Citations

Abstract Introduction While Large Language Models (LLMs) offer generative capabilities, generic models often lack domain-specific grounding, leading to hallucinations in high-stakes contexts. However, LLMs can serve as clinical decision support tools if augmented with specific domain data. This study evaluates the utility of Retrieval-Augmented Generation (RAG) applied to open-source LLMs, utilizing a curated knowledge base of authoritative sleep medicine textbooks, to quantify improvement in performance. Methods We evaluated four open-source models—Llama-70B, Llama-8B, Qwen-14B, and Qwen-235B, linked to a RAG system indexing five standard textbooks, including ICSD-3 TR. Models were tested on sleep board–style MCQs and clinical vignettes diagnostic accuracy. Performance was assessed across nine configurations derived from three factors: RAG pipeline complexity (Plain vs. Complicated), textbook preprocessing (Uncleaned vs. Cleaned/TOC-aligned), and retriever type (Dense-only vs. Hybrid). Metrics included MCQ Accuracy and the rates at which the correct diagnosis appeared as the top result or within the top 5 differential diagnosis lists for vignettes. Results RAG consistently outperformed the no-RAG baseline, yielding absolute performance gains of 5.6%–10.7% for MCQs and 8.1%–10.2% for the top diagnosis in cases across all models. For MCQs, Qwen-235B achieved the highest accuracy of 87.3% (vs. 81.7% baseline) using the Plain RAG configuration with Cleaned (TOC-aligned) Hybrid retrieval. Llama-70B followed with 83.6% in the same configuration. For case vignettes, Qwen-235B achieved a correct top diagnosis rate of 66.3% and a correct diagnosis rate within the top 5 differential diagnosis lists of 90.8% using Cleaned Hybrid retrieval configurations. Hybrid retrieval (Dense + Sparse) consistently surpassed Dense-only methods. Notably, while larger models benefited from Cleaned text, smaller models (e.g., Qwen-14B) achieved higher top diagnosis rates with Uncleaned text (57.1% vs. 51.0%), suggesting a dependency on redundant context in lower-parameter settings. Conclusion RAG significantly enhances knowledge performance of open-source LLMs in sleep medicine. Hybrid retrieval and curated, TOC-aligned knowledge bases yield optimal results for large models, whereas smaller models benefit from the redundancy of uncleaned text. These findings suggest that RAG systems can augment LLMs in domain specific knowledge for clinical decision support. Support (if any)

Abstract Introduction Narcolepsy and idiopathic hypersomnia (IH) are characterized by excessive daytime sleepiness. They can be caused by deficiency of orexin/hypocretin, a neuropeptide that regulates sleep and wakefulness. It is estimated that 1 in 2000 people in the United States of America have been diagnosed with some form of narcolepsy or idiopathic hypersomnia. Around the world, about 3 million people are narcoleptic. Little data are available regarding the lifestyle factors in these patients. In this study, we sought to find whether lifestyle factors, including diet and physical activity are associated with the severity of sleepiness in narcolepsy and idiopathic hypersomnia. Methods We collaborated with “Hypersomnia Foundation” and “Wake Up Narcolepsy” who distributed our survey to their subscribers. The survey consisted of a series of four short subsurveys asking about the substance use, diet (MiniEAT screen), exercise (IPAQ questionnaire), and daytime sleepiness (Epworth Sleepiness Scale). The survey was anonymous and included baseline characteristics, diagnosis (Narcolepsy type 1 (NT1), Narcolepsy type 2 (NT2), or Idiopathic Hypersomnia (IH)). We considered hypersomnolence and moderate to severe hypersomnolence to be present if ESS >10 and ≥15, respectively. Results We received total of 377 individual responses. Of those, 191 responders had IH, 97 had NT1 and 89 had NT2. Median age was 31 (25, 42) and 323 identified as females, 44 males and 10 others. Median ESS was 15 (12, 18), where 285 responders had ESS >10 (76%) and 194 (51%) had ESS >/=15. The ressponders with NT1 had significantly higher median ESS: 17 (12,19), than NT2: 15 (10, 17), or IH: 15(12, 17) responders (p< 0.01). In multiple univariate analyses, none of the baseline characteristics, habits (smoking, alcohol or caffeine), dietary consumption (fruit, vegetable, legumes/nuts/seeds, whole or refined grains, dairy and fish/seafood) or exercise (vigourous, moderate or walking) had significant association with the degree of responders’ subjective sleepiness. Conclusion Most survey responders continue to be excessively sleepy, particularly those with NT1. There were no apparent univariate associations of underlying hypersomnolence with the baseline characteristics, habits, diet and exercise levels. Disorders of central hypersomnolence are of complex nature without easily identifiable modifiers. Support (if any) Mayo Clinic CRISP

