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bioRxiv2024

Whole-Plant Physiological Identification and Quantification of Disease Progression

Visual estimates of plant symptoms are traditionally used to quantify disease severity. Yet, the methodologies used to assess these phenotypes are often subjective and do not allow tracking of disease progression from very early stages. Here, we hypothesized that quantitative analysis of whole-plant physiological vital functions can be used to objectively determine plant health, providing a more sensitive way to detect disease. We studied the tomato wilt that is caused by Fusarium oxysporum f. sp. lycopersici. Physiological performance of infected and non-infected tomato plants was compared using a whole-plant pot-based lysimeter functional-phenotyping system in a semi-environmentally controlled greenhouse. Water-balance traits of the plants were measured continuously and simultaneously in a quantitative manner. Infected plants exhibited early reductions in transpiration and biomass gain, which preceded visual disease symptoms. These changes in transpiration proved to be effective quantitative indicators for assessing both plant susceptibility to infection and virulence of the fungus. Physiological changes linked to fungal outgrowth and toxin release contributed to reduced hydraulic conductance during initial infection stages. The functional-phenotyping method objectively captures early-stage disease progression, advancing plant disease research and management. This approach emphasizes the potential of quantitative whole-plant physiological analysis over traditional visual estimates for understanding and detecting plant diseases.

plant biology↗

bioRxiv2024

Physiologically refined cell culture conditions uncover oncogene-dependent metabolic signatures in Ewing sarcoma spheroids

Ewing sarcoma (EwS) cell line culture largely relies on standard techniques, which do not recapitulate physiological conditions. Here, we report on a physiologically improved, feasible, and cost-efficient EwS cell culture technique employing an advanced medium composition, reduced fetal calf serum, and spheroidal growth. Functional in vitro assays and transcriptome profiling demonstrated that these refined conditions better recapitulate proliferation rates of patient tumors as well as hypoxic conditions relevant for EwS pathophysiology. Moreover, transcriptional signatures associated with the oncogenic activity of the EwS-specific FET::ETS fusion transcription factors in the refined culture conditions were shifted from proliferative towards metabolic gene signatures. The herein presented optimized physiological EwS cell culture technique provides a broadly applicable approach for enhanced in vitro modeling relevant to advancing EwS research and the validity of experimental results. MOTIVATIONCell culture remains the main platform to model EwS for research purposes. Yet, concerns exist about the limitations of standard in vitro techniques to adequately reflect physiological conditions. In this study, we refined EwS cell culture methods to increase modeling capacity while ensuring a practical and cost-effective handling, thereby broadening their applicability within the scientific community.

cancer biology↗

bioRxiv2024

Acinetobacter baumannii DacC influences cell shape, biofilm formation, and physiological fitness by manifesting DD-carboxypeptidase and β-lactamase dual-enzyme activities

With the growing threat of drug-resistant Acinetobacter baumannii, there is an urgent need to comprehensively understand the physiology of this nosocomial pathogen. As penicillin-binding proteins are attractive targets for antibacterial therapy, herein we have tried to explore the physiological roles of two putative DD-carboxypeptidases, viz., dacC and dacD in A. baumannii. Surprisingly, the deletion of dacC resulted in a reduced growth rate, loss of rod-shaped morphology, reduction in biofilm-forming ability, and enhanced susceptibility towards {beta}-lactams, whereas, the deletion of dacD had no such effect. Interestingly, ectopic expression of dacC restored the lost phenotypes. The double deletion mutant in which both dacC and dacD were absent showed properties similar to the dacC single knockout. On the other hand, cell-shape reverting efficiency in septuple PBP deleted E. coli and in vitro enzyme kinetics assessments reveal that dacD is a stronger DD-CPase as compared to dacC. The expression of dacC was in the log phase whereas dacD expression takes place in the stationary phase. In summary, we conclude that dacC encodes a dual enzyme, possessing activities of DD-CPase and {beta}-lactamase, which significantly affects the physiology of A. baumannii in various ways whereas dacD encodes a strong DD-CPase and plays a role in cell morphology, though it exerts negligible impact on other physiological aspects like intrinsic antibiotic resistance or biofilm formation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/603720v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@18820c9org.highwire.dtl.DTLVardef@208baeorg.highwire.dtl.DTLVardef@b2673eorg.highwire.dtl.DTLVardef@983aae_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Subjective salience ratings are a reliable proxy for physiological measures of arousal

