The Cerebellum
○ Springer Science and Business Media LLC
Preprints posted in the last 7 days, ranked by how well they match The Cerebellum's content profile, based on 17 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.
Prawiroharjo, P.; Fakhri, A.; Gabrielle, A.; Martalia, V.; Rahmayani, S. A.; Wijaya, V. G.
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Aphasia diagnosis in Indonesia remains challenging due to limited culturally and linguistically appropriate instruments. Widely used tools such as the Boston Diagnostic Aphasia Examination (BDAE) and Western Aphasia Battery (WAB) are not adapted to the Indonesian context, while Tes Afasia untuk Diagnosis, Informasi, dan Rehabilitasi (TADIR) provides screening but lacks diagnostic accuracy. To address this gap, we developed the Instrumen Diagnosis dan Evaluasi Afasia (IDEA) for native Indonesian speakers and evaluated its validity, reliability, and normative cutoff values in cognitively healthy Indonesian adults. Eighty-three cognitively normal adults (screened using MoCA-Ina) with no history of neurological disease were assessed using IDEA, which evaluates six language domains. Items were adapted from existing tools and reviewed by experts. Content validity, internal consistency (Cronbachs alpha), and construct validity (Exploratory Factor Analysis) were analyzed using SPSS v25. A total of 83 participants were included (median age = 55.81 years, 54% secondary education). IDEA demonstrated good feasibility, with an average completion time of 45-60 minutes depending on participant engagement. Content validity was established by unanimous expert consensus. Construct validity showed meritorious sampling adequacy (KMO = .872) and significant sphericity (Bartletts test {chi}^2 (15) = 278.523, p<.001), supporting factor analysis. Internal consistency showed good reliability across six domains (Cronbachs = 0.896). IDEA is a valid and reliable tool for assessing aphasia in Indonesian natives. It is a culturally appropriate assessment tool which offers structured, domain-based evaluation and supports differential diagnosis of both classical and progressive aphasia syndromes. Keywords: Aphasia, Language Assessment, Indonesian, IDEA, Validity
zhong, Q.; Chen, L.; Ji, Y.; Zhu, F.; Zou, X.
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Background The global prevalence of autism spectrum disorder (ASD) has significantly increased over the past two decades. Despite substantial research advances, critical aspects, including etiology, diagnostic biomarkers, and pharmacological interventions, remain incompletely elucidated. This persistent knowledge gap warrants systematic mapping of the field's evolution to inform future research priorities. Methods A bibliometric analysis of ASD-related publications indexed in Web of Science was conducted from January 2020 to May 2025. Following a systematic deduplication process, original articles, reviews, case reports, and clinical trials were included in the analysis. The analytical framework comprised co-authorship networks, institutional collaboration patterns, national research contributions, and keyword co-occurrence structures, all of which were examined using CiteSpace (version 5.8.R3) and VOSviewer. Results After deduplication, 8,162 publications (January 2020-May 2025) were analyzed. The annual output grew steadily, confirming ASD as a sustained priority in neuroscience. Research remains academia-driven, led by the United States, with China as the second-largest contributor. Chinese institutions place greater emphasis on mechanistic and developmental phenotyping, which aligns with national priorities. These studies maintain strong methodological rigor, and their growing volume underscores the central role of ASD in translational neuroscience. Conclusion Future research on ASD should focus on strengthening case identification, refining clinical phenotyping, and expanding large-scale cohort studies to advance our understanding of its etiology and identify reliable diagnostic biomarkers. It is equally important to develop and evaluate targeted interventions for core symptoms and integrate telemedicine into service delivery models. A critical yet understudied priority is improving the quality of life for autistic individuals and their families, an area in which research globally, including in China, requires greater depth and consistency. With China's growing investment in autism research, it is well-positioned to contribute to these pressing international challenges.
Kettlety, S. A.; Akrong, E. R.; Suskauer, S. J.; Roemmich, R. T.; Slomine, B. S.; Svingos, A. M.
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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.
Chi, Z.; Alexander-Bloch, A.; Neufeld, S. A.; Wolstencroft, J.; Skuse, D.; IMAGINE-ID consortium, ; Baker, K.
