Flow-weighted Echo-Planar Imaging

Cerebrospinal fluid (CSF) circulation is tightly coupled to cerebral blood flow under the fixed-volume constraint of the cranial vault, with cardiac pulsations and respiration acting as dominant physiological drivers. Disruption of these flow dynamics has been implicated in various neurological disorders, motivating the need for imaging methods that capture CSF and vascular flow simultaneously and in real time. Conventional phase contrast MRI (PC-MRI) provides quantitative CSF velocity measurements but relies on cardiac gating and velocity encoding, which limit temporal resolution, dynamic range, and sensitivity to non-cardiac fluctuations. Here, we introduce self-gated ultrafast real-time flow-weighted echo-planar imaging (SURF-EPI), an inflow-weighted approach in which signal intensity reflects the replacement of saturated spins by freshly inflowing, unsaturated water molecules, yielding higher signal with higher flow. This allows simultaneous assessment of arterial inflow, venous outflow, and CSF motion at high temporal resolution. SURF-EPI was acquired at the C2-C3 spinal level, enabling real-time imaging of CSF flow dynamics in the cervical spinal canal alongside arterial and venous blood flow in major cervical vessels (frame-rate: 21.7 Hz). In addition to frequency-domain analyses, we leveraged intrinsic arterial signal fluctuations as a timing reference to reconstruct cardiac-resolved CSF dynamics for individual cardiac cycles without external physiological recordings. Frequency-domain analysis revealed distinct spectral signatures in CSF flow compared with neurovascular flow, including broadened cardiac peaks and enhanced respiratory modulation, particularly within the ventral spinal canal. In contrast, dorsal CSF showed increased power within the cardiac frequency band, higher coherence with cervical vasculature at the cardiac frequency, and reduced non-cardiac contributions. Time-domain analysis showed strong correlation between CSF flow waveforms derived from SURF-EPI and PC-MRI. Beyond ensemble-averaged waveforms, SURF-EPI enabled beat-to-beat analysis, revealing substantial cycle-to-cycle variability in CSF flow that is not captured by time-averaged gated approaches. Together, these findings establish SURF-EPI as a rapid, complementary framework to PC-MRI, enabling real-time neurofluid imaging with integrated time- and frequency-domain characterization of CSF and neurovascular flow dynamics.

neuroscience↗

bioRxiv2025

Indirect Deuterium Displacement Exchange Imaging for Non-invasive High-Resolution CSF Production Mapping

Cerebrospinal fluid (CSF) production is central to brain homeostasis, yet existing measurement techniques are invasive, technically demanding, and confounded by intracranial perturbations. Here, we introduce indirect deuterium displacement exchange imaging (CSF-iDDxI), a noninvasive MRI approach for mapping CSF production in vivo. The method leverages intravenously infused deuterium oxide (D2O), which crosses the blood-CSF barrier, replaces existing H2O in CSF, producing concentration-dependent attenuation of proton (1H) signal within CSF spaces. Using high-resolution 3D balanced steady-state free precession MRI in rats, we demonstrate robust and spatially widespread D2O-induced CSF signal loss that is selectively suppressed by acetazolamide, a carbonic anhydrase inhibitor known to suppress CSF production by the choroid plexus. Dynamic imaging during intravenous D2O infusion further revealed that cortical parenchymal signal changes were unaffected by acetazolamide, confirming specificity to CSF production. Exploratory kinetic modeling estimated rapid CSF water turnover (k {approx} 0.09 min-1) under physiological conditions, reduced to k {approx} 0.031 min-1 with acetazolamide suppression, consistent with prior isotope tracer studies. Together, these findings establish CSF-iDDxI as a sensitive, pharmacologically validated tool for quantifying CSF production and turnover.

neuroscience↗

bioRxiv2023

Meningeal CSF transport is primarily mediated by the arachnoid and pia maters during development

BackgroundThe recent characterization of the glymphatic system and meningeal lymphatics has re-emphasized the role of the meninges in facilitating CSF transport and clearance. Here, we characterize small and large CSF solute distribution patterns along the intracranial and surface meninges in neonatal rodents and compare our findings to a rodent model of intraventricular hemorrhage-posthemorrhagic hydrocephalus. We also examine CSF interactions with the tela choroidea and its pial invaginations into the choroid plexuses of the lateral, third, and fourth ventricles. Methods1.9-nm gold nanoparticles, 15-nm gold nanoparticles, or 3 kDa Red Dextran Tetramethylrhodamine constituted in aCSF were infused into the right lateral ventricle of P7 rats to track CSF circulation. 10 minutes post-1.9-nm gold nanoparticle and Red Dextran Tetramethylrhodamine injection and 4 hours post-15-nm gold nanoparticle injection, animals were sacrificed and brains harvested for histologic analysis to identify CSF tracer localization in the cranial and spine meninges and choroid plexus. Spinal dura and leptomeninges (arachnoid and pia) wholemounts were also performed. ResultsThere was significantly less CSF tracer distribution in the dura compared to the arachnoid and pia maters in neonatal rodents. Both small and large CSF tracers were transported intracranially to the arachnoid and pia mater of the perimesencephalic cisterns and tela choroidea, but not the dura mater of the falx cerebri. CSF tracers followed a similar distribution pattern in the spinal meninges. In the choroid plexus, there was large CSF tracer distribution in the apical surface of epithelial cells, and small CSF tracer along the basolateral surface. There were no significant differences in tracer intensity in the intracranial meninges of control vs. intraventricular hemorrhage-posthemorrhagic hydrocephalus (PHH) rodents, indicating preserved meningeal transport in the setting of PHH. ConclusionsDifferential CSF tracer handling by the leptomeninges suggests that there are distinct roles for CSF handling between the arachnoid-pia and dura maters in the developing brain. Similarly, differences in apical vs. luminal choroid plexus CSF handling may provide insight into particle-size dependent CSF transport at the CSF-choroid plexus border.

neuroscience↗

bioRxiv2023

The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes

DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift null deletion in Dnaaf5. Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partial preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. While transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. Together, these findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies. Brief SummaryA mouse model of human DNAAF5 primary ciliary dyskinesia variants reveals gene dosage effects of mutant alleles and tissue-specific molecular requirements for cilia motor assembly.

cell biology↗