Molecular Ecology Resources

Species distribution models (SDMs) increasingly inform conservation and biosecurity decisions in freshwater systems, where the reliability of its uncertainty estimates matters as much as its point predictions. Ensemble SDMs derive prediction intervals from across-replicate variance, but this variance captures systematic error only when replicates disagree about it, an assumption that fails when training data are contaminated with low-accuracy records, the norm in citizen-science datasets. Whether this failure is spatially uniform or concentrates in identifiable parts of a range is unknown. Using a panel of European freshwater crayfish spanning native headwater-associated species and invasive lowland colonizers, we show that contamination-induced calibration failure is strongly spatially structured: it concentrates at stream-network headwaters, the topological tops of the network, where upstream-aggregated predictors are structurally undefined, and scales with contamination severity, replicated across four species and both dominant ensemble protocols (replicate and consensus). The failure is driven by upward prediction bias, not by intervals failing to widen: contaminated ensembles overpredict suitability in headwaters, and because the bias is shared across ensemble members, the intervals do not flag it. This is a conservation-relevant blind spot, because headwaters are both refugia for threatened native crayfish and front lines for invasion; an SDM that silently overpredicts suitability there misdirects survey and management effort toward the segments where its predictions are least trustworthy. Standard leave-one-basin-out conformal calibration, the recommended panel-wide remedy, repairs marginal coverage but leaves headwaters undercovered, because a single calibration threshold is dominated by the abundant non-headwater segments. A group-conditional (Mondrian) variant, calibrating the two populations separately, restores reliable coverage in both at no extra cost and reallocates width where it is needed. We recommend network-position-stratified calibration as a default for ensemble SDMs in dendritic freshwater systems.

AO_SCPLOWBSTRACTC_SCPLOWO_LICommunity assembly graphs (CAGs) summarize which species combinations can coexist and how single-species invasions drive transitions between them, encoding the pathways, alternative endpoints, and cycles that make up a communitys assembly history. Constructing CAGs from dynamical models requires methods that are both computationally tractable and faithful to the underlying ecological dynamics. However, existing methods rely on restrictive assumptions, such as global stability, that exclude alternative stable states and non-equilibrium dynamics known to occur in empirical systems. C_LIO_LIWe develop a computational pipeline that constructs CAGs from any generalized Lotka-Volterra model. Building on the invasion graph framework and its connection to permanence, the pipeline verifies that community dynamics are bounded, identifies which subsets of species coexist in the sense of permanence, determines which single-species invasions are dynamically realized, and assigns each community a topographic height equal to the length of the longest assembly path leading to it. We also provide a numerical algorithm to simulate the dynamics of community assembly. C_LIO_LIWe prove several general properties of the resulting graphs, including that a successful invader is never subsequently excluded and that, in the absence of assembly cycles, permanent communities can be reassembled by introducing their species one at a time in the right order. We prove that the CAG faithfully reproduces the compositional shifts seen in the numerically simulated dynamics of assembly. Applying the pipeline to three empirically based models (a New Zealand grassland, a European pasture, and a Puerto Rican ant community), we show how competition strength and mutualistic feedbacks reshape the assembly landscape and how intransitive competition generates assembly cycles. C_LIO_LIOur approach accommodates alternative stable states and non-equilibrium dynamics without requiring global stability, and it turns the long-standing landscape metaphor into a quantitative, mechanistically grounded object by resolving what "height" means. More broadly, it makes the topography of the assembly pathways measurable, providing a way to compare the historical contingency and predictability of the assembly in ecological systems. C_LI

As population-scale whole-genome sequencing datasets continue to expand, they enable genetic association studies beyond single-nucleotide variants to more complex forms of genetic variation, including classical human leukocyte antigen (HLA) alleles. The HLA region comprises nine highly polymorphic classical HLA genes in extensive linkage disequilibrium that are associated with numerous autoimmune and infectious diseases. However, unlike genome-wide association studies of single-nucleotide variants, there is no general guidance for controlling the multiple-testing burden in HLA allele association analyses. Here, we systematically evaluated the effective number of independent HLA allele tests using sequencing data from diverse genetic ancestries, analytical derivation and simulations. We show that the multiple-testing burden depends on genetic ancestry, allele frequency, and the phenotype model, but remains remarkably stable across minor allele count thresholds, corresponding to approximately 60-70% of the total number of tested HLA alleles. Simulations further demonstrate that the effective number of tests can exceed 90% under realistic disease models. Analyses of 4-field HLA alleles from long-read sequencing showed that higher typing resolution increases the number of alleles but preserves the underlying correlation structure and scales the effective number of independent tests proportionally. Our results provide practical guidance for HLA association studies and support Bonferroni correction based on the total number of tested HLA alleles as a simple and robust approximation when permutation-based approaches are impractical.