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Background: Children and young people (CYP) with intellectual disability (ID) frequently have co-occurring neurodevelopmental (ND) and mental health (MH) difficulties. While copy number variants (CNVs) are identified as an important aetiology of ID, it is unclear whether and how CNV risk scores predict ND and MH characteristics within the CNV-associated ID population. Methods: We analysed data from the UK-based IMAGINE-ID cohort of CYP (aged 4-19 years) with ID and clinically-reported CNVs (N = 1,640). CNVs were annotated with Gencode 19 in ENSEMBL to calculate CNV risk scores, including summed probability of loss-of-function intolerance (pLI) and dosage sensitivity. Multivariate regression models examined the prediction of CNV variables and inheritance on ND and MH characteristics, assessed via the Development and Well-Being Assessment (DAWBA). Post-hoc analyses explored CNV variable stratification (lower vs. higher range pLI). Results: Higher summed pLI scores (indexing CNV genes' intolerance to loss of function) unexpectedly predicted fewer MH difficulties and a lower likelihood of ND diagnoses, even after accounting for demographic factors and CNV inheritance. Post-hoc analyses identified a threshold effect. Within the lower pLI range, higher pLI scores were associated with greater MH difficulties, consistent with findings from population-based samples. In contrast, within the higher pLI range, higher pLI scores were associated with fewer MH difficulties (among individuals more likely to have severe ID). Conclusion: These findings challenge the assumption that CNV genomic "risk scores" universally predict ND and MH difficulties. Instead, within CNV-associated ID, complex relationships exist between CNV risk scores, inheritance and phenotypes. These insights emphasise the necessity of integrating genomic results with familial and developmental context to understand individual vulnerabilities and support needs.
Thomson, A. R.; Hollestein, V.; Arenella, M.; Powell, H.; He, J.; Oakley, B.; Loth, E.; Holt, R.; Buitelaar, J. K.; Colomar, L.; Forde, N. J.; Bourgeron, T.; Falck-Ytter, T.; Bussu, G.; Banaschweski, T.; Aggensteiner, P. M.; Edden, R.; Charman, T.; Pretzsch, C.; Murphy, D.; Arichi, T.; Puts, N.
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Sensory processing differences are a core feature of autism, affecting 60-95% of individuals, yet the associated neural mechanisms remain unclear. An excitation-inhibition (E/I) imbalance in brain circuits has been proposed, but in vivo evidence linking genetic variation in E/I pathways, regional neurochemistry, neural circuit function, and sensory behaviour has been lacking. Here we performed a multimodal investigation in 206 individuals (130 autistic), integrating gene-set polygenic scores for excitatory glutamatergic and inhibitory gamma-aminobutyric acid (GABA)-ergic pathways, magnetic resonance spectroscopy (MRS) measures of regional GABA and Glx (glutamate + glutamine) levels, vibrotactile psychophysical measures of tactile perception, and questionnaire measures of behavioural sensory reactivity. We found that glutamatergic polygenic scores predicted thalamic glutamate levels in neurotypical but not autistic individuals, suggesting altered genotype-neurochemistry coupling in autism. Thalamic Glx:GABA levels associated with tactile perception in both groups, but with opposing directions of effect, indicating that autistic and neurotypical individuals achieve similar perceptual outcomes with potentially differing thalamocortical circuit mechanisms. Within autistic individuals, tactile perceptual differences further related to behavioural sensory reactivity. Together, these findings suggest that autistic sensory processing potentially relies on distinct circuit mechanisms linking genetic variation, neurochemistry and perception. This work thus has important implications for how sensory differences are conceptualised, studied, and interpreted, and ultimately for how interventions and support are developed.
Cole, J. J.; Cohen, J. S.; Sahin, M.; Srivastava, S.; Campbell, C. A.