Pain is an inherently salient multidimensional experience that signals potential bodily threats and promotes nocifensive behaviours. Any stimulus can be salient depending on its features and context. This poses a challenge in delineating pain-specific processes in the brain, rather than salience-driven activity. It is thus essential to salience match control (innocuous) stimuli and noxious stimuli, to remove salience effects, when aiming to delineate pain-specific mechanisms. Previous studies have salience-matched either through subjective salience ratings or the skin conductance response (SCR). The construct of salience is not intuitive, and thus matching through self-report poses challenges. SCR is used as a proxy measure that captures physiological arousal, which overcomes the nebulous construct of salience. However, SCR cannot be used to salience-match in real-time (i.e., during an experiment) and assumes an association between salience and physiological arousal elicited by painful and non-painful stimuli, but this has not been explicitly tested. To determine whether salience and physiological arousal are associated, thirty-five healthy adults experienced 30 heat pain and 30 non-painful electric stimuli of varying intensities. Stimuli were subjectively matched for salience and SCR was measured to each presentation. A linear mixed model found no differences in SCR between salience-matched heat and electric stimuli. A mediation analysis showed that salience fully mediated the relationship between stimulus intensity and SCR (proportion mediated=83%). In conclusion, salience and physiological arousal are associated, and subjective salience ratings are a suitable for salience-matching pain with non-painful stimuli. Future work can thus use subjective salience ratings to delineate pain-specific processes.

neuroscience↗

bioRxiv2024

Centimeter-scale, physiologically relevant intestinal organoids generated entirely from pluripotent stem cells

Over the past decade, intestinal organoids have shown great promise as a platform to study the development of intestine, elucidate the pathogenesis of diseases such as inflammatory bowel disease (IBD), and model physiological features of intestinal tissue for high-throughput drug screening. However, intestinal organoids derived from adult epithelial stem cells lack cellular diversity, especially those resides in the lamina propria. Intestinal organoids derived from embryonic stem (ES) cells or induced-pluripotent stem cells (iPSCs) has greater cellular diversity, but are still limited in size and physiological features such as peristalsis. In this study, we generated centimeter-scale, full-thickness, and physiologically relevant intestinal organoids in suspension culture without usage of Matrigel. Using a series of optimized culture media, multiple lineages of cells were differentiated from iPSCs and spontaneously assembled to achieve the intestinal architecture. These bubble-like organoids have a thickness of 500 microns, exhibit a mature vasculature network, and have smooth muscle-like cells to conduct regular peristalsis. In addition, adipocyte-like cells and granulocyte-like cells are also observed in these organoids, which are important in immune homeostasis. Lastly, these organoids show mature crypt structures, response to lipopolysaccharides (LPS), and increases luminal influx upon forskolin treatment, suggesting the organoids have intact epithelial integrity. Thus, this study provides a highly reproducible approach to produce large and physiologically relevant intestinal organoids that are suitable for different biomedical applications.

cell biology↗

bioRxiv2024

Transcriptomically-measured gene expression predicts physiological variation across single neurons in humans and mice

Single-cell transcriptomics measures the molecular landscape of individual neurons with unprecedented efficiency and scale. This insight has the potential to advance our understanding of the molecular basis of neuronal function, and to identify druggable targets for disease treatments. However, transcriptomics also suffers from greater measurement noise than traditional techniques (e.g., RT-PCR), which raises questions about its ability to offer insight into function at true single-cell resolution. We tested if transcriptomic data could yield insight into function of individual neurons in human and mouse neocortex by analyzing two datasets collected via Patch-Seq, a powerful technique for obtaining transcriptomic and physiology data from the same neuron. We found that computational models trained on single-cell transcriptomic data robustly predicted physiology of individual neurons. Critically, models trained on single cells outperformed those trained on cell type averages when predicting single-cell physiology. Thus, the standard approach of denoising single-cell transcriptomic data by averaging on cell types sacrifices functionally-relevant information. Our analysis also revealed novel relationships between gene expression and physiology, including a potential molecular substrate of human- mouse cross-species differences in the speed of single-neuron computation. Broadly, our findings highlight the promise of Patch-Seq for generating new insight into the molecular basis of neuronal function.

neuroscience↗

bioRxiv2024

Nitrogen nutrition impacts grapevine esca leaf symptom incidence, physiology and metabolism.