TEXT ABSTRACTCatalytic-RNA (cat-RNA) expressed from mobile DNA can record cellular events, such as the uptake of plasmids via horizontal gene transfer, by splicing a barcode onto 16S ribosomal RNA (rRNA) - a system termed RNA addressable modification (RAM). However, scaling RAM to record multiple simultaneous biological events requires large numbers of orthogonal cat-RNA whose signals reflect the biological features under investigation rather than variability arising from the barcode sequence. Here, we explore how to design orthogonal cat-RNA to record information about multiple plasmid-encoded traits in parallel. We show that cat-RNA having tRNA-derived barcodes with sequence variation in the anticodon stem-loop present greater signal consistency within Escherichia coli than mRNA-derived barcodes. When orthogonal cat-RNA designs harboring tRNA-derived barcodes were evaluated in Vibrio natriegens and Pseudomonas putida, increased variance was observed compared with Escherichia coli. Nevertheless, the signal consistency was sufficient to use these orthogonal cat-RNAs to report on the relative activities of four promoters and two origins of replication by sequencing barcoded-rRNA derived from the three organisms. These results show how RAM can be multiplexed to report on mobile DNA features in microbial communities and illustrate the importance of accounting for variability in RNA outputs when designing and interpreting multiplexed RNA barcoding data. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/738544v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@406ebaorg.highwire.dtl.DTLVardef@259751org.highwire.dtl.DTLVardef@1f1512corg.highwire.dtl.DTLVardef@8384b_HPS_FORMAT_FIGEXP M_FIG C_FIG

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.

Cortisol, our stress hormone, exerts widespread influence on neural activity. However, its influence on the aperiodic component of the electroencephalography power spectrum remains to be investigated. Given individual differences in the capacity to cope with stress and adversity, it also remains unclear whether trait resilience moderates this relationship. Hence, the present study examined whether individual differences in trait resilience moderates the association between resting cortisol and aperiodic activity. Participants (N=145) completed various self-report questionnaires (e.g., trait resilience). Electroencephalography was recorded over a 20-minute baseline period, followed by salivary cortisol collection. The results revealed a significant moderating effect of trait resilience in the occipital scalp region. Specifically, higher cortisol concentration was associated with flatter 1/f slopes amongst individuals with low trait resilience, whereas this association was reversed amongst those with high trait resilience. Overall, our findings highlight the role of individual differences in trait resilience in shaping hypothalamic-pituitary-adrenal axis-related neural dynamics.

Abstract Background: Remote clinical reviews have become an integral component of contemporary nursing practice across community and acute care settings. Nurses increasingly make autonomous clinical decisions using telephone, video, and online/digital systems, often with limited sensory information and under conditions of uncertainty. However, empirical understanding of how nurses make clinical decisions via remote reviews remains limited. Aim: To explore and understand how registered nurses (RNs) make clinical decisions about patient care via remote reviews. Methods: A convergent mixed-methods design was employed. Quantitative data (analytic quantitative sample N=53) were collected using validated questionnaires that measured decision-making processes, physician-nurse collaboration, decision-making stress, and perceived decision-making ability. Qualitative data (N=23) were generated through semi-structured interviews. Data collection took place between October 2024 and April 2025. Quantitative data were analysed using descriptive statistics, correlation, and multiple regression. Qualitative data were analysed using framework analysis. Integration was achieved through pillar-building and theory-driven synthesis and illustrated by joint display tables. Results: Most nurses demonstrated a flexible decision-making style, integrating analytical and intuitive reasoning. Both analytical and intuitive processes were positively associated with perceived decision-making ability. Physician-nurse collaboration emerged as a strong predictor of decision-making confidence, while decision-related stress was not a significant predictor. Qualitative findings identified three themes: characteristics of remote review; making adaptive decisions shaped by both internal and external constraints and enablers; and external influencing factors. The integrated findings informed a theory-informed ICE framework to illustrate how nurses make clinical decisions via remote reviews. Conclusion: Remote clinical decision-making is a dynamic cognitive-environmental process rather than a purely individual cognitive act. The ICE framework conceptualises this interaction, extending existing decision-making theories to digitally mediated care. Impact: Understanding remote decision-making supports training design, clinical governance, and the development of Artificial Intelligence-enhanced decision-support tools grounded in ecological bounded rationality. Patient or Public Contribution: Patient and public representatives contributed to stakeholder discussions that informed the development of the interview topic guide and the theoretical model. Patients or members of the public were not involved in recruitment, data collection, analysis, interpretation of findings, or preparation of the manuscript. Keywords: clinical decision-making, remote reviews, telehealth, nursing, mixed methods, ecological bounded rationality