Abstract Patients with extremely rare pathogenic variants pose unique challenges to current healthcare systems. Nano-rare mutations have been defined as mutations with a known prevalence of <30 patients worldwide, but because of the small fraction of humans who have undergone genetic testing, neither the precise prevalence of individual mutations nor the total prevalence of patients with nano-rare mutations is known. n-Lorem is a non-profit founded in 2020 with the mission of equitably discovering, developing, and providing bespoke experimental antisense oligonucleotides (ASOs) for free, for life, to patients with nano-rare mutations that are amenable to ASO treatment. In this perspective, we provide an overview of the n-Lorem processes and systems, the characteristics of the first 329 patients who have applied for treatment for whom initial assessment was completed and suitability for ASO treatment determined, and a summary of the results of ASO treatment for patients treated to date. Detailed data on individual patients and the overall clinical safety and tolerability profiles of the ASOs for which there are clinical data are the subjects of other manuscripts.

Abstract A recent discussion that highlighted the differences between the reported effective orifice area and corresponding incidence of prosthesis-patient mismatch within the 1- and 7-year results of the PERIcardial SurGical AOrtic Valve ReplacemeNt (PERIGON) Trial of the Avalus valve has once again emphasized the instability of such measurements. The effective orifice area, calculated using the continuity equation through measurements of the left ventricular outflow tract diameter, is highly susceptible to measurement variability, as previously demonstrated in literature through both intra- and interobserver variability. To illustrate this problem, a simulation was performed in which the left ventricular outflow tract diameter was systematically altered by −2 mm, −1 mm, 0 mm, +1 mm, and +2 mm. Subsequently, the proportion of severe prosthesis-patient mismatch was recalculated and varied between 13.3%, 6.2%, 3.1% (original), 1.2%, and 0.3%, respectively. These findings demonstrate that small but clinically realistic variability in left ventricular outflow tract measurements can significantly affect the presence of prosthesis-patient mismatch. A measurement variability of 1 mm can nearly double or halve the prevalence of severe prosthesis-patient mismatch. This illustrates that prosthesis-patient mismatch, in its current form, is highly unstable and that indexed effective orifice area-based prosthesis-patient mismatch should not be used in isolation.

Summary Cancer genome sequencing is essential for understanding tumor evolution and advancing precision medicine. 1 However, reference gaps and germline variants obscure detection of small and large somatic variants and methylation in repetitive regions. 1–3 It is common for tumor cells to gain or lose chromosome arms due to somatic structural changes that occur inside highly repetitive satellite DNA sequences in the centromeres. 4 To identify the full spectrum of somatic variants, including complex rearrangements, we construct and curate near-complete, haplotype-resolved assemblies of the most recent common ancestor of an early-passage broadly-consented hypodiploid pancreatic cancer cell line and matched normal tissues. The tumor assembly completely recapitulates all 35 tumor chromosomes observed with karyotyping, with multiple translocation-induced hybrid chromosomes. The hybrid chromosomes contain putative functional dicentric and fused centromeres, nested foldback inversions causing 14 breakpoints with a haplotype switch in a single event, and centromeric satellite tandem duplications up to 136 kbp. Direct comparison of tumor and normal assembly haplotypes uncovers >7,000 variants altering >1 Mbp of sequence in repetitive regions that have been hidden by reference gaps and germline variants. 44 % of somatic small variants change representation because they alter germline variants on GRCh38, impacting mutational signatures and kataegis/omikli clusters. Most somatic LINE insertions originate from two hypomethylated non-reference germline LINE insertions, highlighting their impact on insertion mutation burden. These assemblies demonstrate that centromeric, acrocentric, and telomeric regions conventionally excluded from analysis harbor extensive somatic and epigenetic changes. Resolving complete tumor genomes enables a deeper understanding of cancer structural plasticity and the endpoints of breakage-fusion-bridge cycles. These assembled, curated paired normal-tumor benchmarks will serve as a critical foundation for developing future algorithms to characterize the most intractable regions of cancer genomes.

