Biology subjects

Huebner, M.

Publications and source records attributed to Huebner, M..

5 recordsLinked to original sources

bioRxiv2026

Low-Cost Real-Time Fiber-Optic Distance Sensing for OPM-based Biomagnetic Measurements

Background: Accurate tracking of the distance between magnetic sensors and biological tissue is particularly relevant to biomagnetic measurements in which stable wearable sensor configurations are not feasible, such as optically pumped magnetometer-based magnetomyography (OPM-MMG). In these measurements, movement-induced changes in source-to-sensor geometry can affect the recorded signal nonlinearly and complicate motion artifact control. Because components used near optically pumped magnetometers must be nonmagnetic to minimize magnetic interference, a compact, nonmagnetic method is needed for real-time monitoring of sensor-to-surface distance. Methods: Low-cost, nonmagnetic polymer fiber sensors (Keyence FS-N11MN with FU-6F fibers) were evaluated for real-time distance measurement using a fully automated linear stage over a range of 0-30 mm and at controlled incidence angles from 50 to 90 degrees. The sensors generated analog output voltages from 1 to 5 V, sampled at 2048 Hz, with a response time of 16 ms. Custom scripts were used for signal averaging, noise estimation, uncertainty weighting, calibration, and distance reconstruction. Results: Voltage decreased nonlinearly with increasing distance. For the pooled data obtained at 80 and 90 degrees, weighted Hill1 fits over 0-10 mm and 0-30 mm yielded adjusted R-squared values greater than 0.9990. Across the five sensors, the mean absolute reconstruction error was 0.0282 mm when both calibration and evaluation were restricted to 0-10 mm, and 0.1310 mm when calibration over 0-30 mm was evaluated over 10-30 mm. Periodic modulation was observed beyond 10 mm, remained present when Sensor 1 was operated independently, and was consistent with the discrete internal signal levels of the sensor. Conclusion: Low-cost, nonmagnetic polymer fiber sensing may provide a compact, real-time method for monitoring sensor-to-surface distance over 0-10 mm in optically pumped magnetometer-based biomagnetic measurements. Extension across the full 0-30 mm range will require range-specific calibration and further validation using skin-facing surfaces.

bioengineering↗

bioRxiv2025

Inhibition of Posterior Thalamic Nuclei Attenuates CGRP-induced Migraine-like Behavior in Mice

ObjectiveTo determine whether induction of migraine-like symptoms in mice by calcitonin gene-related peptide (CGRP) requires activation of the posterior thalamic nuclei (PoT) in the brain.BackgroundPrevious research found that both optical activation of the PoT and injection of CGRP into the PoT are sufficient to induce light aversive behavior in mice. The PoT is well known as a sensory integration center of light and pain signals in the brain. However, whether this region is required for touch hypersensitivity and light aversion following peripheral administration of CGRP was not known.MethodsThe PoT was injected in two strains of mice, inbred C57BL/6J and outbred CD-1, with viral vectors expressing inhibitory chemogenetic Designer Receptors Exclusively Activated by Designer Drugs (DREADDs). The inhibitory DREADDs were activated by systemic intraperitoneal (ip) injection of two designer drugs, clozapine N-oxide (CNO) and DREADD agonist compound 21 (C21). We used ip injection of CGRP to induce migraine-like phenotypes and tested whether we could rescue these phenotypes by bilateral chemogenetic inhibition of the PoT. The light/dark assay was used to measure light aversive behavior (a surrogate for photophobia) and the plantar von Frey assay to measure hindpaw touch sensitivity (a surrogate for extracephalic allodynia).ResultsWe successfully induced light aversive and hindpaw touch hypersensitivity phenotypes in mice using ip injections of CGRP. Activation of the inhibitory DREADDs in the PoT using ip CNO (5 mg/kg) was sufficient to partially rescue the touch hypersensitivity phenotype, but with off target effects in the control mice. Lowering the CNO dose to 1 mg/kg alleviated off target effects but was insufficient to rescue the touch hypersensitivity phenotype. On the other hand, C21 (1 mg/kg) fully rescued the touch hypersensitivity phenotype without any off target effects. Treatment with C21 also partially rescued the light aversion phenotype. These results were consistent across both C57BL/6J and CD-1 mouse strains.ConclusionInhibition of the PoT fully rescues CGRP-induced touch hypersensitivity and partially rescues light aversion in mice, indicating that the PoT is necessary for touch hypersensitivity and partially necessary for light aversive behaviors. These data suggest the PoT is part of a central network that receives peripheral CGRP-induced signals and thus could be harnessed for future targeted therapeutics for migraine.Plain language summaryThe posterior thalamus is a central brain region that contributes to migraine pathophysiology when stimulated. In this study, we asked if inhibition of this brain region could alleviate migraine-like phenotypes in mice. We found that inhibition of the posterior thalamus fully rescues touch hypersensitivity and partially rescues light aversive behavior, suggesting that the posterior thalamus is necessary for migraine pathophysiology and could offer a potential therapeutic target for migraine.

