Biology subjects

Chen, J. J.

Publications and source records attributed to Chen, J. J..

At least 19 recordsLinked to original sources

bioRxiv2026

CRISPR-dPCR: A unified multiplex digital PCR framework for quantitative characterization of targeted knock-in

Accurate characterization of CRISPR knock-in requires distinguishing site-specific integration from total donor abundance and donor-derived background while measuring editing at the target site. Here, we present CRISPR-dPCR, a modular multiplex digital PCR framework combining a locked nucleic acid-enhanced cut-site assay with junction-based detection and two orthogonal short-amplicon strategies: Poisson linkage and homology-arm subtraction. We evaluated assay modules across genomic loci, neuroblastoma models and primary human T cells, with selected assays compared on two dPCR platforms. In genotype-defined clones and mixtures with low residual donor, homology-arm subtraction most closely recovered expected knock-in abundance. Linkage provided highly specific evidence of target-cargo association without junction-spanning amplification, whereas junction assays supplied boundary-specific confirmation but were more sensitive to amplicon length and multiplexing. Five-channel panels integrated cut-site editing, donor abundance, copy-number normalization and site-specific knock-in in a single reaction. Residual donor DNA limited quantitative interpretation, particularly in early post-editing samples. Modular extensions quantified defined unintended outcomes, including chromosomal translocations. CRISPR-dPCR integrates complementary measurements into a scalable analytical framework for genome-editing research, cell and gene therapy product development and applications in longitudinal clinical monitoring of targeted integration and transgene persistence.

molecular biology↗

bioRxiv2026

Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990

COVID-19 highlighted the need for antivirals that can be rapidly deployed against both current and future coronavirus threats. CMX990 is a clinical stage coronavirus main protease (Mpro) inhibitor bearing a unique trifluoromethoxymethyl ketone warhead. Here, we broadly evaluate its pan-coronavirus target engagement, antiviral breadth, and pharmacologic differentiation. Across a reporter panel of 24 Mpro enzymes spanning alpha-, beta-, delta-, and gamma-coronaviruses, CMX990 retained robust potent activity, including against nirmatrelvir-resistant SARS-CoV-2 variants. In direct comparison, nirmatrelvir and ensitrelvir showed diminished potency against non-SARS-CoV-2 coronaviruses. Live-virus assays corroborated this breadth, with potent, selective activity against SARS-CoV-2, SARS-CoV-1, MERS-CoV, and additional human coronaviruses. Structural studies revealed a conserved covalent binding mode centered on the catalytic Cys of coronavirus Mpro. In serial-passage studies, resistance emerged only after approximately twice as many serial passages under CMX990 selection as under nirmatrelvir selection, without selecting for the canonical nirmatrelvir-resistance substitution E166V. Extracellular washout experiments revealed superior persistence of antiviral activity relative to nirmatrelvir, consistent with durable target engagement. In a murine SARS-CoV-2 infection model, once-daily CMX990 protected against weight loss and reduced lung viral titers to near baseline levels. Collectively, these findings identify CMX990 as a structurally and functionally validated pan-coronavirus protease inhibitor supporting its potential as a pandemic-ready antiviral candidate.

pharmacology and toxicology↗

bioRxiv2026

Intranasal photobiomodulation as an energy-efficient, largely parameter-insensitive alternative to transcranial photobiomodulation