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IMPORTANCE: Most United States children with neurodevelopmental disorders have not received genetic testing aligned with current guidelines. Integration of genetic counselors into non-genetics departments is a potential strategy to improve uptake, but prevalence and details of integrated care models are unknown. OBJECTIVE: To characterize availability, utilization, and perceived need for genetic counselors across non-genetics departments caring for patients with neurodevelopmental disorders DESIGN: Cross-sectional observational department-level survey SETTING: Child neurology, adult neurology, developmental pediatrics, child psychiatry, and adult psychiatry departments at Intellectual and Developmental Disabilities Research Centers PARTICIPANTS: The survey was distributed to 67 departments across 15 institutions. The departmental response rate was 52% (35/67), with at least one response from 87% (13/15) of institutions. EXPOSURE: Presence/absence of dedicated genetic counselor(s), where "dedicated" was defined as hired by the department MAIN OUTCOME(S) AND MEASURE(S): This was a descriptive study only, with no comparative statistical analyses due to the exploratory nature. RESULTS: One third of departments (34%; 12/35) reported having dedicated clinical genetic counselors. Prevalence was highest in child neurology (67%; 8/12), followed by adult neurology (40%; 2/5) and developmental pediatrics (22%; 2/9), with none in child psychiatry (0/7) or adult psychiatry (0/2). In almost all departments with genetic counselors (92%; 11/12), they directly billed for their services, which universally included pre-test counseling/consent and post-test counseling. In departments without genetic counselors, only 39% (9/23) reported providers ordered their own genetic testing. Among all departments, over half (57%) were interested in adding/increasing genetic counseling support, while 26% were unsure and 17% uninterested. Insufficient funding was the most cited barrier; only one department reported insufficient need. CONCLUSIONS AND RELEVANCE: Though currently implemented in only one third of departments, our findings suggest those with dedicated genetic counselors directly pursue genetic testing (without referring to genetics) more than those without genetic counselors. Interest in increasing or adding genetic counseling support was high, and though funding was a reported barrier, feasible funding models were described. In the context of limited medical geneticists and expanding precision therapies, alternate delivery models for neurodevelopmental genetic testing including genetic counselor integration in non-genetics departments may help to scale and sustain uptake.
Djaafara, B. A.; Elyazar, I. R.; Yosephine, P.; Surya, A.; Silalahi, F. S.; Handito, A.; Thohir, B.; Aryani, D.; Gunawan, D.; Nisa, A. K.; Prianto, E.; Samad, I.; Cook, A. R.; Huang, A. T.; Clapham, H. E.; Bhatt, S.; Mishra, S.
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Estimating dengue force of infection (FOI) is essential for understanding transmission dynamics and targeting intervention programmes, yet surveillance data in endemic settings required for estimations are often incomplete, with varying formats. We developed a Bayesian hierarchical catalytic model that jointly fits age-stratified case data, aggregate case data, and seroprevalence surveys within a single framework, incorporating external covariates to improve parameter identifiability. Synthetic validation showed that covariates alone recovered accurate FOI point estimates even when most districts contributed only aggregate data, but did so with poorly calibrated uncertainty; anchoring the model with a single seroprevalence survey was necessary to bring credible interval coverage close to nominal. Applied to 128 districts across Java and Bali, Indonesia (2016-2024), the model revealed substantial spatial heterogeneity in FOI and reporting rates. Many districts in Java exceeded the WHO-suggested seroprevalence threshold for vaccine introduction, yet were classified as low-priority when using reported incidence as prioritisation criterion, particularly in areas with weak surveillance. Model-based seroprevalence estimation, integrating multiple data sources, offers a more consistent basis for identifying high-priority districts for vaccine introduction, and is less susceptible to surveillance bias than reported incidence.
Liu, J. B.; Chen, Y.-J.; Edelen, M. O.; Pusic, A. L.; Martin, N. E.; Zeng, C.
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Purpose: Nonresponse to routinely collected patient-reported outcome measures (PROMs) threatens the representativeness of aggregated data. We characterized patient-, provider-, and clinic-level factors associated with PROMIS Global-10 nonresponse in routine radiation oncology care. Methods: In this retrospective cohort study, all adults seen at five Mass General Brigham radiation oncology clinics over one year were included. The primary outcome was patient-level nonresponse, defined as never completing the portal-administered Global-10 versus completing it at least once. Using iterative mixed-effects logistic regression, we modeled patient-, provider-, and clinic-level factors. Results: Among 12,214 patients, 71 providers, and five clinics, patient- and appointment-level response rates were 35.4% and 10.9%, with patient-level response ranging nearly fivefold across clinics (12.8% to 66.2%). In Model 1, male sex, lower education, not working, and recent surgery had higher odds of nonresponse, and longer time since diagnosis lower odds. After provider- and clinic-level factors were added, patient sex, education, and employment became nonsignificant, whereas recent surgery (adjusted odds ratio [aOR] 1.97) and longer time since diagnosis (aOR 0.46 for >12 months) persisted. A provider's historical collection rate was protective but attenuated at the clinic level. There, a later program launch (aOR 0.29) and higher historical collection rate (aOR 0.79) correlated with lower nonresponse, whereas academic versus community setting did not. Conclusions: Nonresponse to routinely collected PROMs is a multilevel phenomenon driven substantially by clinic-level implementation factors, not patient characteristics alone. Because response rate is only a proxy for representativeness, PROMs programs and PRO-based performance measures should prioritize representative collection over volume.
