Theoretical and Applied Genetics
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Preprints posted in the last 7 days, ranked by how well they match Theoretical and Applied Genetics's content profile, based on 49 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit.
Harris, Z. N.; Braley, J.; Cassetta, E.; Crain, J.; DeHaan, L.; Van Tassel, D.; Miller, A.; Rubin, M. J.
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Perennial grains represent a promising frontier for sustainable agriculture, but breeding progress is constrained by the accessibility of genotyping and the difficulty of evaluating complex traits expressed for multiple years after establishment across heterogeneous environments. Phenomic selection may help address these challenges by using inexpensive, scalable, high-dimensional phenotypes collected early in development, although the robustness of such predictions across breeding cycles remains uncertain. Here, we compared genomic selection and phenomic selection across two breeding cycles of Thinopyrum intermedium (intermediate wheatgrass; IWG; Kernza(R)), comprising approximately 2,280 individuals from maternal half-sib families evaluated across multiple field sites and years. We constructed relationship matrices from genomic markers and early-life stage phenomic data, including seed and leaf color (HSV), CropReporter multispectral reflectance and indices, and cycle-specific hyperspectral reflectance sensors. Genomic models provided the strongest predictions on average across all field traits in both cycles. Among phenomic predictors, leaf HSV was consistently the most informative, whereas CropReporter and hyperspectral data showed lower and more trait-dependent performance and seed HSV provided little predictive value. Genomic, leaf HSV, and CropReporter models transferred across breeding cycles with little apparent loss of predictive ability relative to within-cycle validation, demonstrating that their predictive signals were not restricted to a single breeding cycle. Early-life stage leaf HSV emerged as a practical, accessible tool for germplasm thinning and early-stage prioritization in perennial breeding programs. Despite limited similarity among relationship matrices, multi-relationship-matrix models rarely improved prediction beyond the stronger constituent single-relationship-matrix model. Together, these results show that early-life stage phenomic data provide reproducible information about agronomic performance expressed years later, but that predictor complexity and data integration do not guarantee improved prediction.
Pereira de Oliveira, L.; Attri, K.; Doran, L.; Leonelli, L. B.; Long, S. P.; Ainsworth, E.
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Accelerating photoprotective regulation to improve carbon assimilation is a promising strategy to increase crop productivity. Although rapid non-photochemical quenching (NPQ) relaxation has been validated as a target through metabolic engineering, it remains unclear whether conventional breeding has improved this trait. Here, we investigated whether more than a century of soybean breeding enhanced NPQ relaxation alongside light-saturated carbon assimilation and seed traits. We evaluated a historical panel of 24 soybean genotypes across vegetative and reproductive developmental stages by integrating NPQ relaxation, gas exchange parameters, xanthophyll-cycle pigment profiles, expression of key photoprotective genes (VDE, PsbS, and ZEP), seed number and seed weight. NPQ relaxation parameters were not consistently associated with genotype release year, seed number, or seed weight at either developmental stage. The only exception was the amplitude of the rapidly relaxing NPQ component (AqE), which was negatively correlated with all three variables during the reproductive stage. In contrast, genotype release year was positively associated with maximum net CO2 assimilation rate (Amax), maximum carboxylation rate of Rubisco (Vcmax), maximum electron transport rate (Jmax), seed number, and seed weight, while Amax and Vcmax were positively correlated with seed number and seed weight. These findings indicate that the greater photosynthetic capacity of modern genotypes was not accompanied by faster photoprotective response. Thus, photoprotective regulation has not kept pace with gains in photosynthetic capacity under field conditions. We conclude that rapid NPQ relaxation remains an important target for synchronizing photoprotection with the high photosynthetic capacity of modern soybean lines.
Singh, J.; Gudi, S.; Maughan, P. J.; Gill, U.; Gupta, R.
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Aegilops peregrina is a wild allotetraploid wheat wild relative and an important source of genetic diversity for stress tolerance and agronomic traits. Here, we report a subgenome-resolved, chromosome-scale reference genome assembly of a drought tolerant and stem rust resistant Ae. peregrina accession PI 604178 generated using PacBio HiFi and Hi-C sequencing. The 10.13 Gb assembly contains 98.81% of sequence anchored to 14 pseudomolecules representing the seven S and seven U chromosomes, with contig and scaffold N50 values of 25.84 and 746.48 Mb, respectively. The assembly achieved a consensus quality value of 74.61, 97.83% k-mers completeness, and 99.9% BUSCO completeness. LTR Assembly Index values of 20.43 and 18.79 for the S and U subgenomes, respectively, further supported high continuity across repeat-rich regions. Repetitive elements comprise 85.93% of chromosome-anchored assembly. We annotated 59,910 high-confidence protein-coding genes, with comparable gene representation across the two subgenomes. This reference genome provides a high-quality genomic framework for comparative analyses, characterization of important loci regulating agronomic and resilience related traits, and sequence-guided exploitation of Ae. peregrina allelic diversity for wheat improvement.
