Journal of Proteome Research

Sonication is a fundamental technique in proteome sample preparation, primarily used for protein solubilization and shearing of genomic DNA. Although the mechanical shearing of DNA is well-characterized, its unintended impact on protein structural integrity remains a significant "blind spot" in high-throughput analytical workflows. In this study, we systematically investigated sonication-induced protein fragmentation by combining gel-based fractionation (PEPPI-MS) with sequence-level compositional analysis and bioinformatic mapping. Our results demonstrate that sonication does not significantly alter overall proteome identification or the recovery of membrane proteins; however, it induces extensive and non-random protein fragmentation. Sonication caused an approximately three-fold increase in the abundance of >45 kDa protein-derived fragments migrating into the <40 kDa fraction, and 1,620 high-molecular-weight (MW) proteins were uniquely detected in the lower-MW fraction upon sonication, an eight-fold increase over non-sonicated controls. Peptide-level amino acid composition analysis revealed subtle but directional shifts in the sonication-derived fragments. This residue-level signature is reinforced by two orthogonal structural analyses (MobiDB peptide-level mapping and protein-level profiling using metapredict V3 software), which show that sonication-susceptible proteins harbor more than twice the disordered content of length-matched controls (median 40% vs. 18%). This study identifies a previously unrecognized "structural bias" whereby intrinsically disordered region (IDR)-rich proteins are selectively compromised during sample preparation. Because these fragments are indistinguishable from enzymatic digestion products in conventional bottom-up proteomics, the underlying structural damage is effectively masked in global quantitative datasets, potentially distorting biological interpretations related to protein size, isoforms, and stability, particularly for IDR-rich classes, such as transcription factors and signaling molecules. We propose that optimizing and standardizing sonication parameters is essential for ensuring the accuracy and reproducibility of quantitative proteomic analyses.

Multi-omics and spatial-omics technologies are exploding in use, producing increasingly complex datasets. Existing bioinformatics tools are developing rapidly but fail to fully enforce the FAIR principles, leaving the field vulnerable to escalating issues in computational reproducibility. Here, we introduce a reproducible-by-design paradigm represented in an omics data processing package, RomicsProcessor. At its core, the "Romics_object", which is a self-contained digital artifact that encapsulates the full history of the data from the original data to the fully processed state, capturing the details of the transformative steps and the required dependencies. This architecture ensures that computational workflows are fully portable and reproducible. In this manuscript, we demonstrate RomicProcessors computational capabilities and scalability on diverse datasets, including bulk proteomics, large-scale multiplexed immunofluorescence, and multi-batch mass spectrometry imaging. Providing a robust framework for truly FAIR Data Principles-based analysis, RomicsProcessor is a blueprint for the next generation of reproducible bioinformatics tools that can dramatically accelerate discovery in multi-omics biology in the era of artificial intelligence.

N-glycolylneuraminic acid (Neu5Gc) has been repeatedly associated with human cancer, but reliable detection has remained elusive, generating controversy regarding its presence in human samples. To address this, matrix-matched calibration curves, which have been pioneered in proteomics and metabolomics for assessing changes in complex mixtures, were measured of released N-glycans at four orders of magnitude dynamic range in defined mixtures, systematically benchmarking Neu5Gc-containing N-glycan detection across multiple LC-MS platforms and sites. Orthogonally, the gold-standard analytical method, consisting of fluorescence detection of labelled monosaccharides separated by LC, was applied to the same samples, yielding absolute concentrations of Neu5Gc. LC-MS demonstrated an extended detection range of three or more orders of magnitude while retaining intact N-glycan measurement, improving assay specificity and enabling detection of the variety of Neu5Gc-bearing N-glycans. By combining orthogonal dimensions of evidence, including chromatographic separation, isotopic distribution matching, and composition-confirming MS/MS, LC-MS confidently resolved Neu5Gc signals from noise, even at low abundance. In comparison, DMB-LC-FLR was limited to two orders of magnitude dynamic range, insufficient for detection of Neu5Gc in commercially available pooled human sera. These findings strongly support that DMB-LC-FLR assay specificity and sensitivity are insufficient for Neu5Gc detection in human samples due to noise overwhelming the Neu5Gc signal. By establishing a reusable benchmarking framework for future glycomic studies, we aim to use LC-MS to improve the measurement of Neu5Gc in clinical samples.