BackgroundPhotobiomodulation (PBM) is an emerging non-invasive light-based brain stimulation technique that can alter cortical oscillations and is currently being pursued for improving cognition and treating neurological and psychiatric conditions. Nearly all human EEG evidence comes from transcranial PBM (tPBM) applied to the forehead, where light must traverse the scalp and thick skull, requiring protocols to compensate with high surface irradiance. Intranasal PBM (iPBM) can reach the anterior skull base at a fraction of that irradiance and has also been shown to modulate cerebrospinal fluid dynamics, yet it has been studied almost exclusively as an adjunct to tPBM, leaving its cortical effects in isolation, and its energy-efficiency relative to the transcranial route, unknown. ObjectiveTo define the spatiotemporal EEG response to pulsed iPBM delivered alone, determine whether stimulation parameters or individual biology moderate it, and compare the energy-efficiency of iPBM and tPBM in the same participants. MethodsHigh-density EEG was collected from forty-six healthy young adults during pulsed iPBM and tPBM spanning a parameter space of varying wavelengths, pulsation frequencies, and irradiances. Percent change in band power from a within-session pre-stimulation baseline was tested with spatiotemporal cluster-based permutation tests. Linear mixed-effects models with backward elimination assessed stimulation and biological moderators (sex, nostril-to-cortex distance). Energy-efficiency, defined as the percent change in band power per J/cm2 of delivered surface energy, was compared between routes within each subject in delivery route-specific cluster regions of interest (ROI) (Wilcoxon signed-rank tests, Benjamini-Hochberg false discovery rate). ResultsiPBM alone produced significant spatiotemporal clusters in theta, beta, and gamma power, with anterior increases and posterior decreases; no delta or alpha clusters survived correction. Beta and gamma effects appeared at stimulation onset and persisted even after stimulation ended, whereas theta effects strengthened after stimulation ended. No predictor survived elimination in any band, time window, or cluster ROI: response magnitude was independent of wavelength, pulsation frequency, irradiance, sex, and nostril-to-cortex distance. Notably, although iPBM delivered roughly twenty times less surface energy than tPBM ([~]0.6-1.1 vs [~]12-24 J/cm2), it produced EEG changes of similar magnitude, and its energy-efficiency exceeded that of tPBM in seven of eight eligible comparisons, with median iPBM-to-tPBM efficiency ratios of 14-32 (all FDR q<0.05) ConclusionsDelivered in isolation, pulsed iPBM elicits a robust cortical EEG signature closely resembling that of tPBM, is insensitive to the stimulation parameters and individual factors tested, and achieves this at a small fraction of the delivered surface energy. As a result, delivery route, not surface irradiance alone, should be treated as a primary variable in PBM dose reporting and protocol design.

physiology↗

bioRxiv2026

A lipid nanoparticle platform for high yield CRISPR-targeted homology directed repair enables fully non-viral CAR T cell generation

CRISPR-mediated homology directed repair (HDR) enables targeted CAR integration with improved fitness and therapeutic potential of CAR T cells. However, current methods for generating HDR-engineered CAR T cells rely on viral transduction or electroporation, approaches that limit global implementation and constrain patient access due to their cost, toxicity, and requirement for centralized manufacturing. Through a screen of ionizable lipids, we identified LNP systems that enable CRISPR-mediated gene knock-in (KI) in primary human T cells and are amenable to hand mixing by ethanol injection as a research tool or machine formulation for larger scale manufacturing. Modifying the linear dsDNA HDR template with truncated Cas9 target sequences (tCTS) enhanced HDR rates across multiple LNP systems. We optimized two LNP formulations capable of HDR-mediated KI of a large 4kB CD19 CAR-EGFR HDR template into the TRAC locus with rates of [≥]8% and >10x improved edited cell yields compared to electroporation. We demonstrate that LNP-generated CAR T cells exhibited similar growth kinetics, activation states, differentiation states, and killing capacity compared to electroporation-generated CAR T cells. Our LNP platform components are fully disclosed, commercially sourced, and enable efficient fully non-viral CRISPR-HDR cell engineering across diverse applications.

bioengineering↗

bioRxiv2026

Orientation Dependence of R2' in White Matter: Digital Characterization, Modelling and Implications for Studying Brain Physiology