Varela, S.; Ruhter, J.; Sacks, E.; Zheng, X.; Allen, D.; Hale, A.; Landry, C.; Kuang, X.; Long, B.; Zhu, Y.; Proma, S.; Kaur, S.; Jarquin, D.; Morrison, J.; Leakey, A.
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The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (GxE) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams--including remote sensing, environmental, and management data--toward data-driven decision making in agriculture.
Ogunbawo, A. R.; Mulim, H. A.; Hidalgo, J.; Ventura, H. T.; Souza, N. O.; Oliveira, H. R.
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The exponential increase in the number of genotyped animals, combined with the availability of high-density SNP chips has introduced computational challenges for routine genomic evaluations, particularly during the construction of the genomic relationship matrix. Although higher-density SNP panels can facilitate the identification of causal mutations, their use substantially increases computational requirements without a proportional gain in genomic prediction performance. To optimize computational efficiency while maintaining accuracy of genomic predictions, this study compared five SNP selection strategies (i.e., random sampling, random sampling with inclusion of informative SNPs, linkage disequilibrium (LD)-based pruning, a Shannon entropy-based machine learning approach, and [[EQUATION]]-based prioritization) to develop reduced-density panels for Nellore cattle. Using high-density (HD) genotype data comprising 437,650 SNPs from 304,782 animals (after quality control) as reference, three reduced-density panels (25K, 45K, and 65K SNPs) panels were tested across five traits (i.e., Age at first calving, Stayability, Weaning weight, Yearling weight, Muscling) with diverse genetic architectures. Genomic estimated breeding values (GEBVs) derived from these reduced panels were compared to those obtained from the HD reference panel using Pearsons correlations, under both genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) methods. In the GBLUP model, prediction accuracy generally improved with increased marker density. Random selection with and without the informative SNPs consistently yielded the highest accuracies, whereas the [[EQUATION]]-based approach showed the lowest agreement with the HD reference across all densities. In contrast, ssGBLUP demonstrated strong robustness to marker reduction, producing uniformly high correlations {approx}1.00) across all SNP densities and selection strategies. These findings indicate that optimized low-density SNP panels maintain prediction accuracy comparable to HD panels, offering a cost-effective tool for large-scale genomic evaluations.
Ding, Y.; Zhang, P.; Ociepa, T.; Nucia, A.; Guan, H.; Kowalczyk, K.; Park, R. F.; Okon, S.
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Blumeria graminis f. sp. avenae (Bga), the causal agent of oat powdery mildew, is one of the most host-specialized members of the B. graminis species complex. Despite its agricultural importance, the lack of a high-quality reference genome has limited studies of host specialization, virulence evolution and comparative genomics in this pathogen. Here, we generated the first chromosome-scale genome assembly of Bga using an integrative approach combining long- and short-read sequencing, Hi-C scaffolding and transcriptome data. The Bga genome exhibits hallmark features of powdery mildew fungi, including extensive repeat content and low gene density. Comparative analyses revealed that genome expansion is primarily associated with historical transposable element proliferation rather than recent transpositional activity. Genome organization is consistent with a functionally stratified "one-speed" model, in which genes associated with pathogenicity, including predicted effectors and infection-responsive genes, are preferentially located in transposable element-rich regions characterized by reduced synteny conservation and extended intergenic spaces. In contrast, conserved genes are concentrated in compact genomic regions and maintain strong syntenic conservation across cereal-infecting formae speciales. Hi-C analyses demonstrated a highly structured chromatin architecture and revealed genome organization patterns associated with infection-related gene expression. Comparative genomic analyses indicated that host specialization in Bga is driven by localized diversification of a relatively small subset of genes rather than large-scale genome restructuring. These results provide the first high-quality genomic resource for Bga and offer new insights into the evolutionary mechanisms underlying host specialization in powdery mildew fungi.