Abstract Chronic low‐grade inflammation characterizes type 2 diabetes mellitus (T2DM) and underlies the development of peripheral neuropathy, symptoms of which include mechanical allodynia and an exaggerated exercise pressor reflex. The purpose of this study was to determine whether mechanical allodynia and/or specific concentrations of inflammatory mediators coincide with the presence of an exaggerated exercise pressor reflex. Haemoglobin A1c was assessed to detect diabetes onset (threshold ≥5.6%) in male University of California Davis (UCD)‐T2DM rats ( n = 18). Age‐matched, healthy Sprague–Dawley rats ( n = 18) served as controls. Monthly measurements assessed mechanical allodynia (via paw withdrawal threshold), insulin and inflammatory mediators (via ELISA and multiplex kits). Paw withdrawal threshold was not different between groups prior to diabetes onset. However, by 8 weeks post‐onset, T2DM rats demonstrated a significant decrease in pain threshold compared to that before diabetes onset, which persisted for 8 weeks. This is the same period in diabetes progression as when the exercise pressor reflex is exaggerated. Prior to diabetes onset, UCD‑T2DM rats had significantly higher circulating levels of IL‑6 and IL‑1β, and these elevations persisted throughout disease progression, with only CRP showing a significant increase at 8 weeks post‑onset. These findings offer a useful foundation for further exploration into the assessments of mechanical allodynia and inflammation to determine when those with T2DM are at an increased risk for experiencing adverse cardiovascular events.

This multicenter, single-arm, phase 1/2 study evaluated the safety and efficacy of CD19-directed allogeneic chimeric-antigen-receptor (CAR) immunotherapy CTX110 in adult patients with relapsed/refractory (r/r) B-cell non-Hodgkin lymphoma (NHL). Patients received 1 or 2 treatment courses: standard lymphodepletion, followed by 1 CTX110 infusion at dose levels (DLs) 1-4 (3-60 × 107 CAR T-cells; dose escalation, N=32), or 2 infusions at DL4 on days 1 and 35 (cohort expansion, N=31). Primary endpoints in dose escalation and cohort expansion were incidence of dose-limiting toxicities and objective response rate, respectively. CTX110 was administered to 63 heavily pretreated patients: 59% primary refractory, 43% with ≥3 prior treatment lines. Among 57 patients whose first infusion was DL≥3, rates of objective and complete response (CR) were 65% and 39%, respectively. Among 22 patients achieving CR, 5 (23%) had ongoing CR at data cutoff, with 15-50 (median 34) months follow-up. The 2-infusion regimen appeared to prolong response duration compared to 1 infusion (hazard ratio 0.65). Cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) were reported in 54% and 13% of treated patients, respectively, including 2 grade ≥3 cases each. The most common grade ≥3 adverse events were neutropenia (59%), and anemia and thrombocytopenia (35% each). Serious adverse events occurred in 32% of treated patients, including CRS (14%), ICANS (8%), and febrile neutropenia (6%). In this r/r NHL population, CTX110 was well-tolerated, resulting in clinically meaningful responses at DL≥3, with a second infusion demonstrating evidence of further clinical benefit. This trial (NCT04035434) was registered at www.clinicaltrials.gov.

Background Frontotemporal dementia is an umbrella term that encompasses several clinical syndromes with impaired behavioral, language, and motor functions. These syndromes show considerable overlap in clinical features and imaging patterns. Therefore, there is a need to investigate the syndromic heterogeneity in FTD using unbiased data-driven approaches. Methods We used data-driven clustering analysis of structural magnetic resonance imaging (MRI) data on 400 patients with clinical FTD diagnoses [behavioral variant of frontotemporal dementia (bvFTD), semantic variant of primary progressive aphasia (svPPA), right temporal variant of frontotemporal dementia (rtvFTD), apraxia of speech with agrammatic aphasia (AOS-PAA), primary progressive apraxia of speech (PPAOS), progressive supranuclear palsy (PSP), corticobasal syndrome (CBS) and primary progressive aphasia who did not fit into the other diagnostic categories (PPA-other)]. MR images were w-scored relative to cognitively unimpaired individuals, and principal component analysis was performed. A clustering ensemble approach, including hierarchical algorithms, was applied to the MR-based principal components, and imaging and clinical characteristics of the clusters were investigated. Various numbers of clusters ( K = 2, 3, or 4) were evaluated. Results The K = 3 solution offered the most clinically meaningful separation of FTD syndromes. The first cluster captured mostly frontal MRI abnormalities related to the speech, language and behavioral clinical dimensions, including patients with AOS-PAA, PPAOS, PPA-other, and bvFTD. The second cluster captured mostly temporal abnormalities and included mainly patients with svPPA and rtvFTD, but also bvFTD, AOS-PAA, and PPA-other. The third cluster captured cortical and subcortical atrophy, particularly in the midbrain, and included atypical Parkinsonian syndromes, with all PSP and CBS patients captured in this cluster, as well as most PPAOS patients. Considerable overlap of clinical syndromes was noted across these clusters, whereby patients with AOS-PAA, svPPA, PPA-other, and bvFTD were captured in more than one cluster. Discussion Our findings highlight heterogeneity in FTD, which mainly exists along three axes: speech, language and behavioral deficits reflecting frontal atrophy, language deficits reflecting temporal atrophy, and motor and motor speech deficits reflecting mostly midbrain and subcortical atrophy, with cortical involvement.