Background: Post-stroke dysphagia (PSD) contributes to aspiration, pneumonia, malnutrition, prolonged hospitalization and mortality. We evaluated the discrimination, validity and readiness of machine learning and data-driven prediction models for PSD-related outcomes. Methods: Following a prospectively registered protocol (PROSPERO CRD420261419259), we searched PubMed/MEDLINE, Embase, Web of Science Core Collection, CINAHL and CENTRAL from inception through June 7, 2026. Eligible studies developed or validated multivariable prediction models for PSD-related outcomes in adults with stroke. We used PROBAST and PROBAST+AI to assess risk of bias and applicability and TRIPOD+AI to evaluate reporting. Area under the curve (AUC) estimates were pooled on the logit scale with random-effects models. Results: Twenty-four studies were included and ten contributed to meta-analysis. Four studies predicting early or incident PSD yielded a pooled AUC of 0.94 (95% CI 0.60-0.99; I2 = 95.6%). Pooled AUCs were 0.84 (95% CI 0.71-0.92) for aspiration or penetration-aspiration and 0.89 (95% CI 0.24-1.00) for severe dysphagia. The exploratory analysis of all ten risk-prediction models produced an AUC of 0.90 (95% CI 0.80-0.95), but heterogeneity was substantial (I2 = 90.3%) and the prediction interval was 0.51-0.99. Every study had high risk of bias because of analysis-domain concerns; calibration and external validation were uncommon. Conclusions: Reported discrimination was often high, but the evidence does not establish reliable performance in care. Independent validation, calibration, complete model reporting and clinical-impact studies are needed before these models guide post-stroke swallowing care. Keywords: Post-stroke dysphagia; Stroke; Deglutition disorders; Machine learning; Clinical prediction model; Area under the curve; Meta-analysis

Introduction Parkinson's disease (PD) is a multifactorial disorder, affecting multiple neurotransmitter systems, including the cholinergic system. Cholinergic denervation is heterogeneous across patients and difficult to predict based on clinical presentation. In this study, we assessed the sensitivity of structural MRI (sMRI) and functional MRI (fMRI) to cholinergic degeneration related to PD and to cognitive functioning in PD. We compared our results to results from previously reported [18F]Fluoroethoxybenzovesamicol ([18F]FEOBV) PET imaging, which is considered the gold standard for cholinergic imaging. Methods 34 PD patients and 10 healthy controls underwent structural T1-weighted MRI. A subset of 14 patients and 9 controls also underwent resting-state fMRI. We extracted the bilateral volumes of the nucleus basalis of Meynert (NBM) from the sMRI images. Functional connectivity (FC) from the NBM to the cortex (NBM-FC) was determined using fMRI data. Principal component analysis (PCA) was applied to reduce the dimensionality of the NBM-FC images. We assessed performances for NBM-FC in distinguishing patients from controls using stepwise logistic regression. Similarly, NBM volume was used using logistic regression. Furthermore, the relation between these measures and cognitive function in several domains was investigated with (stepwise) linear regression. Leave-one-out cross validation (LOOCV) and bootstrapping was performed to assess robustness of the results. Results NBM-FC was well able to discriminate patients from controls with an AUC of 0.84 (95% CI: 0.62-1). NBM volume showed lower performance, but was still better than chance: AUC: 0.75 (95% CI: 0.57-0.93). Significant correlations were found between 1) cognition in the attentional domain and NBM-FC (r=0.63; p=.015) and 2) global cognition and NBM volume (r=0.55, p=.001). These results were inferior to those previously reported using [18F]FEOBV tracer uptake (see Chapter 6). Bootstrapping revealed that NBM volume of only the left hemisphere was stably related to PD diagnosis and global cognition in PD patients. We found that a lower NBM-FC in specific brain areas, including the fusiform gyrus, supramarginal gyrus and dorsolateral prefrontal cortex, was related to PD diagnosis. Bootstrapping revealed no stable NBM-FC pattern related to attention. Conclusion Although MRI results were slightly inferior to [18F]FEOBV PET data, MRI may provide a cheaper and more widely available alternative for cholinergic imaging. We recommend testing the utility of MRI as predictor and monitor of cholinergic treatment effect in a longitudinal study.