Stutz, S. S.; Edquilang, R.; Bernacchi, C. J.; Ort, D. R.
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Water-use efficiency (WUE), the ratio of accumulated plant biomass to water lost through transpiration has conventionally been determined using a destructive single-point measurement. Recent advances in high-throughput phenotyping now enable repeated, non-destructive estimation of biomass and WUE. However, these digital measurements must be statistically validated against conventional destructive methods to validate their use as reliable proxies. Therefore, we compared digital biomass determined point clouds produced from multispectral camera scanners with destructive harvests across eight harvests using Samsun tobacco grown under both drought and high-water conditions. WUE efficiency, calculated using the digital biomass estimated from a point cloud and gravimetric water use determinations, were compared to destructive harvest determinations. The coefficient of variation (CV) showed there were no significant differences in digital and destructive measurements for either biomass or WUE. Indicating that digital measurements can be used in place of destructive measurements. Drought plants used significantly less water and were significantly smaller than high-water plants from Harvests 4 through 8. However, there were no significant differences in the ratio of evapotranspiration to leaf area or WUE, indicating that drought plants were simply smaller and used less water than the high-water plants. This work validates that estimating plant biomass from a digital point coupled with continuous gravimetric determination of water use provides a reliable nondestructive measure of WUE in high-throughput measurements across the full plant life cycle.
Yamada, Y.; Tatsumi, Y.; Inagaki, A.; Shitan, N.; Sato, F.
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Although the biosynthetic pathways of benzylisoquinoline alkaloids (BIAs) have been extensively investigated in several plant species, their transcriptional regulatory mechanisms remain only partially understood. Jasmonate (JA)-responsive group IX APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors (TFs) are well-known regulators of specialized plant metabolism, including the biosynthesis of various alkaloids. However, their specific roles in BIA biosynthesis remain largely elusive. Here, we isolated five novel group IX AP2/ERF TFs, designated Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE1-5), from Coptis japonica. Phylogenetic analysis revealed that Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE) proteins belong to subclades distinct from group IXa, which contains well-known AP2/ERF TFs involved in alkaloid biosynthesis. Transient expression analyses in C. japonica protoplasts demonstrated that certain BJEs, particularly CjBJE3 and CjBJE5, positively regulated BIA biosynthetic genes through a mutual regulatory network among BJE members. Moreover, CjBJE3 expression was regulated by CjbHLH1, a unique-type basic helix-loop-helix (bHLH) TF specific to BIA-producing plants. Furthermore, heterologous expression of CjBJE3 and CjBJE5 in cultured Eschscholzia californica cells significantly enhanced the overall BIA production, particularly by increasing end-product benzophenanthridine BIAs, highlighting several uncharacterized biosynthetic genes clustered in the genome. Our findings suggest that BIA-producing species have developed a specific regulatory network comprised of CjbHLH1 and BJE TFs, providing valuable clues for identifying novel biosynthetic enzymes.
Chaturvedi, R. R.; Gracner, T.; Perez-Arce, F.; Suen, S.-c.; Jin, J.; Orriens, B.; Pacula, R. L.; Sexton Ward, A.; Haile, R.; Kapteyn, A.
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Importance: Evidence on GLP-1/GIP therapies is largely derived from trials enrolling selected populations or medical records that miss utilization outside healthcare channels. No nationally representative cohort has characterized real-world uptake, indications, and access. Objective: To characterize GLP-1/GIP prevalence, indication, clinical profile, and access. Design: Prospective cohort study with three GLP-1/GIP surveillance waves (March 2024, December 2024, October 2025). Setting: The Understanding America Study, an address-based, nationally representative panel of approximately 15,000 US adults aged 18+ years initiated in 2014. Participants: UAS participants responding to at least one surveillance wave (n=9150). Exposures: GLP-1/GIP use status (never vs any use, comprising current and former use), self-reported primary indication (diabetes, weight loss, or other), and access pathway (traditional vs non-traditional). Main Outcomes and Measures: Survey-weighted prevalence of GLP-1/GIP use, overall and by indication and access pathway; sociodemographic, cardiometabolic, treatment, and access characteristics; and smartwatch-derived resting heart rate, heart rate variability, maximum activity heart rate, step count, and sleep duration and variability. Results: Among n=9150 adults (1274 with any use; 60.9% female; median age 53 years), weighted prevalence increased 46%, from 8.2% (March 2024) to 12.0% (October 2025) representing 32 million. Weight-loss indications grew, reaching nearly half of use (4.1% to 5.6%); diabetes-indicated use was stable (5.3% to 5.4%). Users carried high cardiometabolic burden (obesity, 68.2%; diabetes, 53.6%) but diverged by indication: diabetes-indicated users were older (median, 59 vs 49 years), whereas weight-loss-indicated users were more often female (69.9% vs 51.3%) and healthier. One in three users (~9 million) had non-traditional access, especially in weight-loss-indicated users, of whom 33% had no conventional prescription; 41% used compounding, online, or foreign pharmacies; and, 43% lacked coverage. Non-traditional users were five times as likely to report an unlisted, likely compounded formulation (19.8% vs 4.1%). All p<0.05. Conclusions and Relevance: Real-world GLP-1/GIP use has grown rapidly and diversified substantially in indication, access, and population profile. One in 3 users obtained treatment through nontraditional channels largely invisible to claims data, raising long-term safety, efficacy, and coverage questions. GLIMMER provides a public, nationally representative longitudinal evidence base for future payer and provider decisions.
