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Background/aim: Basket designs have been utilized in recent oncology clinical trials due to an increased interest in precision medicine. One current successful basket trial is the American Society for Clinical Oncology Targeted Agent and Profiling Utilization Registry (TAPUR) study, a pragmatic phase II trial where patients are matched based on their tumor genomic profile to treatments that target specific genomic alterations. Despite its success, recruiting patients with rare genomic alterations remains challenging. This study aims to introduce and evaluate a Bayesian approach for integrating data from ongoing independent basket trials that share similar primary aims to improve interim decisions and final analyses and reduce necessary to evaluate treatments.
Methods: We introduce a Bayesian two-stage phase II single-arm trial specifically for rare cancers utilizing a hierarchical Bayesian random effects model that incorporate data from ongoing trials. We compare this approach with the standard Simon two-stage design through extensive numerical simulations and apply it to real-world scenarios.
Results: Simulation results demonstrate that in rare populations our Bayesian approach has attractive operating characteristics. The simulations show that our approach performs well across a broad set of scenarios with fixed and variable numbers of trials.
Conclusion: Our proposed Bayesian two-stage approach effectively integrates data from multiple ongoing basket trials, enhancing the ability to recruit and analyze patients with rare genomic alterations. This approach improves the timing of interim decision-making and final analysis, making it a valuable tool for trials with slow accrual rates.
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http://dx.doi.org/10.1177/17407745251358233 | DOI Listing |
Stat Med
September 2025
Berry Consultants, Abingdon, UK.
Confidence distributions are a frequentist alternative to the Bayesian posterior distribution. These confidence distributions have received more attention in the recent past because of their simplicity. In rare diseases, oncology, or in pediatric drug development, single-arm trials, or platform trials consisting of a series of single-arm trials are increasingly being used, both to establish proof-of-concept and to provide pivotal evidence for a marketing application.
View Article and Find Full Text PDFBioinformatics
September 2025
Department of Mathematical Sciences, The University of Texas at Dallas, TX United States.
Motivation: The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context. Understanding gene functions and interactions in different spatial domains is crucial, as it can enhance our comprehension of biological mechanisms, such as cancer-immune interactions and cell differentiation in various regions. It is necessary to cluster tissue regions into distinct spatial domains and identify discriminating genes that elucidate the clustering result, referred to as spatial domain-specific discriminating genes (DGs).
View Article and Find Full Text PDFWater Res
August 2025
School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China. Electronic address:
Global phosphorus (P) resources are facing a depletion crisis, and pyrolysis of P-rich sewage sludge (SS) offers significant resource potential. Optimizing pyrolysis conditions remains key yet challenging for enhancing P retention and bioavailability. This study conducted a correlation-prediction-causation integrated framework (CPCIF) to investigate how heating temperature (HT), heating rate (HR), and retention time (RT) influence total P enrichment rate (BTPE), relative inorganic P transformation rate (BITP), and relative apatite P transformation rate (BAIP) from SS to biochar during pyrolysis.
View Article and Find Full Text PDFComput Chem Eng
July 2025
Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
The global energy market faces significant challenges due to increasing demand, growing competition, and the ongoing shift toward renewable sources. Addressing these complexities requires advanced methodologies that can effectively navigate uncertainty and optimize investment and operational decisions. This study presents a flexible scenario-based framework for capacity-related decision making and investment planning in energy systems comprising solar, wind, and natural gas facilities.
View Article and Find Full Text PDFPLoS Biol
August 2025
School of Psychology, University of Nottingham, Nottingham, United Kingdom.
Recall of stimuli is biased by stimulus history, variously manifested as an attractive bias toward or repulsive bias from previous stimuli (i.e., serial dependence).
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