PurposeR2*, the transverse relaxation rate, reflects local magnetic field inhomogeneities from susceptibility differences with R2, the reversible component sensitive to blood oxygenation. Orientation dependence of R2 and R2* in white matter (WM) are attributed primarily to myelin, with vascular contributions to R2 uncharacterized. This study examined WM R2 orientation dependence, evaluated existing models, and developed an improved model combining myelin and blood. MethodsSimulations used BOLDswimsuite with 2D WM voxels (5,000 fibres). Spin-echo (TE = 70ms) and gradient-echo (TE = 35ms) signals were simulated across 30 fibre orientations (0{degrees}-90{degrees}). R2' was calculated as R2* - R2. Oxygenation, cerebral blood volume (CBV), vessel size, and vessel geometry were varied. Four published models and a novel Myelin-Blood model were fitted to R2' data and compared using R2 and RMSE. ResultsR2 and R2* showed strong orientation dependence. Parallel and mixed vessel geometries produced greater R2' amplitude and orientation dependence than random geometries; decreasing oxygenation and increasing CBV amplified orientation effects. Vessel size altered peak locations. Existing vascular models performed poorly, and the Empirical Myelin Model erred near the magic angle. The Myelin-Blood model provided near-perfect fits (mean R2 = 0.999, RMSE = 0.007 Hz), reducing RMSE by ~74%. DiscussionWM R2' cannot be explained by vascular or myelin effects alone. Myelin is the primary determinant of orientation dependence, but vascular contributions were evident near the magic angle and low oxygenation. The Myelin-Blood model improves WM R2 characterisation and may reduce orientation-dependent bias and improve interpretation of WM BOLD fMRI signals.

neuroscience↗

bioRxiv2026

Hemodynamic Responses in the White Matter (WM): Reduced Blood Flow in Deep WM During Hypercapnia Revealed by Multi-Delay pCASL in Healthy Young Adults

The white matter (WM) cerebrovascular response remains poorly understood compared with grey matter (GM), partly due to technical challenges in perfusion quantification. Previous studies of cerebrovascular reactivity (CVR) have mostly been performed using BOLD MRI, and it is unclear to what extent they reflect changes in cerebral blood flow (CBF). In this work, we used multi-delay pseudo-continuous arterial spin labeling (pCASL) to quantify hypercapnia-induced CBF changes ({Delta}CBF) while accounting for regional variability in arterial transit time. Twenty-five healthy young adults underwent MRI during normocapnia and hypercapnia (inhalation of a 4% CO2 gas mixture). Hypercapnia induced robust positive {Delta}CBF in cortical GM (26.7 {+/-} 13.5%), superficial WM (17.2 {+/-} 12.6%), periventricular regions (13.6 {+/-} 10.6%), and subcortical GM (25.7 {+/-} 14.1%) (all p < 0.0001). In contrast, deep WM exhibited a near-zero group-mean CBF response (1.0 {+/-} 8.9%, p = 0.57), with 10 of 25 participants demonstrating negative {Delta}CBF. Negative CBF responses were consistently localized to the corona radiata, centrum semiovale, and optic radiation. Quality-control analyses showed that deep-WM {Delta}CBF estimates are robust, supporting the reliability of these findings. Moreover, across tissue compartments, higher baseline CBF was associated with reduced hypercapnic responsiveness, and deep-WM responses were strongly coupled with cortical GM responses across individuals. These results demonstrate that hypercapnia-induced cerebrovascular responses are highly heterogeneous across tissue depths and provide evidence that negative CBF responses can occur in healthy deep WM in the presence of vasodilation elsewhere. The findings challenge the assumption of uniformly positive perfusion responses during hypercapnia and support a potential role for flow redistribution arising from regional differences in vascular resistance and reserve capacity.

neuroscience↗

bioRxiv2026

Orally Bioavailable SARS-CoV-2 Protease Inhibitors Bearing a Hydroxymethyl Ketone Warhead