Abstract Objective: To synthesize the available evidence on the association between SARS-CoV-2-related microvascular thrombosis and acute kidney injury (AKI), with emphasis on renal outcomes, mortality, and renal replacement therapy requirements. Methods: This systematic review followed the PRISMA 2020 statement and was prospectively registered in PROSPERO (CRD420251132701). PubMed/MEDLINE, Scopus, and Embase were searched for systematic reviews, including meta-analyses, and umbrella reviews investigating the association between SARS-CoV-2-related microvascular thrombosis and acute kidney injury. Two reviewers independently performed study selection, data extraction, and methodological quality assessment using AMSTAR-2 and ROBIS. Evidence was synthesized through a structured narrative synthesis supported by quantitative data extracted from the included reviews. Results: Six evidence syntheses evaluating kidney involvement, thrombotic events, and microvascular mechanisms in COVID-19 were included. AKI incidence was 9.2% (95%CI 4.6-13.9) among hospitalized patients and 32.6% (95%CI 8.5-56.6) among critically ill patients. In children with multisystem inflammatory syndrome associated with SARS-CoV-2, AKI incidence was 20% (95%CI 14-28). Microvascular or thrombotic events were associated with adverse renal outcomes (OR 2.14; 95%CI 1.32-3.48). AKI was associated with increased mortality (OR 4.68; 95%CI 1.06-20.70) and greater likelihood of renal replacement therapy requirement (OR 2.87; 95%CI 1.45-5.68). The certainty of evidence ranged from moderate to high for the principal outcomes. Conclusion: Current evidence supports an important association between microvascular thrombotic injury and COVID-19-associated AKI. These findings reinforce the relevance of endothelial dysfunction and thromboinflammatory pathways in kidney involvement during COVID-19 and highlight the need for early renal monitoring, risk stratification, and kidney-protective strategies in high-risk patients. Keywords: COVID-19; Acute Kidney Injury; Microvascular Thrombosis; SARS-CoV-2; Renal Replacement Therapy; Systematic Review

White matter lesion (WML) identification, assessment, and characterization using magnetic resonance imaging (MRI) are fundamental for diagnosis and monitoring of multiple sclerosis (MS). Portable ultra-low field (pULF) MRI at 64 millitesla (mT) has been shown to visualize WML with at least one dimension greater than 4 mm. An automated WML segmentation tool catered to pULF-MRI can provide standardized and accurate quantitative measurements of WML volume. In this study, we sought to investigate and compare the accuracy of machine-learning (ML) and deep-learning (DL) pULF MRI segmentation tools. Same-day paired pULF (64mT) and high-field (HF, 3T) MRI scans from 84 adults with MS or suspected-MS (mean age {+/-} SD: 48 {+/-} 13, 62 females) included T2-FLAIR and T1w images. Reference WML segmentations were manually annotated on pULF T2-FLAIR for all scans, with WML confirmed with registered HF T2-FLAIR. HF reference WML segmentations were created. Four automated segmentation methods were applied to pULF scans: Method for Inter-Modal Segmentation Analysis (MIMoSA), an ML algorithm trained on HF WML masks; WMH-SynthSeg, a convolutional neural network model with flexible segmentation capabilities across field strengths and resolution; nnU-Net, a DL algorithm trained on pULF reference WML masks; and Pseudo-Label Assisted nnU-Net (PLAn), a DL algorithm pre-trained on HF reference WML masks and refined with 64mT reference WML masks. Two models were trained with nnU-Net, one using T2-FLAIR images only (nnU-Net-FL) and one using T1w and T2-FLAIR images (nnU-Net-FL/T1). The same was done with PLAn, creating PLAn-FL and PLAn-FL/T1. The six automated WML segmentation outputs were compared to the manual segmentations to determine Dice Similarity Coefficient (DSC) scores. Associations of WML volume estimates with clinical measures were investigated. DSC scores with pULF reference WML masks from PLAn-FL (DSC mean {+/-} SD: 0.50 {+/-} 0.24) outperformed MIMoSA (0.24 {+/-} 0.20, p < 0.0001), WMH-SynthSeg (0.30 {+/-} 0.18, p < 0.0001), nnU-Net-FL (0.41 {+/-} 0.24, p < 0.0001), and nnU-Net-FL/T1 (0.41 {+/-} 0.26, p = 0.0004). Worse Expanded Disability Status Scale (EDSS) and Scripps Neurologic Rating Scale (SNRS) scores were correlated with higher WML volumes in the pULF and HF reference masks. They were also correlated with WML volumes derived from WHM-SynthSeg, nnU-Net-FL, nnU-Net-FL/T1, PLAn-FL, and PLAn-FL/T1, but not MIMoSA. After adjusting for age, WHM-SynthSeg, nnU-Net FL, nnU-Net-FL/T1, PLAn-FL, and PLAn-FL/T1 had significant associations with EDSS and SNRS scores. nnU-Net and PLAn performed best in segmenting WML on pULF-MRI at 64 mT, providing accurate quantitative estimates of WML burden. Moreover, WML volumes estimated by these algorithms were associated with clinical measures of disability, underscoring their utility for reflecting clinical and radiological disease severity. Given pULF-MRI's mobility and lower cost, these findings highlight its relevance in clinical trials, particularly in involving more participants who face logistical constraints and barriers.