Retinopathy of prematurity (ROP) is caused by hyperoxic exposure of prematurely born infants. The mouse model of oxygen-induced retinopathy (OIR) recapitulates pathological features of both phase I and phase II ROP. We here looked at the retinal proteins that change in response to hyperoxia in phase I of the mouse model of OIR. Using tandem mass tag labeled proteomics, we found several differentially expressed proteins (DEPs) in phase I of OIR. Of all the DEPs, we investigated the role of previously unknown protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 4-like 2 (NDUFA4L2). NDUFA4L2 protein and its paralog NDUFA4 are both mitochondrial complex I proteins; however, here we demonstrate that NDUFA4L2 changes in both phases of OIR, with no changes in its paralog NDUFA4, implying its unique function in pathophysiology of the disease. We demonstrate that NDUFA4L2 is an oxygen-sensitive protein and regulates retinal endothelial cell migration by rescuing isocitrate dehydrogenase flux impaired by hyperoxia in phase I of OIR.

Importance Sleep-disordered breathing (SDB) is common in childhood and is associated with attentional and behavioral impairments despite largely preserved sleep macrostructure and minimal abnormalities in conventional electroencephalographic measures. This discrepancy has contributed to the perception that sleep is relatively preserved in pediatric SDB and has limited understanding of the physiological mechanisms underlying morbidity. Objective To determine whether pediatric SDB is associated with disruption of the regional organization and homeostatic dynamics of slow-wave activity (SWA), a key physiological marker of sleep-dependent neural recovery and development. Design, Setting, and Participants Cross-sectional study of 62 children aged 4 to 12 years who underwent overnight polysomnography with high-density electroencephalography in a laboratory setting. Participants were recruited from clinical referrals and the community, spanning the full spectrum of SDB severity. Exposures SDB severity indexed by hypopnea index (HI), apnea-hypopnea index (AHI), and obstructive apnea index (OAI). Main Outcomes and Measures Regional electroencephalogram-derived SWA (0.5 to 4 Hz) topography and exponential decay parameters derived from frontal and posterior cortical regions. The frontal-to-posterior decay-rate ratio was evaluated as a summary measure of regional sleep homeostasis. Results In children with lower hypopnea index, SWA demonstrated the expected developmental pattern, with posterior predominance in younger children and a progressive shift toward a more balanced anterior-posterior distribution with age. Increasing HI was associated with attenuation or reversal of this spatial organization. Global SWA showed no meaningful association with SDB severity. In contrast, regional frontal and posterior decay parameters were strongly associated with HI (adjusted R2 = 0.53; p < 1e-6) but not OAI (adjusted R2 = 0.05; p = .95). The frontal-to-posterior decay-rate ratio showed the strongest association with HI {beta} = 4.15; 95% CI, 3.17-5.13; p < 1e-10; adjusted R2 = 0.55. Conclusions and Relevance Pediatric SDB was associated with regional disruption of slow-wave sleep homeostasis rather than global loss of deep sleep. These alterations affected both the spatial organization and temporal dynamics of SWA during a period of active cortical maturation and were not captured by conventional sleep metrics. Regional SWA dynamics may provide a developmentally sensitive marker of physiological disease burden in children with SDB.