Weerasinghe, C.; Osowicki, J.; Simpson, J. A.; Crocker-Buque, T.; McCarthy, J.; Williams, E.; Price, D. J.
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Controlled human infection models (CHIMs) are increasingly used in infectious disease research to study pathogen dynamics and evaluate interventions under controlled conditions. However, these studies are resource-intensive and involve ethical and safety constraints, making efficient study design critical. Dose-finding is a key early component in CHIMs, where the aim is to identify a challenge dose that achieves a target infection probability. Traditional rule-based designs are commonly used but can be inefficient, motivating the use of model-based adaptive approaches such as the Bayesian Continual Reassessment Method (CRM). Although CRM has been extensively studied and widely adopted in Phase I oncology trials for identifying the maximum tolerated dose of therapeutics, its application in CHIM settings remains limited, particularly when the endpoint of interest is infection. This tutorial provides step-by-step guidance for implementing a Bayesian CRM in dose-finding CHIMs, using an oropharyngeal Neisseria gonorrhoeae challenge as a motivating case study. The framework outlines key design components, including dose-grid specification, dose-response model, prior elicitation, Bayesian updating, decision rules, and stopping criteria, with particular emphasis on a clinically interpretable parameterisation. Trial operating characteristics are evaluated through simulation studies under multiple dose-response scenarios and prior-predictive analyses, and compared with a commonly used '3+3' type rule-based design. This work highlights the advantages of Bayesian model-based designs for dose-finding in CHIMs over classic rule-based designs and provides a structured, reproducible framework for implementing CRM, supporting their application in future CHIM studies.
Prosty, C.; Butler-Laporte, G.; Brophy, J.; Frenette, C.; Loo, V.; Coburn, B.; Hota, S.; Longtin, Y.; Kong, L.; Muller, M.; Steiner, T.; Valiquette, L.; Daneman, N.; Daley, P.; Nott, C.; MacFadden, D. R.; Kandel, C.; Chen, Y.; Perez- Patrigeon, S.; Lee, T. C.; McDonald, E.
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Background and Aims The optimal treatment for first episodes and first recurrences of Clostridioides difficile infections (CDI) is unknown and there is emerging evidence for pulse and taper (P-T) regimens. Therefore, we sought to estimate the relative efficacy of treatment options. Methods MEDLINE and CENTRAL were searched from database inception to May 21, 2025 and unpublished conference abstracts were searched from recent infectious disease conferences. RCTs on the treatment of first episodes or first recurrences of CDI comparing fixed-dose or P-T regimens of fidaxomicin or vancomycin were included. The primary and secondary outcomes were 40- and 56-day CDI recurrence, respectively. A random-effects network meta-analysis on the risk ratio (RR) scale was conducted using a standard regimen (10-14 days) of vancomycin as the comparator. Treatments were ranked using the surface under the cumulative ranking curve (SUCRA). Results 8 RCTs were included comprising a total of 2181 patients. For 40-day recurrence, fidaxomicin P-T had the highest probability of ranking best (RR=0.10, 95%Confidence Interval [95%CI]=0.10-0.49, SUCRA=1.00), followed by vancomycin P-T (RR=0.49, 95%CI=0.32-0.76, SUCRA=0.61), fixed-dose fidaxomicin (RR=0.61, 95%CI=0.49-0.76, SUCRA=0.39), and, finally, fixed-dose of vancomycin (SUCRA=0.00). The treatments ranked in the same order for 56-day recurrence, though only 3 RCTs reported on this timepoint. Conclusion Vancomycin P-T, fidaxomicin P-T, and fixed-dose fidaxomicin were all superior to a fixed-dose vancomycin. Head-to-head comparative effectiveness RCTs are needed to quantify their relative effect sizes of and impact on long-term prevention of recurrent CDI.
Brochu, H. N.; Shi, Q.; Song, K.; Zhang, Q.; Munroe, J.; Harris, N. J.; Britt, N.; Zeng, Q.; Kapuria, K.; Chappell, J.; Norvell, B. M.; Peavy, L.; Williams, J. D.; Harris, A. B.; Chaitram, J.; Hutson, C. L.; Deng, J.; McGrath, D.; Boles, D.; Dale, S. E.; Gigante, C. M.; Iyer, L. K.