Chronic kidney disease and heart failure disproportionately burden populations of African ancestry, yet Mendelian randomisation (MR) studies of the causal relationship between kidney function and heart failure subtypes have been conducted exclusively in European ancestry populations. We performed a forward two-sample MR analysis to evaluate the causal effect of genetically predicted estimated glomerular filtration rate (eGFR) on heart failure with preserved ejection fraction (HFpEF) and heart failure with reduced ejection fraction (HFrEF) in individuals of African ancestry. Genetic instruments were selected from an African ancestry eGFR genome-wide association study (N = 67,943) at genome-wide significance, with linkage disequilibrium clumping using an African ancestry reference panel. Heart failure subtype summary statistics were obtained from the Million Veteran Program (HFpEF: 5,379 cases / 113,041 controls; HFrEF: 9,104 cases / 109,632 controls). Six independent SNPs (F-statistics 30.5 &#8211 107.3; R&#178 = 0.62%) were retained as instruments. The primary inverse-variance weighted analysis provided no evidence of a causal effect of eGFR on HFpEF (OR 0.92, 95% CI 0.80 &#8211 1.06, p = 0.248) or HFrEF (OR 0.98, 95% CI 0.78 &#8211 1.23, p = 0.878). Sensitivity analyses were directionally consistent. There was no evidence of heterogeneity or directional pleiotropy. Minimum detectable effects at 80% power were OR 1.28 for HFpEF and OR 1.22 for HFrEF. These null findings should be interpreted as inconclusive given current power constraints; larger ancestry-matched studies are needed.

Objective: Photobiomodulation therapy has emerged as a promising modality to facilitate scar healing and pain management in dermatology and plastic surgery. However, its role in postoperative care following spine surgeries remains understudied. This double-blinded, placebo-controlled study aimed to investigate the effects of photobiomodulation in patients with chronic lower back pain undergoing lumbar decompression, with postoperative wound healing as the primary outcome and pain reduction and functional recovery as secondary outcomes. Methods: Patients were randomized to receive either active photobiomodulation braces (N=13) or placebo braces (N=12). Follow-up assessments were performed at 2, 4, 6, 8, and 12 weeks postoperatively. Outcomes included wound healing (Stony Brook Scar Evaluation Scale), back and leg pain (Visual Analog Scale), quality of life (EuroQol 5D), and functional status (Oswestry Disability Index). Results: Compared to the placebo group, the photobiomodulation treatment group had a 4.12-fold cumulative improvement in final scar scores, with significant between-group differences at postoperative weeks 6, 8, and 12 (p = 0.0062, 0.010, 0.042). Among patients with severe preoperative disability, treatment resulted in a 1.89-fold faster improvement in back pain (p=0.025) and a 1.80-fold faster improvement in ODI scores (p=0.025); and superior treatment effect on wound healing were again observed at weeks 6, 8, and 12. Among patients with poor initial scars, treatment led to a significantly better scar outcome than placebo at week 6 and a 1.94-fold faster EQ5D improvement (p=0.052), with significant gains observed as early as two weeks after surgery. There were no adverse events associated with photobiomodulation treatment. Conclusions: Photobiomodulation significantly promoted postoperative wound healing following lumbar decompression surgery, with therapeutic benefits preserved even in patients with poor baseline scar scores and functional impairment. This indicates that the efficacy of photobiomodulation is not limited by the initial scar condition or disability, supporting its broad clinical applicability. Additionally, patients with severe preoperative disability experienced greater benefits from photobiomodulation than placebo, including faster reduction in back pain and more rapid improvement in functional capacity, highlighting its role in postoperative pain management and rehabilitation. These therapeutic effects are likely mediated by photobiomodulation-induced reduction of inflammation and enhancement of tissue repair. Together, this study suggests that photobiomodulation can be a promising adjunct therapy to facilitate postoperative recovery in patients undergoing spine surgery.