Prenatal alcohol exposure (PAE) is a major cause of neurodevelopmental disorders, yet most children are diagnosed late or misdiagnosed. Neuroplacentology suggest that placental factors released into maternal and/or umbilical cord blood contribute to fetal brain development. Consistently, a preclinical inter-organ transcriptomic database revealed that PAE disrupts the expression ratio of angiogenic and inflammatory factors suggesting an angio-inflammatory response. This study aimed i) to assay, by multiplex immunoassay, angiogenic and inflammatory factors in maternal and umbilical cord blood from alcohol-consuming women and ii) to perform a maternofetal analysis according to neonatal sex. Afterwards, dysregulated factors from mothers who gave birth to females or males were submitted to STRING and ShinyGO analyses. Results showed that PAE differently altered the distribution profiles of dysregulated angiogenic and inflammatory factors in maternal and umbilical cord blood. Moreover, sex-specific differences were observed, with 36% of dysregulated proteins specific to males, 48% to females, and 16% common to both. STRING analysis revealed robust functional protein-protein interactions linking together inflammatory and angiogenic clusters while the ShinyGO analysis identified enriched pathways related to vascular shear stress. These findings provide the first maternofetal analysis of combined angiogenic and inflammatory factors from alcohol-consuming mothers.

Reactive nitrogen species (RNS), particularly peroxynitrite generated from the reaction of superoxide and nitric oxide, are implicated in thermally-induced oxidative stress but remain difficult to resolve in live coral cells. We optimized fluorescent dye strategies to directly quantify superoxide, nitric oxide, and peroxynitrite production in thermally stressed Pocillopora acuta cell suspensions. Thermal stress was associated with an increase in intracellular peroxynitrite concentration, but not in its precursors, nitric oxide and superoxide, highlighting challenges with the application of fluorescent probes and their controls to live coral cells. Compounds developed for mammalian systems often translate poorly to non-model systems such as corals: strong endogenous fluorescence and multiple membrane barriers within the coral symbiocyte, for instance, limited the function of the nitric oxide probe, DAF-2DA. Despite these limitations, the detection of peroxynitrite in live, thermally stressed P. acuta cells represents a step forward in understanding the mechanism of coral bleaching. We also outline strategies for improving the performance of commercial dyes in non-model systems, including media optimization with EDTA treatment to preserve both cell viability and probe performance.

The apnea-hypopnea index (AHI), the conventional metric of obstructive sleep apnea (OSA) severity, is typically studied using scalar summaries of sleep architecture, such as the total time spent in each sleep stage. Although clinically interpretable, these summaries fail to capture the temporal organization of overnight sleep-stage sequences and may obscure stage-specific associations with OSA severity. Modeling the complete sleep-stage trajectory provides substantially richer temporal information; however, because total sleep duration varies across individuals, sleep-stage trajectories are observed over subject-specific domains, limiting the applicability of conventional functional regression methods that assume a common observation interval. We therefore applied Variable-Domain Functional Regression (VDFR) to overnight polysomnographic data from the APPLES study (n= 1,103), treating the epoch-by-epoch sleep-stage sequence as a continuous, variable-length functional predictor of AHI. We compared three levels of sleep-stage granularity: five stages (Wakefulness, N1, N2, N3, REM), three stages (Wakefulness, Non-REM, REM), and binary staging (Wakefulness vs. Sleep). Functional sleep-stage terms were significant across all staging granularities and model structures (all p-values [&le;]0.001). Wake, N1, and N2 were positively associated with AHI, whereas N3 and REM were negatively associated, with REM exhibiting the strongest association. These effects were attenuated under coarser staging representations, highlighting the importance of preserving fine-grained sleep architecture. To our knowledge, this is the first application of VDFR to overnight polysomnographic data in OSA, showing that accommodating subject-specific sleep durations enables the identification of stage-specific temporal associations with AHI severity that are attenuated or obscured by coarser staging and conventional scalar analyses.