The use of covalent warheads targeting the catalytic cysteine has been a cornerstone in coronavirus main protease (Mpro) inhibitor development, where various electrophilic motifs have been used including aldehydes, nitriles, ketoamides, and hydroxymethyl ketones (HMKs). Recent efforts have been mostly centered around nitrile warheads, given the success of compounds like Nirmatrelvir and Ensitrelvir in the clinic. However, finding and advancing alternative chemotypes with differentiating chemical and pharmacological profiles is essential for future pandemic preparedness. Among such alternatives, HMKs hold special interest because they balance reduced intrinsic electrophilicity with an excellent selectivity profile. Nevertheless, early HMK-based compounds, such as the clinical-stage Mpro inhibitor PF-00835231, suffered from poor oral bioavailability and therefore required intravenous administration, with or without prodrug derivatization of the hydroxyl group. Here, we describe our efforts in advancing the HMK field via the discovery of mCMX110, a lead that has superior potency, increased unbound exposure in vivo, and favorable oral bioavailability in preclinical studies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/725542v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@40222aorg.highwire.dtl.DTLVardef@831b88org.highwire.dtl.DTLVardef@184a910org.highwire.dtl.DTLVardef@779095_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Characterization and Validation of Compressed Sensing for Time-of-Flight MRI Angiography of the Human Brain at 3T and 7T

BackgroundCerebral vasculature is a key biomarker of brain health, and time-of-flight (TOF) magnetic resonance angiography (MRA) provides noninvasive assessment of vascular anatomy. However, conventional TOF-MRA requires long scan times, increasing patient burden and susceptibility to motion artifacts. Compressed sensing (CS) offers a feasible acceleration strategy. PurposeTo quantitatively evaluate CS acceleration in TOF-MRA at 3T and 7T using automated whole-FOV vascular segmentation and semi-automatic segmentation of representative vessels. Study typeProspective Population23 healthy human participants (3T) and 8 healthy human participants (7T). Field Strength/SequenceCS TOF-MRA (CS factors 4 and 8 at 3T; 8 at 7T) was compared against non-accelerated (CS0) TOF-MRA. AssessmentVisual comparison and vascular segmentation were performed using automated whole-FOV methods and semi-automatic segmentation of the posterior cerebral artery and anterior choroidal artery. Statistical TestsContrast-to-noise ratio (CNR), voxel count, and vessel diameter were assessed using two-tailed paired t-tests. ResultsWhole-FOV CNR differed significantly across CS factors at 3T (CS0 > CS4: p < 0.001, d = 0.77; CS0 < CS8: p = 0.008, d = 0.36; CS4 < CS8: p < 0.001, d = 1.11) and 7T (CS0 < CS8: p = 0.002, d = 0.54), with semi-automatic segmentation yielding consistent findings (p < 0.01 for all comparisons). The diameter measurements for segmented vessels are also higher with high CS-factors (PCA 7T: left: p = 0.006, d = 0.93, right: p = 0.045, d = 0.43; AChA 7T: left: p < 0.001, d = 0.66, right: p = 0.009, d = 1.06; PCA 3T: p < 0.001 for all comparison dLeft = 0.52 (CS0 vs. CS4), 0.56 (CS4 vs. CS8), 1.11 (CS0 vs. CS8) and dRight = 0.78 (CS0 vs. CS4), 0.57 (CS4 vs. CS8), 1.17 (CS0 vs. CS8)). Data ConclusionCS shows promise for enhancing clinical applicability of TOF-MRA, with advantages most pronounced at 7T.

bioengineering↗

bioRxiv2026

Loss of Mast cells and histaminergic signaling link diet to platelet-mediated NETosis and mammary cancer recurrence