Introduction Hospitalised community-acquired pneumonia (CAP) is heterogeneous in aetiology, severity, and outcome. Phenotyping and endotyping approaches offer potential to stratify patients biologically and guide targeted therapy, but require well-characterised cohorts with linked biosamples. We describe the PARIS (Pneumonia: Acute Respiratory Infection +/- Sepsis) study: a prospective observational cohort of hospitalised patients with pneumonia, designed to characterise functional outcomes and to provide a biobank for translational immunological research. Methods Adults admitted with CAP to a single NHS district general hospital were enrolled within 24 hours of admission between December 2020 and March 2022. Clinical, functional, and physiological data were collected at enrolment, hospital discharge, and 6-8 week follow-up. Serial blood samples were collected for flow cytometry, transcriptomics, pathogen DNA detection, and plasma biobanking. Results Forty-seven patients were enrolled (15 without and 32 with sepsis [SOFA >=2] at enrolment); 87% met sepsis criteria by 24 hours post enrolment. Most patients (30/47, 64%) were managed as COVID-19, microbiologically confirmed in 27. Mean age was 57 years (SD 16), 70% were male, and baseline comorbidity burden was low. Severity was moderate (median NEWS2 4 at enrolment, rising to 6 by 24 hours post enrolment; p<0.001). Mortality was 4/47 (8.5%), with 44/47 (94%) alive at hospital discharge. Median length of stay was 8 days (IQR 5.5-11). Translational samples were collected from the majority: fresh flow cytometry (44/47, 94%), transcriptomics from the sepsis subgroup (31/32, 97%), pathogen DNA sampling (35 samples received across study timepoints; see Table 5), and stored plasma (29/47, 62%). The primary outcome of functional decline (Barthel score decrease >=1.85) occurred in only 1/29 patients with paired assessments (3.4%). Persistent CRP elevation (>3 mg/L) at 6-8 week follow-up was present in 16/31 (52%) survivors with available data. Conclusions The PARIS cohort provides a well-characterised clinical platform and linked biobank to support translational studies of pneumonia and sepsis. The low rate of functional decline reflects the younger, lower-comorbidity, COVID-predominant population recruited. Primary protocol endpoints were not achieved owing to pandemic-related disruption. Data and samples underpin a programme of linked translational studies.

Background: Actigraphy-derived rest-activity rhythm (RAR) features are widely used to characterize clinical states in bipolar disorder (BD). Both mean levels and temporal variability of these features have been associated with mood episodes; however, variability measures are often statistically coupled with the mean, particularly in skewed distributions. This raises a question as to whether variability reflects a separate characteristic of the data or whether the observed association arises from statistical properties of the data. Objective: In this study, we aim to determine whether temporal variability of actigraphy-derived RAR features provides standalone information on mood episodes in BD beyond mean activity levels after accounting for mean-variance dependence. Methods: We analyzed actigraphy data from a subset of 72 participants with BD drawn from a larger longitudinal study, extracting 22 daily RAR features aggregated weekly as sample mean (MEAN) and within-week temporal variability computed as sample standard deviation (VAR). Variance-stabilizing transformations (Box-Cox or Yeo-Johnson) were applied to the entire study cohort to reduce mean-variance dependence. Associations with mood episodes and remission (mania: n=34; depression: n=58 annotated participants) were evaluated using generalized linear mixed-effects models with a logistic link function, including univariate (MEAN or VAR) and multivariate (MEAN+VAR) specifications, assessed by likelihood-based metrics and the area under the receiver operating characteristic curve (AUC). Results: Transformations reduced mean-absolute correlations from 0.43 to below 0.06. Temporal variability remained significantly associated with clinical state for 11/22 RAR features in mania and 16/22 features in depression, with all significant associations remaining after false discovery rate correction (p<0.05). Joint models showed modest incremental gains (AUC 3%-4% overall; up to 12% in mania, 7% in depression), with absolute performance remaining limited (AUC 0.50-0.66). In both mania and depression, nearly all significant variability-based regressors contributed incremental information beyond mean-based models. Only sleep duration and activity changes around wake time (+-1 hour), did not improve discrimination between mania and remission. Conclusions: Temporal variability in RAR features can be considered a standalone state marker of mood episodes not captured by mean activity. We found it to be more consistently associated with depression than mania. Its incremental discriminative contribution is modest, suggesting greater utility within multivariate or multimodal frameworks.