Nitrogen plays a crucial role in plant growth and defence mechanisms, yet its role in plant-pathogen interactions is complex and remains largely unexplored, especially in perennial crops. This study aimed to investigate the effects of controlled nitrogen nutrition levels on disease incidence, fungal communities, and plant physiology and metabolism. Esca is a widespread grapevine vascular disease affecting physiology, xylem integrity and metabolism. Naturally infected Vitis vinifera L. cv. Sauvignon blanc were subjected to three ammonium nitrate treatments across three seasons, resulting in reduced esca incidence under nitrogen deficiency compared with medium nutrition levels, while excess nitrogen had no significant impact. Nitrogen treatments significantly impacted vine physiology and leaf metabolites but did not affect fungal wood communities. Nitrogen deficiency significantly reduced stem diameter, photosynthesis, and leaf area, likely decreasing whole-plant transpiration, while excess nitrogen increased these factors suggesting a key role of plant transpiration in esca incidence. Additionally, nitrogen deficiency led to significantly higher production of phenylpropanoids, particularly flavonoids, in leaf metabolomes compared to the medium level. These findings highlight the pivotal role of nitrogen in the development of esca through alterations in vine morphology, physiology and metabolism. Fertilization practices may be crucial in the management of plant diseases.

plant biology↗

bioRxiv2024

A Statistically-Robust Model Of The Axomyelin Unit Under Normal Physiologic Conditions With Application To Disease States

Despite tremendous progress in characterizing the myriad cellular structures in the nervous system, a full appreciation of the interdependent and intricate interactions between these structures is as yet unfulfilled. Indeed, few more so than the interaction between the myelin internode and its ensheathed axon. More than a half-century after the ultrastructural characterization of this axomyelin unit, we lack a reliable understanding of the physiological properties, the significance and consequence of pathobiological processes, and the means to gauge success or failure of interventions designed to mitigate disease. Herein, we highlight shortcomings in the most common statistical procedures used to characterize the axomyelin unit, with particular emphasis on the underlying principles of simple linear regression. These shortcomings lead to insensitive detection and/or ambiguous interpretation of normal physiology, disease mechanisms and remedial methodologies. To address these problems, we syndicate insights from early seminal myelin studies and use a statistical model of the axomyelin unit that is established in the accompanying article. Herein, we develop and demonstrate a statistically-robust analysis pipeline with which to examine and interpret axomyelin physiology and pathobiology in two disease states, experimental autoimmune encephalomyelitis and the rumpshaker mouse model of leukodystrophy. On a cautionary note, our pipeline is a relatively simple and streamlined approach that is not necessarily a panacea for all g ratio analyses. Rather, it approximates a minimum effort needed to elucidate departures from normal physiology and to determine if more comprehensive studies may lead to deeper insights.

neuroscience↗

bioRxiv2024

Parental care modifies the role of early-life size and growth in shaping future physiology

Size and growth early in life are associated with physiological development and these traits influence fitness. Life history theory predicts that the relationship between traits reflect constraints involving allocation and acquisition of resources. Using longitudinal data from 113 wild nestling barn swallows (Hirundo rustica erythrogaster), we first characterized developmental changes in glucose metabolism, a physiological trait involved in energy mobilization and response to stress. Next, we used these data to test hypotheses from life history theory about allocation and acquisition of resources based on associations of nestling size and growth with glucose physiology and assessed whether these relationships are modified by parental care. We found that larger nestlings had higher baseline blood glucose and larger magnitude of change in glucose in response to a stressor. Further, this relationship was most pronounced among birds in nests that received the lowest amount of parental care. Given that glucose metabolism fuels activity and is critical in the vertebrate stress response, these results suggest that physiological constraints may contribute to the early-life disadvantage of being smaller, especially in the context of lower parental care. While these findings are inconsistent with a trade-off involving differential allocation of resources between life history traits, they align with the differential acquisition hypothesis.

evolutionary biology↗

bioRxiv2024

Investigation of the effect of physiological factors on resting-state and task-based functional connectivity