Chowdhury, A. R.; Chowdhury, B.
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Background: Consumer use of AI chatbots for health advice is rising, yet triage safety relative to established services remains unclear. Australia's Healthdirect, a government-backed symptom checker with 2.4 million uses in FY2024-25, remains unevaluated against frontier large language models (LLMs), and whether premium subscriptions improve triage safety remains unexplored. This study compared the triage accuracy and safety of Healthdirect against six LLM configurations across ChatGPT, Claude, and Gemini, assessed whether paid subscriptions improve triage safety, and characterised each system's error patterns. Methods: Forty-five clinical vignettes from the Semigran et al. benchmark spanning emergency, non-emergent, and self-care categories (15 each) were evaluated across seven systems. Healthdirect was tested following a seven-rule interaction protocol. LLMs were evaluated using first-person patient-language prompts under free-tier and paid-tier conditions. Outcomes were triage accuracy, emergency sensitivity, under-triage, and critical misses, analysed using Cochran's Q, Bonferroni-corrected McNemar tests, Cohen's kappa, and Wilson intervals. Findings: Triage accuracy differed significantly (Cochran's Q = 36.79, p < 0.001). Healthdirect achieved 48.9% accuracy (95% CI 35.0% to 63.0%; kappa = 0.233) versus 73.3% to 86.7% for LLMs (kappa = 0.600 to 0.800). Healthdirect operated under conservative interactive defaults while LLMs received complete information in a single prompt, which may have disadvantaged Healthdirect. Emergency sensitivity was 46.7% versus 80.0% to 86.7% for LLMs. Healthdirect produced two critical misses; no LLM produced any across 270 evaluations (95% CI 0% to 1.4%). When LLMs undertriaged, they recommended GP care rather than self-care. No tier differences were significant (all p > 0.05), and most systems over-triaged self-care cases. Interpretation: Frontier LLMs demonstrated higher triage accuracy and safer error profiles than Healthdirect. All LLMs avoided critical misses; Healthdirect did not. Premium subscriptions did not significantly improve triage safety. These findings support clinical governance decisions about whether LLMs warrant formal evaluation alongside government-backed symptom checkers.
ye, y.; Zeng, Z.; Tian, X.; Yuan, Z.; Wang, J.; Zhu, Y.
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Artificial intelligence applied to routine electrocardiograms (ECGs) has largely focused on detecting existing disease or predicting individual cardiovascular outcomes. Whether ECGs can support prediction of multiple future diseases across organ systems remains unclear. We developed ECG-RISK, a multitask survival model for 67 incident three-character ICD-10 endpoints using ECG waveforms, demographic characteristics and routinely collected laboratory data from 86,673 MIMIC-IV patients. Discrimination was highest for heart, brain, kidney and lung endpoints, with organ-level C-indices ranging from 0.796 to 0.825, whereas liver and pancreatic endpoints showed lower discrimination. The ECG-only model achieved strong discrimination across most endpoints, whereas the incremental improvement gained by incorporating ECG and laboratory inputs beyond demographic information varied substantially across endpoints. Across the nine exploratory aggregated outcomes, Kaplan Meier curves showed clear separation among model-score tertiles. Discrimination was highest for dementia (C-index, 0.891) and heart failure (C-index, 0.857). These findings support the feasibility of ECG-based longitudinal risk prediction across multiple diseases. External validation and competing-risk analyses are required to assess generalisability and clinical utility.