Background. UK clinical guidance recommends that structured risk prediction tools and risk stratification should not be used in self-harm, to predict suicide or determine who is offered treatment. Underpinning this position is the premise that routinely collected health data contain no useful predictive signal, which has received little direct scrutiny. Objective. To test whether routinely collected electronic health record data can distinguish groups at higher and lower risk of severe outcomes following paracetamol overdose. Methods. We analysed 4,095 adults presenting to NHS Lothian emergency departments with paracetamol overdose (2017-2023). Elastic-net logistic regression was fitted to 37 routinely collected electronic health record features to predict a composite of death or mental health inpatient admission at 0-7, 8-30 and 31-365 days following attendance, evaluated on a held-out 20% test set with bootstrapping. Findings. Events occurred in 5.5% of patients at 0-7 days, 2.0% at 8-30 days and 7.9% at 31-365 days, dominated by mental health admission. Bootstrap AUROC 95% confidence intervals lay above 0.5 in every window (0.65-0.82, 0.63-0.90, 0.71-0.85): models ranked patients better than chance. Calibration slopes (1.04, 1.14, 1.07) were close to one. Ranking drew primarily on mental health-related features. Conclusions. Routinely collected health data carried predictive signal for severe outcomes after paracetamol overdose, although discrimination fell short of what is needed for individual-level clinical use. Clinical implications. These models are not proposed for clinical deployment; however, treating risk prediction as a settled question will redirect research efforts, potentially excluding this patient population from machine learning advances driving improvements in care in other medical specialties.

Background with objective: Detecting EGFR mutations is critical for treating lung adenocarcinoma with highly effective targeted therapies. However, standard genetic testing is expensive, complex, and often unavailable in resource-limited settings like Bangladesh. Because elevated serum CEA has been linked to these genetic alterations, it could serve as an accessible screening tool. This study aims to evaluate the association between serum CEA levels and EGFR mutation status to determine if routine CEA testing can reliably predict these mutations and guide treatment. Methodology: In this cross-sectional analytical study, we recruited 58 patients with histologically confirmed treatment naive lung adenocarcinoma. The presence of EGFR mutations in the ctDNA was determined via ARMS (Amplification Refractory Mutation System) PCR. Patient data was statistically analyzed to assess the diagnostic correlation between serum CEA levels and the presence of EGFR mutations. Result: The overall EGFR mutation rate was 43.1% with exon 19 deletion (48%) and exon 21 mutations (44%) were the predominant types. Median serum CEA levels were significantly higher in patients with EGFR mutations compared to wild-type cases (14.6 ng/ml vs 2.8 ng/ml, p<0.001). A multivariate analysis revealed a 14% increased likelihood of an EGFR mutation for 1 ng/ml rise in serum CEA. Furthermore, serum CEA showed strong diagnostic accuracy for ctDNA samples at a 6.39 ng/ml cut-off (AUC 0.82, sensitivity 68.0%, specificity 84.8%). Conclusion: Serum CEA is a valuable, cost-effective, and non-invasive biomarker demonstrating significantly higher levels and strong diagnostic accuracy in EGFR-mutated lung adenocarcinoma compared to wild-type cases.