Understanding the brains functional network through functional connectivity (FC) is crucial for gaining deeper insights into brain functional mechanism and identifying a potential biomarker for diagnosing neurological disorders. Despite the development of various FC measures, their reliability under different conditions remains under-explored. Moreover, physiological noise can obscure true neural activity, and accordingly, introduce errors into FC patterns. This issue necessitates further investigation. In this study, we evaluate and compare the performance of various methods using Local Field Potential and Blood-Oxygen-Level-Dependent signals across different conditions. We also examine the impact of physiological artifacts on BOLD-FC results. Our comprehensive assessment covers multiple modalities of brain signals, diverse task paradigms, and varying noise levels. Our findings reveal that while Granger Causality-based methods exhibit significant limitations, particularly with BOLD data, multivariate techniques (e.g. partial correlation) demonstrate greater robustness in distinguishing between different types of connections within the network. Notably, our results indicate that physiological artifacts substantially affect FC values, leading to erroneous connectivity estimates, especially with bivariate methods. This research offers a foundational analysis of the effects of physiological artifacts on FC results and provides valuable insights for future studies.

neuroscience↗

bioRxiv2024

Protein catabolites as blood-based biomarkers of aging physiology: Findings from the Dog Aging Project

Our understanding of age-related physiology and metabolism has grown through the study of systems biology, including transcriptomics, single-cell analysis, proteomics and metabolomics. Studies in lab organisms in controlled environments, while powerful and complex, fall short of capturing the breadth of genetic and environmental variation in nature. Thus, there is now a major effort in geroscience to identify aging biomarkers and to develop aging interventions that might be applied across the diversity of humans and other free-living species. To meet this challenge, the Dog Aging Project (DAP) is designed to identify cross-sectional and longitudinal patterns of aging in complex systems, and how these are shaped by the diversity of genetic and environmental variation among companion dogs. Here we surveyed the plasma metabolome from the first year of sampling of the Precision Cohort of the DAP. By incorporating extensive metadata and whole genome sequencing information, we were able to overcome the limitations inherent in breed-based estimates of genetic and physiological effects, and to probe the physiological and dietary basis of the age-related metabolome. We identified a significant effect of age on approximately 40% of measured metabolites. Among other insights, we discovered a potentially novel biomarker of age in the post-translationally modified amino acids (ptmAAs). The ptmAAs, which can only be generated by protein hydrolysis, covaried both with age and with other biomarkers of amino acid metabolism, and in a way that was robust to diet. Clinical measures of kidney function mediated about half of the higher ptmAA levels in older dogs. This work identifies ptmAAs as robust indicators of age in dogs, and points to kidney function as a physiological mediator of age-associated variation in the plasma metabolome.

systems biology↗

bioRxiv2024

Human internal exposures of bisphenol A and six data-poor analogues predicted by physiologically based kinetic models with multimodal parameterization

BackgroundBisphenols (BP) AF, B, E, F, M, and S have been introduced as substitutes for bisphenol A (BPA) and are increasingly used in consumer products. Despite widespread human exposure and potential adverse health outcomes related to BPF, BPB, BPS, and BPAF, their physiological disposition in humans is poorly characterized, which hinders assessment of associated risks. ObjectivesOur goal was to simulate the kinetic behavior of prevalent bisphenol analogs in organs of toxicological interest. To enable predictions of physiologically relevant internal concentrations of a family of structurally similar compounds with limited available human data, we aim to establish a reproducible framework using multimodal parameterization methods. MethodsHerein we developed physiologically based kinetic (PBK) models, following oral exposure. Their parametrization was primarily based on structural, physiological and experimental values, as well as quantitative structure-activity relationship (QSAR) predictions. Outputs were evaluated against available biomonitoring data for BPA and BPS. Critical parameters were identified by sensitivity analysis and iteratively re-sampled in Monte Carlo (MC) simulations to quantify uncertainties. ResultsAmong human models parametrized for males and females of different ages, we predicted that bisphenols reached the highest concentrations in 5-year-old males. Environmentally relevant exposure levels resulted in maximum concentrations in the blood and testes for BPS, and in the thyroid for BPM. After 96 hours, steady-state concentrations were not yet reached in the breasts for BPA, BPAF, BPB, BPE, BPF and BPM. ConclusionsThe data from this study suggest significant variability in internal concentrations for identical exposures to different bisphenols analogs that further depend on age, sex and organ. This diversity in toxicokinetic behavior should be considered for health risk assessment of these substitutes.

pharmacology and toxicology↗

bioRxiv2025

Proteome analysis of daily urine samples of pregnant rats unveils developmental processes of fetus as well as physiological changes of mother rats