Background: Prolonged unsupplemented spiritual fasting (USF), complete caloric abstinence motivated by spiritual practice, is undertaken by many communities worldwide, yet its physiological consequences remain poorly characterized. No prior study has documented continuous real-time monitoring during free-living fasting beyond 10 days. Methods: We conducted a self-controlled observational study of 23 experienced Jain practitioners undergoing USF. Seventeen completed at least 8 days of fasting (11 completed eight days, six continued to 30 days); six discontinued early. Continuous glucose monitoring (CGM) and blood biomarkers at baseline (Day-0), post-fasting (Day-9), and 60-day follow-up (Day-69) were obtained. Mood was assessed daily using PANAS. Within-participant comparisons used both parametric and non-parametric t-tests. Results: CGM revealed near-complete suppression of glycaemic variability within 24-48 hours of fasting onset, sustained throughout with no clinical hypoglycaemia in either cohort. Blood biomarkers showed transient perturbation during fasting -- including rises in hepatic enzymes, bilirubin, uric acid, creatinine, and lipid fractions -- broadly reversible by follow-up (Day-69). hsCRP rose during fasting then fell below baseline at follow-up (5.52{+/-}13.67 to 3.68{+/-}13.18 mg/L, p=0.034). HDL significantly rose above baseline (45.71{+/-}112.32 to 48.97{+/-}111.19, p=0.045) and LDL similarly declined below baseline (122.33{+/-}132.10 to 106.96{+/-}131.62 mg/dL, p=0.035); and then both significantly improved by follow-up. Thyroid axis suppression fully normalized by follow-up. Psychological wellbeing was maintained throughout. Conclusions: Extended USF produces a safely reversible pattern of acute physiological adaptation with net cardiometabolic benefit. Absence of clinical hypoglycaemia during 30-day water-only USF, documented here for the first time with CGM, provides empirical grounding for future controlled trials.

Natural product synthesis by non-ribosomal peptide synthetases (NRPS) is greatly defined by the substrate selectivity of the adenylation (A) domains. Previous assays for specificity determination were mainly performed in vitro and were requiring protein purification. In this work, we developed - based on NRPS engineering - a novel in vivo assay suitable for high-throughput application named ASCR (A domain screening). Using the recently described XUT fusion sites, A domains and their upstream condensation domains were assembled as di-domains to characterized NRPS model system, which allowed detection of defined tripeptide products via mass spectrometry directly after cell culture extraction. We evaluated the assay by screening in total 54 A domains from five known and seven uncharacterized NRPS, covering a broad range organism taxonomy and GC content of the investigated NRPS-encoding genes. Additionally, we applied the assay to elucidate and confirm the structures of novel cyclic pentapeptides derived from three novel NRPS from Photorhabdus temperata K122.

Background: Short-chain fatty acids (SCFAs) are microbial metabolites with immunoregulatory properties. Human milk contains SCFAs which have been proposed as potential modulators of infant immune development. We aimed to examine associations between human milk SCFA concentrations and infant allergic disease outcomes in a high-risk cohort of infants of atopic mothers. Methods: SCFAs were measured by targeted liquid chromatography-mass spectrometry in human milk samples collected at 3 and 6 months postpartum from atopic mothers enrolled in the Infant Fish Oil Supplementation (IFOS) Study (n=147). Associations between milk SCFA concentrations and early childhood allergic disease outcomes (atopic dermatitis, food allergy, allergic rhinitis, and allergen sensitisation at 1 and 2-3 years) were examined using logistic regression. Results: Human milk SCFA concentrations were broadly stable between 3 and 6 months postpartum, except for acetate which was significantly elevated at 6 months. No significant associations were observed between human milk SCFA concentrations and any allergic disease outcome after correction for multiple comparisons (all p>0.05). Conclusions: Human milk SCFA concentrations are not associated with allergic disease outcomes up to 4 years of age. These findings suggest that oral SCFA exposure via human milk is insufficient to reduce infant allergy risk, and that gut SCFA production may be a more relevant target for future allergy prevention research.