neuroscience↗

bioRxiv2024

PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction

In silico modeling of transcriptional responses to perturbations is crucial for advancing our understanding of cellular processes and disease mechanisms. We present PertEval-scFM, a standardized framework designed to evaluate models for perturbation effect prediction. We apply PertEval-scFM to benchmark zero-shot single-cell foundation model (scFM) embeddings against base-line models to assess whether these contextualized representations enhance perturbation effect prediction. Our results show that scFM embeddings do not provide consistent improvements over baseline models, especially under distribution shift. Overall, this study provides a systematic evaluation of zero-shot scFM embeddings for perturbation effect prediction, highlighting the challenges of this task and revealing the limitations of current-generation scFMs. Our findings underscore the need for specialized models and high-quality datasets that capture a broader range of cellular states. Source code and documentation can be found at: https://github.com/aaronwtr/PertEval.

bioinformatics↗

bioRxiv2022

CGRP Administration into the Cerebellum Evokes Migraine-like Behaviors Predominately in Female Mice

The neuropeptide calcitonin gene-related peptide (CGRP) is a major player in migraine pathophysiology. Previous preclinical studies demonstrated that intracerebroventricular administration of CGRP caused migraine-like behaviors in mice, but the sites of action in the brain remain unidentified. The cerebellum has the most CGRP binding sites in the central nervous system and is increasingly recognized as both a sensory and motor integration center. The objective of this study was to test whether the cerebellum, particularly the medial cerebellar nuclei (MN), might be a site of CGRP action. In this study, CGRP was directly injected into the right MN of C57BL/6J mice via a cannula. A battery of behavioral tests was done to assess migraine-like behaviors. CGRP caused light aversion measured as decreased time in the light zone even with dim light. The mice also spent more time resting in the dark zone, but not the light, along with decreased rearing and transitions between zones. These behaviors were similar for both sexes. In contrast, significant responses to CGRP were seen only with female mice in the open field assay, von Frey test, and automated squint assay, indicating anxiety, tactile hypersensitivity, and spontaneous pain, respectively. In male mice, the responses had the same trend as females but did not reach statistical significance. No detectable effect of CGRP on gait was observed in either sex. These results suggest that CGRP in the MN causes light aversion in males, while in females, light aversion is accompanied by increased anxiety, tactile hypersensitivity, and spontaneous pain. A caveat is that we cannot exclude contributions from other cerebellar regions in addition to the MN due to diffusion of the injected peptide. These results reveal the cerebellum as a new site of CGRP actions that may contribute to migraine pathophysiology and possibly its prevalence in females.

neuroscience↗

bioRxiv2020

Quantification of Brucella abortus population structure in a natural host

Cattle are natural hosts of the intracellular pathogen, Brucella abortus, which inflicts a significant burden on the health and reproduction of these important livestock. The primary routes of infection in field settings have been described, but it is not known how the bovine host shapes the structure of B. abortus populations during infection. We utilized a library of approximately 106 uniquely barcoded B. abortus strains to temporally and spatially quantify population structure at the strain level during colonization of cattle through a natural route of infection. Introducing 108 bacteria from this barcoded library to the conjunctival mucosa resulted in expected levels of local lymph node colonization at a one-week timepoint. We leveraged variance in strain abundance in the library to demonstrate that only 1 in 10,000 brucellae introduced at the site of infection reached the parotid lymph nodes. Thus, cattle restrict the overwhelming majority of B. abortus introduced via the ocular conjunctiva at this dose. Individual strains were spatially restricted within the host tissue, and the total B. abortus census was dominated by a small number of distinct strains in each lymph node. These results define a bottleneck that B. abortus must traverse to colonize local lymph nodes from the conjunctival mucosa. The data further support a model in which a small number of spatially isolated granulomas founded by unique strains are present one-week post infection. These experiments demonstrate the power of barcoded transposon tools to quantify infection bottlenecks and to define pathogen population structure in host tissues. Significance statementUnderstanding microbial population dynamics during infection has important implications for disease management, transmission and pathogen evolution. A quantitative analysis of microbial population structure requires the ability to track individual strains. We used a pool of individually barcoded strains to measure changes in Brucella abortus population structure during infection of bovine hosts via the ocular conjunctiva, a natural route of entry. Cattle exert a severe bottleneck on the bacterial population entering through the conjunctival mucosa such that individual cells have a 0.0001 probability of colonizing a local draining lymph node. The populations in lymph nodes, even on different sides of the same animal, are distinct and dominated by a small number of highly abundant, spatially distinct clones.

microbiology↗