Background: International Classification of Diseases (ICD) codes are often used in epidemiological studies to track disease rates over time. Objective: This evaluation of ICD-code-based algorithms for electronic medical record (EMR) studies of Alzheimers disease (AD) and related dementias (ADRD) examines the impact of incorporating Centers for Medicare and Medicaid (CMS) data as an additional source of diagnostic and treatment information in Department of Veterans Affairs (VA) EMR studies. Methods: We performed a chart review of 100 VA Million Veteran Program (MVP) participants to evaluate algorithm performance. We also assessed genetic associations across algorithms in a large MVP cohort (n=396k). Results: Adding CMS data increased the number of detected cases, sensitivity, and positive predictive value, but decreased specificity and negative predictive value. Genetic analyses showed that broader (ADRD/dementia) algorithms with just VA data performed similarly to narrow (AD-focused) algorithms incorporating both VA and CMS ICD codes. Additionally, narrow AD algorithms based solely on VA data yielded the highest ORs, indicating the largest proportion of late-onset AD cases. Conclusions: We recommend using a broad (ADRD) algorithm without CMS or medication data, particularly for epidemiological studies or a strict AD algorithm including CMS and medication cases for genetic discovery of late-onset AD associations in VA EMR, and a strict AD algorithm without CMS data for applications focused solely on AD and sensitive to misspecification. Careful evaluation of algorithm performance is warranted in different EMR systems, as ICD coding practices vary by institution, as demonstrated by this comparison of VA EMR and CMS data.

Magnetic Resonance Imaging (MRI) derived brain age varies substantially between individuals, but it remains unclear whether early deviations from normal brain ageing precede future cognitive decline and whether they provide predictive value beyond conventional MRI measures. Here, we investigated whether MRI-derived brain age gap estimation (BrainAGE) identifies early structural brain ageing differences among cognitively normal individuals who later develop mild cognitive impairment (MCI) or dementia. We analysed longitudinal structural MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and replicated the main findings in the population-based Kuopio Osteoporosis Risk Factor and Prevention Study (OSTPRE). Individuals who later converted to MCI or dementia had higher BrainAGE values several years before diagnosis and, in ADNI, showed steeper longitudinal increases than stable individuals. Elevated BrainAGE values were also associated with increased risk of future conversion to MCI in cognitively healthy individuals and faster subsequent memory decline. Cross-sectional differences and the association between BrainAGE and risk of future conversion were replicated in OSTPRE. Importantly, adding BrainAGE to models including demographic, APOE4, cognitive, and MRI-derived measures consistently improved prediction of future cognitive outcomes, with the greatest benefit observed for individuals who converted after longer follow-up. These findings show that structural brain ageing begins to diverge years before the onset of MCI. BrainAGE captures this early divergence, providing complementary information beyond conventional structural MRI measures that may improve the early identification of cognitively normal individuals at increased risk of future cognitive decline when integrated with other biomarkers.

Introduction: The Diabetes Prevention Program Outcomes Study (DPPOS) is an established cohort of aging persons with pre-diabetes and type 2 diabetes with 25 years of median follow-up. In 2022 DPPOS added Alzheimer's disease (AD), and AD related dementias (ADRD) phenotyping using the National Alzheimer's Coordinating Center (NACC) Uniform Data Set (UDSv3), which included a standardized neurological examination across 25 clinical sites, administered by clinical staff and interpreted centrally by clinicians. Methods: A DPPOS video-based asynchronous neurological examination (DPPOS-VANE) was developed iteratively through consensus from research clinicians and staff feedback to harmonize with UDSv3 to identify common neurological diagnoses aside from dementia including diabetic cranial neuropathies, stroke and parkinsonism. DPPOS-VANE was designed to be conducted without direct participant contact by the examiner, reproducible, and independent of clinical skills of PCs. An iPad camera recorded the video exam, comprised of assessments of extraocular and facial movements, visual fields, speech, gross motor strength, pronator drift, praxis and parkinsonism. A 10-minute training video demonstrated the examination step-by-step with scripts and instructions in English and Spanish. Site-specific performance review, feedback, and staff certification preceded central reading of video recordings by physicians. After two years of implementation, 1286 DPPOS-VANEs led to 1284 examination reviews. Of these, 1204 (93%) were completed by having the examiner follow the standard script. Overall, 1237 examinations (96%) were delivered as planned, 41 (3%) had minor errors but were still usable, and 6 (0.4%) had major deviations in exam technique; two additional recorded evaluations were not usable as recorded videos were inaccessible due to technical errors. Each examination was completed within 10-15 minutes. Each site on average completed 51.4 examinations (range 14-92). Discussion: Engaging 55 research staff across 25 sites and 3 physician-reviewers, this study is the first to demonstrate feasibility of a VANE as an efficient neurological examination model enabled by commonly used devices. Such a multisite standardized VANE represents a novel paradigm for large epidemiological studies.