Bipolar androgen therapy (BAT) exploits the paradoxical vulnerability of castration-resistant prostate cancer (CRPC) cells to rapid cycling between castrate and supraphysiologic androgen concentrations, but clinical BAT uses testosterone, which can also activate wild-type androgen receptor (AR) in androgen-responsive tissues, causing systemic side effects. 5{beta}-dihydrotestosterone (5{beta}-DHT) is a naturally occurring testosterone metabolite generally considered androgenically inactive because it binds wild-type AR weakly, yet its activity against clinically relevant AR mutants has not been systematically evaluated. Here, we tested whether 5{beta}-DHT and related 5{beta}-reduced testosterone metabolites activate AR signaling and growth programs in prostate cancer models that carry AR mutations. In C4-2 cells, 5{beta}-DHT and 3{beta}-etiocholanediol (3{beta}-ecdiol) increased canonical AR target genes, including KLK3 and TMPRSS2, with weaker activity than testosterone, whereas other 5{beta} metabolites showed limited activity. In androgen-responsive LNCaP and C4-2 models, 5{beta}-DHT and 3{beta}-ecdiol promoted cell growth under androgen-depleted conditions, and this effect was suppressed by enzalutamide, supporting AR dependence. RNA-seq confirmed that 5{beta}-DHT and 3{beta}-ecdiol induced androgen-response gene sets substantially overlapping with testosterone, albeit at lower transcriptional magnitude. Further, we found that 5{beta}-DHT, but not 3{beta}-ecdiol, suppresses cell proliferation of LNCaP, C4-2, and PC-3 cells stably expressing the clinically relevant AR gain-of-function mutants W742C and H875Y through activating AR-induced senescence-like features after high-dose exposure, consistent with the therapeutic logic of BAT. These findings identify 5{beta}-DHT as an overlooked mutant-AR agonist capable of BAT-like tumor suppression and propose it as a testosterone surrogate in BAT with potentially reduced systemic androgenic side effects. HighlightsO_LI5{beta}-DHT and 3{beta}-ecdiol promote AR-dependent prostate cancer cell growth C_LIO_LIBoth are weaker AR agonists than testosterone by RNA-seq and qPCR C_LIO_LISupraphysiologic 5{beta}-DHT suppresses growth via AR-mediated senescence C_LIO_LIGrowth suppression extends to AR mutants W742C and H875Y C_LIO_LI5{beta}-DHT may be a lower-androgenicity testosterone surrogate for BAT C_LI

Study Objectives Co morbid insomnia and sleep apnea (COMISA) is challenging clinically and difficult to treat. Our goal was to assess how much COMISA is the mere addition of two phenotypes or display features indicative of genuine statistical interactions. Methods A total of 152,487 patients from 240 sleep centers across 30 US states were included. Insomnia was defined as difficulty initiating/maintaining sleep with daytime fatigue/sleepiness occurring "often"/"always". OSA was defined as having an Apnea Hypopnea Index (AHI) more than 15 events/h. Modified Poisson regression was conducted to evaluate multiplicative interactions between insomnia and OSA on common comorbidities and sleep symptoms. Additive interactions were also examined. Linear regression models were used to evaluate additive interactions for PSG parameters. The false discovery rate was controlled using the Benjamini Hochberg procedure. Results After adjustment for confounders, insomnia and OSA demonstrated positive interactions for depression, chronic muscular pain, headache, subjective excessive daytime sleepiness (EDS), naps, and pre-sleep anxious and muscular tension (adjusted p < 0.05). Furthermore, insomnia and OSA demonstrated positive interactions for parameters related to respiratory disturbance, including AHI, oxygen desaturation index (ODI), respiratory disturbance index (RDI), total arousal index (AI) and respiratory AI, and negative interactions for minimum oxygen saturation and percentage of rapid eye movement stage (REM%) (adjusted p < 0.05). Furthermore, the adverse effects of insomnia and OSA on AHI, ODI, RDI and REM% were substantially amplified in males. Conclusions Our findings demonstrate that insomnia and OSA do not merely coexist but genuinely interact synergistically to amplify selected adverse clinical outcomes.