Kremer, P.; Schlicker, N.; Hasnaj, R.; Bamberger, J.; Witte, T.; Haase, I.; Mayr, A.; Schmidt, C.; Osteras, N.; Baraliakos, X.; Kuhn, S.; Krusche, M.; Knitza, J.
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Objectives To evaluate whether access to a certified large language model (LLM)-based clinical decision support system improves physician diagnostic performance in rheumatology compared with conventional diagnostic resources alone. Methods In this multicentre, open-label, randomised controlled trial, 82 physicians from seven hospitals in two countries were randomised 1:1 to conventional diagnostic resources plus Prof. Valmed or conventional resources alone. Participants assessed three rheumatology vignettes before and after assistance. The primary outcome was top-1 diagnostic accuracy. Secondary outcomes included top-3 accuracy, diagnostic reasoning, confidence, case-processing time and perceived support quality. Results Top-1 accuracy increased from 22.2% to 33.3% in the intervention group and from 23.3% to 35.0% in the control group, with no between-group difference in improvement (adjusted OR 0.99, 95% CI 0.45 to 2.19; p=0.979). Differences in top-3 accuracy, diagnostic reasoning and confidence were also not significant. Assisted case-processing time was substantially shorter with LLM support (94 vs 206 s; adjusted mean difference -112 s, 95% CI -141 to -83; p<0.001). Information timeliness and perceived diagnostic support quality were rated significantly higher in the intervention group. Exploratory analyses showed persistent overconfidence and substantial AI over-reliance. Conclusions Certified LLM-based diagnostic support did not improve diagnostic accuracy compared with conventional resources, but substantially reduced case-processing time and improved perceived support quality. These findings suggest potential workflow benefits while highlighting overconfidence and over-reliance as important safety considerations.
Singh, A. M.; Yeh, T.-C.; DeBoer, C.; Al-Moujahed, A.; Lin, J. B.; Smith, S. J.; Sanislo, S.; Janjua, K. A.; Lin, T.-C.; Almeida, D. R. P.; Mruthyunjaya, P.; Mahajan, V. B.
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Purpose: To evaluate the safety, procedural performance, sample recovery, and surgeon preference of an ophthalmic needle designed specifically for anterior chamber (AC) paracentesis. Methods: In this multicenter study, AC paracentesis was performed in clinic and operating-room settings using a 32-gauge x 4-mm needle with low dead space. The procedure was evaluated using a standardized physician survey. Prespecified outcomes included procedure-related adverse events (primary outcome), needle entry and handling, aspiration and sample recovery, comparative performance versus a 30-gauge needle, and physician preference for future use. Results: A total of 110 needle uses by eight surgeons were included. No ocular complications occurred, including lens or iris injury, hyphema, AC collapse, wound leak, hypotony, infection, or retinal complication, and no procedure required needle exchange or conversion to another device. Two technical events without ocular sequelae were noted, in which needle entry was partial thickness and did not reach the AC (1.8%; exact 95% CI, 0.2%-6.4%). Physicians rated needle entry, handling and sample recovery as good or excellent. Compared with a 30-gauge needle, the study needle was rated as at least comparable across all assessed domains. All surgeons rated it better or much better for intra-procedural safety and preferred it for future AC taps. Conclusions and Relevance: This short, 32-gauge low-dead-space ophthalmic needle demonstrated a favorable safety profile and was preferred over a 30-gauge needle by all surgeons. As aqueous humor liquid biopsy expands in clinical diagnostics and trials, an ophthalmic-specific needle design may help improve the consistency and safety of aqueous humor collection for molecular analysis and broader clinical use. Keywords: Anterior chamber paracentesis; Aqueous humor; Liquid biopsy; Low dead space; Ophthalmic needle
Patil, A.; Barathe, R.; Tate, D. M.; Kate, K.; Pande, S.; Gawande, N.; More, A.; Mahadik, S.; Berde, K.; Singhvi, R.