Breast cancer recurrence remains a clinical challenge. The period after the treatment of the primary tumor while cancer cells that evaded initial treatment lay dormant, provides a unique window of opportunity for interventions to prevent recurrence. Specific modifiable factors such as consumption of high fat diets or elevated circulating cholesterol are associated with decreased time to recurrence. Mechanistically, oxidized cholesterol and lipid species have been implicated in the regulation of the tumor microenvironment. This suggests that consumption of food prepared under oxidizing conditions such as pan-frying, may be an underappreciated risk. Using murine models of mammary cancer dormancy, we found that a diet enriched with fat from fried, cured bacon (cfBF) decreased dormancy latency times. Resulting lesions had fewer mast cells (MCs). Loss of MCs alone resulted in reemergence from dormancy. Elevated expression of a MC gene signature in breast tumors was associated with improved progression free and overall survival, highlighting the human relevance of these findings. MCs are a major source of tissue histamine, and lesions from mice fed cfBF had decreased concentrations. Importantly, antagonists of the histamine receptor 2 (H2R) sparked reemergence from dormancy. H2R antagonists are over-the-counter drugs are taken to alleviate gastroesophageal reflux disease. Chronic treatment of mice with H2R-antagonists sensitized platelets towards activation and crosstalk with neutrophils, and subsequent formation of neutrophil extracellular traps (NETs). The loss of platelet or NETosis activity mitigated the H2R-antagonist stimulated reemergence from dormancy. Therefore, we establish a novel metastatic axis which links diet to recurrence via MCs, histaminergic signaling and NETosis: Diet -- MC -- H2R -- (decreased) Platelet Activity -- (decreased) Neutrophil-NETosis -- (decreased) Reemergence from Dormancy. Our data reveal several potential intervention strategies: lifestyle, MC stabilization, histaminergic signaling, and neutrophil and platelet activity.

cancer biology↗

bioRxiv2026

Intranasal photobiomodulation: an energy efficient paradigm for cortical and subcortical stimulation

Previous studies have shown the hemodynamic response to transcranial photobiomodulation (tPBM) in localized cortical regions during and after forehead irradiation. However, it is unclear if tPBM can reach deeper regions such as subcortical tissue. It is also unclear whether the manner of regional neurovascular coupling predominantly studied using tPBM extends to all brain regions. As an alternative to forehead delivery, intranasal PBM (iPBM) uses the pathway of the cribriform plate, which is thin and directly leads to the orbitofrontal cortex, rather than the prefrontal cortex in the case of forehead PBM. Thus, it is possible that iPBM can stimulate the brain more efficiently (i.e. with less power). In this study, healthy young adults underwent different iPBM protocols differing in wavelength, frequency and irradiance. We utilized functional magnetic resonance imaging (fMRI) to quantify regional blood oxygenation (BOLD) and perfusion. We further model the neurovascular interactions underlying the fMRI response. We uncovered three distinct temporal signatures, varying by brain region. Specifically, a significant response in the thalamus was observed, with a time-locked BOLD response. Overall, iPBM was found to be associated with much higher efficiency at eliciting BOLD fMRI responses than its forehead (tPBM) counterpart. Lastly, in addition to the expected dose dependence, there were extensive sex differences in the fMRI response to iPBM, surpassing those observed for tPBM. Collectively, these findings highlight the feasibility and efficacy of iPBM and establish a foundation for personalizing PBM protocols for optimal outcomes.

neuroscience↗

bioRxiv2025

Loss of cilia drives centriole clustering and elimination during mammalian spermatogenesis

Cilia are microtubule-based organelles essential for signaling and motility, and their dysfunction causes ciliopathies often associated with infertility. In male germ cells, two types of cilia are present: zygotene primary cilia and sperm flagella. To define the role of cilia in spermatogenesis, we conditionally ablated the distal appendage protein CEP164, required for basal body docking and ciliogenesis, in male germ cells. CEP164 localized to the mother centriole/basal body throughout spermatogenesis, and its loss led to male infertility accompanied by absence of both zygotene cilia and sperm flagella. Despite defective ciliogenesis, meiotic chromosome pairing and DNA double-strand break repair proceeded normally. However, round spermatids exhibited basal body docking and flagellogenesis defects, and frequently formed supernumerary centriole clusters that were subsequently eliminated via residual bodies. Live-cell imaging revealed that centrioles were highly mobile, and centriole pairs from neighboring cells often associated through intercellular bridges, forming aggregates. These results establish that basal body docking is crucial for retaining centrioles within spermatids, and its disruption leads to centriole clustering and loss. In contrast, zygotene cilia are dispensable for meiotic chromosome pairing and DNA repair during mammalian spermatogenesis.

developmental biology↗

bioRxiv2025

The fMRI response to transcranial photobiomodulation: the effect of wavelength, irradiance, frequency and skin tone on the BOLD and CBF response in healthy young adults