Autonomic dysfunction is a common sequela of mild traumatic brain injury (mTBI). Physical activity progression is an integral component of mTBI rehabilitation, particularly in addressing autonomic dysfunction. However, clinicians often rely on point-in-time evaluation of orthostatic and exercise intolerance to guide activity recommendations. Commercially available wearable devices (e.g., Fitbits) provide an opportunity to evaluate heart rate response to activity in a real-world setting. Previous work has used physiologic (heart rate) and activity (step count) data to identify subgroups of adults with stroke that may be used to guide activity recommendations. This method may be useful to subgroup youth post-mTBI to identify those who have abnormal physiologic responses to activity. We aimed to identify subgroups using heart rate and step count data in adolescents presenting for specialty care after diagnosed mTBI. Eighty participants aged 13-18 within six months of mTBI diagnosis were recruited to wear a Fitbit Sense 2. Data from seven days and two nights collected within fourteen days of enrollment were included. A group-based steps per minute (SPM) threshold (25th percentile; 10 SPM) and individualized heart rate threshold (20% heart rate reserve (HRR)) were used to classify each minute of active daytime data into one of four quadrants: SPM>10 & HRR>20% (QI), SPM<10 & HRR>20% (QII), SPM<10 & HRR<20% (QIII), and SPM>10 & HRR<20% (QIV). We used percentage of minutes in each quadrant, mean steps per day, percentage of minutes with zero steps, mean SPM in QI, and resting heart rate in a k-means clustering algorithm to identify subgroups. We evaluated subgroup differences by clustering variables using Kruskal-Wallis tests. Sixty-one participants were included. Three subgroups emerged: Sedentary (n=12), Active (n=23), and Atypically Elevated Heart Rate (AEHR; n=26). Subgroups varied significantly on all clustering variables (p<0.01). The Active subgroup took a high number of steps per day, had lower sedentary time, and had the highest activity intensity (mean SPM in QI). The Sedentary subgroup took fewer steps per day compared to the Active subgroup, had high sedentary time, and showed the highest resting heart rate. The AEHR subgroup took fewer steps per day compared to the Active subgroup and had high sedentary time. The AEHR subgroup also spent a higher percentage of time with an atypically high heart rate response to low levels of activity compared to the other subgroups. Our findings suggest that data from wearable devices can identify subgroups of adolescents with mTBI with distinct physiologic/physical activity profiles, which may ultimately be used to inform personalized activity prescriptions. Future work should aim to understand how the identified subgroups relate to longitudinal outcomes.

Background: Female chronic pelvic pain disorders (CPPDs) are highly prevalent and frequently accompanied by sleep disturbance and autonomic nervous system (ANS) dysregulation. Heart rate variability (HRV), a non-invasive index of ANS function, may provide an objective, physiological correlate of sleep health and can be monitored using wearable devices, enabling a continuous, scalable approach. Objectives: This study examined whether wearable-derived daily HRV metrics are associated with self-reported sleep disturbance in women with CPPD(s) compared with healthy controls, using epoch-level data and generalized additive models. Methods: We conducted a retrospective observational study using up to 90 days of data from a mobile health research app. Participants were 128 women with CPPD(s) and 63 demographically matched healthy controls, who completed a daily PROMIS-based 3-item sleep disturbance questionnaire and wore Fitbit devices that provided 5-minute HRV epochs. Primary predictors were high frequency (HF) and low frequency (LF) power and root mean square of successive differences (RMSSD), with group (CPPD vs control), daily pain severity, and menstrual status as covariates. We fit separate generalized additive mixed models (GAMMs) for each HRV metric with a nonlinear smooth term and an HRV x Group interaction. Results: Higher HF and RMSSD were associated with lower sleep disturbance scores, and these associations were stronger in controls than in the CPPD group (HF x group B {approx} -1.59, p < 0.00010; RMSSD x group B {approx} -0.58, p < 0.0001). LF showed a more complex pattern but also differed by group (B {approx} -0.531, p < 0.0001). HRV smooth terms were highly nonlinear, and models explained ~8-9% of deviance in sleep disturbances. Pain severity and menstrual bleeding were strongly associated with worse sleep. Conclusion: These findings indicate small but consistent associations between wearable-derived HRV metrics and daily sleep disturbances in women with CPPD(s) and healthy controls, with weaker associations in CPPD(s). Integrating continuous HRV with symptom tracking could support low-burden and multimodal monitoring of sleep health in chronic pelvic pain, but prospective validation is needed before HRV can be used for diagnostic or treatment response decision making.