Significant physiological changes occur in both fetus and mother during pregnancy. Urine proteins have been shown to reflect a wide range of physiological and pathological changes in the body. To comprehensively explore the daily changes in urine proteins during pregnancy, this study employed low-abundance protein-enriched magnetic nanobeads to conduct an in-depth analysis of the daily changes in urine proteins throughout the entire pregnancy of rats. Based on the 3,455 identified urine proteins, fetal and maternal dynamic changes were observed in the pregnancy group compared to the control group, including blastocyst formation and cell division in the early stage of pregnancy, embryonic development and organ morphogenesis in the intermediate and mid-to-late stages of pregnancy, and maternal-specific change such as lactation in the late stage of pregnancy. These results indicate that urine protein can reflect the fetal and maternal dynamic physiological alterations during pregnancy, which suggests the potential value of urine protein analysis in pregnancy health monitoring. It is emphasized that the analysis focuses on the daily variations in the urine proteins, as these daily changes are expected to reveal more dynamic and detailed information about the physiological processes during pregnancy.

developmental biology↗

bioRxiv2025

Deconvoluting drug interactions based on M. tuberculosis physiologic processes:Transcriptional disaggregation of the BPaL regimen in vivo

Identification of optimal antibiotic combination treatments for tuberculosis (TB) in preclinical studies is impeded by the limited information conventional pharmacodynamic (PD) markers provide about drug interactions. Measurement of individual drug activity based on colony forming units (CFU) does not reliably predict the activity of drug combinations, potentially because one drug may affect the physiology of Mycobacterium tuberculosis (Mtb) in a way that either favors or disfavors the activity of a second drug. SEARCH-TB is a novel candidate PD approach which uses targeted in vivo transcriptional profiling to evaluate the effects of drugs on Mtb physiology. To test the capacity of SEARCH-TB to elucidate drug interactions, we deconstructed the BPaL (bedaquiline, pretomanid, linezolid) regimen in the BALB/c high-dose aerosol mouse infection model, measuring the effect of 2, 7, and 14-day treatment with drugs in monotherapy, pairwise combinations, and as a 3-drug combination. Monotherapy rapidly induced drug-specific Mtb transcriptional responses by day 2 with continued evolution over 14 days. Bedaquiline dominated pairwise combinations with both pretomanid and linezolid. The pretomanid-linezolid combination gave a blended response, inducing transcriptional profiles "intermediate" between either drug. In the 3-drug BPaL regimen, the addition of both pretomanid and linezolid to bedaquiline yielded a greater transcriptional response than expected based on pairwise results. This work demonstrates that physiologic perturbations induced by a single drug may be modified in complex ways when drugs are combined. This establishes proof of concept that SEARCH-TB is a highly granular readout of drug interactions in vivo, providing information distinct from CFU burden and suggesting a future in which regimen selection is informed by in vivo molecular measures of Mtb physiology.

genomics↗

bioRxiv2025

Tubulin transforms Tau and -synuclein condensates from pathological to physiological

Proteins phase-separate to form condensates that partition and concentrate biomolecules into membraneless compartments. These condensates can exhibit dichotomous behaviors in biology by supporting cellular physiology or instigating pathological protein aggregation1-3. Tau and - synuclein (Syn) are neuronal proteins that form heterotypic (Tau:Syn) condensates associated with both physiological and pathological processes. Tau and Syn functionally regulate microtubules8-12, but are also known to misfold and co-deposit in aggregates linked to various neurodegenerative diseases4,5,6,7, which highlights the paradoxically ambivalent effect of Tau:Syn condensation in health and disease. Here, we show that tubulin modulates Tau:Syn condensates by promoting microtubule interactions, competitively inhibiting the formation of homotypic and heterotypic pathological oligomers. In the absence of tubulin, Tau-driven protein condensation accelerates the formation of toxic Tau:Syn heterodimers and amyloid fibrils. However, tubulin partitioning into Tau:Syn condensates modulates protein interactions, promotes microtubule polymerization, and prevents Tau and Syn oligomerization and aggregation. We distinguished distinct Tau and Syn structural states adopted in tubulin-absent (pathological) and tubulin-rich (physiological) condensates, correlating compact conformations with aggregation and extended conformations with function. Furthermore, using various neuronal cell models, we showed that loss of stable microtubules, which occurs in Alzheimers disease and Parkinsons disease patients13,14, results in pathological oligomer formation and loss of neurites, and that functional condensation using an inducible optogenetic Tau construct resulted in microtubule stablization. Our results identify that tubulin is a critical modulator in switching Tau:Syn pathological condensates to physiological, mechanistically relating the loss of stable microtubules with disease progression. Tubulin restoration strategies and Tau-mediated microtubule stabilization can be potential therapies targeting both Tau-specific and Tau/Syn mixed pathologies.