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Introduction: Polyendocrine metabolic ovarian syndrome (PMOS), formerly known as polycystic ovary syndrome (PCOS), is a common endocrine disorder affecting women of reproductive age. Besides reproductive and metabolic disturbances, PMOS negatively impacts psychological well-being and quality of life. Despite available treatment options, there remains a need for safe and effective therapies that improve both clinical symptoms and fertility outcomes. Aim: To compare the efficacy of VAMHA and MYRHA tablet combination therapy with standard non-hormonal therapy in restoring regular menstruation. Secondary objectives included assessment of ovulation, menstrual symptoms, polycystic ovarian morphology, hormonal and metabolic parameters, anthropometric measures, and skin manifestations. Study Design: Open-label, randomized, multicentre, prospective comparative clinical study. Methods: Seventy-one women with PMOS were randomized to Group A (n=37) or Group B (n=34). Group A received VAMHA and MYRHA tablets (2 tablets each), while Group B received Metformin 500 mg plus Myoinositol 600 mg (1 tablet), twice daily for 180 days. Data were recorded in Case Report Forms. Statistical Analysis: Continuous variables were summarized using mean and standard deviation, while categorical variables were expressed as frequencies and percentages. Appropriate statistical tests, including Chi-square, were used. A p-value [≤]0.05 was considered significant. Results: Significantly more participants in Group A achieved regular menstrual cycles than Group B (31 vs. 22; p<0.05). Ovulation occurred in 16 participants in Group A compared with 6 in Group B (p<0.05). Both groups showed significant improvement in menstrual irregularity and related symptoms. Significant reductions in Anti-Mullerian Hormone (AMH), fasting insulin, and body mass index (BMI) were observed in both groups (p<0.05). Resolution of polycystic ovarian morphology occurred in 13 participants (38.23%) in Group A and 10 (33.33%) in Group B. Both treatments were well tolerated with no major safety concerns. Conclusions: VAMHA and MYRHA combination therapy was superior to standard non-hormonal therapy in improving menstrual regularity and ovulation. It also produced favourable metabolic, hormonal, and ultrasonographic outcomes, suggesting its potential as a safe and effective option for comprehensive PMOS management and fertility enhancement.
Choudhuri, G.; Akhundova-Unadkat, G.; Naidoo, N.; Morales-Castillo, M.; Guillaume, X.; Duijnhoven, R. G.; Safaei, A.; Swain, M. G.
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Background & Aims: Fatigue is a central symptom of chronic liver disease (CLD), substantially impacting health-related quality of life (HRQoL). This study aimed to further understand CLD symptomatology, including fatigue, and its impact on HRQoL from a patient perspective. Methods: Abbott Global Assessment of Patients unmet needs (aGAP) was a multinational, cross-sectional survey in adults with compensated CLD in China, India and Mexico, conducted between July and November 2024. Adult participants who self-reported that they had physician-diagnosed CLD and were experiencing fatigue completed a quantitative survey to assess symptom burden and included three HRQoL patient-reported outcome (PRO) questionnaires (Patient-Reported Outcomes Measurement Information System [PROMIS]-29+2, Work Productivity and Activity Impairment - Specific Health Problem version 2.0 [WPAI: SHP], Multidimensional Fatigue Inventory [MFI]). Results: Overall, 505 participants (China: 200; Mexico: 105; India: 200) completed the study. Participants reported that their CLD-related fatigue sometimes, often or always affected their self-esteem/confidence (45.1%) and ability to maintain or acquire new employment (38.6%). Most participants reported moderate (51.3%) or serious (26.9%) fatigue, with 33.5% experiencing fatigue every day or almost every day. Many participants felt their social life was negatively impacted by their fatigue (47.3%) and that there were related financial difficulties (53.9%). Use of validated PRO tools demonstrated severe fatigue (MFI: overall mean [SD] 13.9 [3.4] general fatigue and 13.4 [3.6] physical fatigue) as well as substantial levels of work and activity impairment (WPAI: SHP overall mean [SD] 53.0 [26.4]) and high levels of anxiety, pain interference, depression and sleep interference (PROMIS T-scores [≥]54). Conclusions: Fatigue has a substantial impact on HRQoL among adults with CLD across several countries, highlighting a global unmet need for targeted interventions to effectively identify and manage the condition.
Tecchio, P.; Schlaffke, L.; Bolsterlee, B.; Hahn, D.; Raiteri, B. J.