Background: Plasma phosphorylated tau-217 (pTau-217) measurements for use in Alzheimer disease (AD) identification require thresholds to define positivity and there exist different approaches to operationally defining the boundary. We compared amyloid {beta} (AB) PET-anchored and distribution-based positivity cut-off values and explored how these mapped onto latent biomarker states. Methods: We analysed plasma pTau-217 measured in the Bio-Hermes-001 cohort (N = 990) using an immunoassay (Lilly) and mass spectrometry assay (University of Gothenburg). Gaussian mixture models were used to identify latent classes and thresholds were derived in two ways: achieving 90% specificity for AB PET positivity and exceeding the mean + 2SDs of the lowest latent class. We explore classes in reference to AB PET status and clinical diagnosis, as well as agreement between approaches using Cohen kappa for both assays. Results: In both assays, three latent biomarker classes were identified with monotonic increases in AD clinical diagnosis and AB PET positivity. PET-anchored thresholds showed lower specificity but higher sensitivity to amyloid positivity than distribution-based thresholds. Overall agreement between the approaches was acceptable (k = 0.678 for Lilly and 0.575 for University of Gothenburg), with disagreement concentrated in the intermediate latent class. Classes with the lowest and highest pTau-217 concentrations were classified consistently using both thresholds Discussion: The two thresholding approaches yielded similar classifications at both the negative and positive tail of the observed biomarker distribution, but classify intermediate concentrations differently. The boundary definition influenced pTau-217 positivity more than the analytical platform itself. Thresholding approaches may capture different pTau-217 biomarker states, therefore such methodological decisions should be grounded in the context of the intended application.

Stress-related psychiatric disorders and inflammatory bowel diseases share high co-morbidity and contribute to the symptom severity of one another. In mice, ten days of Chronic Social Defeat Stress (CSDS) is sufficient to reduce gut microbiome diversity and the relative abundance of Firmicutes, which are hallmarks of inflammatory bowel diseases. However, mechanisms by which stress causes gut microbiome dysbiosis are largely unknown. Here, we demonstrate that pharmacologically inhibiting {beta}-adrenergic receptors (ARs), which are activated by (nor)adrenaline during stress, mitigates gut dysbiosis otherwise caused by CSDS. Compared to vehicle-treated mice following CSDS, propranolol-treated mice displayed a modest increase in sociability, increased alpha diversity, and increased abundance of anaerobic commensal Clostridia. Abundance of short-chain fatty acid-producing anaerobic Firmicutes abundance correlated with sociability following CSDS across all treatments. Pharmacologically blocking -ARs during stress increased subsequent sociability, but had little effect on gut microbiome composition. Together, our findings support the hypothesis that {beta}-AR activation contributes to stress-induced changes of the gut microbiome. One Sentence SummaryPharmacologically inhibiting beta-adrenergic receptors during chronic stress mitigates reductions in anaerobic, short-chain fatty acid-producing bacteria in the gut.