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Background The 2022-2023 global mpox outbreak highlighted the critical need for robust genomic surveillance capabilities to track mpox virus (MPXV) evolution and transmission dynamics. Methods Building upon our established SARS-CoV-2 sequencing infrastructure, we implemented a Molecular Loop probe-based long-read sequencing approach using Pacific Biosciences Sequel II technology for comprehensive MPXV genomic surveillance across the United States (US). From August 2024 to June 2025, we generated 326 high-quality whole genome sequences from residual mpox-positive clinical specimens collected by Labcorp across all 10 US Department of Health and Human Services regions. Results Our analysis identified two samples containing clade Ib MPXV in January and June 2025 and captured shifting trends in clade IIb diversity, with 13 distinct lineages observed. We also identified multiple instances of large (~1.6-17.6kb) deletions proximal to the inverted terminal repeats in clade IIb genomes. APOBEC3 mutation analysis indicated substantial evidence of human-to-human transmission among both clades. Further, we observed significantly higher APOBEC3-associated SNPs per kilobase (P<0.001) in clade IIb genomic variable regions relative to their central conserved region. Our assay exhibited strong reproducibility across biological replicates from individual patients and accuracy was confirmed via parallel sequencing of select specimens by US Centers for Disease Control and Prevention (CDC) using metagenomic sequencing. We also demonstrated via custom simulation that our assay discriminates all known MPXV clades and lineages, including those we have not observed in the US. Conclusions Our integrated nationwide surveillance system facilitates real-time genomic tracking of outbreak evolution, with demonstrated capacity across SARS-CoV-2 and MPXV, positioning this platform for rapid deployment during future pathogen emergence.
Kamelian, K.; Pascall, D. J.; Cheng, M. T. K.; Meng, B.; Altaf, M.; Morse, R. M.; Aggio, J. B.; Egan, D. J. S.; Chen-Xu, M.; Trivioli, G.; Sutton, B.; Richter, A.; Gonzalez-Vazquez, L. D.; Cormie, C.; Kemp, S.; Yeadon, R.; Hyatt, B.; Wong, A.; Thesin Pelamkulangara, N.; Fraser, E.; McCarthy, B.; Novaes, F.; Stott, S.; Galvin, A.; Bellis, K. L.; De Angelis, D.; Harrison, E. M.; Martin, D.; Smith, R. M.; Gupta, R. K.
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Background: Monoclonal antibodies have emerged as a prophylactic strategy to prevent symptomatic SARS-CoV-2 infection in immunocompromised individuals. However, the evolutionary and clinical implications of breakthrough infections under this regime remain unclear. Methods: A male in their 80s with a haematological/oncological diagnosis received a 2000 mg intravenous infusion of sotrovimab in March 2023 and was diagnosed with COVID-19 by RT-qPCR from a nasopharyngeal swab in August 2023. Weekly samples (n=24) were collected through February 2024 (171 days). All samples underwent whole-genome sequencing, with select mutations subjected to functional assessment. Findings: Sequencing identified the GE.1 lineage at all timepoints. An intra-host recombination event in ORF1ab (positions 8942-12458) was detected prior to 23 weeks post-detection, followed by a 14-fold increase in viral load (7.42e+06 to 1.00e+08 RNA copies/mL) and a marked shift in the viral population. E340D, a sotrovimab resistance mutation, was detected at low abundance (46%) within the first week post-infection, fluctuated over time, and was nearly fixed by week 15 (107 days) post-detection. We assessed five spike mutations - V36M, S98F, and V213G in the N-terminal domain, Y505P in the receptor-binding domain, and P681Q near the S1/S2 cleavage site - and additionally evaluated the impact of E340D. V36M conferred the highest infectivity across all cell lines, with the most significant effect in low-TMPRSS2 cells. While all mutations showed enhanced infectivity with the addition of E340D, the effect was most pronounced in mutations with lower baseline infectivity. The addition of E340D significantly decreased relative neutralizing titres for V36M, S98F, and V213G, enabling escape from neutralizing antibodies in XBB-responsive individuals, illustrating an enhanced phenotypic advantage. Patient neutralizing activity was absent pre-sotrovimab, and sotrovimab-induced neutralization was further compromised by selection of E340D. Interpretation: Sotrovimab pre-exposure prophylaxis in an immunocompromised patient did not prevent SARS-CoV-2 infection, and selected for resistant mutation E340D, with unexpected fitness consequences across non-receptor binding domain spike regions.