BackgroundTranscranial photobiomodulation (tPBM) utilizes near-infrared light to penetrate the skull to stimulate neural tissue. However, the in vivo physiological response and the factors influencing this response in the human brain have yet to be understood. MethodsIn this study, we utilize functional magnetic resonance imaging (fMRI) to evaluate the effect of tPBM on the blood-oxygenation (BOLD) and cerebral blood flow (CBF), while varying stimulation parameters such as wavelength, irradiance, and frequency. We further examine the influence of skin tone and sex. We further model the neurovascular interactions underlying the response. ResultsOur results show that the fMRI responses to tPBM is not restrained to the site of irradiation, but quickly spreads to distal sites. Certain regions display an fMRI response sustained after tPBM cessation. Importantly, the responses are dependent on biological and stimulation parameters. Lastly, biophysical modeling revealed a consistent neurovascular coupling-like behaviour underlying these responses. ConclusionEmpirical characterizations of dose dependence are critically important to brain stimulation methods in general but have yet to be demonstrated in most cases. This is the first tPBM study to do just that, establishing the foundation for precision medicine using tPBM, and sets a valuable precedent for the field of brain stimulation.

bioengineering↗

bioRxiv2025

Association between white-matter lesion volume and heart-rate variability: A comparison of T1, T1-T2 and T1-FLAIR-based segmentations using FreeSurfer SAMSEG

BackgroundHeart disease is a crucial risk factor for brain degeneration, but the exact mechanisms are still under investigation. Notably, a growth in white-matter lesion (WML) volume, a hallmark of cerebral small-vessel disease (cSVD) with connections to progressive neurodegeneration and cognitive decline, has been linked to cardiovascular disease. As such, measures of cardiovascular function such as heart rate variability may represent early and accessible predictors of WML development. MethodsThis study used data from healthy adults drawn from the Leipzig Study for Mind-Body-Emotion Interactions (LEMON) dataset to examine heart function through measures of heart rate variability (HRV), as well as their relationship to cSVD as quantified through WML volumes, using FreeSurfer SAMSEG. WML volumes were segmented using 3T T1+FLAIR, T1+T2 or T1 images alone. ResultsResults indicate that both young and old adults exhibited WMLs, and that lower HRV was associated with higher WML volume. This was particularly strong for high-frequency HRV across both young and older adults, but it was low-frequency HRV that was related to WML volume in an age-specific manner. Moreover, we showed that the WML-HRV relationship that is apparent using T1+FLAIR or T1+T2 based WML volumes could be observed even with T1w-based WML estimation alone. ConclusionsThese results suggest HRV not only as an avenue through which cardiovascular risk translates into brain degeneration, but also as a potential early and readily measurable non-invasive predictor of later WML development and cognitive impairment. Research Perspective- Differences in heart rate variability show consistent associations with the volume of white-matter lesions in the brain, with low-frequency heart rate variability uniquely sensitive to age effects on lesion volume. - Associations between heart rate variability and white matter lesion volume are detectable using T1-weighted volume estimation in absence of more intensive T1-weighted + T2-weighted or T1-weighted + FLAIR lesion estimations. - The neuroanatomical basis for this relationship, particularly the difference in high- and low-frequency heart rate variability associations, will require incorporating lifestyle, hormonal, and genetic factors, as well as targeted examination of high-versus low-frequency heart rate variability bands.

neuroscience↗

bioRxiv2025

Real-time spatial evolution of the fMRI response to photobiomodulation in the healthy human brain