Background. Post acute sequelae of COVID 19 (PASC) is clinically heterogeneous and mechanistically unresolved, and single-analyte studies have struggled to explain it. Methods. We profiled matched plasma proteomics, metabolomics and whole-blood transcriptomics at acute infection and convalescence (mean 86 days later) in a Belgian cohort, using linear mixed models, multiomic gene-set enrichment, and a degree-matched differential-correlation approach to quantify how each node's interactions were rewired between patients who developed PASC and those who recovered; seven axis proteins were additionally quantified by multiplex immunoassay as orthogonal validation. Findings. Single omic testing yielded few FDR significant features, yet multi-omic enrichment showed sustained complement cascade involvement from acute illness to follow-up in PASC. Correlation networks re-organised topologically toward C3 and lost the immunoglobulin V gene coexpression seen in recovery. The most rewired nodes, heparin cofactor II (SERPIND1), alpha 1 antitrypsin (SERPINA1), complement factor H related 5 (CFHR5), prothrombin/thrombin (F2) and immunoglobulin V gene transcripts (notably IGLV3 21), changed in their co-expression structure rather than in abundance. In multiplex validation, acute CRP was elevated in patients who developed PASC (FDR = 0.012), whereas the directly measured abundances of the network-nominated proteins were unchanged. Interpretation. These trajectory aware, cross omic networks nominate a thrombo inflammatory axis in which complement and coagulation regulation remain dysregulated in PASC at the level of wiring rather than abundance, providing a systems framework for validation and for exploring interventions at the complement coagulation platelet interface.

BACKGROUND In line with International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) recommendations for high-sensitivity cardiac troponin assays, analytical validation and reference limit assessments are required to confirm that an assay meets performance criteria. This study evaluated the analytical performance and established the 99th percentile upper reference limit (URL) for the SPINCHIP High-Sensitivity Cardiac Troponin I (SPINCHIP hs-cTnI) point-of-care assay. METHODS Analytical performance characteristics, including the limit of blank (LoB), limit of detection (LoD), and limit of quantification (LoQ), were assessed. Additionally, 1,053 plasma samples and 1,055 whole-blood samples were used to determine the URL. Imprecision around the 99th percentile URL was evaluated as part of the analytical validation. High-sensitivity criteria were assessed by confirming measurable cTnI in [&ge;]50% of healthy individuals (n=432 plasma; n=431 whole blood) and achieving imprecision <10% at the 99th percentile (plasma, n=960; whole blood, n=480). RESULTS SPINCHIP hs-cTnI demonstrated a LoB of 0.3 ng/L; LoDs of 0.8 ng/L (plasma) and 0.9 ng/L (whole blood); and LoQs of 1.1 ng/L (plasma) and 1.4 ng/L (whole blood). The analytical measuring range was 1.1-9,000 ng/L. Imprecision at the common 99th percentile URL (14 ng/L) was 5.8%; for men (URL=16 ng/L) 5.6% and for women (URL=10 ng/L) 6.3%. Greater than 85.2% (94.0% and 76.1% in men and women, respectively) of healthy individuals showed measurable cTnI above the LoD. CONCLUSIONS The SPINCHIP hs-cTnI assay meets the IFCC high-sensitivity requirements, demonstrating <10% imprecision at the 99th percentile, reliable low-concentration precision and cTnI detection in more than half of healthy individuals.

BackgroundTuberculosis remains a leading global infectious killer, with BCG offering inconsistent adult protection and rising drug-resistant strains demanding novel vaccine strategies. We report the first multi-epitope vaccine construct simultaneously targeting three previously unexplored Mycobacterium tuberculosis virulence proteins; EccB3, MycP, and polyketide synthase which collectively govern nutrient acquisition, ESX secretion integrity, and innate immune evasion. MethodsUsing a reverse vaccinology pipeline, B-cell, CTL, and HTL epitopes were predicted, filtered for allergenicity, toxicity, and IFN-{gamma} induction, then assembled into an 823-residue chimeric construct incorporating beta-defensin and PADRE adjuvants with AAY/GPGPG linkers, covering [~]90% global HLA diversity. The construct underwent AlphaFold structure prediction, 3DRefine refinement, disulfide engineering, PROCHECK/ProSA validation, ClusPro 2.0 docking against TLR1/TLR2, and C-IMMSIM immune simulation. ResultsThe construct (82.3 kDa, instability index 32.48) showed strong structural quality (94.7% favoured Ramachandran residues), stable TLR1/TLR2 binding (weighted energy: -1,371.0 kcal/mol), and robust in silico immune responses and durable memory cell formation following booster simulation. ConclusionThis computationally validated construct represents a promising multi-target TB vaccine candidate warranting experimental advancement.