Gu, S.; Petrovitch, D.; Hall, O. T.; Lambert, J. W.; Kember, R. L.; Nahid, N. A.; Ma, Q.; Sprague, J. E.; McDonough, C. W.; Johnson, J. A.
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Background: Opioid use disorder (OUD) is heritable, yet most genome-wide association studies (GWAS) have focused on European populations, leaving the genetic architecture of OUD in non-European populations underexplored. Methods: We conducted GWAS of OUD across three ancestries using electronic health records and genomic data from 52,357 All of Us Research Program participants (8,912 cases; 43,445 matched opioid-exposed controls; 48.5% female). Participants were stratified into European (EUR), African (AFR), and Admixed American (AMR) ancestry groups for logistic regression GWAS, with independent replication in the Million Veteran Program. We then applied the deep-learning model AlphaGenome to predict the tissue-specific transcriptomic and splicing consequences of top risk variants across 13 reward-pathway brain regions. Results: We identified and replicated a novel DDX6 risk locus, alongside established OPRM1 and FURIN signals. AlphaGenome predicted the DDX6 regulatory allele downregulates the stress-resistance gene FOXR1 in the nucleus accumbens, while the protective OPRM1 variant (rs1799971) upregulates OPRM1 expression across reward networks. Other signals of interest included IL6R and SHISA9 (EUR); GHR (AFR); and ASTN2 (AMR). Conclusions: This study identifies DDX6 as a novel OUD risk locus, replicates associations with OPRM1 and FURIN, and highlights biologically plausible ancestry-specific signals in AFR and AMR populations. We also replicated top variants in an independent population. Finally, integrating GWAS with deep-learning annotations provides specific, localized biological hypotheses to guide future experimental validation and targeted therapeutics.
van Boven, M.; Bootsma, M. C.
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Stochastic epidemic models are a cornerstone of infectious disease epidemiology and are often used to study intervention scenarios. However, large run-to-run variability can make intervention effects difficult to estimate precisely. We revisit the epidemic Sellke construction, which assigns each individual an infection threshold for the cumulative infection hazard such that, conditional on the thresholds, the epidemic trajectory becomes deterministic. This enables coupling of simulations with and without an intervention, yielding low-variance effect estimates even when outcomes such as final size or peak incidence vary widely between runs. We develop an exact, event-driven implementation that maintains infection and recovery events in priority queues. Cumulative infection-hazard updates require O(log N) time per event, yielding overall complexity O(Elog N) for E events in a population of size N. The implementation achieves computational performance comparable to the classical Gillespie algorithm while naturally accommodating non-Markovian infectious periods and complex infectiousness profiles. We illustrate the approach using distance-dependent spread of avian influenza between poultry farms in the Netherlands and a multilayer population with households, schools, and workplaces. In both examples, coupling enables efficient within-run comparisons of intervention scenarios across stochastic realisations.
Venkatesh, S.; DelSignore, M.; Wu, X.; Morris, M.; Kerr, W. T.; Visweswaran, S.; Wang, Y.; Xia, Z.
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Background. Early diagnosis and intervention are crucial in multiple sclerosis (MS), yet diagnostic delays are common. Large language models (LLMs) such as generative pre-trained transformers (GPTs) may help streamline diagnostic workflows by extracting MS diagnostic signals from clinical notes. Objective. To derive MS diagnosis status from the first neurology note using a computable algorithm based on the 2017 McDonald criteria and applying GPT-4 for node-level reasoning within a structured decision framework. Methods. We analyzed first neurology notes from 125 randomly selected patients (including those with MS, related disorders, and controls) enrolled in a clinic cohort between 2017 and 2023. We included the clinical history and diagnostic testing sections but redacted the assessment and plan. We converted the 2017 McDonald criteria into a decision tree and provided expert-curated clinical knowledge to guide GPT-4 reasoning at each decision node. GPT-4 generated binary decisions at each node to traverse the tree and classified MS diagnoses at terminal nodes. We evaluated performance against neurologist-assessed diagnoses and characterized hallucinations (non-factual, incongruent, irrelevant, over-reliant, and logical reasoning errors). Results. In this study cohort (mean age 40{+/-}13 years; 81% women) representative of the clinic population, GPT-4 performed well in predicting MS diagnosis (84% accuracy, 79% precision, 74% recall, 91% specificity) using first neurology notes. Hallucinations occurred in 32 cases (26%), most commonly incoherence (75%) and overreliance (47%). Conclusion. A structured, LLM-guided decision framework can flag MS diagnoses from early clinical documentation. Large-scale studies are needed to mitigate hallucinations, validate this approach, and test implementation in clinical settings.