Photobiomodulation (PBM) is a non-invasive therapeutic technique that uses low-level near-infrared light to influence mitochondrial metabolism and stimulate neural function. While PBM is increasingly used to improve cognitive and clinical outcomes, its in vivo physiological mechanisms in humans remain poorly characterized. In this study, we used BOLD-fMRI to investigate and quantify the temporal and spatial dynamics of transcranial PBM-induced brain activity in young, healthy adults, while incorporating multiple stimulation parameters (wavelength, irradiance, frequency) and transcranial delivery sites (right forehead and intranasal). A time-lagged correlation analysis revealed distinct spatiotemporal patterns of positive and negative BOLD responses that evolved over tens of seconds across both cortical surface and subcortical regions during stimulation. Notably, these effects propagated across brain regions that are potentially mediated by functional networks, were dose-dependent, and were modulated by individual skin tone. This work provides the first real-time, whole-brain mapping of PBM-induced hemodynamic changes in humans, offering new insights into dose-response characteristics and delivery-specific dynamics underlying PBM neurophysiology.

physiology↗

bioRxiv2025

Linking Electrophysiological Metrics to Oxidative Metabolism: Implications for EEG-fMRI Association

Resting-state functional magnetic resonance imaging (rs-fMRI) is widely used to study brain function, yet its biophysiological basis remains incompletely understood. Building on our recent work, we investigated how EEG activity and cerebral metabolic rate of oxygen (CMRO2) are related to one another, and how they jointly underpin rs-fMRI metrics. Using a multimodal dataset with macrovascular correction applied to all rs-fMRI metrics, we first examined associations between EEG metrics and CMRO2, then applied mediation analysis to evaluate how CMRO2 mediates EEG-fMRI associations. We found that bandlimited EEG theta and alphafractional power was significantly associated with CMRO2. Bandlimited EEG coherence was also associated with CMRO2 across all the bands. Bandlimited EEG fractional power and coherence were also significantly associated with cerebral blood flow (CBF) and oxygen extraction fraction (OEF) in a manner that varied by frequency. EEG broadband temporal complexity was positively associated with CMRO2 and EEG coherence was negatively associated with OEF. Notably, there are pronounced sex differences in these relationships, which suggests that the biophysical underpinnings of rs-fMRI are sex dependent. Moreover, the baseline metabolic and hemodynamic variables did partially mediate EEG-fMRI associations, with CMRO2 serving as the primary mediator. However, most of the mediations are partial, highlighting the complex interplay among electrophysiological activity, oxidative metabolism, and hemodynamics. This study advances our understanding of the biophysical basis of rs-fMRI and provides a foundation for developing sex-specific diagnostic and therapeutic strategies for neurological disorders.

neuroscience↗

bioRxiv2025

Evaluating BOLD functional MRI biophysical simulation approaches: impact of vascular geometry, magnetic field calculations, and water diffusion models

Biophysical simulations have guided the development of blood oxygenation level-dependent (BOLD) functional MRI (fMRI) acquisitions and signal models that relate the BOLD signal to the underlying physiology, such as calibrated BOLD and vascular fingerprinting. Numerous simulation techniques have been developed, however, few of them have been directly compared, thus limiting the assessment of the accuracy and interchangeability of these methods as well as the accuracy of the quantitative techniques derived from them. In this work, we compared the accuracy and computational demands of eight previously published simulation approaches that adopt different geometries (ranging from infinite cylinders to synthetic vascular anatomical networks (VANs)), field offset calculations (analytical and Fourier-based), and water diffusion implementations (Monte Carlo and convolution-based), all of which are available in an open-source Python toolkit, BOLDs{omega}imsuite. The reference simulation approach for comparison used three-dimensional infinite cylinders, analytical field offsets, and Monte Carlo diffusion. When compared with the reference approach, most of the simulations, including two- and three-dimensional geometries, were in excellent agreement when assuming the intravascular signal contribution was small. Two commonly employed simulation approaches were notably biased; both used two-dimensional geometries with overly simplified vasculature or field offset calculations. In general, the simulated intravascular signal was the least consistent across approaches, thus potentially resulting in larger errors when the intravascular signal contribution is large. Lastly, the VAN results were in good agreement with the reference but they diverged slightly, yet systematically, from each other at smaller radii ([lsim] 3 m), primarily driven by intravascular signal differences. We conclude, therefore, that the reference approach is an attractive option for exploratory simulations in the many cases where anatomical and hemodynamic realism is not needed, balancing ease of implementation, accessibility, versatility, computational efficiency, accuracy of results, and interpretability. These findings help pave the way for a broader adoption of forward modelling of the BOLD signal and more reliable interpretations of biophysical simulations aiming to develop quantitative models of the BOLD signal.