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Muscle architecture shapes muscle function and changes with age, growth, training and disease, yet quantifying three-dimensional (3D) muscle architecture in vivo remains challenging. We introduce a hybrid fascicle tractography approach for freehand 3D ultrasound data that accurately reconstructs 3D muscle fascicles with respect to an objective, anatomically relevant coordinate system defined by the muscle's central aponeurosis. The hybrid approach combines Hessian-based fascicle detection with wavelet-based refinement to generate volumetric fascicle orientations. In a synthetic dataset with known ground truth, fascicle orientations and lengths were estimated with errors of [≤]2{degrees} and ~1.5%, respectively. In vivo, the approach detected physiologically plausible fascicle lengthening in the human tibialis anterior following a passive plantar flexion rotation, whereas diffusion tensor imaging of the same muscle did not. The proposed method enables anatomically relevant, objective and non-invasive quantification of 3D muscle architecture in vivo, providing a practical framework for applications in clinical and applied muscle physiology.
Oyarzun-Silva, R. A.; Hernandez-Hernandez, P.; Fernandez-Vaquero, M. A.; De Luis-Cabezon, N.
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Background. Videolaryngoscopy still requires adjuncts or hyperangulated rescue in a clinically important minority, and bedside screening discriminates modestly. Point-of-care ultrasound (POCUS) of the anterior airway is a promising alternative, but existing prediction models are opaque or assume a pre-specified functional form. We developed and internally validated a parsimonious, fully disclosed POCUS risk equation whose form is recovered from data and whose structural properties are machine-checked by formal proof - to our knowledge the first formally verified clinical risk predictor - following TRIPOD+AI 2024. Methods. In a prospective single-centre, single-operator cohort of 259 adults undergoing elective videolaryngoscopy (no-Easy airway 68/259, 26.3%), Sequentially Thresholded Least Squares with bootstrap stability selection (B=300) screened a 71-term library of nine POCUS features and retained a seven-term logistic equation; a two-term bootstrap-stable model was pre-specified as robustness analysis. Internal validation used 5x10 repeated cross-validation plus temporal and device hold-outs, with pre-specified overfitting and optimism assessments. Five behavioural properties of the deployed equation were machine-checked in Lean 4. Results. Two interactions met the |c|/sigma_c>2 stability criterion: skin-to-epiglottis x skin-to-hyoid-bone distance and tongue volume x sagittal tongue area. The seven-term equation reached a 5x10 cross-validated C-statistic of 0.966 (optimism-corrected 0.968) and held across temporal and device hold-outs (0.94-0.97). Calibration-in-the-large matched prevalence, with cross-validated slope 0.90 attenuating to 0.625 out-of-time; standard recalibration restored 0.92 without loss of discrimination. The pre-specified two-term robustness model reproduced this performance (C-statistic 0.964-0.968; events-per-parameter 34; shrinkage 0.99), confirming the result is not an artefact of the screening stage. Net benefit over a clinical baseline was positive across 10-50% thresholds. All five Lean 4 theorems compiled without sorry. Conclusions. A sparse, formally verified POCUS equation predicts difficult videolaryngoscopy with high internally validated discrimination and quantified, modest overfitting. Because the equation was developed in a single-operator cohort and its inputs are operator-dependent, external validation requires prior harmonisation of the measurement protocol and operator credentialing.
Yendewa, G.; Chengsupanimit, T.; Dehghani, A.; Ahmed, A.; Mohareb, A.; Freeman, M.; Cohen, C.; Ofotokun, I.; Dube, K.
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Human immunodeficiency virus (HIV) and hepatitis B virus (HBV) coinfection is associated with accelerated liver disease, but whether coinfection is associated with newly documented social determinants of health (SDoH) is unclear. We conducted a retrospective cohort study using TriNetX across 110 U.S. healthcare organizations (2010-2026). We propensity score matched adults with HIV/HBV to adults with HIV or HBV monoinfection. We organized newly documented SDoH indicators using a dynamic individual-level framework with four clinically recognized domains of social disadvantage: material vulnerability, healthcare access and engagement, interpersonal adversity, and psychosocial vulnerability. Matched cohorts included 10,071 HIV/HBV-HIV pairs and 9,659 HIV/HBV-HBV pairs (mean age, 47 years; 79% male; 66% non-White; median follow-up, 3.3 years). Over 178,900 person-years, HIV/HBV was associated with higher risk of the primary SDoH composite compared with HIV (11.5% vs 9.7%; incidence rate, 2.50 vs 1.97 per 100 person-years; hazard ratio [HR], 1.25; 95% confidence interval [CI], 1.15-1.37) and HBV (11.0% vs 6.4%; incidence rate, 2.39 vs 1.67; HR, 1.50; 95% CI, 1.35-1.67). HIV/HBV was also associated with higher material vulnerability and healthcare access and engagement composites in both comparisons, including housing instability, food insecurity, financial insecurity, insurance instability, and care disengagement/nonadherence (HR range, 1.22-3.33 vs HIV; 1.31-1.94 vs HBV). In the HBV comparison, HIV/HBV was additionally associated with interpersonal adversity, primary support stressors, and violence or victimization (HR range, 1.36-2.16). Findings were robust across sensitivity analyses. HIV/HBV was associated with more newly documented SDoH than monoinfection, supporting dynamic SDoH assessment.