biophysics↗

bioRxiv2025

Neuroscientific Insights into the Built Environment: A Systematic Review of Empirical Research on Indoor Environmental Quality, Physiological Dynamics, and Psychological Well-Being in Real-Life Contexts

The research aims to systematize the current scientific evidence on methodologies used to investigate the impact of indoor built environment on well-being, focusing on Indoor Environmental Quality (IEQ) variables such as thermal comfort, air quality, noise, and lighting. This systematic review adheres to the Joanna Briggs Institute framework and PRISMA guidelines to assess empirical studies that incorporate physiological measurements like heart rate, skin temperature, and brain activity, captured through various techniques in real-life contexts. The principal results reveal a significant relationship between the built environment and physiological as well as psychological states. For instance, thermal comfort was found to be the most commonly studied IEQ variable, affecting heart activity and skin temperature. The research also identifies the need for a shift towards using advanced technologies like Mobile Brain/Body Imaging (MoBI) for capturing real-time physiological data in natural settings. Major conclusions include the need for a multi-level, evidence-based approach that considers the dynamic interaction between the brain, body, and environment. The study advocates for the incorporation of multiple physiological signals to gain a comprehensive understanding of well-being in relation to the built environment. It also highlights gaps in current research, such as the absence of noise as a studied variable of IEQ and the need for standardized well-being assessment tools. By synthesizing these insights, the research aims to pave the way for future studies that can inform better design and policy decisions for indoor environments.

neuroscience↗

bioRxiv2025

A physiologically-based model of bile acid metabolism in humans

Altered serum BA profiles have been reported for several chronic liver diseases. However, relevant modifications in bile acid disposition are difficult to investigate mechanistically due to the interference of the various physiological processes involved at various levels of bile acid metabolism. In this regard, validated computational models represent a promising tool to understand the functional effect of disease-related alterations on bile acid composition along the gut-liver-axis through mechanistic analyses of the underlying physiological processes. We applied a physiologically-based models of bile acid metabolism in humans comprising the five predominant bile acids. The model describes various physiological aspects of bile acid metabolism including synthesis, enterohepatic circulation, hepatic and microbial conversions, postprandial gall bladder emptying as well as excretion via feces and urine. Model development was based on 39 previously published studies in patients without any liver diseases. In the future, the established model may serve as reference for analysis of the role of bile acids in health and disease.

systems biology↗

bioRxiv2025

Adaptive Reconstruction of Pupil Dynamics During Blink Data Loss: A Physiologically-Informed Exponential Recovery and Noise Modelling Framework

This paper presents a novel, physiologically inspired framework for reconstructing missing pupil data during blink-induced interruptions. Pupillometry has become integral to studies of cognition, emotion, and neural function, yet the frequent data gaps caused by blinks can compromise the accuracy of inferences drawn from pupil measurements. This approach addresses these challenges by introducing an exponential recovery model that dynamically adjusts its time constant in proportion to blink duration, thus capturing the non-linear dynamics of pupil responses more effectively than traditional interpolation methods. A localised noise estimation procedure further enhances realism by incorporating both signal-dependent and baseline noise derived from statistical properties of the data surrounding each blink. Additionally, a Savitzky-Golay filter is selectively applied to the reconstructed intervals, preserving key physiological features while mitigating high-frequency artefacts. To facilitate the implementation of our framework, we introduce PRPIP, a Python package that implements our methodology. This work demonstrates the effectiveness of this method using empirical pupil data from visual tasks, illustrating that the reconstructed signals maintain physiological fidelity across a range of blink durations. These findings underscore the potential of combining physiological principles with data-driven noise modelling to generate robust, continuous pupil traces. By offering a more accurate reconstruction of pupil size, this framework stands to advance pupillometric research in fields ranging from cognitive psychology to clinical neuroscience.

bioinformatics↗