neuroscience↗

bioRxiv2025

The link between steady-state EEG and rs-fMRI metrics in healthy young adults: the effect of macrovascular correction

To improve the clinical utility of resting-state fMRI (rs-fMRI), enhancing its interpretability is paramount. Establishing links with electrophysiological activities remains the benchmark for understanding the neuronal basis of rs-fMRI signals. Existing research, while informative, suffers from inconsistencies and a limited scope of rs-fMRI metrics (e.g., seed-based functional connectivity). Phenotypic variables like sex and age are suspected to obscure reliable fMRI-EEG associations. A major contributing factor to these inconsistencies may be the neglect of macrovascular correction in rs-fMRI metrics. Given that macrovascular contributions can inflate rs-fMRI connectivity and power, they may lead to misleading fMRI-EEG associations that do not reflect genuine neuronal underpinnings. In this study, we addressed this by applying macrovascular correction and performing a systematic, inter-participant analysis of multiple rs-fMRI and EEG metrics. Our key findings demonstrate that: 1) Macrovascular correction enhances the relationship between EEG and rs-fMRI metrics and improves model fit in many instances; 2) sex significantly modulates EEG-fMRI associations; 3) EEG complexity is significantly associated with resting-state functional activity (RSFA). This research provides crucial insights into the interplay between rs-fMRI and EEG, ultimately improving the interpretability of rs-fMRI measurements and building upon our prior work linking fMRI and metabolism.

neuroscience↗

bioRxiv2025

Real-Time EEG Response to Pulsed Transcranial Photobiomodulation in Healthy Young Adults: Effects of Stimulation Parameters and Skin Tone

ObjectivesTranscranial photobiomodulation (tPBM) modulates cortical activity, but how specific stimulation parameters shape the electrophysiological response remains unclear. We tested whether pulsed forehead tPBM produces frequency band-specific EEG changes, whether pulsation frequency entrains endogenous oscillations, and whether wavelength, pulsation frequency, irradiance, sex, and skin tone significantly modulate the response. Materials and MethodsForty-six healthy young adults (24M/22F, 20-32 years) each completed four 12-minute EEG recordings (256-channel; PRE-DURING-POST, 4 min each) with pulsed NIR light delivered to the right forehead. The parameter space included two wavelengths (808 nm, 1064 nm), two pulsation frequencies (10 Hz, 40 Hz), and three irradiances (100, 150, 200 mW/cm2). Forehead skin tone (ITA) and sex were included as biological moderators. EEG band power (delta through gamma) was expressed as percent change from a pre-stimulus baseline. Spatiotemporal cluster-based permutation tests (10,000 permutations, FWER alpha=0.05) identified significant electrode clusters. Linear mixed-effects models with backward elimination and FDR correction (q=0.05) quantified parameter and biological contributions. ResultstPBM produced bilateral, bidirectional EEG changes: frontal gamma enhancement and posterior theta, alpha, and beta suppression, emerging gradually during stimulation and persisting post-stimulation. Wavelength qualitatively shaped the response: 808 nm drove broadband posterior suppression while 1064 nm selectively enhanced frontal gamma. Contrary to entrainment predictions, 10 Hz pulsation produced significantly larger gamma increases and theta reductions than 40 Hz. Sex was the most consistent biological modulator: females showed greater alpha suppression during stimulation and males showed greater posterior beta and gamma suppression. Irradiance and skin tone were not significant. ConclusionsPulsed forehead tPBM produces robust, parameter-dependent EEG changes that are not consistent with neural entrainment. Wavelength determines the character of the cortical response, pulsation frequency modulates its magnitude, potentially through photobiological rather than oscillatory mechanisms, and sex is a significant biological moderator. These findings contribute toward a human-specific foundation for informing optical tPBM parameter selection.

physiology↗