Huang, Y.-H.; Arana, K.; Rachimi, S.; Tam, H.; Spegarova, J. S.; Engelhardt, K. R.; Griffin, H.; Mee, M.; Miano, M.; Raggi, F.; Grossi, A.; Rusmini, M.; Ceccherini, I.; Dell'Orso, G.; Ferro, J.; Giarratana, M. C.; Pillai, V.; Banka, S.; Garcez, T.; Briggs, T. A.; Mellouli, F.; von Hardenberg, S.; Beier, R.; Auber, B.; Baumann, U.; Tawamie, H.; Behrens, E.; Oldridge, D. A.; Cabrera, E. C.; Xu, Y.; Ouyang, S.; Hambleton, S.; Romberg, N.; Cyster, J. G.
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The X-linked G-protein coupled receptor GPR174 is highly expressed in T and B lymphocytes and has immunoregulatory roles in mice, but its function in humans is unknown. We describe a cohort of six individuals who have function-disrupting variants in GPR174 and a clinical phenotype of lymphadenopathy and autoimmunity. Histological analysis of two patient lymph nodes revealed necrotizing lymphadenitis and lymphoproliferation resembling Kikuchi-Fujimoto disease. In-depth analysis of three patients and related carriers revealed overaccumulation of CD8 terminally differentiated effector memory cells re-expressing CD45RA (TEMRA). Patient cells and GPR174-deficient CD8 T cells generated from controls showed less repression of proliferation by the GPR174 ligand lysophosphatidylserine (lysoPS) and an effector-biased gene expression program. GPR174-deficient CD4 T cells were resistant to lysoPS-mediated suppression of IL2 production. In mice, chronic viral infection led to over-accumulation of GPR174-deficient effector CD8 T cells. We describe an inborn error of immunity associated with dysregulated lymphocyte responses that we propose predisposes to exaggerated lymphoproliferation and autoimmunity following viral infection.
Hussein, M. A.; Doshi, R.; He, L.; Reynolds, T.
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Patients and caregivers seek informational and emotional support throughout medical care, especially when interpreting unfamiliar laboratory test results. Although resources such as patient portals and online health communities (OHCs) help address questions, gaps remain. The emergence of large language models (LLMs) offers the potential to be a complementary source of support to assist patients and caregivers in understanding and using their test results. The objective of our study is to empirically compare LLM responses to patients online questions containing their laboratory test results to responses written by peers in an OHC. We compared the 519 peer replies to 122 laboratory test-related posts from an OHC to 488 responses generated from four LLMs using mixed computational and qualitative methods. LLMs frequently provided clear explanations of medical terminology and structured interpretations of numeric results but were longer and less readable. Peers offered more personalized, context-specific emotional support. Overall, LLMs have the potential to complement peer responses in OHCs, but require greater emotional depth, reasoning transparency, and alignment with community norms.
Sriram, R.; Nenadic, I.; Shahrabani, E.; Goonewardena, S.; Yao, S.; Farrell, B.; Loring, Z.; Murthy, V. L.
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We conducted a scaling evaluation of unlabeled pretraining for electrocardiogram foundation model performance. One-dimensional vision transformer masked autoencoders were pretrained across increasing ECG volumes and fine-tuned for rhythm, morphology, diagnostic, and structural heart disease tasks. Models pretrained below 400,000 ECGs failed to consistently exceed controls without self-supervised pre-training, whereas 600,000 to 800,000 ECGs improved AUROC across tasks, suggesting a minimum threshold for effective ECG representation learning.
John, A.; Pike, C.; Olga, L.; Sovio, U.; Wong, H. S.; Smith, G. C.; Aiken, C.