Chukwuoha, C. M.; Ovenseri-Ogbomo, G.; Azuamah, Y. C.; Odimegwu, N. E.; Obioma-Elemba, J. E.; Ugwoke, G.; Nkeremuzor, E. C.; Eronini, Y.; Ikoro, N. C.; Esenwah, E. C.
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Abstract Objective: Glaucoma is a chronic disorder that impairs ocular health and may exacerbate ocular surface disease leading to tear film instability, dry eye symptoms and decreased quality of life. This study compared changes in tear quantity among glaucoma subjects living with and without diabetes mellitus, attending an eye clinic in Nigeria. Methods: A comparative cross sectional research design was used. 157 subjects which comprised 74 glaucoma subjects living with diabetes mellitus and 83 glaucoma subjects living without diabetes mellitus participated in the study. Tear quantity assessment included the Schirmer I test and tear meniscus height (TMH) measurement. Descriptive statistics, independent samples t-test and Chi-square test were used to examine the data at 0.05 level of significance. Results: Glaucoma subjects living with diabetes mellitus showed substantially decreased tear production (11.4 +/- 6.8 mm) compared with glaucoma subjects living without diabetes mellitus (19.6 +/- 9.6 mm; p < 0.001). Tear meniscus height in glaucoma subjects living with diabetes mellitus (0.8 +/- 0.3 mm) was significantly greater than in subjects living without diabetes mellitus (0.7 +/- 0.3 mm; p = 0.034). Conclusion: Diabetes mellitus dramatically deteriorates the ocular surface function in glaucoma subjects by decreasing tear production, altering the tear meniscus height and increasing the severity of ocular surface symptoms. Routine glaucoma care, especially in patients with diabetes mellitus, should include a full ocular surface evaluation including Schirmer I test, TBUT, TMH, and OSDI assessment to allow early detection and management of ocular surface disease, better treatment adherence, and improved visual outcomes. Keywords: Glaucoma, Diabetes Mellitus, Tear production, Tear Meniscus Height, Ocular Surface Disease.
Gorobets, O.; Vinh-Hung, V.
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Background: Prostate cancer enzalutamide treatment is approved at a standard dose of 160 mg daily. Concerns for real-world patients -- older and more fragile than those enrolled in clinical trials -- have prompted consideration of initiating treatment with lower doses, but the long-term efficacy of this approach remains unknown. We evaluate the long-term survival and longevity in patients treated with standard versus upfront low-dose enzalutamide. Methods: Retrospective analysis of 151 patients treated with enzalutamide (102 receiving 160 mg; 49 receiving [≤]80 mg) between 2014--2021 at the Centre Hospitalier Universitaire de Martinique, with complete follow-up through end of life (98.7% completeness of follow-up). Primary outcomes were overall survival (OS), progression-free survival (PFS), and longevity (attained age). Results: Doses [≤]80 mg were associated with longer median OS (36.3 vs. 20.7 months), improved restricted mean OS (difference of 0.7 years, p=0.05), and enhanced longevity (median 82.5 vs. 78.3 years, p=0.004). PSA response rate at 12 weeks was higher with lower-dose (71.4% vs. 48.8%, p=0.016). In multivariable models adjusted for prognostic factors, [≤]40 mg compared with 160 mg was non-inferior regarding OS (HR=0.61, 95% CI 0.36--1.06), superior regarding PFS (HR=0.59, 95% CI 0.35--0.99), and superior regarding longevity (HR=0.48, 95% CI 0.28--0.84). Bone metastasis, poor performance status, PSA response, time to PSA nadir, and disease duration were independent predictors of outcomes. A post-hoc analysis revealed a strong association between dose and physician-prescribing profiles, ranging from "endorse-lowest-dose" to "never-deviate-from-full-dose". Conclusions: Lower doses of enzalutamide were non-inferior to full-dose. Dose-adapted strategies warrant further investigation.