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Background: Children born prematurely (before 37 weeks) or admitted to the neonatal unit (NNU) are at increased risk of adverse long-term physical health outcomes. It is also recognised that there is an association with later academic performance and special educational needs, however it is not clear whether these broad risk factors could be used as stand-alone heuristics to identify children who may benefit from additional support in educational settings. We aimed to examine the associations between neonatal unit (NNU) admission and educational attainment in mid-childhood. Methods and Findings: Pregnancy data from a prospective birth cohort (Pregnancy Outcome Prediction Study, Cambridge, United Kingdom, 2008-2012) were linked to national educational outcomes (Department for Education, United Kingdom). Multivariable regression models adjusted for maternal, child, and socioeconomic factors were used to evaluate associations between (i) all NNU admissions, (ii) at term NNU admissions >48 hours, (iii) preterm birth without ongoing physical health needs, and educational outcomes at ages 5-11 years. Children who required any NNU care were more likely not to meet expected educational standards across multiple ages and domains in early and mid-childhood: age 5 early year foundation (aOR 1.64, 95% CI 1.19-2.27, p=0.003), phonics at age 6 (aOR 2.43, 95% CI 1.72-3.57, p<0.001), and at age 7 (here assessments were divided into multiple domains): reading (aOR 1.67, 95% CI 1.18-2.38, p=0.004), writing (aOR 1.72, 95% CI 1.25-2.38, p<0.001), mathematics (aOR 1.56, 95% CI 1.09-2.22, p=0.020), and science (aOR 1.85, 95% CI 1.22-2.78, p=0.003). Similar patterns were observed among both at term-born infants who stayed >48hrs in NNU (phonics assessment at age 6 aOR 2.26, 95% CI 1.51-3.36, p<0.001) and in children born preterm without long-term physical health sequelae (phonics assessment at age 6 aOR 3.07, 95% CI 1.96-4.81, p<0.001). These associations were robust to adjustment for demographic, perinatal, and socio-economic factors. By age 11, differences in academic attainment were attenuated and no longer clearly distinguishable across all exposure groups. However, there was an increased likelihood of special educational needs (SEN) at age 11 associated with any NNU admission (aOR 1.78, 95% CI 1.15-2.73, p=0.009), at term NNU admission for >48hrs (aOR 1.88, 95% CI 1.19-3.00, p=0.007), and children born preterm without long-term physical health sequelae (aOR 1.50, 95% CI 1.00-2.25, p=0.049). Predictive performance of any NNU admission for SEN at age 11 was moderate (AUC 0.70, 95% CI: 1.14-2.65, p=0.010), with balanced sensitivity and specificity and high negative predictive value. Conclusions: NNU admission, for both term and preterm infants, is associated with poorer educational outcomes and an increased likelihood of special educational needs in mid-childhood.
Aung, K. W.; Scuffell, J.; Podlasek, A.; Engamba, S.; Jones, F.; Edwards, A.; Chew-Graham, C. A.; Sanyaolu, L.; Busse-Morris, M.
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Background Post-infection conditions (PICs), such as Long Covid, are associated with heterogeneous, fluctuating symptoms that profoundly affect daily functioning. Despite moderate-certainty evidence from the NIHR-funded LISTEN trial (COV-LT2-0009) that personalised self management support improves outcomes and may reduce societal and economic impacts of Long Covid, many people living with PICs still receive condition-specific services, generic advice, or stand-alone digital tools that do not address their complex needs. Aim To map care approaches in general practice and synthesise UK evidence for PIC management. Design and setting Scoping review and online survey. Method A two-phase study was conducted: (1) a scoping review of UK evidence on PIC management in general practice; and (2) a supplementary online survey of practitioners working in UK general practice to provide contextual insights. Results The scoping review identified 32 studies focused on Long Covid. One study included a comparator group (ME/CFS). Study populations were predominantly white ethnicity and female. Evidence for non-Covid PICs in UK general practice was largely absent. The supplementary survey (n=46) provided preliminary practice-level insights. Healthcare practitioners reported varied PIC presentations, diagnostic uncertainty, limited referral pathways, inequitable access, and low confidence in managing PICs. Conclusion Evidence informing PIC management in UK general practice remains predominantly Long Covid-focused and may not reflect the range of PICs encountered in practice. While survey findings are preliminary and require confirmation in larger samples, they highlight uncertainty around PIC management. Further research is needed to evaluate whether existing Long Covid pathways should be expanded or complemented by broader PIC models. Keywords general practice; Long Covid; self-management; post-viral syndromes